Chemical Physics Letters

Published by Elsevier BV

Print ISSN: 0009-2614


Modified Becke'05 method of nondynamic correlation in density functional theory with self-consistent implementation
  • Article
  • Full-text available

February 2012


137 Reads



Becke's B05 method for nondynamic correlation is simplified for self-consistent implementation. An alternative form is proposed for the nondynamic correlation factors that do not require solving a complicated nonlinear algebraic equation. The four linear parameters of B05 are re-optimized together with one extra parameter entering a modified expression for the second-order same-spin energy contribution. The latter is co-linear with the exact-exchange energy density and does not require higher moments of the relaxed exchange hole. Preliminary tests of this method show that it leads to a slight improvement over the resolution-of-identity B05 results reported previously for atomization energies, and to a definite improvement for reaction barriers of Hydrogen abstraction.

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Two-photon excitation of 2,5-diphenyloxazole using a low power green solid state laser

January 2011


73 Reads

This Letter concerns two-photon excitation of 2,5-Diphenyloxazole (PPO) upon illumination from a pulsed 532 nm solid state laser, with an average power of 30 mW, and a repetition rate of 20 MHz. A very agreeable emission spectrum position and shape has been achieved for PPO receiving one- and two-photon excitation, which suggests that the same excited state is involved for both excitation modes. Also, a perfect quadratic dependence of laser power in the emission intensity function has been recorded. We tested the application of a small solid state green laser to two-photon induced time-resolved fluorescence, revealing the emission anisotropy of PPO to be considerably higher for two-photon than for one-photon excitation.

Acetylene weak bands at 2.5μm from intracavity Cr2+:ZnSe laser absorption observed with time-resolved Fourier transform spectroscopy

February 2006


51 Reads






The spectral dynamics of a mid-infrared multimode Cr(2+):ZnSe laser located in a vacuum sealed chamber containing acetylene at low pressure is analyzed by a stepping-mode high-resolution time-resolved Fourier transform interferometer. Doppler-limited absorption spectra of C(2)H(2) in natural isotopic abundance are recorded around 4000 cm(-1) with kilometric absorption path lengths and sensitivities better than 3 10(-8) cm(-1). Two cold bands are newly identified and assigned to the ν(1)+ν(4) (1) and ν(3)+ν(5) (1) transitions of (12)C(13)CH(2). The ν(1)+ν(5) (1) band of (12)C(2)HD and fourteen (12)C(2)H(2) bands are observed, among which for the first time ν(2)+2ν(4) (2)+ν(5) (-1).

2D IR photon echo study of the anharmonic coupling in the OCN region of phenyl cyanate

February 2009


52 Reads

The vibrations in the OCN stretching region of phenyl cyanate are examined by two-dimensional infrared spectroscopy. In water and THF, these spectra display three diagonal peaks having cross peaks characteristic of anharmonically coupled transitions. The pattern of the spectra is reproduced by coupling of two overtones with the OCN fundamental.

Single-scan 2D NMR spectroscopy on a 25 T bitter magnet

August 2007


37 Reads

2D NMR relies on monitoring systematic changes in the phases incurred by spin coherences as a function of an encoding time t(1), whose value changes over the course of independent experiments. The intrinsic multiscan nature of such protocols implies that resistive and/or hybrid magnets, capable of delivering the highest magnetic field strengths but possessing poor temporal stabilities, become unsuitable for 2D NMR acquisitions. It is here shown with a series of homo- and hetero-nuclear examples that such limitations can be bypassed using recently proposed 2D "ultrafast" acquisition schemes, which correlate interactions along all spectral dimensions within a single scan.

2D IR photon echo spectroscopy reveals hydrogen bond dynamics of aromatic nitriles

February 2009


48 Reads

The CN vibrations of two aromatic nitriles, cinnamonitrile, PhCH=CH-CN and benzonitrile, PhCN, representative of components of common enzyme inhibitors, are examined by two dimensional infrared spectroscopy. In methanol, these spectra display cross peaks between the two CN components whose evolution exposes the few picosecond (4.5 ps for CIN and 5.3 ps for BN) equilibrium dynamics of hydrogen bond making and breaking. The main features of the 2D IR spectra are reproduced by simulations only with exchange incorporated. The lowest free energy state is the non-hydrogen bonded form. Both alkyl and aryl nitriles have now shown this picosecond exchange process.

