PAETE.ORG FORUMS
Paetenians Home on the Net

HOME | ABOUT PAETE | USAP PAETE MUNISIPYO  | MEMBERS ONLY  | PICTORIAL PAETE | SINING PAETE  | LINKS  |

FORUM GUIDELINES
please read before posting

USAP PAETE Forum Index USAP PAETE
Discussion Forums for the people of Paete, Laguna, Philippines
 
 FAQFAQ   SearchSearch    UsergroupsUsergroups   RegisterRegister 
 ProfileProfile   Log in to check your private messagesLog in to check your private messages   Log inLog in 

(Chem) Spectroscopy: NMR Spectroscopy

 
Post new topic   Reply to topic   printer-friendly view    USAP PAETE Forum Index -> Science Lessons Forum
View previous topic :: View next topic  
Author Message
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Thu Feb 09, 2006 6:44 am    Post subject: (Chem) Spectroscopy: NMR Spectroscopy Reply with quote






Nuclear magnetic resonance (NMR) spectroscopy: Understanding antimalarial drugs
STAR SCIENCE By Angel C. De Dios, Ph.D.
The Philippine STAR 02/09/2006

Malaria is among the top causes of death in the developing world. The disease is responsible for about one to three million deaths per year. Almost half of the entire population of the world is exposed to various species of Plasmodium, the parasite responsible for this disease. This exposure translates into several hundreds of millions of people carrying the parasite. The disease is therefore a major concern in developing countries. Affordable medicine against the disease is imperative and its non-lucrative nature unfortunately does not draw interest among top pharmaceutical companies. For this reason, efforts in designing drugs against this deadly disease have been confined within academic research institutions in the United States, as an example. The widely used drug against malaria is chloroquine. Unfortunately, there are now strains in all three continents – Africa, Asia and South America – that are resistant to chloroquine. With the emergence of drug-resistant strains, it has become timely to understand how antimalarial drugs work in the hope of intelligently designing new drugs against malaria.

The most common drugs used against malaria, including chloroquine, are based on quinoline, a heteroaromatic compound (similar to naphthalene, except with one carbon replaced by nitrogen). Its target is believed to be the heme fragment, a byproduct of the metabolism of hemoglobin. The malaria parasite feeds on this human blood protein for its amino acid source. Unlike humans, the parasite cannot metabolize heme and this turns out to be toxic to the parasite. The heme, however, precipitates out and crystallizes into hemozoin, making it innocuous to the parasite. Crystals of hemozoin, commonly referred to as malaria pigment, are found in red blood cells infected by the malaria parasite. Antimalarial drugs such as quinine, chloroquine and amodiaquine are thought to inhibit heme crystallization. By understanding the underlying mechanisms and chemical properties behind the interaction between the drug and its target heme, it is hoped that new drugs can be designed in an effective and speedy manner. This desired increase in understanding could only come with a detailed knowledge of these molecules. The drugs and their target are very small, about a million times smaller than the parasite, preventing their direct observation by even the most powerful microscope. Spectroscopic techniques are required to probe systems at the atomic resolution level. To understand spectroscopy a little bit, a simple analogy can be made. These techniques are similar to listening carefully to what tunes atoms and molecules are singing. Hearing a love song brings us certain emotions. Similarly, the frequencies atoms and molecules display can reveal information regarding their environment and structure, allowing our naked eyes to probe into the ultramicroscopic world of atoms and molecules. Extraction of chemical information from these techniques, however, is not straightforward. Analysis is required and nowadays, computers are necessary to model the systems and to evaluate the interactions between molecules from first principles.

Our research group at Georgetown University employs nuclear magnetic resonance (NMR) spectroscopy and molecular simulations in the study of antimalarial drugs. NMR spectroscopy is a widely used technique in chemistry. This type of spectroscopy employs a magnet (similar to magnetic resonance imaging, MRI) in which samples containing the molecules to be studied are placed. Inside the magnet, the nuclei (the core of atoms that contain protons and neutrons) begin to spin at their characteristic frequencies, their unique tunes. Sophomores in college chemistry are usually introduced to this method as a tool for characterizing and identifying small organic compounds. In NMR spectroscopy each nucleus in a unique chemical setting will report a particular frequency, a "signature" NMR chemical shift. NMR spectroscopy, similar to other techniques in chemistry, provides us with a glimpse into the world of atoms our naked eyes would normally not see. Since its discovery in the 1950s, the NMR chemical shift, demonstrating a great sensitivity to the electronic environment around a nucleus, has likewise become of value in elucidating the secondary structures of proteins in solution. Proteins can be regarded as large molecules and the arrangement of their atoms, what chemists would refer to as structure, leads to the properties and functions these proteins exhibit in human health and disease. Changes in NMR chemical shifts can be observed by simply altering the solvent, the medium in which we place atoms or molecules. Interactions between molecules manifest in this ubiquitous observable. One example that demonstrates the sensitivity of the NMR chemical shift is the fact that nuclei in the vicinity of molecules that contain aromatic rings exhibit changes in the chemical shift, which can then provide clues regarding their position and distance from these aromatic centers. In chemistry, an aromatic molecule is one in which electrons are free to cycle around circular arrangements of atoms. Aromaticity is relevant to the study of malaria since most antimalarial drugs and their target, heme, are aromatic. The aromatic rings, due to the electrons freely circulating above and below a molecular plane, are able to perturb the NMR spectrum of a nearby molecule. Aromatic compounds make nuclei sing a different tune.

There are other parameters in NMR spectroscopy in addition to the chemical shift. Coupling constants, which arise from either a direct interaction between nuclear spins or from an indirect interaction mediated by electrons, are also excellent reporters of the environment in the vicinity of the nucleus. There are duets, trios, and even choral singing. Equally important are relaxation times, as these provide a wealth of information regarding the structure and dynamics of chemical systems. Relaxation times refer to the rate at which a nucleus returns to its equilibrium spin state after we have forced it to sing its tune. Nuclei are like singers that need some break before they could sing their tune again. Unlike other spectroscopies, relaxation in NMR is not spontaneous, as it requires agents or mechanisms, such as unpaired electrons, other nuclear spins, and molecular motion. And in the presence of unpaired electrons, nuclei relax a lot faster. And the closer they are to the source of unpaired electrons, the less time they take to relax.

At the center of heme is a ferric ion, which is paramagnetic (having unpaired electrons). One can clearly see this by simply seeing that the number of electrons in a ferric ion is not even, thus, no matter how these electrons are distributed, complete pairing is not possible. In molecules with unpaired electrons, how fast a nucleus can return to its equilibrium spin state can serve as a clue of how the various nuclei are situated with respect to the unpaired electron. The most widely studied nucleus in NMR is the proton. Biologically relevant compounds, like other organic compounds, contain plenty of hydrogen atoms. Thus, through an NMR spectrometer, one can see a view of what is going on through the eyes of a hydrogen nucleus. And a compound usually will have several unique hydrogens, with each one offering its own vantage point. In the presence of heme, the NMR spectra of the antimalarial drugs are significantly perturbed. The paramagnetic heme affords an efficient relaxation mechanism for the quinoline nuclear spins, that their lines in the NMR spectrum become much broader when the quinoline molecule becomes closer to a heme fragment. In the presence of a relaxing agent, they can sing very often, but their tunes are not long lasting. The enhancement in the relaxation rates can be carefully measured. Each hydrogen nucleus in the quinoline drug will have a relaxation time, which can be analyzed to extract its distance from the paramagnetic heme. With all the hydrogens in the antimalarial drug reporting a distance from the ferric center of heme, one can perform some sort of a triangulation procedure to draw the position of the drug molecule with respect to its target, the heme. Thus, it has been demonstrated that via NMR spectroscopy, one can determine solution structures, the three-dimensional arrangement of atoms, of heme-antimalarial drug complexes.

The NMR chemical shifts are likewise perturbed when aromatic systems become close to each other. The interaction between heme and an antimalarial drug is suggested to be noncovalent (no chemical bonding is involved). The interaction is believed to arise from the aromatic rings of the porphyrin group in heme and the drug molecule. These aromatic rings are characterized by electrons lying primarily above and below a molecular plane. These electrons extend a bit further compared to other electrons found in systems that have only single bonds. These electrons can influence the NMR chemical shift of nearby nuclei. By monitoring the NMR chemical shift, one can also gain information regarding how far an aromatic ring is from any given nucleus or vantage point since these interactions are very much distance-dependent. Hence, NMR chemical shifts have likewise been utilized in deciphering how antimalarial drugs approach a heme fragment. Furthermore, NMR chemical shifts can be used to study drug-drug interactions as these antimalarial drugs all contain the aromatic quinoline ring. NMR spectroscopy has been utilized, for example, in the study of self-aggregation of various antimalarial drugs. Solution structures for chloroquine dimers have been proposed. Mixed aggregates are also important in cases where one drug interacts strongly with another, suggesting that a mixed cocktail of antimalarial drugs may not be a wise choice at all times.

The ultimate goal in these studies is to understand at the molecular level how antimalarial drugs work. With this understanding, it is hoped that new drugs can be designed in a systematic fashion. Work on antimalarial drugs involves computational work. Since the NMR chemical shift is electronic in origin, one can calculate this NMR parameter from first principles, those we learned from Newton, Schrödinger, Einstein, Dirac, Ramsey and others. The NMR chemical shift reported at each site originates from the electronic or bonding makeup near that atom. Particularly interesting for the antimalarial drugs are the chemical shifts of the aromatic nuclei. Preliminary calculations indicate that there may be a heterogeneity or non-uniformity in the NMR chemical shifts of aromatic nuclei, an indication perhaps of the non-uniform distribution of electrons in the region above and below the aromatic plane. This non-uniform distribution of charges can lead us to the more familiar case of electrostatic interactions, the simple principle that states unlike charges attract. Substitutions on a quinoline ring as exemplified by the well-known drugs chloroquine, quinine and amodiaquine, enhance this non-uniform distribution. These subtle differences may partly explain the interactions found between aromatic rings, the interaction believed to be at the heart of the drug-target complex in malaria. Therefore, NMR spectroscopy may not only provide detailed pictures of drug-target complexes at atomic resolution, but may likewise provide insights regarding the origin of the properties of these drug molecules. With each tune played by a nucleus, we learn more about what atoms see.

*************************************************************

Questions to explore further this topic:

What is light?

http://scienceofspectroscopy.i.....s_light%3F
http://cse.ssl.berkeley.edu/light/measure.html

What are wavelength and frequency?

http://scienceofspectroscopy.i....._Frequency

What is the energy associated with light?

http://scienceofspectroscopy.i.....tle=Energy

What is Beer-Lambert Law?

http://scienceofspectroscopy.i.....ambert_Law

How is light created?

http://scienceofspectroscopy.i.....is_Created

How does light interact with matter?

http://scienceofspectroscopy.i.....and_Matter

How does light affect matter?

http://scienceofspectroscopy.i....._on_Matter

What is a spectrum?

http://www.colorado.edu/physic.....index.html
http://www.astro.uiuc.edu/~kal.....emspectrum

What is spectroscopy?

http://chemistry.about.com/lib.....21302a.htm

What is Ultraviolet-visible spectroscopy?

http://scienceofspectroscopy.i.....ectroscopy
http://www.shu.ac.uk/schools/s.....visab1.htm

What is infrared (IR) spectroscopy?

http://scienceofspectroscopy.i.....ectroscopy
http://www.shu.ac.uk/schools/s.....rspec1.htm

What is NMR spectroscopy?

http://scienceofspectroscopy.i.....ectroscopy
http://www.shu.ac.uk/schools/s.....c/nmr1.htm
http://www.cis.rit.edu/htbooks/nmr/inside.htm

How are xrays used in chemistry?

http://scienceofspectroscopy.i.....ectroscopy

What is microscopy (in chemistry)

http://scienceofspectroscopy.i.....Microscopy

What is fluorescence?

http://scienceofspectroscopy.i.....uorescence

What is phosphorescence?

http://scienceofspectroscopy.i.....horescence

What is chemiluminescence?

http://scienceofspectroscopy.i.....minescence

What is a laser?

http://scienceofspectroscopy.i.....SER_Theory

Is spectroscopy used only in chemistry?

http://scienceofspectroscopy.i.....ce_Imaging
http://www.nrc-cnrc.gc.ca/educ.....ibd_e.html
http://www.planetary.org/explo.....scopy.html

What are aromatic compounds?

http://bouman.chem.georgetown......bexamp.htm
http://www.biocrawler.com/encyclopedia/Aromatic
http://jchemed.chem.wisc.edu/J.....8/MENU.HTM

What is quinoline?

http://www.biocrawler.com/encyclopedia/Quinoline

What is heme?

http://omlc.ogi.edu/spectra/hemoglobin/hemestruct/

GAMES

http://www.nasa.gov/audience/f.....index.html


Last edited by adedios on Sat Jan 27, 2007 4:13 pm; edited 3 times in total
Back to top
View user's profile Send private message Visit poster's website
TonyB



Joined: 05 Jan 2006
Posts: 178

PostPosted: Thu Feb 09, 2006 8:28 am    Post subject: Congratulations! Reply with quote

Dear Angel,

Congratulations! I also heard the good news about the little one coming soon.

On the articles about science, I hope you can publish more in the future. I shall be writing to PhilStar about moving their science/tech articles to a more prominent space in the main webpage much like other online editions of the major networks.

cheers!
tony.basa
_________________
Usap Business | LDP Batch '89 | This Side Of Town
Back to top
View user's profile Send private message
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Thu Feb 09, 2006 12:53 pm    Post subject: Reply with quote

Thanks, Tony. I hope PhilStar listens to your suggestion. There is actually a pipeline for these articles (that is probably worth several months since only one article gets published each week). We are hoping to attract other Filipino scientists to contribute articles. It is difficult to write since most of us are trained to write in scientific peer-reviewed journals, not in popular media.

We just had a checkup and we are relieved to hear the heartbeat for the first time. The previous ones were just through ultrasound, but now that ten weeks have passed, we could actually hear the heartbeat.
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Mon Oct 02, 2006 8:15 pm    Post subject: One-of-a-kind imaging probe reveals secrets useful for drug Reply with quote

One-of-a-kind imaging probe reveals secrets useful for drug discovery
University of Florida

Filed under Research, Health on Monday, October 2, 2006.GAINESVILLE, Fla. — Good things may indeed come in small packages for scientists eager to find natural substances to help cure diseases. The challenge is to analyze material that is smaller than the proverbial gnat’s eyelash.

But using a refined version of nuclear magnetic resonance technology, or NMR, scientists have unlocked secrets hidden in tiny amounts of venom taken from spindly insects called common two-stripe walking sticks, which are relatively harmless, plant-eating creatures common in the eastern United States.

