56 results match your criteria Chemical Physics[Journal]


Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters.

Chem Phys 2019 May 17;521:69-76. Epub 2019 Jan 17.

Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.

We calculate the nearest-neighbour enthalpies and entropies at 5 salt concentrations of 18 RNA sequences, each for at least 9 different species concentrations, totalling 757 melting temperatures, using a melting temperature optimization method. These new parameters do not need to be salt-corrected and are shown to provide overall improved melting temperature predictions. They show a marked quadratic dependence with salt concentrations which are compensated to form linear Gibbs free energies. Read More

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http://dx.doi.org/10.1016/j.chemphys.2019.01.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6784847PMC

Hydrogen bonding between hydrides of the upper-right part of the periodic table.

Chem Phys 2018 May 4;507:34-43. Epub 2018 Apr 4.

Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.

One of the most important electrostatic interactions between molecules is most definitely the hydrogen bond. Understanding the basis of this interaction may offer us the insight needed to understand its effect on the macroscopic scale. Hydrogen bonding is for example the reason for anomalous properties in compounds like water and naturally life as we know it. Read More

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http://dx.doi.org/10.1016/j.chemphys.2018.03.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6197068PMC
May 2018
3 Reads

Graphical representation methods: How well do they discriminate between homologous gene sequences?

Chem Phys 2018 Sep 26;513:156-164. Epub 2018 Jul 26.

Physics Department, Jadavpur University, Jadavpur, Kolkata 700032, India.

Graphical representation methods constitute a class of alignment-free techniques for comparative study of biomolecular sequences. In this brief commentary, we study how well some of these methods can discriminate among closely related genes. Read More

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http://dx.doi.org/10.1016/j.chemphys.2018.07.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116999PMC
September 2018

Optical Properties of Meloxicam in the Far-Infrared Spectral Region.

Chem Phys 2018 ;512

Department of Chemistry, Middle East Technical University, Ankara 06100, Turkey.

One of the most commonly used nonsteroidal anti-inflammatory active pharmaceutical ingredient called Meloxicam has been characterized spectroscopically both by Terahertz (THz) time domain spectroscopy (THz-TDS) and by Fourier Transform Infrared (FTIR) spectroscopy in far-IR regions of electromagnetic spectrum; 0.2 THz to 20 THz. While many relatively sharp features are observed in the far-IR range between 2 THz to 20 THz as expected for being an organic substance, very distinct and relatively strong absorption bands are also observed at 1. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03010104183023
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http://dx.doi.org/10.1016/j.chemphys.2018.04.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463309PMC
January 2018
19 Reads

Photochemical Dynamics of a Trimethyl-Phosphine Derivatized [FeFe]-Hydrogenase Model Compound.

Chem Phys 2018 ;512

Department of Chemistry and Physics, Hood College, 401 Rosemont Ave., Frederick, MD, 21701-8524, USA.

Though there have been many studies on photosensitizers coupled to model complexes of the [FeFe]-hydrogenases, few have looked at how the models react upon exposure to light. To extract photoreaction information, ultrafast time-resolved UV/visible pump, IR probe spectroscopy was performed on Fe(μ-SCH)(CO)(PMe) () dissolved in heptane and acetonitrile and the photochemical dynamics were determined. Excitation with 532 and 355 nm light produces bleaches and new absorptions that decay to half their original intensity with time constants of 300 ± 120 ps and 380 ± 210 ps in heptane and acetonitrile, respectively. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03010104173076
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http://dx.doi.org/10.1016/j.chemphys.2017.12.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6459200PMC
January 2018
25 Reads

Crystal and electronic structures of substituted halide perovskites based on density functional calculation and molecular dynamics.

Chem Phys 2017 Mar;485-486:22-28

Department of Environmental Chemistry and Chemical Engineering, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan.

Durability of organo-lead halide perovskite are important issue for its practical application in a solar cells. In this study, using density functional theory (DFT) and molecular dynamics, we theoretically investigated a crystal structure, electronic structure, and ionic diffusivity of the partially substituted cubic MAXPbI (MA = CHNH, X = NH or (NH)CH or Cs). Our calculation results indicate that a partial substitution of MA induces a lattice distortion, resulting in preventing MA or X from the diffusion between A sites in the perovskite. Read More

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http://dx.doi.org/10.1016/j.chemphys.2016.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364368PMC
March 2017
3 Reads

Molecular Dynamics Simulation and NMR Investigation of the Association of the β-Blockers Atenolol and Propranolol with a Chiral Molecular Micelle.