A correlated ab initio study of the Ã2Π ← Χ̃ 2Σ+ transition in MgCCH

August 1997


14 Reads

The A2 pi <-- X2 sigma+ transition in MgCCH was studied with correlation consistent basis sets and single- and multireference correlation methods. The A2 pi excited state was characterized in detail; the x2 sigma+ ground state has been described elsewhere recently. The estimated complete basis set (CBS) limits for valence correlation, including zero-point energy corrections, are 22668, 23191, and 22795 for the RCCSD(T), MRCI, and MRCI + Q methods, respectively. A core-valence correction of +162 cm-1 shifts the RCCSD(T) value to 22830 cm-1, in good agreement with the experimental result of 22807 cm-1.

Ab initio predictions on the rotational spectra of carbon-chain carbene molecules

January 1993


15 Reads

We predict rotational constants for the carbon-chain molecules H2C=(C=)nC, n=3-8, using ab initio computations, observed values for the earlier members in the series, H2CCC and H2CCCC with n=1 and 2, and empirical geometry corrections derived from comparison of computation and experiment on related molecules. H2CCC and H2CCCC have already been observed by radioastronomy; higher members in the series, because of their large dipole moments, which we have calculated, are candidates for astronomical searches. Our predictions can guide searches and assist in both astronomical and laboratory detection.

Ab initio study of C + H+3 reactions

April 1991


9 Reads

The reaction C + H3+ --> CH(+) + H2 is frequently used in models of dense interstellar cloud chemistry with the assumption that it is fast, i.e. there are no potential energy barriers inhibiting it. Ab initio molecular orbital study of the triplet CH3+ potential energy surface (triplet because the reactant carbon atom is a ground state triplet) supports this hypothesis. The reaction product is 3 pi CH+; the reaction is to exothermic even though the product is not in its electronic ground state. No path has been found on the potential energy surface for C + H3+ --> CH2(+) + H reaction.

A comparative electron correlation treatment in H2S-benzene dimer with DFT and wavefunction-based ab initio methods

June 2007


29 Reads

Three major conformations of H(2)S-benzene dimer have been located with a variety of density functional theories (DFT) and second order Møller-Plesset perturbation (MP2). In line with an experiment, MP2 results indicate that the tilted C(s)-symmetry structure is a stable dimer, yet a C(2v)-symmetry structure is only a second-order saddle point. Although all of the examined DFT methods also predict the binding between H(2)S and benzene as MP2 and the coupled cluster method with single and double excitations and perturbative triples (CCSD(T)) do, they considerably underestimate binding energies as compared with CCSD(T) results. However, PW91LYP and MPWB1K reproduce the binding sequence obtained with MP2 for the dimers, and provide the best binding energies among the tested DFT methods. The method of increments with the orbitals of H(2)S and π orbitals of the benzene recovers 99% of the total binding from the full CCSD(T).

On-the-fly free energy parameterization via temperature accelerated molecular dynamics

September 2012


45 Reads

We discuss a method for parametric calculation of free energy functions in arbitrary collective variables using molecular simulations. The method uses a variant of temperature accelerated molecular dynamics to evolve on-the-fly the parameters of the free energy function to their optimum values by minimization of a cumulative gradient error. We illustrate how the method performs using simple examples and discuss its application in the derivation of effective pairwise potentials for multiscale molecular simulations.

Quantifying accumulation or exclusion of H(+), HO(-), and Hofmeister salt ions near interfaces

December 2008


56 Reads

Recently, surface spectroscopies and simulations have begun to characterize the non-uniform distributions of salt ions near macroscopic and molecular surfaces. The thermodynamic consequences of these non-uniform distributions determine the often-large ion-specific effects of Hofmeister salts on a very wide range of processes in water. For uncharged surfaces, where these nonuniform ion distributions are confined to the first few layers of water at the surface, a two-state approximation to the distributions of water and ions, called the salt ion partitioning model (SPM) has both molecular and thermodynamic signiicance. Here, we summarize SPM results quantifying the local accumulation of H(+), exclusion of HO(-), and range of partitioning behavior of Hofmeister anions and cations near macroscopic and molecular interfaces. These results provide a database to interpret or predict Hofmeister salt effects on aqueous processes in terms of structural information regarding amount and composition of the surface exposed or buried in these processes.