The analytical technique, described in the current issue of ACS Chemical Biology by scientists at the McKnight Brain Institute of the University of Florida and the Center for Medical, Agricultural and Veterinary Entomology at the Gainesville U.S. Department of Agriculture, could aid in the search for natural substances to make medicines. It also shows that scientists can obtain volumes of information from very tiny samples, which could be useful in efforts to understand Alzheimer’s disease and other disorders.

“There are many potent, useful molecules made by plants and animals, but they are usually produced in such small quantities it takes a huge amount of material to characterize them,” said Arthur Edison, an associate professor of biochemistry and molecular biology. “In this case, it previously required hundreds of milkings to get enough walking stick venom for analysis. We were able to get great data from just one milking.”

Researchers at the McKnight Brain Institute’s Advanced Magnetic Resonance Imaging and Spectroscopy equipped an NMR spectrometer with a special probe to examine the venom, which the walking stick sprays to defend itself from predators.

Similar to the magnetic resonance imagers used to examine patients in hospitals, this analytical tool uses much stronger magnetic fields to study smaller samples, allowing scientists to study molecules atom by atom.

But what made this particular method unique is not the extreme power of the magnet, which at 600 megahertz is fairly standard, but the extreme sensitivity of the probe — the component that is inserted into the magnet to obtain chemical information from the samples.

Developed by scientists at the National High Magnetic Field Laboratory at UF and in Tallahassee, and a manufacturer of NMR equipment, the probe is only about 2 inches in diameter, and the space for the sample itself is about 1 millimeter in diameter.

When in use, the probe is cooled to lower than 400 degrees Fahrenheit below zero to reduce electrical signals that would interfere with the analysis. But the sample area itself is kept warm to protect the specimen.

“It is now possible to approach problems we couldn’t think about before,” said Edison, who said he welcomes collaboration with other scientists interested in using the new probe. “For example, in mouse models of Parkinson’s or Alzheimer’s disease, there is not a lot of tissue to work with, especially if you’re studying a sample from a single animal. But this is a way we could obtain potentially important chemical information about disease from small amounts of brain tissue.”

Scientists used walking stick venom to demonstrate the technique partly because it combined lead researcher Aaron Dossey’s passion for studying insects with his formal training in biochemistry.

“I’ve raised different species of walking sticks, which are well known to spray defensive venom,” Dossey said. “We thought if this technique really can look at small samples, well, a milking of a single walking stick is very small. It’s worth a try.”

They discovered compounds not previously known to be present in these animals, as well as chemical differences in secretions from the same walking stick at different times. Notably, they found a high concentration of glucose, a simple sugar and vital cellular fuel.

“Glucose is an expensive molecule to spray at your predators,” Edison said. “But why is the glucose there? It may be something the walking stick uses to enable it to safely store the toxic material in the insect’s gland until it is ready for use as a venom, to improve the properties of the spray or some other reason we haven’t yet considered. It’s the kind of thing that may provide hints about drug discovery in future.”

More than 40 years ago, Jerrold Meinwald, an emeritus professor of chemistry and chemical biology at Cornell University, led landmark chemical studies of walking stick venom. He was pleased to know the insect was being studied in Florida.

“We used not dozens but thousands of walking sticks to get enough secretions to do analyses and, no, it’s not easy to do,” Meinwald said. “When we started you could hardly work with natural materials in terms of milligrams. Now you can do chemistry on the microgram scale. NMR has made enormous progress — it has thousands of times the sensitivity it used to have. The findings in Florida represent the great improvement that has taken place in the state of the art. It’s nice to see it applied to this insect.”
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Sun Mar 04, 2007 8:12 am    Post subject: Natural antibiotics yield secrets to atom-level imaging tech Reply with quote

University of Michigan
3 March 2007

Natural antibiotics yield secrets to atom-level imaging technique

ANN ARBOR, Mich. -- Frog skin and human lungs hold secrets to developing new antibiotics, and a technique called solid-state NMR spectroscopy is a key to unlocking those secrets.

That's the view of University of Michigan researcher Ayyalusamy Ramamoorthy, who will discuss his group's progress toward that goal March 3 at the annual meeting of the Biophysical Society in Baltimore, Md.

Ramamoorthy's research group is using solid-state NMR to explore the germ-killing properties of natural antibiotics called antimicrobial peptides (AMPs), which are produced by virtually all animals, from insects to frogs to humans. AMPs are the immune system's early line of defense, battling microbes at the first places they try to penetrate: skin, mucous membranes and other surfaces. They're copiously produced in injured or infected frog skin, for instance, and the linings of the human respiratory and gastrointestinal tracts also crank out the short proteins in response to invading pathogens.

In addition to fighting bacteria, AMPs attack viruses, fungi and even cancer cells, so drugs designed to mimic them could have widespread medical applications, said Ramamoorthy, who is an associate professor of chemistry and an associate research scientist in the Biophysics Research Division.

While researchers have identified hundreds of AMPs in recent years, they're still puzzling over exactly how the peptides wipe out bacteria and other microbes. Unlike conventional antibiotics, which typically inhibit specific bacterial proteins, AMPs get downright physical with invaders, punching holes into their membranes. But they're selectively pugnacious, targeting microbes but leaving healthy host cells alone.

"They're like smart bombs," Ramamoorthy said. "We'd like to exploit their properties to design super-smart bombs, but before we can do that, we need to understand how these AMP smart bombs interact with membranes to destroy bacteria. We need to know how they're shaped before, during and after the process of attaching to bacteria and how they attach."

Solid-state NMR spectroscopy is an ideal tool for answering such questions because it provides atom-level details of the molecule's structure in the complex and challenging cell membrane environment, Ramamoorthy said. "Just as an MRI produces a detailed image of our internal organs, solid-state NMR spectroscopy is used to construct a detailed image of a peptide or protein and to reveal how it sits in the cell membrane," providing clues for modifications that might make synthetic AMPs even more effective in overcoming ever-increasing bacterial resistance. For instance, rearranging parts of the molecule might make it fit into the membrane better, resulting in greater effectiveness with smaller amounts of AMP.

"Our overall mission is to use the kind of basic physical data we obtain from solid-state NMR spectroscopy to help interpret biological functions," Ramamoorthy said. The work is highly interdisciplinary, involving not only Ramamoorthy's lab and several other groups in the Chemistry Department, but also researchers from the College of Engineering, the School of Dentistry, the Medical School and the Biophysics Research Division, as well as collaborators in Canada, Japan, India and the U.S. pharmaceutical companies Genaera Corporation and Eli Lilly and Company. Ramamoorthy was awarded support from the National Institutes of Health and the National Science Foundation, through an NSF Faculty Early Career Development Award.

A leader in this area of research, he has organized two major international symposia on the field at the University of Michigan, edited a special issue in the journal BBA-Biomembranes, published a number of papers in leading journals, and brought out a book on NMR Spectroscopy of Biological Solids. Ramamoorthy says that this area of research will grow considerably at U-M from implementing plans to set up a high magnetic field solid-state NMR spectrometer facility and an NIH-funded program.

###
EMBARGOED FOR RELEASE AT NOON EST SATURDAY, MARCH 3, 2007

For more information:

Ayyalusamy Ramamoorthy---http://www.umich.edu/~michchem/faculty/ramamoorthy/ and http://www.umich.edu/~ramslab

Biophysical Society---http://www.biophysics.org/
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed May 16, 2007 9:09 am    Post subject: NMR advance relies on microscopic detector Reply with quote

NMR advance relies on microscopic detector
Technology could vastly improve diagnostics
Anne Trafton, News Office
May 15, 2007


Detecting the molecular structure of a tiny protein using nuclear magnetic resonance (NMR) currently requires two things: a million-dollar machine the size of a massive SUV, and a large sample of the protein under study.

Now, researchers from MIT's Center for Bits and Atoms report the development of a radically different approach to NMR. The new highly sensitive technique, which makes use of a microscopic detector, decreases by several orders of magnitude the amount of protein needed to measure molecular structure.

The new technology could ultimately lead to the proliferation of tabletop NMR devices in every research laboratory and medical office. Among other things, such devices could prove invaluable in diagnosing a variety of diseases.

"It's revolutionary," said Shuguang Zhang, one of the authors and associate director of MIT's Center for Biological Engineering. "It's not just incremental progress."

The research team reports the work in the online and print editions of the Proceedings of the National Academy of Sciences the week of May 14. Lead author Yael Maguire, a former MIT graduate student who earned his Ph.D. for this work, will give a talk on it May 16 at the VII European Protein Symposium in Stockholm.

NMR, along with X-ray crystallography, is commonly used to determine the structure of proteins and other molecules. NMR probes normally consist of a coil that surrounds the sample being studied. The coil creates a magnetic field that interacts with the nuclear spin of atoms in the sample, and those interactions reveal how the atoms are connected.

With current NMR machines, you need about 1017 (more than a million billion) molecules of a protein to determine its molecular structure. Some researchers have tried to make tiny coils to study smaller samples, but it has proven very difficult to scale these to small sizes to analyze tiny samples and to create high throughput methods.

Instead, research originally aimed at improving quantum computing led the MIT researchers to a completely different approach based on guiding waves.

"We were trying to get away from coils and see if we could find a new way to look at it," said Maguire, now a visiting researcher at MIT and chief technology officer of Cambridge-based ThingMagic.

How it works

The new approach starts with technology similar to the Wi-Fi antennas found in laptop computers. These antennas consist of a flat strip of metal. Using a laser, the MIT team made a microscopic defect (a slot) in such a conducting structure, known as a strip line. In that location a little bit of the magnetic field leaks out of the line, creating a uniform, concentrated magnetic field. That field allows the slot to be used as an NMR probe, in place of a coil.

The detector described in the PNAS paper is a plastic card about one-third the size of a credit card and is easy and inexpensive to produce. To get structural information, the new detector must still be placed in a massive machine housing a superconducting magnet, just as the coil probes are. However, the MIT researchers anticipate that the microslot's small sample volume will allow much smaller tabletop spectrometers to be developed.

Zhang said such NMR devices could prove especially valuable in diagnosing diseases caused by misfolded proteins, such as Alzheimer's and Huntington's, or prion diseases like Creutzfeld-Jakob disease. It could also allow early detection of glaucoma and cataracts, which could be diagnosed by testing a single teardrop. "You could detect it so early it will become treatable," Zhang said.

The new technology could dramatically improve the rate of biomedical research, because it can take up to a year to obtain enough material for an NMR study using the coil probes, said co-author Professor Neil Gershenfeld, director of MIT's Center for Bits and Atoms. That is "a major limiting step in drug discovery and studying biological pathways," he said.

The probes could also be used to make portable devices for diagnostics or soil analysis. And because the smaller devices are cheaper to make, they should be affordable even in developing countries where NMR machines are now rare, said Zhang.

Asking big questions

Maguire got the idea for the project after talking to Zhang and asking him what kind of new device would make the biggest impact in biology. For Zhang, the answer was immediate: improving NMR.

Elucidating structure is critically important for biologists because structure determines function, said Zhang. The goal for the project was to create an NMR detector sensitive enough to detect structural information using the amount of protein in a spot on a two-dimensional gel used for electrophoresis (about 1014 molecules).

The task was daunting. "Nobody in their right mind would try to take one spot from that gel and get a molecular structure from it," said Zhang.

However, Zhang said that he believes in the sentiment expressed by Francis Crick, the legendary biologist who determined the double helix structure of DNA along with James Watson: You need to ask big questions in order to get big answers.

Zhang adds that the project probably never would have happened without interdisciplinary collaboration: "Biologists would never have thought of this type of machine, but a physicist would never have asked the question," he said.

Before starting this project, Maguire and Gershenfeld, with co-author Isaac Chuang, had already used NMR to create early quantum computers. Their effort to improve the computing capabilities turned out to be surprisingly relevant to detecting molecular structures, an "unexpected spinoff," said Gershenfeld.

"We were not at all thinking about biology, but this turned out to be exactly what was needed to improve biological sensitivity," Gershenfeld said.

The research was funded by the National Science Foundation.
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Mon Jul 23, 2007 9:39 am    Post subject: Fingerprinting with light shows promise for improved crime-f Reply with quote

Fingerprinting with light shows promise for improved crime-fighting
23 July 2007
Analytical Chemistry

In a finding that should get a “thumbs up” from CSI fans, researchers in the United Kingdom are reporting development of a fast new fingerprinting method that shows promise for improving the collection and analysis of fingerprints from crime scenes. The finding is scheduled for publication in the August 1 issue of ACS’ Analytical Chemistry, a semi-monthly journal.

Standard methods for collecting fingerprints at crime scenes, such as dusting, can sometimes alter the prints and erase valuable forensic clues, including traces of chemicals that may be in the prints. In the new study, Sergei G. Kazarian of Imperial College London and colleagues used a special gelatin tape to collect fingerprints from several different surfaces including a door handle, a mug handle, a curved glass surface, and a computer screen. They exposed the imprinted gels to a highly sensitive instrument that used a beam of infrared light and an array detector to obtain images of the collected fingerprints.

The method revealed valuable chemical information about the composition of the prints, potentially giving information about the individual depositing them (e.g. smoker, vegetarian), and the presence of contaminants within the prints, which could provide clues about what possible suspects had handled (e.g. foodstuffs, drugs) and, thus could be useful in identifying a criminal, the report said. In addition, the new method kept the original fingerprints intact and available for further analysis, the researchers added.

ARTICLE #4 FOR IMMEDIATE RELEASE
“Spectroscopic Imaging of Latent Fingermarks Collected with the Aid of a Gelatin Tape”

DOWNLOAD PDF
http://pubs.acs.org/cgi-bin/sa.....70580j.pdf

DOWNLOAD HTML
http://pubs.acs.org/cgi-bin/sa.....0580j.html
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Oct 17, 2007 11:57 am    Post subject: NMR researchers unlock hydrogen’s secrets to spot polymorphi Reply with quote

NMR researchers unlock hydrogen’s secrets to spot polymorphism in pharmaceuticals

University of Warwick
17 October 2007



Researchers at the University of Warwick and Astra Zeneca have found a new way to use solid-state NMR equipment to crack the secrets of hydrogen atoms and thus spot unwanted polymorphs in pharmaceuticals.

Pharmaceuticals companies are constantly battling the problem of polymorphism in which an active drug can actually exist in more than one form or crystal structure which can cause the drug to act in very different ways. Now researchers at the University of Warwick and Astra Zeneca have devised a new method of using solid-state NMR (nuclear magnetic resonance) equipment to spot unwanted polymorphs that should be adopted as a routine tool by pharmaceutical companies.