Chem Phys 2015 Aug;457:133-146

Department of Biochemistry and Molecular Biology, Howard University College of Medicine, Howard University, 520 W Street NW, Washington, DC 20059.

Molecular dynamics simulations and NMR spectroscopy were used to compare the binding of two β-blocker drugs to the chiral molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The molecular micelle is used as a chiral selector in capillary electrophoresis. This study is part of a larger effort to understand the mechanism of chiral recognition in capillary electrophoresis by characterizing the molecular micelle binding of chiral compounds with different geometries and charges. Read More

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http://dx.doi.org/10.1016/j.chemphys.2015.05.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4527343PMC
August 2015
14 Reads

Infrared, Raman, and Ultraviolet Absorption Spectra and Theoretical Calculations and Structure of 2,3,5,6-Tetrafluoropyridine in its Ground and Excited Electronic States.

Chem Phys 2015 Jul;456:28-33

Department of Chemistry, Texas A&M University, College Station, TX 77843-3255 USA.

Infrared and Raman spectra of 2,3,5,6-tetrafluoropyridine (TFPy) were recorded and vibrational frequencies were assigned for its S electronic ground states. and density functional theory (DFT) calculations were used to complement the experimental work. The lowest electronic excited state of this molecule was investigated with ultraviolet absorption spectroscopy and theoretical CASSCF calculations. Read More

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http://dx.doi.org/10.1016/j.chemphys.2015.04.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476468PMC
July 2015
8 Reads

Sub-100-ps structural dynamics of horse heart myoglobin probed by time-resolved X-ray solution scattering.

Chem Phys 2014 Oct;422:137-142

Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea ; Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea.

Here we report sub-100-ps structural dynamics of horse heart myoglobin revealed by time-resolved X-ray solution scattering. By applying the time-slicing scheme to the measurement and subsequent deconvolution, we investigate the protein structural dynamics that occur faster than the X-ray temporal pulse width of synchrotrons (~100 ps). The singular value decomposition analysis of the experimental data suggests that two structurally distinguishable intermediates are formed within 100 ps. Read More

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http://dx.doi.org/10.1016/j.chemphys.2014.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4323384PMC
October 2014
26 Reads

The enzymatic reaction catalyzed by lactate dehydrogenase exhibits one dominant reaction path.

Chem Phys 2014 Oct;442(17):132-136

Department of Chemistry and Biochemistry, University of Arizona, P.O. Box 210041, 1306 East University Blvd., Tucson, AZ 85721, USA.

Enzymes are the most efficient chemical catalysts known, but the exact nature of chemical barrier crossing in enzymes is not fully understood. Application of transition state theory to enzymatic reactions indicates that the rates of all possible reaction paths, weighted by their relative probabilities, must be considered in order to achieve an accurate calculation of the overall rate. Previous studies in our group have shown a single mechanism for enzymatic barrier passage in human heart lactate dehydrogenase (LDH). Read More

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http://dx.doi.org/10.1016/j.chemphys.2014.02.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4215548PMC
October 2014
1 Read

A Molecular Dynamics Simulation Study of the Association of 1,1'-Binaphthyl-2,2'-diyl hydrogenphosphate Enantiomers with a Chiral Molecular Micelle.

Chem Phys 2014 Aug;439:36-43

Department of Biochemistry and Molecular Biology, Howard University College of Medicine, Howard University, 520 W Street NW, Washington, DC 20059.

Molecular dynamics (MD) simulations were used to investigate the binding of 1,1'-binaphthyl-2,2'-diyl hydrogenphosphate (BNP) enantiomers to the molecular micelle poly-(sodium undecyl-(L,L)-leucine-valine) (poly(SULV)). Poly(SULV) is used as a chiral selector in capillary electrophoresis separations. Four poly(SULV) binding pockets were identified and either (R)-BNP or (S)-BNP were docked into each pocket. Read More

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http://dx.doi.org/10.1016/j.chemphys.2014.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112194PMC
August 2014
17 Reads

Real-time tracking of CO migration and binding in the α and β subunits of human hemoglobin via 150-ps time-resolved Laue crystallography.

Chem Phys 2013 Aug;422:98-106

Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.