Enhanced Fluorescence Emission of Me-ADOTA by Self-Assembled Silver Nanoparticles on a Gold Film

July 2009


58 Reads

We report a multi-fold enhancement of the fluorescence of methyl-azadioxatriangulenium chloride (Me-ADOTA*Cl) in PVA deposited on a 50 nm thick gold mirror carrying an evaporation induced self-assembly of colloidal silver nanoparticles (Ag-SACs). The average measured increase in fluorescence emission of about 50-fold is accompanied by hot spots with a local enhancement in brigthness close to 200. The long lifetime of the dye allows for the first direct determination of the correlation between the enhancement of emission intensity and the decrease in fluorescence lifetime. The Ag-SACs surface preparation and observed enhancements are highly reproducible. We believe that these robust plasmonic surfaces will find use in sensing platforms for ultrasensitive detection.

A SERS study of the molecular structure of alkanethiol monolayers on Ag nanocubes in the presence of aqueous glucose

September 2009


47 Reads

We report progress towards the surface-enhanced Raman scattering (SERS) characterization of self-assembled monolayers (SAMs) on uniform Ag nanocubes. This study quantifies changes in the SAMs induced by the presence of aqueous glucose. The SAMs were prepared from dodecanethiol and they were representative of highly ordered monolayers as indicated by SERS analysis. We examined the SAMs response to glucose and observed conformational changes in the alkanethiolate SAMs. Analysis of the trans and gauche bands as well as the C-H stretching modes of the SAMs suggest that the analyte-SAM interactions were superficial and there was no penetration for the glucose molecules into the monolayers.

Gold Nanoparticle Based Surface Enhanced Fluorescence For Detection of Organophosphorus Agents

July 2008


80 Reads

Organophosphorus agents (OPA) represent a serious concern to public safety as nerve agents and pesticides. Here we report the development of gold nanoparticle based surface enhanced fluorescence (NSEF) spectroscopy for rapid and sensitive screening of organophosphorus agents. Fluorescent from Eu(3+) ions that are bound within the electromagnetic field of gold nanoparticles exhibit a strong enhancement. In the presence of OPA, Eu(3+) ions are released from the gold nanoparticle surface and thus a very distinct fluorescence signal change was observed. We discussed the mechanism of fluorescence enhancement and the role of OPA for fluorescence intensity change in the presence of gold nanoparticles.

Using ultrafast infrared multidimensional correlation spectroscopy to aid in vibrational spectral peak assignments

December 2003


20 Reads

Ultrafast infrared heterodyne detected vibrational stimulated echoes with full phase information are used to obtain the vibrational correlation spectrum from a mixture of metal-carbonyl compounds. The linear absorption spectrum displays four peaks in the carbonyl stretching region. In the absence of knowledge of the molecules that make up the mixture, the absorption spectrum could arise from four molecules that each produces a single peak to one molecule with four peaks. In contrast, the correlation spectrum displays four peaks on the diagonal and off-diagonal peaks that make it straightforward to determine which peaks belong to a particular molecule.

The Effects of Regularly Spaced Glutamine Substitutions on Alpha-Helical Peptide Structures. A DFT/ONIOM Study

August 2011


64 Reads

The side-chains of the residues of glutamine (Q) and asparagine (N) contain amide groups. These can H-bond to each other in patterns similar to those of the backbone amides in α-helices. We show that mutating multiple Q's for alanines (A's) in a polyalanine helix stabilizes the helical structure, while similar mutations with multiple N's do not. We suggest that modification of peptides by incorporating Q's in such positions can make more robust helices that can be used to test the effects of secondary structures in biochemical experiments linked to proteins with variable structures such as tau and α-synuclein.

Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation

March 2008


82 Reads

Molecular dynamics (MD) simulations are performed for N-methylamide (NMA) in water at 300 K with different force fields. Compared to the three all-atom force fields (CHARMM22, AMBER03, and OPLS-AA), the united-atom force field (GROMOS96) predicts a broader distribution of the peptide OCNH dehedral angle. A map constructed by fitting the npi* and pipi* transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue-shifted npi* and pipi* energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins.