NMR equipment is already used to detect polymorphism in pharmaceuticals. However the standard technique looks at the carbon 13C nuclei in the drugs by a method called cross-polarisation magic-angle spinning (CP MAS). This is a very insensitive technique as only 1 in 100 carbon nuclei are the 13C isotope. This means that 99 out of 100 carbon nuclei are a NMR-invisible form of carbon. Only one-dimensional spectra are routinely possible from such an experiment.

Researchers have long wished to be able to couple this carbon based solid–state NMR technique with one that looks at hydrogen nuclei. It has been possible to look at hydrogen when the sample is a solution (solution-state NMR) but this is not as easy in solid-state NMR as the extensive network of coupled together 1H nuclei leads to broad lines in the spectrum that are hard to tell apart. This makes it almost useless when you are examining a tablet. Tablets are also particularly difficult to examine as the active drug within the tablet is combined with a mixture of other filler compounds (excipients).
This breakthrough by the Warwick team opens up hydrogen nuclei to useful study by solid-state NMR which will bring immense benefits to the study of polymorphism in drugs and organic molecules in general. This is because hydrogen atoms are central to hydrogen bonding (as opposed to carbon atoms which "observe" from afar). Hydrogen bonding is often the driving force in determining how organic molecules do differ in their methods of "3D packing" forming polymorphs or pseudo-polymorphs (pseudo-polymorphism referring to crystal structures that differ through the inclusion or non inclusion of small molecules, eg with or without water). This new NMR technique can identify which pseudo polymorph of an active pharmaceutical is present in a complete tablet.

The research team led by Dr Steven Brown from the University of Warwick’s Department of Physics have exploited recent developments in NMR hardware and pulse sequence design allowing them to gain high-resolution 1H solid-state NMR spectra by a method called CRAMPS (combined rotation and multiple-pulse spectroscopy). By using this high-resolution two-dimensional 1H CRAMPS solid-state NMR they obtained a spectrum for a tablet formulation in less than 2 hours, which is equivalent to the time required for a good 13C CP MAS one dimensional spectrum.

Dr Steven Brown said: "This Hydrogen 1H solid-state NMR method gives powerful new insight that complements established Carbon 13C based techniques - this new approach should be adopted as a routine tool in pharmaceutical characterisation"

Notes for editors:

The research paper entitled "Distinguishing Anhydrous and Hydrous Forms of an Active Pharmaceutical Ingredient in a Tablet Formulation Using Solid-State NMR Spectroscopy" by John M. Griffin, Dave R. Martin, and Steven P. Brown has just been published in Angewandte Chemie Volume 119, Issue 42 , Pages 8182-8184

The research received funding and support from Astra Zeneca (UK) EPSRC and BBRSC.
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Jan 09, 2008 11:46 am    Post subject: Hope Diamond's phosphorescence key to fingerprinting Reply with quote

Penn State
8 January 2008

Hope Diamond's phosphorescence key to fingerprinting

Shine a white light on the Hope Diamond and it will dazzle you with the brilliance of an amazing blue diamond. Shine an ultraviolet light on the Hope Diamond and the gem will glow red-orange for about five minutes. This phosphorescent property of blue diamonds can distinguish synthetic and altered diamonds from the real thing, and it may also provide a way to fingerprint individual blue diamonds for identification purposes, according to a team of researchers from the Naval Research Laboratory, the Smithsonian Institution and Penn State.

Other colors of diamonds do not phosphoresce, but fluoresce, emitting visible light only as long as they are stimulated with ultraviolet radiation. Blue diamonds that phosphoresce emit light even after the ultraviolet lamp is turned off. Unlike the Hope, however, most blue diamonds produce a bluish light rather than reddish light.

The red phosphorescence is rare enough that researchers thought that those blue diamonds that did glow red must have come from the parent of the Hope – an original 112-carat blue diamond mined in India in the mid-1600s. That diamond was cut down to 67 carats to become the French Blue owned by French kings and, after being lost during the French Revolution, appeared 20 years later in 1812 as the 45-carat stone known today as the Hope Diamond.

The research, reported in the current issue of Geology, confirms that all blue diamonds have a red phosphorescent component and that, through spectroscopic analysis, each blue diamond can be individually identified.

"The Hope Diamond is the most popular museum object in the world," says Peter J. Heaney, professor of geosciences at Penn State. "Even so, the Smithsonian considers the specimens in the museum objects of scientific value. They have an enormous number of gemstones in their collection and they encourage scientific research to figure out how the stones formed, and what gives them their special properties."

As popular as the Hope Diamond is, it is always on display at the Smithsonian. Heaney and the other researchers worked on the gems in the morning and after the museum closed.

"If you want to study the Hope diamond using spectroscopy, you need to bring the machine to the Hope diamond," says Heaney. "You cannot bring the Hope to the machine."

The researchers, who included Heaney; first author Sally Eaton-Magana, Gemological Institute of America, formerly of the Naval Research Laboratory; Jaime Freitas, Paul Klein and James E. Butler, NRL; Roy Walters, Ocean Optics, Inc.; and Jeffery E. Post, curator of gems and minerals, Smithsonian Institution, used a portable spectrometer manufactured by Ocean Optics that could be set up at the museum. They tested a variety of blue stones known to be natural including the Hope Diamond, the Blue Heart – the second largest blue diamond known, the Portuguese Diamond – another large stone, and 64 other blue diamonds, many of which came from the Aurora Butterfly – a collection of 240 stones temporarily on display at the museum.

Of these, only five did not phosphoresce. Those five turned out to be a different type of diamond than the blue Hope and the other 62 diamonds tested.

Spectroscopic analysis is a noninvasive process that shines light on an object and then measures the wavelength of the light emitted by the object. The researchers used two different wavelengths of ultraviolet light – short and long. Exposed to short ultraviolet, the researchers saw bands at 500 nanometers, corresponding to blue-green and 660 nanometers, corresponding to red. Under short ultraviolet, only the red wavelength occurred.

"Even though many blue diamonds appear pink or bluish when exposed to ultraviolet light, we found that all blue diamonds do have red phosphorescence," says Heaney. "Unlike the Hope Diamond, some blue diamonds' red light is overpowered by the blue green."

Impurities in the carbon that makes up a diamond create the color. For blue diamonds, boron impurities make the diamond blue in natural light. For yellow diamonds, nitrogen in the diamond creates the yellow hue. The spectrometer captures the properties of the impurities. Natural blue diamonds have high levels of boron and low levels of nitrogen impurities, and the interaction of these two elements probably causes the red phosphorescence.

When the researchers compared the peak intensities of the 500 and 660 nanometer bands against half the time it took for 660-nanometer light to dissipate, they realized that each diamond had an individual signature. They used the 660 band because the 500 band always disappears faster than the 660. That simple mathematical ratio produces a unique value for every natural blue diamond.

The researchers then tested three artificial diamonds – artificially created diamonds doped with boron. According to Heaney, companies can manufacture synthetic blue diamonds or heat treat other diamonds to create blue ones that are difficult to discern as artificial or altered with the naked eye, but using spectroscopy, these blue diamonds are not the same as the natural ones. All three of the synthetic diamonds lacked a peak at 660 nanometers.

The researchers from the Naval Research Laboratory have a long interest in diamonds because while white diamonds are insulators, colored diamonds, which have minute quantities of elements other than carbon, are semiconductors similar to the silicon currently used in most of today's electronics.

"Diamond's properties are superior to silicon because diamonds are one of the best conductors of heat, and smaller electronics need large capacities to dissipate heat," says Heaney.

The Penn State scientist is interested in methods to non-invasively fingerprint diamonds because of the problems with conflict diamonds – diamonds sold to support military action against legitimate governments – that have been a focus of Heaney's work for some time. Understanding the phosphorescence of blue diamonds may make it possible to physically identify individual blue diamonds to add to the current Kimberly Protocols, a paper trail method that ensures diamonds come from legitimate sources.
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Mon Jul 21, 2008 8:53 am    Post subject: Insightful Light Reply with quote

Insightful Light
By Ashley Yeager
July 18th, 2008

Raman spectroscopy may offer doctors, dentists and forensic scientists a better tool for molecular detection

From CT, PET and MRI to the original X, a vast alphabetical arsenal of tools tells doctors what is going on inside the body. But despite their successes, these tools often fail to detect the subtle changes that signal the imminent onset of illness. Mischief at the molecular level often evades doctors’ current imaging and detection abilities. So for sensing such changes, biomedical scientists are taking a tip from chemists. Using a method known as Raman spectroscopy, medical detectives are moving ever closer to exploiting the power of light to improve disease detection.

For the full article:

http://sciencenews.org/view/fe.....tful_Light
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Mon Aug 04, 2008 8:23 am    Post subject: New imaging technique reveals hidden details of a lost Van G Reply with quote

New imaging technique reveals hidden details of a lost Van Gogh painting
Analytical Chemistry
4 August 2008

European researchers are reporting the first use of a powerful new imaging technique to reveal with unprecedented detail a Van Gogh under a Van Gogh — the portrait of a woman hidden underneath one of the fabled Dutch Master's landscapes. Their study, which could provide new insights into the hidden details of other paintings, was scheduled for the July 29 online issue of ACS' Analytical Chemistry, a bi-weekly publication.

Joris Dik and colleagues note that Vincent van Gogh, one of the founding fathers of modern painting, saved canvas by painting-over as many as one-third of his early period works with new or modified pictures. However, current imaging tools used by museums are unable to clearly visualize many of these hidden images, which offer unique and intimate insights into the artist's works, the researchers say.

In the new study, the researchers used their new non-destructive technique, called Synchrotron Radiation-based X-Ray Fluorescence (XRF) Elemental Mapping, to analyze Van Gogh's Patch of Grass painting. Although conventional imaging techniques previously showed that the painting contained the hidden image of a woman's head, the details were blurred. The new technique reveals more detailed information about the chemical composition of the hidden paint layers. As a result, the scientists could construct a clearer and more colorful image of the hidden head. The image even includes brush strokes and facial features such as eyes, nose, mouth, and chin. The reconstructed image shows the dark, somber-head of a Dutch peasant woman, similar to a series of head portraits from Van Gogh's early career, the researchers say. — MTS

ARTICLE #1 FOR IMMEDIATE RELEASE
"A Lost Painting by Vincent van Gogh Visualized by Synchrotron Radiation-based XRF Elemental Mapping"

DOWNLOAD FULL TEXT ARTICLE
http://dx.doi.org/10.1021/ac800965g
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Mon Dec 15, 2008 1:08 pm    Post subject: Reply with quote

E/Z Conformation and the Vibrational Spectroscopy of Me2NN(O)=NOMe
D. Scott Bohle, Joseph Ivanic, Joseph E. Saavedra, Kamilah N. Smith, and Yan-Ni Wang
Journal of Physical Chemistry A 2005, 109, 11317-11321