We have developed the method of picosecond Laue crystallography and used this capability to probe ligand dynamics in tetrameric R-state hemoglobin (Hb). Time-resolved, 2 Å-resolution electron density maps of photolyzed HbCO reveal the time-dependent population of CO in the binding (A) and primary docking (B) sites of both α and β subunits from 100 ps to 10 μs. The proximity of the B site in the β subunit is about 0. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.12.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020136PMC
August 2013
7 Reads

Simplified and economical 2D IR spectrometer design using a dual acousto-optic modulator.

Chem Phys 2013 Aug;422:8-15

Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706.

Over the last decade two-dimensional infrared (2D IR) spectroscopy has proven to be a very useful extension of infrared spectroscopy, yet the technique remains restricted to a small group of specialized researchers because of its experimental complexity and high equipment cost. We report on a spectrometer that is compact, mechanically robust, and is much less expensive than previous designs because it uses a single pixel MCT detector rather than an array detector. Moreover, each axis of the spectrum can be collected in either the time or frequency domain via computer programming. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.08.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959789PMC
August 2013
33 Reads

Structural Consequences of Chromophore Formation and Exploration of Conserved Lid Residues amongst Naturally Occurring Fluorescent Proteins.

Chem Phys 2014 Jan;429:5-11

Chemistry Department, Connecticut College, New London, CT06320, USA.

Computational methods were used to generate the lowest energy conformations of the immature precyclized forms of the 28 naturally occurring GFP-like proteins deposited in the pdb. In all 28 GFP-like proteins, the beta-barrel contracts upon chromophore formation and becomes more rigid. Our prior analysis of over 260 distinct naturally occurring GFP-like proteins revealed that most of the conserved residues are located in the top and bottom of the barrel in the turns between the β-sheets. Read More

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http://dx.doi.org/10.1016/j.chemphys.2013.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899699PMC
January 2014
15 Reads

EPFR Formation from Phenol adsorption on Al2O and TiO: EPR and EELS studies.

Chem Phys 2013 Aug;422:277-282

Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

We have examined the formation of environmentally persistent free radicals (EPFRs) from phenol over alumina and titania using both powder and single-crystal samples. Electron paramagnetic resonance (EPR) studies of phenol adsorbed on metal oxide powders indicates radical formation on both titania and alumina, with both oxides forming one faster-decaying species (lifetime on the order of 50-100 hours) and one slower-decayng species (lifetimes on the order of 1000 hours or more). Electron energy loss spectroscopy (EELS) measurements comparing physisorbed phenol on single-crystal TiO(110) to phenoxyl radicals on the same substrate indicate distinct changes in the π-π* transitions from phenol after radical formation. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03010104120045
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http://dx.doi.org/10.1016/j.chemphys.2012.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891583PMC
August 2013
30 Reads

Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories.

Chem Phys 2013 Aug;422:229-237

Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.

Folding and unfolding rates for the ultrafast folding villin subdomain were determined from a photon-by-photon analysis of fluorescence trajectories in single molecule FRET experiments. One of the obstacles to measuring fast kinetics in single molecule fluorescence experiments is blinking of the fluorophores on a timescale that is not well separated from the process of interest. By incorporating acceptor blinking into a two-state kinetics model, we show that it is possible to extract accurate rate coefficients on the microsecond time scale for folding and unfolding using the maximum likelihood method of I. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.08.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892999PMC
August 2013
3 Reads

Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-cage.

Chem Phys 2013 Aug;422

Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.

Using the miniprotein Trp-cage as a model, we show that D-amino acids can be used to facilitate the delineation of protein folding mechanism. Specifically, we study the folding-unfolding kinetics of three Trp-cage mutants where the native glycine residue near the C-terminus of the α-helix is replaced by a D-amino acid. A previous study showed that these mutations increase the Trp-cage stability, due to a terminal capping effect. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S03010104130005
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http://dx.doi.org/10.1016/j.chemphys.2013.01.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844134PMC
August 2013
12 Reads

Nanosecond Dynamics of InfluenzaA/M2TM and an Amantadine Resistant Mutant Probed by Time-Dependent Red Shifts of a Native Tryptophan.

Chem Phys 2013 Aug;422

Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School - UMDNJ, Piscataway, New Jersey 08854 ; Department of Biochemistry, Robert Wood Johnson Medical School - UMDNJ, Piscataway, New Jersey 08854.