Amide I Band and Photoinduced Disassembly of a Peptide Hydrogel

August 2013


24 Reads

Peptide hydrogels are promising candidates for a wide range of medical and biotechnological applications. To further expand the potential utility of peptide hydrogels, herein we demonstrate a simple yet effective strategy to render peptide hydrogels photodegradable, making controlled disassembly of the gel structure of interest feasible. In addition, we find that the high-frequency amide I' component (i.e., the peak at ~1685 cm(-1)) of the photodegradable peptide hydrogel studied shows an unusually large enhancement, in comparison to that of other peptide fibrils consisting of antiparallel β-sheets, making it a good model system for further study of the coupling-structure relationship.

Photophysics of a Fluorescent Non-natural Amino Acid: p-Cyanophenylalanine

March 2010


107 Reads

The non-natural amino acid p-cyanophenylalanine (Phe(CN)) has recently emerged as a useful fluorescent probe of proteins; however, its photophysical properties have not been systematically examined. Herein, we measure the fluorescence quantum yield and the fluorescence lifetime of Phe(CN) in a series of solvents. It is found that the fluorescence lifetime of Phe(CN) shows a linear dependence on the Kamlet-Taft parameter α of the protic solvents used, indicating that the solute-solvent hydrogen bonding interactions mediate the non-radiative decay rate. Thus, results of this study provide a basis for quantitative application of Phe(CN) fluorescence in protein conformational studies.

Rapid synthesis of small silver nanocubes by mediating polyol reduction with a trace amount of sodium sulfide or sodium hydrosulfide

January 2007


155 Reads

This paper describes the fastest route to monodispersed silver nanocubes. By adding a trace amount of sodium sulfide (Na(2)S) or sodium hydrosulfide (NaHS) to the conventional polyol synthesis, the reaction time was significantly shortened from 16-26 hours to 3-8 minutes. By merely adjusting the reaction time, monodispersed silver nanocubes of 25-45 nm in edge length were rapidly and routinely produced on relatively large scales. These small nanocubes are of great interest for biomedical applications by way of generating gold nanocages with plasmon resonance peaks tunable to the near-infrared region through a galvanic replacement reaction.

Fig. 1. The starting function y(x) defined via Eq. (7). This function is discontinuous at x = 2.
Fig. 2. The required function x(y) constructed from numerical estimates. The point of discontinuity at y = 0 is also a branching point.
Table 2 (continued)
Table 3 Mean absolute errors (MAE) for atomization energies D e (kcal/mol, no ZPE) of 39 molecules, and MAE for bond lengths R e (A ˚ ) in 36 molecules (45 bonds)
Analytical representation of the Becke-Roussel exchange functional

April 2008


158 Reads

The unique meta-GGA (generalized gradient approximation) exchange functional of Becke and Roussel (BR89) and the correlation functional of Becke related to it (B94) are represented for the first time in an analytical form. All functional derivatives are then obtained analytically, which allows an efficient self-consistent implementation. A brief assessment of this "BR89B94" meta-GGA scheme is made considering molecular atomization energies and equilibrium geometries, with the latter being reported for the first time. The hybrid version of it yields one of the most accurate atomization energies to date, but its bond distances are less satisfactory. Some interesting features of the BR exchange hole are discussed.

Angular-Dependent Metal-Enhanced Fluorescence from Silver Island Films

April 2008


50 Reads

In this letter we report the observation of angular-dependent Metal Enhanced Fluorescence (MEF) from fluorophores deposited onto silver island films (SiFs). When illuminated with laser light (473 nm) at angles of 45 and 90 degrees from the surface, SiFs scattered light at wide observation angles biased by the direction of the incident light. We observed angular-dependent MEF (10-fold) from FITC-HSA immobilized onto the SiFs, again slightly biased with respect to the direction of the incident light. We also measured the photostability of FITC from the back of the glass substrate at angles of 225 and 340 degrees.

Quenching of p-Cyanophenylalanine Fluorescence by Various Anions

March 2013


57 Reads

To expand the spectroscopic utility of the non-natural amino acid p-cyanophenylalanine (PheCN), we examine the quenching efficiencies of a series of commonly encountered anions toward its fluorescence. We find that iodide exhibits an unusually large Stern-Volmer quenching constant, making it a convenient choice in PheCN fluorescence quenching studies. Indeed, using the villin headpiece subdomain as a testbed we demonstrate that iodide quenching of PheCN fluorescence offers a convenient means to reveal protein conformational heterogeneity. Furthermore, we show that the amino group of PheCN strongly quenches its fluorescence, suggesting that PheCN could be used as a local pH sensor.