The use of nitric oxide (NO) in chemistry and biochemistry has grown in importance over the recent years. Nitric oxide has various physiological functions such as: vasodilations (narrowing of the blood vessels),(1) platelet aggregation (clumping of platelets),(2) and neurotransmission (passage of ‘messages’ across an organ)(3) to name a few roles. Due to the vital role and growing interest, reactions where nitric oxide is produced have been further examined. One example of this is the examination of the nitrogen-bounded diazeniumdiolate ions. “Diazen” represents the N=N linkage, “ium” the formal positive charge, and “diolate” indicates the two negatively charged oxygens.(4) Nitrogen-bound diazeniumdiolates have a planar O-N-N-O system where two different orientations (isomers) can form. One is the Z (cis) configuration where the oxygens are on the same side of the double bond nitrogens; the other orientation is the E (trans) configuration where the oxygens are on opposite sides of the double bond.
The difference between these two isomers is not only configuration, but also the ability to produce nitric oxide. Many nitrogen-bound diazeniumdiolate ions have been shown to hydrolyze under physiological conditions to release two equivalents of NO, showing that this class of compounds are nitric oxide donors. However, nitric oxide is produced with only the Z isomer. The E isomer remains unknown as a non-ring condensed product. Despite the fact that the formation of diazeniumdiolates has been known for years, very few examples of the E (trans) configuration have been observed.
Authors of this paper explore a diazeniumdiolate with the structure R’R’NN(O)=NOR’ where R’=CH3. Previous theoretical investigations on similar diazeniumdiolates have indicated that these species could adopt both the E and Z configuration. The authors have attempted before to isolate and observe the E (trans) isomer of this particular diazeniumdiolate by Proton NMR, but this technique proved to provide inconclusive evidence. Therefore it was thought that another tool that may be more sensitive would be vibrational spectroscopy.(5)
Vibrational spectroscopy measures the excitation of a compound by the degree of rotation or vibration it exhibits when excited by light. There are two methods for measurement in vibrational spectroscopy, infrared spectroscopy and Raman spectroscopy. In infrared (ir) spectroscopy, light of all different frequencies is passed through a sample and the intensity of the transmitted light is measured at each frequency. On the other hand, in Raman Spectroscopy, the transmitted light isn’t observed, but instead the light scattered by the sample.(7)
The object of the study was to synthesis O2-methyl-1-(N,N-dimethylamino)diazen-1-ium-1,2-diolate [Me2NN(O)=NOMe]. Raman and infrared (FT-IR) vibrational studies were then performed on the structure. Next the spectrums were then compared to density functional theory calculations. These calculations were done at the B3LYP/aug-cc-pVDZ level for both the Z (cis) and E (trans) isomers. Through comparison of the two spectrums and the theory calculations, it was hoped that there was evidence of the E configuration and to be able to quantify how much of the trans isomer was present, which was previously unreported.
O2-methyl-1-(N,N-dimethylamino)diazen-1-ium-1,2-diolate [Me2NN(O)=NOMe] was prepared from sodium 1-(N,N-dimethylamino)diazen-1-ium-1,2-diolate. Proton and Carbon 13 NMR was conducted to indicate that Me2NN(O)=NOMe was produced. Vibrational studies were conducted by Raman and infrared (FT-IR) spectrometers. Computations were carried out at the restricted Hartree-Fock (RHF), density functional theory (DFT), and second-order Moler-Plesset (MP2) levels of theory. Vibrational frequencies were calculated for the optimized structures cis and trans along with their Raman intensities.
There are six tables presented in the paper, three for Raman bands and three for IR bands. For both Raman and IR, there was a table for the low-energy, a table of the fingerprint region and a table for the C-H stretching region. Each table had: the calculated intensity of the band for the cis and trans isomer, the experimental (actually observed) intensities of the band, and the difference between the two. The information presented for the calculated intensities are values from the DFT results. There was very good agreement between DFT and MP2 calculations, therefore there was no need to report both. Both methods agree on the nature of the vibrations, and so the calculated relative intensities are likely to reflect the relative amounts of the Z and E isomers.(5)
If there was a center of inversion, then a mode could not be both IR and Raman active. This is called the mutual exclusion rule.(6) However, since there is no center of inversion in the structure that is being examined, then it’s possible that a mode can be both IR and Raman active. There are three figures presented in the paper that show excellent correspondence between the observed frequencies of both Raman and IR spectra. In addition, the experimental frequencies also agree quite closely with the predicted DFT and MP2 vibrational frequencies.(5)
There were three vibration modes in the IR fingerprint region that were closely examined to determine if both cis and trans isomers were present. These three modes were chosen for three reasons. First, previous work done by some of the same authors demonstrated that diazeniumdiolate have strong coupling of the vibrational modes for the substituents and the O-N-N-O framework.(5) This known vibration movement between the substituent and the framework varies if the structure is cis or trans. This coupling and deformation of the O-N-N-O framework was calculated (by DFT) to occur at 1295.3 cm -1 (along with 1270.2 cm-1) for the cis isomer and 1352.2 cm -1 for the trans isomer. Second reason is that there is no other energies of bands in the region 1400 cm-1 to 1197 cm-1 except for the bands related to the deformation of the O-N-N-O framework. Therefore, if there was a peak to appear in the stated range, then it would have to be related to the O-N-N-O framework deformation. Finally, the calculated intensity for the band at 1295.3 cm-1 for the cis and 1353.2 cm-1 for the trans isomers are to be strong (the band at 1270.2 cm-1 for the cis isomer was calculated to have a medium intensity). Therefore, the bands should be easily seen on the IR spectra if the bands are expected to have strong intensities.
When the region between 1400 cm-1 to 1197 cm-1 was examined on the IR spectra, there was in fact three intensity bands as predicted but all three were shifted by 30-40 cm-1. Thus, the observed peaks at 1260.2 and 1222.9 cm-1 were for the cis isomer, and 1314.1 cm-1 was for the trans isomer. The intensity for the cis isomer bands were also as expected, strong for the band in the 1260.2 cm-1 range and medium intensity for the band at 1222.9 cm-1. The intensity band for the trans isomer was calculated to be strong, however it was observed to be very weak. Even though the band is very weak, the appearance of the band in the IR (and also present in the Raman) spectra, suggests that the trans isomer might be detected using vibrational spectroscopy.
The difference between the calculated and observed intensity of the trans band is most likely due to the concentration of trans isomer present compared to the concentration of cis isomer present. If the extinction coefficients for the cis and trans isomers are similar, then the relative concentrations within the isolated material can be determined by the integrated band intensities. The extinction coefficients are similar, and the calculations in the gas phase suggest that these modes do indeed have similar intensities, 87.0 km/mol for the cis (for band 1295 cm-1) and 87.6 km/mol for the trans (for band 1352 cm-1). Thus, integration is a good approximation of their relative concentrations. This means, that even though the trans was calculated to have a strong intensity, it was observed to be very weak because the concentration of the trans isomer was extensively less than the cis isomer. In fact, when integration of the 1260 and 1314 cm-1 bands in the IR were computed, it was concluded that the concentration of trans isomer was 1/200 that of the cis diazeniumdiolate.
Vibrational spectra for the diazeniumdiolate Me2NN(O)=NOMe indicates that if the E isomer is present, it corresponds to <0.002% of the total composition. When the concentration was attempted to be determined with proton NMR spectroscopy, the data proved to be inconclusive. It was determined that if the E isomer was present, it must represent <1% of the total composition. Vibrational spectroscopy proved to be a more sensitive technique, thus lowering the detection limit. Although there is very good correlation between the calculated and experimental results for the known Z isomer, the only way to verify the results for the unknown E isomer would be to synthesis the E isomer. Since there is a lack of a known preparative route to E-Me2NN(O)=NOMe, this will remain unknown. A general synthetic approach to both of these isomers remains an important challenge in this chemistry.(5)

References:
1. Vasodilation. Wikipedia, the free encyclopedia. http://en.wikipedia.org/wiki/Vasodilation. Wikimedia Foundation, Inc. 8 December 2008
2. Adhesion and aggregation. Wikipedia, the free encyclopedia. http://en.wikipedia.org/wiki/P.....gregation. Wikimedia Foundation, Inc. 8 December 2008
3. Neurotransmission. Wikipedia, the free encyclopedia. http://en.wikipedia.org/wiki/Neurotransmission. Wikimedia Foundation, Inc. 8 December 2008
4. Hrabie, Joseph; Keefer, Larry. Chem. Rev. 2002, 102, 1135-1154
5. Bohle, Scott; Ivanie, Joseph; Saavedra, Joseph; Smith, Kamilah; Wang, Yan-Ni. J. Phys. Chem. A. 2005 109, 11317-11321
6. Harris, Daniel C.; Bertolucci, Michael D.; “Symmetry and Spectroscopy.” An introduction to Vibrational and Electronic Spectroscopy. Dover Publications, Inc. New York ©1989. Pg. 159
7. Harris, Daniel C.; Bertolucci, Michael D.; “Symmetry and Spectroscopy.” An introduction to Vibrational and Electronic Spectroscopy. Dover Publications, Inc. New York ©1989. Pg. 93-94

Further Understanding:
What is NMR?
http://chem.ch.huji.ac.il/nmr/.....isnmr.html

What is Infrared (IR) Spectroscopy?
http://www.mtholyoke.edu/~mlyo.....tIsIR.html
http://www.wag.caltech.edu/hom.....frared.htm

What is Raman Spectroscopy?
http://carbon.cudenver.edu/pub...../raman.htm

What does it mean to be cis or trans?
http://www.chemguide.co.uk/bas.....etric.html

What are nitric oxide donors?
http://www.emdbiosciences.com/.....ursors.htm

What are the vibration modes for IR?
http://www.emdbiosciences.com/.....ursors.htm
http://www.reciprocalnet.org/e.....se.html#Ra

What is density functional theory?
http://www.physics.ohio-state.edu/~aulbur/dft.html

What is the Moller-Plesset perturbation theory?
http://en.wikipedia.org/wiki/M.....ion_theory

What is resticted Hartree-Fock?
http://vergil.chemistry.gatech.....intro.html

What is the center of inversion?
http://www.reciprocalnet.org/e.....rsion.html
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Tue Dec 16, 2008 9:08 am    Post subject: Reply with quote

Kelly Bogle


Near-Infrared Spectroscopy


Near-infrared spectroscopy (NIRS) is a technique that passes light through a sample using the near infrared region of the electromagnetic spectrum (approximately from 800 nm to 2500 nm). Information about that sample is then obtained from analysis of the resulting spectrum. NIR light has enough energy to cause overtones and combinations of molecular vibrations. Overtones occur when a single photon excites a mode beyond the v = 1 energy level. Combination bands occur when more than one vibration is observed from excitation by a single photon. NIRS is advantageous in not requiring much sample preparation.

In an article written by Arnold and coworkers, NIRS was used to determine glucose in whole blood and the scattering and absorption effects were analyzed. Since diabetes is so prevalent and is increasing rapidly, there is a need for simple and effective methods to measure glucose in whole blood. Whole blood is made up of several components, mostly red blood cells and plasma. The components in the blood having a different refractive index with respect to the plasma is a factor that give rise to light scattering. Glucose concentration has been shown to have an effect on the light scattering properties1.

Arnold and coworkers obtained measurements over the overtone region (10 000 –

5400 cm-1) and the combination region (5000 – 4000 cm-1). Bovine blood was used as a model for human blood. A glucose/lactate analyzer using a small sample of blood was used to measured glucose concentration in the bovine blood. The rest of the blood was allowed to flow through the sample cell of the IR spectrometer while spectra was being collected. Different quantities of dried glucose were then successively added to the blood for five different spectroscopy measurements. Calibration models for the spectral data were made using partial least-squares (PLS) algorithm. PLS is a statistical method that maximizes the overlap between variances in the spectral and concentration data matrices1. It was found that increase in glucose concentration resulted in lowered transmission of light through the blood in both the overtone and combination spectral regions1. Since the enormity of the decrease in intensity was too large to be attributed to the absorbance of glucose in the specified spectral regions, the decline in intensities was thought to be due to the scattering properties of the blood. The effect of glucose concentration on refractive index may be determined by the equation n = 1.325 + 2.73 x 10-5 x [Cg], where [Cg] is the millimolar concentration of glucose. A significant difference in refractive mismatch of the components in the blood is necessary to result in the increase in scattering observed with increasing glucose concentration. Therefore, glucose is the primary affects the scattering effects of whole blood. From the PLS calibration model for glucose measurements in the combination region spectra, it was found that both the prediction and calibration data points followed the unity line. The same results were obtained for the first overtone spectral region but there was slightly more scatter. Thus, the best calibration model was obtained from the combination spectra.



1. Arnold, M. A.; Amerov, A. K; Chen, J.; Small, G.W. Anal. Chem. 2005, 77, 4587–4594.


Questions to further explore this topic:

What is near-infrared spectroscopy (NIRS)?

http://www.spectroscopynow.com.....amp;page=1

http://elchem.kaist.ac.kr/vt/c.....ib/nir.htm

What is the electromagnetic spectrum?

http://imagine.gsfc.nasa.gov/d.....ctrum.html

http://csep10.phys.utk.edu/ast.....ctrum.html

What are overtones?

http://books.google.com/books?.....#PPA164,M1

What are combination bands?

http://books.google.com/books?.....#PPA164,M1

How does NIRS detect compounds?

http://www.800mainstreet.com/irsp/eir.html

What is refractive index?

http://www.brooklyn.cuny.edu/b......Main.html

http://www.matter.org.uk/Schoo.....index.html

What are energy levels?

http://cas.sdss.org/dr6/en/pro.....levels.asp

http://www.colorado.edu/physic.....bohr2.html

What is a calibration model?

http://www.icalibra.com/index......;Itemid=25

What is the partial least-squares (PLS) algorithm?

http://www.statsoft.com/textbook/stpls.html

http://www.ats.ucla.edu/stat/sas/library/pls.pdf

http://www.thermo.com/com/cda/.....29,00.html

What is absorbance?

http://www.uwplatt.edu/chemep/.....strans.htm

What is wavelength?

http://www.lindahall.org/educa.....riment.pdf

How is concentration related to the absorbance?

http://teaching.shu.ac.uk/hwb/.....beers1.htm

How is intensity related to absorbance?

http://elchem.kaist.ac.kr/vt/c.....erslaw.htm

http://teaching.shu.ac.uk/hwb/.....beers1.htm

What does an infrared spectrum look like?

http://www.spectroscopynow.com.....amp;page=1

What are the components of whole blood?

http://www.aabb.org/Content/Ab.....dwhole.htm

http://www.cancer.org/docroot/.....onents.asp

What is glucose?

http://www.elmhurst.edu/~chm/v.....ucose.html

FUN TRIVIA

http://www.funtrivia.com/playq.....e26d8.html
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:23 am    Post subject: Reply with quote

Katy Sherlach

NMR Spectroscopy

Professor de Dios

December 15, 2009

Final Paper

The mineral copper has important roles in the biology of the human body. Typically stored in the liver, muscles, and bones, copper is involved in the action of several enzymes, the absorption of iron, and the metabolism of fats. Low levels of copper can lead to anemia-like symptoms, while high levels of copper cause the symptoms associated with Wilson’s disease.1 For those who are afflicted with Wilson’s disease, a mutated recessive gene causes the body to be unable to remove excess copper from the liver in the form of bile. The subsequent build-up results in toxic effects. As a result, the copper enters the blood and moves to other organs in the body, such as the brain, kidneys and eyes. The build-up of copper in the iris leads to the characteristic discoloration known as Kayser-Fleischer rings. Other symptoms of Wilson’s disease include the swelling of the liver and spleen, tremors, and behavioral changes. The effects on the liver are so severe that Wilson’s disease, if not treated, can lead to death through liver failure. Wilson’s disease is typically diagnosed through an examination for Kayser-Fleischer rings in the eye, or through laboratory tests on blood, urine and liver tissue. Genetic testing can also be used, focusing on the mutated ATP7B gene that causes the disease. However, the symptoms are similar to those of other disorders, and may be misdiagnosed due to the rarity of Wilson’s disease.2

In their paper, “Estimation of free copper ion concentrations in blood serum using T1 relaxation rates”, published in the Journal of Magnetic Resonance, Blicharska, Witek, Fornal, and MacKay demonstrate a new method of measuring copper ion concentrations in blood serum, which can potentially be used as a new method of diagnosing Wilson’s disease. The authors utilize a nuclear magnetic resonance (NMR) spectrometer to determine the level of copper 2+ ions (Cu2+). NMR is a chemical method used to examine compounds in a very strong magnetic field, tens of thousands times more powerful than the earth’s magnetic field. Atomic nuclei respond to radio-frequency energy differently in the strong magnetic field, depending on the chemical environment in which they are located. The radio-frequency energy excites the nuclei, which relax at measurable rates. The parameter T1 is inversely proportional to the relaxation rate.

Copper’s nucleus is not very responsive to NMR examination, so direct quantification is not feasible. However, the authors chose to take advantage of a chemical property of copper in their examination. Cu2+ is known as a paramagnetic species, meaning it has an unpaired electron. Paramagnetic species have a significant impact on the NMR properties of other compounds in the sample. In the case of this study, the unpaired electron in Cu2+ is altering the relaxation rate of the hydrogen atoms of water molecules present in the blood serum, shortening their T1 time. In order to relate the T1 of water in blood serum to the amount of Cu2+ present, the authors used a compound known as D-penicillamine (D-PEN). D-PEN reacts with Cu2+, forming a stable compound that significantly reduces copper’s paramagnetic effect. By adding D-PEN to a sample of blood serum and examining the changes in water’s T1, the initial concentration of free Cu2+ ions in the blood can be calculated. A larger change in T1 would indicate a Wilson’s disease sample. Samples with high levels of copper ions were found to have a change in the T1 time of up to 16 seconds as D-PEN is added to the sample.