Proteins involved in functions such as electron transfer or ion transport must be capable of stabilizing transient charged species on time scales ranging from picoseconds to microseconds. We study the influenza A M2 proton channel, containing a tryptophan residue that serves as an essential part of the proton conduction pathway. We induce a transition dipole in tryptophan by photoexcitation, and then probe the dielectric stabilization of its excited state. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.12.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833813PMC
August 2013
3 Reads

Simulations of Two-dimensional Infrared and Stimulated Resonance Raman Spectra of Photoactive Yellow Protein.

Chem Phys 2013 Aug;422

We present simulations of one and two-dimensional infrared (2DIR) and stimulated resonance Raman (SRR) spectra of the dark state (pG) and early red-shifted intermediate (pR) of photoactive yellow protein (PYP). Shifts in the amide I and Glu46 COOH stretching bands distinguish between pG and pR in the IR absorption and 2DIR spectra. The one-dimensional SRR spectra are similar to the spontaneous RR spectra. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827784PMC
August 2013
8 Reads

Reconstruction of Calmodulin Single-Molecule FRET States, Dye-Interactions, and CaMKII Peptide Binding by MultiNest and Classic Maximum Entropy.

Chem Phys 2013 Aug;422

Department of Chemistry, University of Kansas, Lawrence, Kansas, 66045, United States.

We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.11.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819237PMC
August 2013
1 Read

Structural changes in single membranes in response to an applied transmembrane electric potential revealed by time-resolved neutron/X-ray interferometry.

Chem Phys 2013 Aug;422

Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104.

The profile structure of a hybrid lipid bilayer, tethered to the surface of an inorganic substrate and fully hydrated with a bulk aqueous medium in an electrochemical cell, was investigated as a function of the applied transbilayer electric potential via time-resolved neutron reflectivity, enhanced by interferometry. Significant, and fully reversible structural changes were observed in the distal half (with respect to the substrate surface) of the hybrid bilayer comprised of a zwitterionic phospholipid in response to a +100mV potential with respect to 0mV. These arise presumably due to reorientation of the electric dipole present in the polar headgroup of the phospholipid and its resulting effect on the thickness of the phospholipid's hydrocarbon chain layer within the hybrid bilayer's profile structure. Read More

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http://dx.doi.org/10.1016/j.chemphys.2013.01.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821765PMC
August 2013
1 Read

Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics.

Chem Phys 2013 Aug;422

Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA ; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA.

As it remains practically impossible to generate ergodic ensembles for large intrinsically disordered proteins (IDP) with molecular dynamics (MD) simulations, it becomes critical to compare spectroscopic characteristics of the theoretically generated ensembles to corresponding measurements. We develop a Bayesian framework to infer the ensemble properties of an IDP using a combination of conformations generated by MD simulations and its measured infrared spectrum. We performed 100 different MD simulations totaling more than 10 µs to characterize the conformational ensemble of αsynuclein, a prototypical IDP, in water. Read More

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http://dx.doi.org/10.1016/j.chemphys.2013.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810979PMC
August 2013
12 Reads
3 Citations
1.652 Impact Factor

Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin.

Chem Phys 2013 Aug;430:88-97

Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States.

Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Read More

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http://dx.doi.org/10.1016/j.chemphys.2013.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772081PMC
August 2013
13 Reads
1.652 Impact Factor

Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from molecular dynamics.

Chem Phys 2013 Aug;422:156-164

Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States.

molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the N and N positions of the imidazole group to estimate the p' Anticipating our results, we will see that the estimated p for the first protonation event of the M2 channel is in good agreement with experimental estimates. Read More

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http://dx.doi.org/10.1016/j.chemphys.2013.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4407280PMC
August 2013
7 Reads

A spectroscopic and computational study of Al(III) complexes in cryolite melts: Effect of cation nature.

Chem Phys 2013 Feb;412(C):22-29

Kazan National Research Technological University, K. Marx Str., 68, 420015 Kazan, Republic of Tatarstan, Russia.

Lithium, sodium and potassium cryolite melts are probed by Raman spectroscopy in a wide range of the melt composition. The experimental data demonstrate a slight red shift of main peaks and a decrease of their half-widths in the row Li(+), Na(+), K(+). Quantum chemical modelling of the systems is performed at the density functional theory level. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568921PMC
February 2013
7 Reads

Counting Single Rhodamine 6G Dye Molecules in Organosilicate Nanoparticles.

Chem Phys 2012 Oct;406:41-46

Institute of Physics, Chemnitz University of Technology, Reichenhainer Str. 70, D-09126 Chemnitz, Germany.