Vibrational echo experiments on red blood cells: Comparison of the dynamics of cytoplasmic and aqueous hemoglobin

February 2004


34 Reads

Ultrafast spectrally resolved stimulated vibrational echo experiments measure the dephasing of the CO stretching mode of hemoglobin-CO (Hb-CO) inside living human erythrocytes (red blood cells). A method is presented to overcome the adverse impact on the vibrational echo signal from the strong light scattering caused by the cells. The results are compared to experiments on Hb-CO aqueous solutions. It is demonstrated that the dynamics of the protein as sensed by the CO ligand are the same inside the erythrocytes and in aqueous solution, but differences in the absorption spectra show that the cell affects the protein's potential energy surface.

Computational study of the cerium(III) ion in aqueous environment

June 2012


123 Reads

This work comprises the first quantum chemical simulation study of the Ce(3+) ion in aqueous environment. The structural and dynamical properties have been investigated by means of the quantum mechanical charge field (QMCF) molecular dynamics (MD) approach and the results, where applicable, have been compared to experimental data. Besides conventional analytical tools, angular radial distribution functions have been employed to gain deeper insight into the structure of the hydrate. The ion-oxygen stretching motion's wavenumber, further characterising the Ce-O bond, is in excellent agreement with experimental results, same as the structural values obtained from the simulation.

Close coupling results for inelastic collisions of NH3 and Ar. A stringent test of a spectroscopic potential

September 1994


39 Reads

We have calculated state-to-state total cross sections for rotational excitation and inversion of NH3 by collisions with Ar using the close coupling method. The Ar-NH3 interaction potential has been obtained from a fit to the spectrum of this van der Waals molecule. The calculated cross sections agree to within about 30% with the measured values; the estimated error in the latter is 10% to 20%.

Fluorescence Quenching/Enhancement Surface Assays: Signal Manipulation Using Silver-coated Gold Nanoparticles

April 2008


122 Reads

Gold nanoparticles covalently attached to the indium tin oxide coated glass slide drastically quench fluorescence of a surface immunoassay (approximately 5-fold). Silver electrochemically deposited over the gold particles leads to fluorescence amplification: signal increases approximately 7-8 times if compared to the signal on gold particles not covered with silver. This phenomenon allows enhancing of the surface immunoassays utilizing both types of nanoparticles. (c) 2008 Elsevier B. V. All rights reserved.

The reaction of atomic oxygen with methanethiol. A theoretical study of the structures and the potential energy surface

May 1993


78 Reads

Ab initio calculations at the Hartree-Fock, MP2 and MP4 levels were performed to find structures of the equilibrium and transition states and the reaction energies and energies of activation of several competing reaction pathways of O (3P)+CH3SH. A 6-31G* basis set was used in all calculations. The mechanism of hydrogen atom abstraction from the S-H group methanethiol was found to be very competitive with the oxygen atom addition to the sulfur atom.

A combined DFT/Green's function study on electrical conductivity through DNA duplex between Au electrodes

June 2009


59 Reads

Electrical conducting properties of DNA duplexes sandwiched between Au electrodes have been investigated by use of first-principles molecular simulation based on DFT and Green's function to elucidate the origin of their base sequence dependence. The theoretically simulated effects of DNA base sequence on the electrical conducting properties are in qualitative agreement with experiment. The HOMOs localized on Guanine bases have the major contribution to the electrical conductivity through DNA duplexes.

Metal-Enhanced S(2) Fluorescence from Azulene

January 2007


120 Reads

In this paper, we report the first observation of metal-enhanced S(2) emission at room and low temperature (77K). The S(2) emission intensity of Azulene is enhanced by close proximity to Silver island films (SiFs). In this regard, a ≈ 2-fold higher S(2) fluorescence intensity of Azulene was observed from SiFs as compared to a glass control sample. This suggests that S(2) excited states can couple to surface plasmons and enhance S(2) fluorescence yields, a helpful observation in our understanding the interactions between plasmons and lumophores, and our continued efforts to develop a unified plasmon-lumophore/fluorophore theory.

Efficient self-consistent DFT calculation of nondynamic correlation based on the B05 method

June 2010


86 Reads

Becke's B05 method of describing nondynamic electron correlation in Density Functional Theory is implemented self-consistently with computational efficiency. Important modifications of the method are proposed in order to make the self-consistency feasible. Resolution-of-identity technique is used to reduce dramatically the cost of the required exact-exchange energy density. The method is briefly validated on a variety of properties. It describes accurately for the first time the subtle energetics of the NO dimer, an exemplary system of strong nondynamic correlation. The efficient algorithm for the exact-exchange energy density can be applied to other functionals that use this quantity.