The use of NMR T1 examination of blood samples in testing for the elevated copper levels associated with Wilson’s disease is promising. The process is quick and inexpensive, making it attractive to medical professionals. Additionally, unlike other laboratory tests, this method is specific for free, unassociated copper ions, which are much more toxic than copper ions which may be contained in proteins in the blood. In the future, NMR spectroscopy may become a large part of diagnosing Wilson’s disease before significant and detrimental symptoms manifest.3


Questions to further explore this topic:


What is copper?

http://www.chemicalelements.com/elements/cu.html

http://en.wikipedia.org/wiki/Copper


What is the role of copper in the body?

http://www.essortment.com/all/.....l_rszx.htm

http://en.wikipedia.org/wiki/C.....gical_role


How much copper is in your body?

http://www.webelements.com/copper/biology.html


What is Wilson’s disease and what are some of its symptoms?

http://digestive.niddk.nih.gov.....bs/wilson/

http://www.mayoclinic.com/heal.....se/DS00411


What is NMR?

http://www.weizmann.ac.il/Chem.....s_NMR.html
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:24 am    Post subject: Reply with quote

Kayla Lincoln

NMR Spectroscopy

Professor de Dios

December 15, 2009


Nuclear magnetic resonance (NMR) is a very useful technique for identifying structural elements in compounds. In this particular study, the heteronuclear single quantum coherence (HSQC) NMR technique was employed to test for the presence of lignins in pear, kiwi, rhubarb, and wheat bran samples. The detection of lignins was important because they are an essential part of dietary fiber, which has many health benefits and is a fundamental part of a daily diet.

Dietary fibers have been known to benefit human health through the processes of laxation, and/or blood cholesterol attenuation, and/or blood glucose attenuation. These fibers are composed of polysaccharides, oligosaccharides, lignin, and associated plant substances, but for the sake of this work only the lignin component of dietary fibers will be investigated. This is due to the fact that lignins are a main component of insoluble dietary fibers and have been shown to be efficient antioxidants. Most reports of sufficient sources of lignins only investigate wheat bran, but since lignins seem to have many health benefits (composing dietary fibers and acting as antioxidants), it was of interest to investigate other systems that may contain them. Since brans are well-known sources of lignins, the authors turned to fruits and vegetables – namely kiwi, pear, and rhubarb – to investigate the amount of lignins present that comprise insoluble dietary fibers.

The 1D 1H and 2D HSQC NMR methods were used to obtain structural information and assign appropriate lignin peaks among the samples. The 1D 1H NMR was used to determine the environment of the different protons attached to carbon atoms in the lignins. The 2D HSQC NMR experiment was used to determine the connectivity of the 1H and 13C atoms of the molecules. Since the wheat bran is a known source of insoluble dietary fiber, its spectrum was used as the standard, which the other spectra were compared to. It is not difficult to identify specific lignins that constitute dietary fibers, as they tend to show considerable diversity in NMR spectra. Based on the heteronuclear single quantum coherence spectra obtained, it was determined that the kiwi, pear, and rhubarb were all significant sources of dietary fiber. There was no clear consensus as to which of the fruits and vegetables was most comparable to wheat bran, as where one lignin was prominent in one it was weak in another. However, through this NMR experiment it was shown that dietary fiber could be obtained in adequate amounts from sources other than wheat bran.


References:

Bunzel, M.; Ralph J. J. Agric. Food Chem. 2006, 54, 8352-8361.




Questions to further explore these topics:


What is lignin?

http://en.wikipedia.org/wiki/Lignin


How much dietary fiber does the average human need per day?

http://www.carbs-information.c.....-needs.htm

http://www.healthcalculators.o...../fiber.asp


What are other sources of dietary fiber?

http://www.wehealny.org/health.....index.html


What are the health benefits of dietary fiber?

http://www.carbs-information.c.....nefits.htm


What are the health benefits of the kiwi?

http://kiwi-fruit.info/kiwi-fr.....Kiwi+Fruit

of the pear?

http://www.juicing-for-health......-pear.html

of rhubarb?

http://www.zhion.com/herb/Rhubarb.html


What is heteronuclear single quantum coherence spectroscopy?

http://en.wikipedia.org/wiki/HSQC
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:25 am    Post subject: Reply with quote

One doesn’t always think about the relevance of cheese to their daily life. It calmly sits in your refrigerator and makes a nice complement to a cracker or on a sandwich, but cheese holds an important place in history. Although the origins of cheese are unknown, it is a very ancient thing. It was referred to in Homer’s Odyssey. Mass production of cheese was documented on the Italian peninsula just around 800 BCE. It is said to have been partly responsible for the ability of Roman armies to expand and dominate the Mediterranean. Having a mobile food source high in fat content and proteins allowed the Roman military to travel far from their home and conquer. It is from this tradition that many of the world’s most famous cheese find their origins.

One such example is grana padano, produced in the Padano River valley south of Milan. It is probably very similar to the types of cheeses used by the ancient Romans. It is very hard, has a relatively high fat content, and doesn’t spoil for several years. A great deal of chemistry takes place in each wheel before it is consumed. Although the milk and enzymes used in each day’s batches are the same, the end product can vary greatly due to the conditions while it “ripens”. The water content throughout the sample of cheese and amino acid content can be altered by the season, the humidity, how the fat distributes itself, as well as many other variables.

How the cheese ripens as well as whether a wheel of cheese has had sufficient time to ripen can be determined by use of nuclear magnetic resonance of various samples. The advantage to using NMR to study cheeses is that it is non-damaging and it can study all of the materials in the sample simultaneously. The content of water throughout the sample as well as the amount of free versus bonded amino acids throughout the cheeses elucidate a great deal about the cheese in question. The NMR studies can determine what atoms are bound on what and therefore where they are all located relative to one another.

Water can be either free to move or trapped in specific locations in the cheese. Looking at the hydrogen atoms of the water molecules, you can determine how much of the water is freely moving and how much is trapped. This helps determine what the texture of the cheese will be like at that point. In addition to looking at the water, seeing whether the proteins from the milk have broken down into their more elementary amino acid pieces is important to the taste of the cheese. The proteins are primarily broken down by the casein enzyme. This also produces lactic acid as it breaks them down. The lactic acid is a big component in the taste of cheese. Studying a wheel of cheese from different batches of the cheese allow the NMR to see how they differ from batch to batch. Comparing the resulting cheese to the conditions it ripened under would therefore give them an understanding of how those conditions affect the final product. It can also quickly remove any wheels that may have spoiled or are more immature than the rest to ensure quality control.

This new analytical method for the cheese has granted people a great deal more insight into how the cheese ripens. It also gives a noninvasive ways to quantitatively measure the effects of the different conditions on the outcome of the cheese. In addition to these two benefits, it can weed out bad cheese and improve the quality control for grana padano cheese producers. Although the production of grana padana hasn’t changed in a millennium, this technique can give interesting new insight into this age old tradition. Innovative science can have a direct impact in today’s world even for something as ubiquitous as cheese.


Reference:

Amino acid profile in the ripening of Grana Padano cheese: a NMR study

S. de Angelis Curtis, R. Curini, M. Delfini, E. Brosio, F. D'Ascenzo, B. Bocca


What is cheese?

http://www.cheese.com/facts1.asp

http://www.cheesesociety.org/d.....iclenbr=51

Who is Homer?

http://www.online-literature.com/homer/

http://facstaff.gpc.edu/~shale.....homer.html

What is the Odyssey?

http://books.google.com/books?.....mp;f=false

http://www.sparknotes.com/lit/odyssey/

http://classics.mit.edu/Homer/odyssey.html

Who were the Romans?

http://www.roman-empire.net/

http://www.historyforkids.org/learn/romans/

http://www.pbs.org/empires/romans/

Where is the Mediterranean?

http://www.worldatlas.com/aatl.....medsea.htm

http://www.geographicguide.net.....ranean.htm

http://iam.classics.unc.edu/

How is Grana Padano cheese made?

http://www.igourmet.com/granapadano.asp

http://entertaining.about.com/.....padano.htm

http://www.nydailynews.com/lif.....ano_v.html

What is fat?

http://kidshealth.org/kid/stay.....d/fat.html

http://www.americanheart.org/p.....ifier=4582

http://health.nytimes.com/heal.....rview.html

What are amino acids?

http://www.biology.arizona.edu.....aa/aa.html

http://www.chem4kids.com/files/bio_aminoacid.html

http://www.wisegeek.com/what-are-amino-acids.htm

http://www.nyu.edu/pages/mathm.....life1.html

What is hydrogen?

http://www.webelements.com/hydrogen/

http://education.jlab.org/itselemental/ele001.html

What is casein?

http://www.wisegeek.com/what-is-casein.htm

http://vegetarian.about.com/od.....Casein.htm
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:26 am    Post subject: Reply with quote

NMR of SARS-CoV

Lisette Fred – December 15, 2009

Severe acute respiratory syndrome coronavirus (SARS-CoV) plagued areas of China during the mid-2000s causing uproar and fear throughout the entire world. SARS-CoV consists of two envelope proteins, S1 and S2, which control the binding and fusion of the viral cell membrane with the target human cell membrane. Glycoprotein S2, which controls the fusion of the membranes, undergoes a series of secondary structure conformational changes from the prefusion to transition and finally postfusion states. S2 contains areas that are highly prone to form helices called HR2 and HR1. It has been previously determined, in the postfusion state, that HR1 and HR2 associate individually into a bundle of three helices and then associate with one another in an antiparallel manner to form a “6 helix bundle”. Like in the postfusion state, the prefusion state also consists of a set of three coiled coils that undergoes a conformation change into a single unstructured transition state.

A dynamic understanding of the conformational changes between the prefusion and the transition states can give insight into design of antiviral drugs that disrupt the formation of this “6 helix bundle” in the postfusion state. Using nuclear magnetic resonance (NMR) experiments, the hydrogen and nitrogen nuclear environments of the protein can be studied by analysis of spectral density mapping, relaxation times, and hydrogen Nuclear Overhauser Effect (HNOE) in both the prefusion and transition states.

Generally speaking, when a protein is tightly coiled it tumbles quickly in solution – fast correlation time - and when a protein contains no secondary structure it tumbles slowly in solution – slow correlation time. Using spectral density maps, the change in correlation time of the amino acid residues in HR1 and HR2 can be monitored at different frequencies. Thus an increase in spectral density map indicates a decrease in correlation time. On the other hand, no change in spectral density signifies an unstructured form in agreement with the spectral density map of a denatured protein. Under the different solvent conditions for each respective state, the spectral density map agreed with the expectations.

Furthermore, determination of heteronuclear relaxation rates of nitrogen and hydrogen also provides evidence for the change in secondary structure in the two individual states. In order to distinguish between the two states, properties of protein solvents were changed. The solvents needed to replicate the prefusion state contained tetrafluoroethlyene (TFE) to induce the helical state of the coiled coils. Similarly to mimic the transition state, the viscosities of the solvents were decreased and the temperature was increased to induce the unstructured conformation. The results from the determination of longitudinal relaxation time under these conditions are consistent with the understanding that correlation time is directly related to longitudinal relaxation time, which is time it takes for the nuclear spins of the nitrogen atoms to return to its original state. Thus, as expected the longitudinal relaxation time, as well as the correlation time, increased from the prefusion to the transition state. Decrease in HNOE calculations show in the transition state the nitrogen and hydrogen atoms are no longer close enough in space for the nitrogen to transfer it excess energy to hydrogen, consistent with the idea that the transition state is unstructured. The transverse relaxation time also decreases from the prefusion to the transition state indicating for the unstructured transition state the signal in the spectrometer from nitrogen decays faster than the signal from nitrogen in the prefusion state.

Clearly, NMR is an excellent tool to provide evidence for the structure of the prefusion and transition states of the SARS-CoV S2. Each experiment and corresponding calculation showed a deeper understanding of the nitrogen and hydrogen environment in the protein, providing insight into its secondary structure under different conditions.

McReynolds, S., Shaokai, J., Rong, L., Caffrey, M. Dynamics of SARS-coronavirus HR2 domain in the prefusion and transition states. Journal of Magnetic Resonance. 2009. 201: 218-221.

What is a virus?

http://www.ucmp.berkeley.edu/alllife/virus.html

http://www.mcb.uct.ac.za/tutorial/virwhat.html

http://www.slic2.wsu.edu:82/hu.....hap11.html

What are cell membranes?

http://users.rcn.com/jkimball......ranes.html

http://micro.magnet.fsu.edu/ce.....brane.html

What is membrane fusion?

http://www-bioc.rice.edu/bios5.....usion.html

What is a glycoprotein?

http://www.ncbi.nlm.nih.gov/bo.....part=A1531

What is a peptide bond?

http://www.peptideguide.com/peptide-bond.html

http://phschool.com/science/bi...../pepb.html

http://www.wisc-online.com/obj.....jID=BIC007

What is secondary structure?

http://www.chembio.uoguelph.ca.....6lec01.htm

http://en.wikipedia.org/wiki/S.....References

What is an alpha helix?

http://www.web-books.com/MoBio/Free/Ch2C4.htm

http://www.youtube.com/watch?v=eUS6CEn4GSA

What is a conformation change in proteins?

http://www.cryst.bbk.ac.uk/PPS.....oj_Vun.htm

http://www.stolaf.edu/people/g.....enzyme.swf
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:27 am    Post subject: Reply with quote

Alexander Gorka December 15, 2009

CHEM-525 Prof. de Dios


Elucidating the Behavior of Heme in Aqueous and Mixed Aqueous Solution via UV-Vis and Nuclear Magnetic Resonance (NMR) Spectroscopy


Hemoglobin is a large protein responsible for the transport of oxygen through the bloodstream to the various cells and tissues that require it to perform their daily functions. The portion of the protein directly involved in this process is called heme, or more precisely ferriprotoporphyrin IX (Fe(III)PPIX). Hemoglobin contains four such molecules, each of which consists of a paramagnetic ferric ion (Fe3+) surrounded by a large planar aromatic system. Two propionic acid side chains protrude from one side of the aromatic plane. It is this ferric center that binds an oxygen molecule and enables the role of hemoglobin as the body’s oxygen highway. Of course, much has been studied regarding the structure, chemical kinetics, signaling, and intermolecular interactions of hemoglobin and its oxygen transport. However, it is the lesser known role of heme in the propagation and treatment of disease that will become the focus of this article.


Heme has been implicated in several conditions affecting humans. The improper release of heme from proteins such as hemoglobin has been shown to occur in atherogenesis (buildup of plaque on the walls of arteries) and some cancers. Once liberated, this free heme has the potential to indiscriminately damage cells and tissues through oxidative stress and the formation of reactive free radicals. Several bacteria including Staphylococci and Streptococci scavenge heme for iron, which is necessary for their growth and metabolism. The human malarial parasite Plasmodium falciparum degrades host cell hemoglobin for amino acids, liberating heme in the process. Not unlike the host, this free heme is particularly toxic to the parasite. Its evolution has therefore favored the development of an elaborate heme detoxification pathway, in which free heme is crystallized into a nontoxic substance called hemozoin (malaria pigment). This crystallization process immediately emerges as a potential drug target – i.e. if one can inhibit the detoxification of heme, the parasite’s proliferation can, in theory, be slowed and eventually stopped completely. Quinoline-based drugs such as chloroquine and quinine have long been effective at inhibiting heme crystallization but are quickly becoming less and less potent as drug resistant parasite strains spread. Existing drug pharmacophores (the active part of the molecule) must continuously be modified and new ones developed to counter the spread of resistance. Paramount to achieving such a goal is to not only understand the drugs themselves but the nature of their heme target.