Rhodamine 6G (R6G) dye molecules have been embedded into organosilicate nanoparticles to improve thermal and chemical stability of these marker molecules. We demonstrate that the well-established method of optical single-particle microscopy can be used to determine the number of dye molecules per nanoparticle in such hybrid materials. Analysing the fluorescence intensity of R6G in single nanoparticles, we obtain an average number of 1. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.02.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532437PMC
October 2012

A Benchmark Test Suite for Proton Transfer Energies and its Use to Test Electronic Structure Model Chemistries.

Chem Phys 2012 May 6;400:8-12. Epub 2012 Mar 6.

Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431.

We present benchmark calculations of nine selected points on potential energy surfaces describing proton transfer process in three model systems, H(5)O(2) (+), CH(3)OH…H(+)…OH(2), and CH(3)COOH…OH(2). The calculated relative energies of these geometries are compared to those calculated by various wave function and density functional methods, including the polarized molecular orbital (PMO) model recently developed in our research group and other semiempirical molecular orbital methods. We found that the SCC-DFTB and PMO methods (the latter available so far only for molecules consisting of only O and H and therefore only for the first of the three model systems) give results that are, on average, within 2 kcal/mol of the benchmark results. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.01.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516617PMC
May 2012
3 Reads

On the Performance of Local Density Approximation in Describing the Adsorption of Electron Donating/Accepting Molecules on Graphene.

Chem Phys 2012 Oct 27;406:78-85. Epub 2012 Aug 27.

Computational Chemistry Laboratory, Department of Natural Science, Albany State University, Albany, GA 31705, United States.

In order to asses performance of the LDA in describing physisorption on graphene, adsorptions of TCNE, TCNQ, TNF, TTF, and DMPD as well as four benzene derivatives on C(54)H(18) and C(110)H(30) were explored with a variety of DFTs such as MPWB1K, M06-2X, PBE-D and LSDA. Although it is well known that the LDA considerably overestimate non-covalent interaction, the LSDA predicted adsorption energies except for TCNE on C(110)H(30) are systematically lower than those from the M06-2X by 0.4-3. Read More

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http://dx.doi.org/10.1016/j.chemphys.2012.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501752PMC
October 2012
10 Reads

A peptide's perspective of water dynamics.

Chem Phys 2011 Nov 11;390(1):1-13. Epub 2011 Aug 11.

Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.

This Perspective is focused on amide groups of peptides interacting with water. The 2D IR spectroscopy has already enabled structural aspects of the peptide backbone to be determined through its ability to measure the coupling between different amide-I modes. Here we describe why nonlinear IR is emerging as the method of choice to examine the fast components of the water dynamics near peptides and how isotopically edited peptide links can be used to probe the local water at a residue level in proteins. Read More

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http://dx.doi.org/10.1016/j.chemphys.2011.07.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404498PMC
November 2011
2 Reads

Large-scale motions in the adenylate kinase solution ensemble: coarse-grained simulations and comparison with solution X-ray scattering.

Chem Phys 2012 Mar;396:84-91

Department of Chemistry, University of Wisconsin - Madison, 1101 University Avenue, Madison, Wisconsin 53706.

While coarse-grained (CG) simulations provide an efficient approach to identify small- and large-scale motions important to protein conformational transitions, coupling with appropriate experimental validation is essential. Here, by comparing small-angle X-ray scattering (SAXS) predictions from CG simulation ensembles of adenylate kinase (AK) with a range of energetic parameters, we demonstrate that AK is flexible in solution in the absence of ligand and that a small population of the closed form exists without ligand. In addition, by analyzing variation of scattering patterns within CG simulation ensembles, we reveal that rigid-body motion of the LID domain corresponds to a dominant scattering feature. Read More

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http://linkinghub.elsevier.com/retrieve/pii/S030101041100371
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http://dx.doi.org/10.1016/j.chemphys.2011.08.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375699PMC
March 2012
12 Reads

Likelihood functions for the analysis of single-molecule binned photon sequences.

Authors:
Irina V Gopich

Chem Phys 2012 Mar;396:53-60

Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

We consider the analysis of a class of experiments in which the number of photons in consecutive time intervals is recorded. Sequence of photon counts or, alternatively, of FRET efficiencies can be studied using likelihood-based methods. For a kinetic model of the conformational dynamics and state-dependent Poisson photon statistics, the formalism to calculate the exact likelihood that this model describes such sequences of photons or FRET efficiencies is developed. Read More

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http://dx.doi.org/10.1016/j.chemphys.2011.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375684PMC
March 2012
2 Reads

Structural distributions from single-molecule measurements as a tool for molecular mechanics.