A hoard of researchers dating back to the late 1940s have shown evidence for the complex speciation behavior of Fe(III)PPIX in aqueous and mixed aqueous-organic solution. That is, depending on the pH, salt concentration, heme concentration, and organic solvent, the heme molecule can assume a variety of supramolecular conformations. These include monomer, π-π dimmers (in which the planar aromatic system of one heme interacts with that of another), μ-oxo dimmers (in which two heme molecules are bridged by an oxygen atom to form an Fe—O—Fe bond), and π-stacked aggregates of μ-oxo dimers. Building on previous findings from others in the field and their own laboratory, Egan and colleagues out of South Africa employ UV-visible and NMR spectroscopy in generating a unified picture of the behavior of heme in aqueous and mixed aqueous solution. The full bibliographic information for this study as well as links to some general knowledge information on the topics presented appear at the end of the article.


Before considering their findings, let’s first examine why these spectroscopic methods are applicable to probing the behavior of heme in solution. UV-vis spectroscopy takes advantage of the transitions of electrons between electronic energy levels in molecules. When these electrons move between these levels, they either absorb or emit a photon of energy corresponding to the magnitude of the transition. Monomeric heme absorbs light (photons) at a characteristic wavelength, as does π-π dimeric and μ-oxo dimeric heme. This absorption phenomenon is recorded by the instrument as a peak in a spectrum. Tracking the wavelength at which the maximum peak occurs enables one to determine which species predominates in a given solution.


NMR spectroscopy utilizes a large magnet to gain insight into the structural characteristics of molecules. Take, for example, a solution of heme. The solution is placed into a narrow glass tube which is then placed inside the magnet of the spectrometer. The proton and electron-containing cores (nuclei) of the atoms that make up the molecule are themselves tiny magnets, and thus begin to interact with the large magnet by spinning at characteristic frequencies. This unique frequency is manifested in the main output parameter of the NMR spectrum – the chemical shift. Monomeric heme has a specific chemical shift signature; a signature that responds in a definite manner when that monomer interacts with the π system or paramagnetic iron center of another. For example, when the π-π dimer forms, peaks that were once sharp in the monomer NMR spectrum become broad and may shift to a higher or lower frequency in the spectrum depending on the nature of the interaction. Other NMR parameters such as coupling and relaxation also respond in characteristic ways. The latter is especially effected by the paramagnetic iron center, whose unpaired electron efficiently brings about the relaxation, or return to equilibrium, of the nuclei.


Using these two spectroscopic methods, and variations on the same, Egan and coworkers explore the effect of organic solvent, salt concentration, pH (a measure of the acidity of the solution), temperature, and monomeric heme concentration on the formation of the various heme solution structures. In making their assignments, the authors rely on previously established UV-vis and NMR profiles for the π-π and μ-oxo dimer. Of particular importance are the magnetic moments (μ) of these complexes as determined by a special type of NMR measurement called magnetic susceptibility or the Evan’s method (see link describing the same). By comparing the known magnetic moments of the dimers with the species observed in solution, it is possible to pinpoint which predominates under a given set of conditions. The authors report the following key behaviors for heme: (1) Fe(III)PPIX forms μ-oxo dimer in 40% (v/v) aqueous DMSO at pH 10 but not aqueous methanol at the same pH, (2) aprotic solvents such as DMSO, acetone, DMF, and THF all promote μ-oxo dimer formation at pH 10 while protic solvents such as methanol, ethanol, and ethylene glycol give rise to mostly π-π dimer under the same conditions, and (3) high salt concentration (4.25 M NaCl) reveals the formation of π-stacked aggregates of μ-oxo dimers at pH 10. It should be noted that another dimer form exists. This is the head-to-tail dimer in which the propionic acid side chains of one monomer hydrogen bond to those of another. The pH 10 condition ensures these carboxylic acid groups are deprotonated, and thus have no hydrogens with which to hydrogen bond.


The importance of these findings, as well as a wealth of studies that precede it, is twofold. On one hand, knowing the predominant species of heme in a particular solvent system greatly aids in vitro (not within a living organism) experimentation regarding heme-heme and heme-drug interaction. That is, if a particular drug is known to interact with the μ-oxo dimer, the correct solvent conditions can immediately be selected for testing. On the other hand, the biochemist now has a basis for comparison of in vivo (within a living organism) results. For example, a researcher has isolated a cellular compartment of a malarial parasite which is known to have a very specific salt concentration. Using the results of the Egan study, that researcher will know (or be able to quickly determine via similar UV-vis and NMR experiments) the predominant form of the heme drug target in that isolate. Rational drug design is thus facilitated, as the pharmacophore can be fine tuned to its intended target.


NMR experiments will undoubtedly continue to be an integral tool in drug development for not only malaria, but a wide range of human afflictions. It is in this capacity that NMR is not only a means of chemical analysis but an instrument at the frontlines of the fight against drug resistance – an instrument quite literally played by the frequencies of the nuclei inside its magnet.



Bibliographic Information


Asher, C.; de Villiers, K. A.; Egan, T. J. Speciation of Ferriprotoporphyrin IX in Aqueous and Mixed Aqueous Solution Is Controlled by Solvent Identity, pH, and Salt Concentration. Inorg. Chem. 2009, 48, 7994-8003.


Useful Links


Hemoglobin & Heme

http://sickle.bwh.harvard.edu/hemoglobin.html

http://www.umass.edu/molvis/tutorials/hemoglobin/

http://omlc.ogi.edu/spectra/he.....index.html


What is an aromatic compound?

http://www.cem.msu.edu/~reusch.....react3.htm


What is a paramagnetic substance?

http://www.ndt-ed.org/Educatio.....cMatls.htm


Malaria (these links go to general sites which then link to a variety of topics including drug resistance, antimalarial drugs, etc.)

http://www.cdc.gov/malaria/index.htm

http://www.who.int/topics/malaria/en/

http://www.malaria.org/

Laboratory Website of Timothy Egan

http://web.uct.ac.za/depts/cem.....c/egan.htm


What is UV-Vis Spectroscopy?

http://www.cem.msu.edu/~reusch.....ectrum.htm

http://www.sci.sdsu.edu/TFrey/.....scopy.html


What is NMR Spectroscopy?

http://www.cem.msu.edu/~reusch.....r/nmr1.htm

http://www.cis.rit.edu/htbooks/nmr/


Organic Chemistry Acronyms

http://www.chem.wisc.edu/areas.....ronyms.pdf


Properties of Common Organic Solvents

http://organicdivision.org/organic_solvents.html


What is a Protic vs. Aprotic Solvent?

http://www.usm.maine.edu/~newt.....vents.html


What is a Carboxylic Acid? What is Propionic Acid?

http://www.chemguide.co.uk/org.....round.html

http://en.wikipedia.org/wiki/Propionic_acid


What is Hydrogen Bonding?

http://www.elmhurst.edu/~chm/v.....nbond.html


What is a Magnetic Moment?

http://hyperphysics.phy-astr.g.....agmom.html


What is a Magnetic Susceptibility Measurement and How is it Performed?

http://www.cem.msu.edu/~cem472/magsus.pdf
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:27 am    Post subject: Reply with quote

NMR and Orange Trees

Kaitlyn Gerhart

First seen in Brazil in 1999, citrus sudden death syndrome (CSD) is a disease that plagues sweet orange and mandarin orange trees that are grafted on Rangpur lime and Citrus volkameriana rootstocks. Infecting more than 400 million trees, CSD is a grave threat to the citrus industry in Brazil because 85% of their 200 million sweet orange trees are grafted on Rangpur lime rootstock. The underlying cause of CSD is still unknown, but there are a few theories as to its origin. One theory is that it is caused by a virus similar to Citrus tristeza virus (CTV) because the diseases share similar traits. CTV is a virus transmitted by certain aphids which also kills citrus trees. Scientists have analyzed CTV samples from CSD trees, but have found no differences between those trees affected with CSD and those that are unaffected. A second theory about the cause of CSD is that an entirely new virus from the Marafivirus genus is at fault or that this virus works in conjunction with CTV. This new virus is fittingly called Citrus sudden death-associated virus (CSDaV).

There are several outward symptoms of CSD in orange trees. Afflicted trees have fewer than the normal number of new shoots, no internal shoots, and discoloration and loss of leaves. These symptoms become worse as the disease progresses and eventually the tree dies. Studies have shown that the bark near the tree buds undergoes several profound physical changes. These changes include degradation, reduction in size, and overproduction of the phloem, the tissue responsible for transporting nutrients throughout the tree. There is also necrosis and collapse of sieve tubes, which are part of the phloem. In addition to affecting the leaves and buds of the tree, CSD also destroys the roots from the tips up. The eventual death of the tree is ultimately caused by the inability to absorb large amount of water in times of need, such as when producing fruits and developing new shoots.

In order to study CSD and also rapidly identify affected trees, nuclear magnetic resonance (NMR) was employed. One of the original ways CSD was identified in trees was by looking for a yellow stain on the bark of the Rangpur lime rootstock. This way is not always reliable, however, so NMR determination of the oil content in the rootstock bark has been proposed as a complementary method for identifying afflicted trees. Using low resolution NMR, 300 samples can be screened per hour. The technique used was performed directly on freeze dried bark samples and ultimately measured the strength of the free induction decay signal (FID) at 70 microseconds after the pulse. This value is related to the concentration of certain apolar lipids (oils) in the rootstock bark. Prestes’ group found that the concentration of oils in the rootstock bark increases by a measurable amount when the plant is infected with CSD.

Prestes’ group also found higher concentrations of sugars and lipids in fresh bark samples of symptomatic CSD plants by proton NMR. This method is rapid and could be used to determine if plants are infected with CSD, but it is very sensitive to the moisture content of the sample. The oil content of dry bark can be determined by high resolution proton NMR, but each sample would take several minutes making this technique not ideal for quick diagnosis.

NMR experiments performed on samples in situ showed interesting trends involving sucrose and lipids. Symptomatic plants showed greater concentrations of these compounds, as well as a greater concentration of proline, an amino acid. These trends are representative of the plant’s response to water stress. This supports the blockage and damage of the phloem by this disease.

Ultimately, the technique most useful for quick and effective screening of CSD infected trees is low resolution proton NMR where the strength of the FID at 70 microseconds is quantified. Although the other techniques reported in Prestes’ paper provide useful information about the disease, they are either too long or too moisture sensitive to be used for quick screening.


Reference

Prestes, R. A.; Colnago L.A.; Forato, L.A.; Carrilho, E; Bassanezi, R.B.; Wulff, N.A. Molecular Plant Pathology. 2009, 10, 51.


What is an orange?

http://en.wikipedia.org/wiki/Orange_%28fruit%29

How can I grow my own oranges?

http://www.gardenguides.com/83.....anges.html

What are the different types of oranges?

http://www.hort.purdue.edu/new.....#Varieties

What other diseases affect oranges?

http://www.hort.purdue.edu/new.....#Varieties

What is citrus sudden death syndrome?

http://edis.ifas.ufl.edu/hs243

What is Rangpur lime?

http://www.hort.purdue.edu/new....._lime.html

How and why are trees grafted?


http://www.midfex.org/m/whygraft.html

http://en.wikipedia.org/wiki/Grafting

http://www.extension.umn.edu/d.....g0532.html
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:30 am    Post subject: Reply with quote

Nuclear Magnetic Resonance (NMR) Spectroscopy: Practical Applications in Civil Engineering

Non-Destructive Testing in Civil Engineering 2003 by Bernd Wolter, Frédéric Kohl, Nina Surkowa, Gerd Dobmann

International Symposium (NDT-CE 2003)


Civil engineering is a discipline within the engineering profession which handles the planning, production and preservation of the physical and naturally built environment, such as such as bridges, roads, canals, dams and gardens. Following the age-long tradition of military engineering, civil engineering is the oldest engineering discipline. Traditionally, civil engineering has been known to compose of several sub-disciplines, including environmental engineering, geotechnical engineering, structural engineering, transportation engineering, municipal engineering, water resources engineering, materials engineering, coastal engineering, surveying, and construction engineering. These forms of civil engineering can be found in all public, private, and federal sectors of development in any rural or municipal area.

The greatest obstacles generally hindering the operations of civil engineering is lack of sufficient tools for accurate measurement of water levels within various construction materials. Currently employed water-monitoring technique is known as Time Domain Reflectometry (TDR) Trase. Developed as the result of World War II radar research, Trase employs the principle of TDR in order to convert the travel time of a high frequency, electromagnetic pulse into volumetric water content. Despite its great effectiveness in the determination of water content in soil, Trase has failed to provide accurate water content data analysis in solid (wooden, brick, concrete, etc.) constructions. Other means of acquiring such data, mainly the A.S.T. drying system, remain arduous to utilize due to their size and require the vaporization of the water from a significant portion of the sample in order for precise measurements to be obtained.

One-Sided Access (OSA) NMR is a new type of instrumentation employed by Bernd Wolter’s research group to determine their properties of water storage and transport in porous materials. Much like an ultrasound reflection sensor, such as the TDR Trase, it can be applied from one side to the specimen, which unlike in Trase can be a building wall, and supplies depth-resolved information about its internal structure of the specimen, including its moisture depth-profile. In addition, this NMR technique can provide detailed data on the porosity, pore-size distribution within almost any construction material. This unique water monitoring technique has already proved itself in a number of geophysical applications, such as subsoil investigations, and architectural monitoring, such as monitoring of the drying process in fresh concrete. Determination of the water tightness within building structures using OSA NMR has allowed detection of environmental durability problems in their early stages, preventing unexpected fallout damage due to moisture ingress. OSA NMR main attribute which spearheads its growing use in civil engineering is its ability to conduct non-destructive testing on the samples used in everyday construction.