Chem Phys 2012 Mar 22;396:61-71. Epub 2011 Jun 22.

Department of Chemistry, Princeton University, Princeton, NJ 08550.

A mechanical view provides an attractive alternative for predicting the behavior of complex systems since it circumvents the resource-intensive requirements of atomistic models; however, it remains extremely challenging to characterize the mechanical responses of a system at the molecular level. Here, the structural distribution is proposed to be an effective means to extracting the molecular mechanical properties. End-to-end distance distributions for a series of short poly-L-proline peptides with the sequence P(n)CG(3)K-biotin (n = 8, 12, 15 and 24) were used to experimentally illustrate this new approach. Read More

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http://dx.doi.org/10.1016/j.chemphys.2011.06.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361908PMC
March 2012
12 Reads

Water Diffusion In And Out Of The β-Barrel Of GFP and The Fast Maturing Fluorescent Protein, TurboGFP.

Chem Phys 2012 Jan 19;392(1):143-148. Epub 2011 Nov 19.

Chemistry Department, Connecticut College, New London, CT06320.

The chromophore of fluorescent proteins is formed by an internal cyclization of the tripeptide 65SYG67 fragment and a subsequent oxidation. The oxidation is slow - the kinetics of this step is presumably improved in fast maturing GFPs. Water molecules can aid in the chromophore formation. Read More

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http://dx.doi.org/10.1016/j.chemphys.2011.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3349357PMC
January 2012
8 Reads

A method to estimate the elastic energy stored in braided DNA molecules using hydrodynamic equations.

Chem Phys 2011 May;383(1-3):50-55

Department of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico 00936-8377.

We present a single-molecule method for measuring the torque exerted by braided DNA molecules undergoing spontaneous unbraiding while attached to a paramagnetic dumbbell in the absence of external manipulation. A magnetic tweezers setup is employed to braid pairs of lambda DNA molecules covalently bound to a surface. Upon removing the magnetic field, the braided DNA molecules undergo spontaneous unbraiding, efficiently transforming the stored elastic energy into enough mechanical energy to rotate the tethered dumbbells for periods as long as 30 minutes. Read More

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http://dx.doi.org/10.1016/j.chemphys.2011.04.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133659PMC
May 2011
1 Read

Covariant Lyapunov vectors for rigid disk systems.

Chem Phys 2010 Oct;375(2-3):296-308

Computational Physics Group, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Wien, Austria.

We carry out extensive computer simulations to study the Lyapunov instability of a two-dimensional hard-disk system in a rectangular box with periodic boundary conditions. The system is large enough to allow the formation of Lyapunov modes parallel to the x-axis of the box. The Oseledec splitting into covariant subspaces of the tangent space is considered by computing the full set of covariant perturbation vectors co-moving with the flow in tangent space. Read More

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http://dx.doi.org/10.1016/j.chemphys.2010.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982751PMC
October 2010
3 Reads

Fluxes of non-interacting and strongly repelling particles through a single conical channel: Analytical results and their numerical tests.

Chem Phys 2010 Oct;375(2-3):523-528

Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892.

Using a diffusion model of particle dynamics in the channel, we study entropic effects in channel-facilitated transport. We derive general expressions for the fluxes of non-interacting particles and particles that strongly repel each other through the channel of varying cross section area, assuming that the transport is driven by the difference in particle concentrations on the two sides of the membrane. For a special case of a right truncated cone expanding in the left-to-right direction, we show how the fluxes depend on the geometric parameters of the channel and on the particle concentrations. Read More

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http://dx.doi.org/10.1016/j.chemphys.2010.04.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2968752PMC
October 2010
8 Reads

Ultrafast Time-resolved Absorption Spectroscopy of Geometric Isomers of Xanthophylls.

Chem Phys 2010 Jul;373(1-2):80-89

Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, USA.

This paper presents an ultrafast optical spectroscopic investigation of the excited state energies, lifetimes and spectra of specific geometric isomers of neoxanthin, violaxanthin, lutein, and zeaxanthin. All-trans- and 15,15'-cis-beta-carotene were also examined. The spectroscopy was done on molecules purified by HPLC frozen immediately to inhibit isomerization. Read More

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http://dx.doi.org/10.1016/j.chemphys.2010.01.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913875PMC
July 2010
3 Reads

Variance of residence time spent by diffusing particle in a sub-domain. Path integral based approach.