NMR’s increasing utilization in the investigation of water content by civil engineers is a result of its ability to provide clear spectra of water distribution within almost any material as well as reliable information about its physical state. The amplitude of the protons (a subatomic particle with a base electric charge of plus one) in 1H-NMR signal represents a measure of the hydrogen density proportional to the water content of the sample. The success of NMR in this highly accurate form of water content measurement stems from its lack of reliance on any changes of physical properties. Rather, NMR directly detects the hydrogen content and with it the moisture content in the material in a form of a direct linear dependence. Imaging of the water content distribution through this method allows precise study of the actual moisture situation within and around a desired site. Rapid acquisition of the data, further allows for the monitoring of time-dependent processes, such as material absorption, desorption and water migration during capillary flow and drying. This allows civil engineers to calculate liquid transport coefficients and storage parameters in a great number of construction materials with the OSA NMR instrumentation. The knowledge of these constants allows architects and other construction experts to conduct basic one- and two-dimensional data calculation of heat and moisture transport in already and soon-to-be constructed buildings.

The time characteristics of the NMR signal, also known as relaxation times T1 and T2, are the parameters employed specifically in quantitative and qualitative characterization of different physical states (gas, liquid, solid) absorbed to solid surfaces or chemically combined with one another. These relaxation times are two means by which any excited magnetic moment (measure of the magnitude and the direction of a momentarily increased magnetic property of an object) relaxes back to equilibrium. Since most construction materials are composed of a variety of compounds, each with a different value of T1 and T2, the relaxation signal graphed by OSA NMR apparatus will produce a curve comprising of several overlapping exponential curves, one for each compound. Through a process of assimilating these curves into a single exponential fit, the relative hydrogen content of each compound in the construction material can be determined.

Pure water generally exhibits relaxation times in the range of seconds at room temperature. This property of water drastically alters once the molecules come into contact or chemically combine with a nearly any surface. In hydration, for example, the hydrogen of water relax at the T2 rate of 10-5 s. In gel pores, a similar process causes a relaxation time of T2 of 10-4 s, while, in concrete, it displays a rate of 10-2 s. Since water exhibits characteristic relaxation times when confined to specific geometries, such as pores within construction materials, the magnitude of the relaxation can be examined through a directly proportional relationship of the inner surface of the material and its volume–both properties of the pore geometry of the material. In this case, the spectra of porous materials with significant water content can be characterized by their broad distribution of the relaxation time values, which correspond to the relative sizes of the pores present in the examined sample. This paramount correlation between the NMR parameter and a physical property of the examined material makes NMR relaxation times a very viable method for determination of pore sizes and their distribution within construction materials.

Several direct applications of the water-content monitoring power of OSA NMR can be found in use today. One of these is the on-site detection of water depth-profiles in concrete pillars, in which the water distribution within the pillars is observed during wetting and drying of the building component. Old building and brand new construction sites alike can be inspected through this method in a completely non-destructive manner, thus preserving both the integrity and appearance of the sample. A similar application of OSA NMR provides accurate determination of density and moisture depth-profiles in wood panels. In this case, detailed analysis of the T2 relaxation curve can distinguish between solid and liquid wood components. Further examination of the acquired spectra can reveal the relative hydrogen content of both components through the use of a single exponential fir function. Through comparable methods, OSA NMR is steadily becoming the most widely employed method of monitoring early-age concrete hardening. All of the past methods, such as the Vicat needle test, the slump test, and the flow table test, did not produce accurate results due to their high dependency on the individual measuring device and procedure. On account of their destructive nature, none of these methods provided a means of continuous monitoring of the material properties as the concrete the hardened. OSA NMR’s final application in civil engineering flourishes in the field of determination of porosity and pore-size distribution in soils. NMR logging tools are commonly employed today for on-site characterization of top-soil earth for porosity, oil and water saturation, pore-size distribution and permeability. In addition to their current use, these tools have been recently used in the exploration of oil and water wells, as well as the determination of building ground stability.


******************************************************************************


Questions to explore the topic further:


What is civil engineering?

http://www.asce.org/

http://www.pubs.asce.org/magazines/CEMag/


What is TDR Trase?

http://www.soilmoisture.com/trace.html


What is the A.S.T. Drying System?

http://www.scottequipment.com/pdfs/AST%20Dryer.pdf


What is subsoil investigation?

http://www.boxvoid.com/surevoi....._eval.html


What is structural integrity engineering?

http://www.sieinc.com/


What is concrete?

http://www.buildeazy.com/newpl.....crete.html


What is absorption?

http://qanda.encyclopedia.com/.....02330.html


What is desorption?

http://en.wikipedia.org/wiki/Desorption


What is capillary flow?

http://science.jrank.org/pages.....ction.html


What is an exponential curve?

http://www.2dcurves.com/expone.....ntial.html


What is hydration?

http://www.cement.org/basics/c.....basics.asp


What is a depth-profile?

http://www.coexploration.org/b.....ation.html


What are oil wells?

http://en.wikipedia.org/wiki/Oil_well


What are wood panels?

http://www.calfinder.com/libra.....d-paneling


What is a Vicat needle apparatus?

http://www.shambhaviimpex.com/.....ratus.html


What is the slump test?

http://www.tpub.com/content/en.....69_550.htm


What is the flow table test?

http://www.astm.org/SNEWS/JULY_2000/july_flow.html


GAMES:

http://www.miniclip.com/games/.....n-yard/en/

http://www.games2win.com/en/fu.....n_site.asp
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:32 am    Post subject: Reply with quote

Nuclear magnetic resonance (NMR) spectroscopy: Identification and structural studies of glycans

Mashal Sultani, Graduate Student, Georgetown University


Introduction to NMR Spectroscopy of Carbohydrates

Johannes F. G. Vliegenthart

Bijvoet Center, Department of Bioorganic Chemistry, Utrecht University,

Padualaan 8,3584 CH Utrecht, The Netherlands

Carbohydrates are organic compounds with the general formula Cm(H2O)n. They consist primarily of carbon, hydrogen and oxygen, the last two in the 2:1 atom ratio. Carbohydrates can be viewed as hydrates of carbon. Saccharides are a large category of natural carbohydrates that function as storage and transport of energy (e.g., starch, glycogen) in living things. Saccharides also serve as structural components in cellulose in plants and chitin in arthropods. Among the simplest of the carbohydrates are the monosaccharides (Greek, one sugar). Monosaccharides are also known as simple sugars and may contain as few as three carbon atoms, but simple sugars that play a crucial role in energy storage will contain six carbons. Glucose is the most common known monosaccharide. When two monosaccharides are combined, they come to form what is called a disaccharide. Disaccharides are important because they serve as reservoirs of glucose that cannot easily be metabolized by glucose-utilizing enzymes. When two disaccharides join together into polymer chains, you obtain a polysaccharide.

Saccharides and their derivatives play key roles in the immune system, fertilization, pathogenesis, and development. A glycan refers to a polysaccharide or oligosaccharide. Glycans may also be used to refer to the carbohydrate portion of a glycoconjugate, such as a glycoprotein, glycolipid, or a proteoglycan. Glycans usually consist primarily of O-glycosidic linkages of monosaccharides. For example, cellulose is a glycan (also known as a glucan) composed of beta-1,4-linked D-glucose, and chitin is a glycan composed of beta-1,4-linked N-acetyl-D-glucosamine. Glycans can be homo or heteropolymers of monosaccharide residues, and is either linear or branched. Glycans can be found attached to proteins as in glycoproteins and proteoglycans. They are generally found on the exterior surface of cells. O- and N-linked glycans are very common in eukaryotes but may also be found, although less commonly, in prokaryotes.

Glycans are extremely important in proper protein folding in eukaryotic cells. Chaperone proteins in the endoplasmic reticulum, such as calnexin and calreticulin bind to the three glucose residues present on the core N-linked glycan. These chaperone proteins then serve to aid in the folding of the protein that the glycan is attached to. N-linked glycans also contribute to protein folding by steric effects and also play an important role in cell-cell interactions. For example, tumor cells make N-linked glycans that are abnormal and are recognized by the CD337 receptor on Natural Killer cells as a red flag that the cell in question is cancerous.

The significance of the understanding of the identity and structure of carbohydrates and glycans is fundamental in the field of scientific research. Carbohydrate NMR is the application of nuclear magnetic resonance (NMR) to structural and conformational analysis of carbohydrate molecules. The study of carbohydrate chemistry today relies heavily on NMR spectroscopy. It is a scientific tool that allows the carbohydrate chemist to determine the structure of monosaccharides and oligosaccharides from synthetic and natural sources. It is also a useful mechanism for determining sugar conformations. Modern high field strength NMR instruments used for carbohydrate samples, usually 500 MHz or greater, are able to run 1D and 2D experiments to determine primary structure and conformation of carbohydrate compounds.

What is NMR spectroscopy? Nuclear magnetic resonance is a phenomenon which occurs when the nuclei of certain atoms are immersed in a static magnetic field and is exposed to a second oscillating magnetic field (radiofrequency range). Only some nuclei experience this phenomenon, depending on whether they possess a property called spin. NMR spectroscopy finds applications in several areas of science. NMR spectroscopy is routinely used by chemists to study chemical structure using simple one-dimensional techniques. Two-dimensional techniques are used to determine the structure of more complicated molecules, such as proteins and nucleic acids. Time domain NMR spectroscopic techniques are used to probe molecular dynamics in solutions while solid state NMR spectroscopy is used to determine the molecular structure of solids. Other scientists have developed NMR methods of measuring diffusion coefficients.

Spectacular developments in the instrumentation, pulse sequences, spectral interpretation, isotope labeling of compounds and molecular modeling techniques have led to new mechanisms of determining the primary structure and the three-dimensional structure of biomolecules in solution. For carbohydrates and glycoconjugates, l H and 13C have proved to be extremely pertinent to determine primary structures. In fact the characterization of (partial) structures of glycoprotein-derived N-glycans has greatly facilitated the elucidation of biosynthetic routes and studying the functional roles of these glycans in complex biological systems. Another significant aspect deals with the confirmation of the identity of glycan structures that are supposed to be identical to known compounds.



Owing to the inherent flexibility of carbohydrate chains, the characterization of the three-dimensional structure in solution is rarely attainable in containing the same detail as proteins and nucleic acids. Nonetheless, important results have been obtained. For the study of the interaction of carbohydrates with complementary compounds NMR spectroscopy has proven to be a valuable tool. Spectra recorded at NMR machines operating at 500 MHz or at higher frequencies contain sufficient details to be used as identity card. For the characterization of compounds described in literature, mostly comparison of the spectral data to reference data is sufficient.


Two groups of signals can be distinguished. The first is the so-called bulk signal containing mainly the non-anomeric protons, present in a rather narrow spectral range between 3.2 and 3.9 ppm. The second is the structural-reporter-group signals that are found outside the bulk region. The chemical shift patterns of the structural reporter groups consisting of chemical shifts and couplings are translated into structural information, based on a comparison to patterns in a library of relevant reference compounds. To assign resonances in the region of the bulk signal and of coinciding structure reporter group signals, 2-D homonuclear correlation type of spectra, such as various COSY or TOCSY experiments are needed. In this way spin systems corresponding to monosaccharide constituents can be traced. The 3-D NMR is also suitable to these molecules due to the small chemical shift dispersion in carbohydrate NMR spectra.


The development of NMR instruments, operating at higher field strengths, has improved the resolution and sensitivity enormously. The advantages of advanced instrumentation are particularly useful for complex molecules like glycoproteins. The characterization of the spatial structure in solution of glycans, free, in a complex with complementary molecules, or covalently attached to other molecules like proteins or lipids, is insightful for the functioning of these molecules and for their recognition by complementary molecules. An oligosaccharide chain exhibits flexibility throughout the whole molecule on a short time scale by fast vibrations at bonds and angles and on a longer time scale by variations of the dihedral angles. lH-lH coupling constants are important for examining the ring conformations of the constituents and for an approximation of the dihedral angle ω for the glycosidic linkages through an exocyclic hydroxymethyl group. The skeleton protons of the constituting monosaccharide can be studied by homonuclear 1Η-ΝΟΕ experiments. Heteronuclear 1H-13C NOEs are useful by giving access to the calculation of distances between carbon atoms and protons.


Complementary approaches are necessary to identify the distinct conformations and to determine their abundance. This is achieved through a combination of Molecular Mechanics (MM) and Molecular Dynamics (MD) calculations. The obtained trajectories of a molecule through space in time make it possible to extract time-dependent parameters like correlation time, diffusion constants, and free energies. The comparison of the conformations of free glycans attached to small peptides with those of glycans in glycoproteins has revealed the dramatic influence arising from the location of the center of mass, as well as the interactions with the protein chain. Therefore, conformational data obtained for free glycans or glycans attached to small peptides should not be generalized to glycoproteins without carrying out further experimental studies. NMR has proven to be an invaluable tool in determining primary and

three-dimensional structures of carbohydrates.


Questions to explore further this topic:


What are carbohydrates?

http://www.visionlearning.com/.....php?mid=61


What are glycans?

http://www.students.uni-mainz......TRU21.html


What are glycoconjugates?

http://en.wikipedia.org/wiki/Glycoconjugate


What is spectroscopy?

http://loke.as.arizona.edu/~ck.....intro.html


What are different types of spectroscopy?

http://chemistry.about.com/od/.....oscopy.htm


What is NMR spectroscopy?

http://www.cem.msu.edu/~reusch.....r/nmr1.htm

http://teaching.shu.ac.uk/hwb/.....c/nmr1.htm


What is carbohydrate NMR?

http://en.wikipedia.org/wiki/Carbohydrate_NMR


How to read NMR spectra?

http://academics.keene.edu/rbl.....eadNMR.pdf


What is 2D NMR?

http://www.cryst.bbk.ac.uk/PPS...../2dnmr.htm


What is 3D NMR?

http://www.cryst.bbk.ac.uk/PPS...../3dnmr.htm


What are carbohydrate conformations?

http://en.wikipedia.org/wiki/C.....nformation


What is molecular modeling?

http://www.netsci.org/Science/.....ure01.html

http://en.wikipedia.org/wiki/Molecular_modelling


What is molecular dynamics?

http://www.ch.embnet.org/MD_tu.....Part1.html

http://en.wikipedia.org/wiki/Molecular_dynamics
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:33 am    Post subject: Reply with quote

Dianne O. Atienza NMR Spectroscopy Paper

Moisture Evaluation of XVI century wall painted by NMR study

Monitoring, conserving and/or restoring cultural heritage property has always been complicated, expensive and requires
extremely specialized people. This is particularly true for wall paintings where a number of special factors need to be
considered. Among which are the changes in weather, humidity, temperature, polluting agents and bacterial attack which all
affect the painted surface adhesion to its surrounding wall. In the case of varying temperature, it weakens the painting
material resulting to the appearance of micro-cracks, detachment and anomalous strains on the surface. Painting material
such as plaster, on the otherhand, requires the right amount of moisture that would maintain the adhesion between the plaster
and the pictorial film.

There are various methods of evaluating the moisture within the wall paintings such as electrical conductivity,
IR thermography and the destructive drilling of solid core necessary to obtain the moisture content. However, these
techniques have disadvantages as electrical conductivity measurements also include the effect of salt present on the wall
painting whereas thermographic investigations can be affected by varying temperature.

In lieu of available methods to determine the moisture content directly on the wall painting, a recent work of
Segre et. al from the Institute of Chemical Methodology employed the non-invasive and more accurate way of determining the
moisture content using unilateral NMR. They have studied the wall painting in the Serra Chapel, XVI century, in the
Chiesa di Nostra Signora del Sacro Cuore in Rome which was frescoed by Pellegrino degli Aretusi, a co-worker of Raphael.
In their study, the researchers use processed NMR results that would enable them to map the distribution of moisture content
of the whole wall. A measurement known as Hanh echo was obtained in different regions of the wall, and, since the Hanh echo
intensity is proportional to the amount of water, the moisture content distribution of the whole wall will be obtained where
degraded wall have been found to have high moisture content.

It has been known that contact of wall paintings with the ground and or with the adjacent walls provides an efficient
source for capillary percolation of moisture. This has been observed in the NMR data map of the damaged wall paintings in
Serra Chapel. Also, they have found that the socle at the foot of the wall prevents humidity exchange process thus, other
possible exchange is attributed to the inner to outer wall structure.

T2, or spin spin relaxation, measurements were also obtained to evaluate the salt outcropping of the wall painting
wherein the longer T2 values indicate higher occurrence of salt outcropping. Salt outcropping causes the detachment of
pictorial film and micro-fractures as a consequence of using organic substances such as egg-yolk, animal glue, wax and
linseed oil. This can be attributed to the moisture adsorbed by the hygroscopic salts where the water in small pores relaxes
rapidly while the water in large pores relaxes more slowly.

In this study, the researchers have shown an innovative way of how we can use NMR data on mapping the moisture
content and salt outcropping effect on wall paintings where experimental results will be highly essential to any restoration
process.

Source:

Proietti, N. et.al. Unilateral NMR study of a XVI century wall painted. J. Magn. Reson. 186 (2007) 311-318.


What/where are the other cultural heritage? http://www.culturalheritage.net/
How do we conserve artifacts? http://nautarch.tamu.edu/crl/c...../File1.htm
what are the famous paintings? http://www.ibiblio.org/wm/paint/
What are the different painting techniques? http://www.faux-painting-techniques.com/
How do I minimize peeling or cracking of my painting? http://www.411homerepair.com/d.....oblems.php
What is electrical conductivity? http://www.scienceclarified.co.....ivity.html
What is IR and thermography? http://www.infraredtraining.com/ir_primer.asp
What is moisture? http://www.epa.gov/athens/lear.....te/mc.html
What is a socle? http://www.websters-online-dic.....tion/socle
What does it mean by hygroscopic? http://msds.chem.ox.ac.uk/glos.....copic.html
What are pores? http://www.google.com/search?h.....d=0CAcQkAE
What is percolation? http://www.websters-online-dic.....ercolation
what is capillary action? http://www.websters-online-dic.....ction.html
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:34 am    Post subject: Reply with quote

“Beer is living proof that God loves us and wants us to be happy.” – Benjamin Franklin


Anna Ivanova


Composition of Beer by 1H NMR Spectroscopy: Effects of

Brewing Site and Date of Production


In order to be able to efficiently control and improve the qualities of beer, its chemical composition and its relation to quality attributes should be understood. The chemical composition of beer is very complex. It depends on water quality, malt, hop, yeasts, the recipe, and the timing of the brewing process. The quality of beer is evaluated based on the product’s appearance (color, foam, properties, and clarity), taste (sweetness, sourness, bitterness, and saltiness), flavor, and aroma. Unfortunately, it is not known how the above properties relate to the chemical composition of beer which leads to the impossibility to control those properties by simply controlling the chemistry/biochemistry of the product. In order to be able to do that, a detailed and comprehensive chemical characterization of beer is required.

Nuclear magnetic resonance (NMR) spectroscopy allows for the detection of several families of compounds at the same time at different concentrations. Therefore, NMR can provide detailed information about the composition of beer, provided that the sample is degassed before analysis. High-resolution NMR and hyphenated NMR (LC-NMR and LC-NMR/MS) have been widely used in the determination of the composition of beer. In fact, high resolution 1H NMR is among the best techniques to detect variations in compounds other than ethanol.

Unfortunately, the 1H NMR spectra of beer is difficult to interpret because there is a significant overlap of the signal. This suggests that a multivariate analysis is required to interpret the data obtained from NMR.

Almeida and coworkers decided to investigate beer samples of the same type produced at different times and different places. They applied 1H NMR and principal component analysis (PCA) to a set of lager beers from three different brewing sites located in three different countries and produced on different days. In that way, the effect of brewing site and time of brewing on the composition of beer can be determined.

Almeida and coworkers selected same brand beer lager (4% v/v alcohol) samples from three different countries (A, B, and C) from three different dates of production (1, 2, and 3) spaced 1-2 months. They took three bottles (a, b, and c) from each date and country so that they had 27 samples in total. The unopened beers were stored at 4oC until the analysis which was made 2-3 months after the production date in order to avoid aging effects. Also, the bottles were opened right before the NMR analysis. The compounds the group chose to quantify were: lactic acid, pyruvic acid, tyrosine, uridine, adenosine and/or inosine, succinic acid, and histidine.

All beer samples underwent ultrasonic degassing for 10 minutes before the NMR analysis and the NMR spectra were obtained at 27oC.

Three different types of compounds were analyzed by PCA after the NMR analysis: aliphatic, sugar, and aromatics based on their corresponding regions in the NMR spectra. Alcohols, organic acids, amino acids, and fatty acids were present in the aliphatic region. Fermentable sugars like glucose and maltose, and dextrins (glucose oligomers with different degrees of branching and polymerization) were present in the sugar region. Aromatic amino acids, nucleosides, aromatic alcohols and polyphenolic compounds were present in the aromatic region. The three regions were investigated separately.

The group concluded that beers from site B have more lactic and pyruvic acids than beers from site A. In addition, site C beers have a lot less lactic acid than site B beers but a little less than site A beers. The significance of pyruvic acid lies in the fact that it is an intermediate in the biosynthesis of ethanol by yeast. Beers with high content of pyruvate might have been produced by yeast that has undergone autolysis (destruction of the cell after its death) during fermentation. Consequently, higher content of pyruvic acid and its reduction product, lactic acid, suggest that the quality of the yeast was poor or that older yeast generations were used. Therefore, site C had the best yeast, followed by A site beers. Site C beers had the worst.

Analysis of the carbohydrate composition showed that site B beers were markedly different from the others. The group concluded that glucose and linear dextrins content was higher in site B and C3 beers. On the other hand, branched dextrins predominated in all other beers. In addition, the researchers were able to calculate the average carbohydrate size and number of branching points. For site B and C3 beers, the average carbohydrate size was five monomers and the branching points were 0.4. Site A and C beers (except C3) had an average carbohydrate size of 6 monomers and 0.5-0.6 branching points. The above proves that site A and most site C beers have more highly branched oligosaccharides. The degree of branching of beer polysaccharides is attributed to the enzyme activity of α- and β-amylases and other enzymes during malting and mashing processes. Consequently, the differences in the carbohydrate contents in the beers are due to differences in the malting and mashing processes from site to site and in the case of C3 beers – the production date.

C3 beers have another distinguishing feature compared to the other beers. They are richer in glucose, trehalose, and maltose than all the other beers. The presence of glucose and maltose suggests that fermentation has not been attenuated. This could be attributed to either premature cooling to complete the flocculation (the clumping together of brewing yeast once the sugar in a beer brew has been fermented into ethanol) of the yeast crop or premature flocculation of the yeast during fermentation.

Analysis of the aromatic region reveals that site A beers have higher content of adenosine and/or inosine and lower content of uridine and tyrosine and/or tyrosol than site B beers. In addition, C3 beers have more 2-phenylethanol and tyrosine and/or tyrosol than C1 and C2 beers. The presence of tyrosol and phenylethanol is suggestive of amino acid degradation. Some amino acids are known to undergo Strecker degradation. This reaction leads to the formation of the corresponding aldehydes during beer production. In addition, aldehydes present during fermentation can be enzymatically reduced to their corresponding alcohols.

In conclusion, Almeida and coworkers used 1H NMR spectroscopy in tandem with PCA to investigate compositional differences in beers produced at different places at different times. The results suggest that beers of the same brand brewed at different places at different times have different aliphatic, sugar, and aromatic contents. The pyruvic and lactic acid contents might reflect yeast quality and/or yeast generation number. The carbohydrate composition reflects the malting and mashing conditions and the resulting enzymatic activities. Finally, the beers can be distinguished by their adenosine/inosine, uridine, tyrosine/tyrosol, and 2-phenylethanol contents which are probably due to Strecker degradation of amino acids. Even though it is not known how the chemical composition affects beer quality, it is shown that it can reveal information about the yeast quality and the performance of malting and/or mashing processes.




Almeida, C.; Duarte, I.F.; Barros, A.; Rodrigues, J.; Spraul, M.; Gil, A.M. Composition of beer by 1H NMR spectroscopy: effects of brewing site and date of production. J. Agric. Food Chem. 2006, 54, 700-706.


The history of beer

http://en.wikipedia.org/wiki/History_of_beer



How to make beer?

http://www.popularmechanics.co.....24487.html


What is yeast?

http://en.wikipedia.org/wiki/Yeast


Beer and breweries by country

http://en.wikipedia.org/wiki/B.....by_country


The different beer styles

http://www.tastings.com/beer/beer_styles.html

http://www.drinkfocus.com/arti...../index.php

http://www.beerhunter.com/beerstyles.html


Top 12 beer myths

http://legendsofbeer.wordpress.....-exploded/


Top 10 beer companies

http://www.globalbusinessinsig.....g0209t.pdf


Free online beer games

http://beer.freeonlinegames.name/

http://www.freegamesonline.dk/...../index.php
Back to top
View user's profile Send private message Visit poster's website
adedios
SuperPoster


Joined: 06 Jul 2005
Posts: 5060
Location: Angel C. de Dios

PostPosted: Wed Dec 16, 2009 9:35 am    Post subject: Reply with quote

Observation of NMR Signals from Proteins Introduced into Living Mammalian
Cells by Reversible Membrane Permeabilization Using a Pore-Forming Toxin, Streptolysin O
By Shinji Ogino, Satoshi Kubo, Ryo Umemoto, Shuxian Huang, Noritaka Nishida, and
Ichio Shimada
Proteins are an important class of biological molecules which are usually involved in many
cellular processes. Understanding how certain proteins behave in cells is very important in
biology but also very difficult. Generally proteins in a cell behave completely different from
thoses in a buffer solution. To study proteins in cells different techniques have been use, in
particular NMR spectroscopy which is noninvasive. However a special type of NMR
specrtoscopy is usually used in the study of proteins in living cells called heteronuclear single
quantum coherence (HSQC). Proteins are made of chains of atoms with some of them being
nitrogen (in the amino acid residues the make up the protein). HSQC is able to detect the
presences of protons and which atom they are attached to (in this case nitrogen). Also if the
nitrogen hydrogen interacts with another protein which they most often do they will give a
different signal which can be seen. This gives additional information on how the protein behaves.
Hydrogens attached to nitrogen in most proteins are involved in the 3D structure of the protein.
In NMR spectroscopy however the naturally abundant nitrogen-14 isotope cannot be seen but
nitrogen-15 isotope can be seen. So special proteins enriched with nitrogen-15 must be used. The
special proteins with the isotope nitrogen-15 allow scientists to able to watch by NMR
spectroscopy how proteins interact in cells. Most cases to use this technique scientist most trick
the cell into making these protein with the nitrogen-15 which is time consuming and expensive.
Also this technique can only done with a few kinds of cells, this leaded the Ichio Shimada and
co workers to develop alternative approach. Using bacterial toxins they were able to make holes
in the cell membrane to shuttle small proteins into any cell type. In this paper researchers have
develop a promising technique that could deliver a variety of proteins to any cells and monitor
the interactions by HSQC NMR spectroscopy with very modification of the protein of interest.
The bacterial toxin in used in the study was streptolysin O (SLO), which has the ability to form
35 nm pores in cell membranes. These pores allow for the entry and exit of small molecules into
the cell. These pores can then be resealed by the presence of calcium ions (Ca2+). The type of cell
studied were 293F (special commercial available cells which contain G actin) and protein used
was an actin sequestering protein (which interacts with G actin) called thymosin beta 4 (T beta 4).
To find out if and how much of the T beta 4 was taken up by the cells, the T beta 4 was attached
to another molecule called fluorescein isothiocyanate (FITC) which can be seen with ultraviolet
(UV) light. After the addition of Ca2+ to reseal the pores, propidium iodide (PI) was used to
stain the cells showing cell membranes damaged. After they found the optimal amount SLO to
use they proceeded to test the technique. Several 293F cells were treated them with SLO then
place in an environment of T beta 4 with FITC. This was followed by resealing with Ca2+ ions.
HSQC NMR spectroscopy was conducted on the cells, looking for the signals of nitrogen 15
isotopic label T beta 4. This was then followed by PI staining. What they found was that the
protein was taken into by the cells but did not give similar signals of T beta 4 interacting with G
actin (done outside cells) but instead the T beta 4 modify by an enzyme in the cell giving
different set of signals. It also should be noted there was very little cell damage afterwards and
large uptake of T beta 4. From these results it can be seen that technique shows promise as a new
less expensive in cell technique that can does not require much modification of the proteins.


What are proteins?
www.bionewsonline.com/5/what_is_protein.htm
What are amino acids?
http://www.biology.arizona.edu.....aa/aa.html
What are isotopes?
http://www.isgs.illinois.edu/r.....what.shtml
What is a cell membrane?
http://www.wisc-online.com/obj.....jid=ap1101
What is ultraviolet light?
http://cycleback.com/blacklight/two.html
What is an ion?
http://www.qrg.northwestern.ed.....n-ion.html

Reference
Ogino, S.; Kubo, S.; Umemoto, R.; Huang, S; Nishida, N.;
Shimada I. J. Am. Chem. Soc. 2009, 131, 10834–10835
Back to top
View user's profile Send private message Visit poster's website
Display posts from previous:   
Post new topic   Reply to topic   printer-friendly view    USAP PAETE Forum Index -> Science Lessons Forum All times are GMT - 5 Hours
Page 1 of 1

 
Jump to:  
You can post new topics in this forum
You can reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum


Powered by phpBB © 2001, 2005 phpBB Group