Chem Phys 2010 May;370(1-3):253-257

Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA.

Path integral based approach is used to analyze the variance of the residence time spent in a sub-domain by a particle diffusing in the presence of an arbitrary potential in a larger domain containing the sub-domain. It is assumed that there is no absorption of the particle within the domain or at its boundaries. Because of the ergodisity, the mean residence time in the sub-domain is a product of the observation time and the equilibrium probability of finding the particle in the sub-domain. Read More

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http://dx.doi.org/10.1016/j.chemphys.2009.10.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880823PMC
May 2010
1 Read

Diffusion in a tube of alternating diameter.

Chem Phys 2010 May 11;370(1-3):238-243. Epub 2009 Nov 11.

Joint Institute for High Temperatures, Russian Academy of Sciences, Izhorskaya 13, Bldg. 2, Moscow 125412, Russia.

The paper deals with diffusion of a particle in a tube that consists of alternating wide and narrow sections. At sufficiently long times the particle motion can be coarse-grained and described as effective free-diffusion along the tube axis. In the coarse-grained description all the details of the tube geometry are packed into the effective diffusion coefficient of the particle. Read More

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http://dx.doi.org/10.1016/j.chemphys.2010.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5774649PMC
May 2010
1 Read

Ultrafast time-resolved absorption spectroscopy of geometric isomers of carotenoids.

Chem Phys 2009 Feb;357(1)

Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT 06269-3060, USA.

The structures of a number of stereoisomers of carotenoids have been revealed in three-dimensional X-ray crystallographic investigations of pigment-protein complexes from photosynthetic organisms. Despite these structural elucidations, the reason for the presence of stereoisomers in these systems is not well understood. An important unresolved issue is whether the natural selection of geometric isomers of carotenoids in photosynthetic pigment-protein complexes is determined by the structure of the protein binding site or by the need for the organism to accomplish a specific physiological task. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823300PMC
February 2009
19 Reads

Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides.

Chem Phys 2009 Feb;357(1-3):188-197

Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.

The light-harvesting apparatus of the purple bacterial photosynthetic unit consists of a pool of peripheral light-harvesting complexes that transfer excitation energy to a reaction center (RC) via the surrounding pigment-protein complex LH1. Recent electron microscopy and atomic force microscopy studies have revealed that RC-LH1 units of Rhodobacter sphaeroides form membrane-bending dimeric complexes together with the polypeptide PufX. We present a structural model for these RC-LH1-PufX dimeric complexes constructed using the molecular dynamics flexible fitting method based on an EM density map. Read More

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http://dx.doi.org/10.1016/j.chemphys.2009.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678753PMC
February 2009
4 Reads

Ultrafast Time-resolved Absorption Spectroscopy of Geometric Isomers of Carotenoids.

Chem Phys 2009 Feb;357(1-3):4-16

Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, USA.

The structures of a number of stereoisomers of carotenoids have been revealed in three-dimensional X-ray crystallographic investigations of pigment-protein complexes from photosynthetic organisms. Despite these structural elucidations, the reason for the presence of stereoisomers in these systems is not well understood. An important unresolved issue is whether the natural selection of geometric isomers of carotenoids in photosynthetic pigment-protein complexes is determined by the structure of the protein binding site or by the need for the organism to accomplish a specific physiological task. Read More

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http://dx.doi.org/10.1016/j.chemphys.2008.07.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2733370PMC
February 2009
18 Reads

Control of laser induced molecular fragmentation of n-propyl benzene using chirped femtosecond laser pulses.

Chem Phys 2009 Jun;360(1-3):47-52

Department of Chemistry, Indian Institute of Technology Kanpur, UP 208016, India.

We present the effect of chirping a femtosecond laser pulse on the fragmentation of n-propyl benzene. An enhancement of an order of magnitude for the relative yields of C3H3+ and C5H5+ in the case of negatively chirped pulses and C6H5+ in the case of positively chirped pulses with respect to the transform-limited pulse indicates that in some fragmentation channel, coherence of the laser field plays an important role. For the relative yield of all other heavier fragment ions, resulting from the interaction of the intense laser field with the molecule, there is no such enhancement effect with the sign of chirp, within experimental errors. Read More

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http://dx.doi.org/10.1016/j.chemphys.2009.04.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2722903PMC
June 2009
5 Reads

Ultrafast Electronic and Vibrational Dynamics of Stabilized A State Mutants of the Green Fluorescent Protein (GFP): Snipping the Proton Wire.

Chem Phys 2008 Jun;350(1-3):193-200

Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA.

Two blue absorbing and emitting mutants (S65G/T203V/E222Q and S65T at pH 5.5) of the green fluorescent protein (GFP) have been investigated through ultrafast time resolved infra-red (TRIR) and fluorescence spectroscopy. In these mutants, in which the excited state proton transfer reaction observed in wild type GFP has been blocked, the photophysics are dominated by the neutral A state. Read More

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http://dx.doi.org/10.1016/j.chemphys.2008.02.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597877PMC
June 2008
3 Reads

New sources and instrumentation for neutrons in biology.

Chem Phys 2008;345(2-3):133-151

Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble cedex 9, France.

Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed. Read More

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http://dx.doi.org/10.1016/j.chemphys.2008.02.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614686PMC
January 2008

The Role of the Tight-Turn, Broken Hydrogen Bonding, Glu222 and Arg96 in the Post-translational Green Fluorescent Protein Chromophore Formation.

Chem Phys 2008 Jun;348(1-3):152-160

Dept. of Chemistry, Connecticut College, New London, CT 06320.

Green Fluorescent Proteins (GFP) and GFP-like proteins all undergo an autocatalytic post-translational modification to form a centrally located chromophore. Structural analyses of all the GFP and GFP-like proteins in the protein databank were undertaken to determine the role of the tight-turn, broken hydrogen bonding, Gly67, Glu222 and Arg96 in the biosynthesis of the imidazolone group from 65SYG67. The analysis was supplemented by computational generation of the conformation adopted by uncyclized wild-type GFP. Read More

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http://dx.doi.org/10.1016/j.chemphys.2008.02.055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597819PMC
June 2008
6 Reads

Two Dimensional Electronic Correlation Spectroscopy of the npi* and pipi* Protein Backbone Transitions: A Simulation Study.

Chem Phys 2007 Nov;341(1-3):29-36

Department of Chemistry, University of California, Irvine, CA 92697 USA.

The two dimensional (2D) photon echo spectrum of the amide ultraviolet (UV) bands of proteins are simulated. Two effective exciton Hamiltonian parameter sets developed by Woody and Hirst, which predict similar CD spectra, may be distinguished by their very different 2DUV spectra. These differences are enhanced in specific configurations of pulse polarizations which provide chirality-induced signals. Read More

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http://dx.doi.org/10.1016/j.chemphys.2007.03.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2564823PMC
November 2007
4 Reads

Extracting single and two-exciton couplings in photosynthetic complexes by coherent two-dimensional electronic spectra.

Chem Phys 2008 Aug;357(1-3):79-84

University of California Irvine, California, United States.

Signatures of "strong" J and "weak" K exciton couplings in the nonlinear femtosecond optical response of the FMO photosynthetic complex are identified. The two types of couplings originate from interactions of molecular transition charge dipoles and change of molecular permanent dipoles in their ground and excited states, respectively. We demonstrate that by combining various two-dimensional optical signals it should be possible to invert spectroscopic data to reconstruct the full exciton Hamiltonian (energies and couplings). Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898157PMC
http://dx.doi.org/10.1016/j.chemphys.2008.10.010DOI Listing
August 2008
5 Reads

Ultrafast excited-state dynamics of RNA and DNA C tracts.

Chem Phys 2008 Jun;350(1-3):165-174

Department of Chemistry, The Ohio State University, 100 W. 18 Ave., Columbus, OH, USA 43210.

The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC)(18) were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Read More

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http://dx.doi.org/10.1016/j.chemphys.2008.01.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435405PMC
June 2008
3 Reads

Time-resolved infrared spectroscopy of the lowest triplet state of thymine and thymidine.

Chem Phys 2008 May;347(1-3):383-392

The Ohio State University Department of Chemistry 100 West 18 Ave. Columbus, OH 43210, USA.

Vibrational spectra of the lowest energy triplet states of thymine and its 2'-deoxyribonucleoside, thymidine, are reported for the first time. Time-resolved infrared (TRIR) difference spectra were recorded over seven decades of time from 300 fs - 3 micros using femtosecond and nanosecond pump-probe techniques. The carbonyl stretch bands in the triplet state are seen at 1603 and ~1700 cm(-1) in room-temperature acetonitrile-d(3) solution. Read More

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http://dx.doi.org/10.1016/j.chemphys.2007.10.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779519PMC
May 2008
6 Reads