Characterization of silicon-carbon clusters by infrared laser spectroscopy. The v1 band of SiC4

June 1995


18 Reads

The nu 1 fundamental vibration of linear SiC4 has been observed by infrared diode laser spectroscopy of a supersonic cluster beam. Twenty-four rovibrational transitions were measured in the spectral region of 2094.6 to 2097.1 cm-1, the rotational temperature was 10 K. A combined least-squares fit of these transitions with previously reported microwave data yielded the following molecular constants: nu 1 = 2095.45806(37) cm-1, B" = 0.051161131(52) cm-1, and B' = 0.0509157(96) cm-1. These results are compared to vibrational spectroscopy measurements of SiC4 trapped in a solid Ar matrix and to ab initio calculations.

Effect of base mismatch on the electronic properties of DNA-DNA and LNA-DNA double strands: Density-functional theoretical calculations

October 2007


37 Reads

The electronic properties of double-stranded octametric DNA-DNA and LNA-DNA with a single-base mismatch were compared with those having fully complementary base pairs to quantify the effect of the base mismatch on hybridization energies (HE). A single T-G mismatch in the LNA-DNA gives rise to a significant reduction in HE, which is consistent with a significant lowering of the melting temperature for mismatched LNA-DNA. By contrast, the hybridization strength of the mismatched DNA-DNA depends strongly on local hydrogen-bonding arrangements in the mispaired T-G. The difference in HE is explained in terms of variation in charge distributions around the hydrogen-bonded base pairs.

Potential-derived point-charge model study of electrostatic interactions in DNA base components

September 1984


9 Reads

Ab initio electrostatic potentials obtained using STO-3G wavefunctions for guanine, cytosine, adenine, and thymine are used to calculate potential-derived (PD) point charges for these base components. Calculated PD point charges are used to estimate the electrostatic contributions to hydrogen-bonding and stacking interaction energies of ten sequence isomers of B-DNA. These estimates are in excellent agreement with the results of the more elaborate segmental multipole moment expansion technique.

Effects of cluster formation on spectra of benzo[a] pyrene and benzo[e] pyrene

April 2008


68 Reads

Absorption and fluorescence emission spectra of the polycyclic aromatic hydrocarbons benzo[a]pyrene (BaP) and benzo[e]pyrene (BeP) in solution and adsorbed on silica have been obtained and compared to examine the spectroscopic effects of clustering. Molecular mechanics calculations with the UFF potential were done to optimize monomer, dimer and trimer geometries, and energy differences were determined by MP2/6-31G* calculations. Fluorescence emission spectra of adsorbed BeP and BaP display a red shift that progresses with increased loading, and the two differ in their photodegradation kinetics. The experimental and theoretical results are found to be consistent.

Water Permeation through DMPC Lipid Bilayers Using Polarizable Charge Equilibration Force Fields

May 2011


43 Reads

We investigate permeation energetics of water entering a model dimyristoylphosphatidylcholine (DMPC) bilayer via molecular dynamics simulations using polarizable Charge Equilibration (CHEQ) models. Potentials of mean force show 4.5-5.5 kcal/mol barriers for water permeation into bilayers. Barriers are highest when water coordination within the bilayer is prevented, and also when using force fields that accurately reproduce experimental alkane hydration free energies. The magnitude of the average water dipole moment decreases from 2.6 Debye (in bulk) to 1.88 Debye (in membrane interior). This variation correlates with the change in a water molecule's coordination number.

Competitive binding effects on surface-enhanced Raman scattering of peptide molecules

October 2007


59 Reads

Surface enhanced Raman scattering (SERS) has been conducted on tryptophan (W), proline (P) and tyrosine (Y) containing peptides that include W-P-Y, Y-P-W, W-P-P-P-Y, Y-P-P-P-W, W-P-P-P-P-P-Y, and Y-P-P-P-P-P-W to gain insight into molecular binding behavior on a metal substrate to eventually apply in protein SERS detection. The peptides are shown to bind through the molecule's carboxylic end, but the strong affinity of the tryptophan residue to the substrate surface, in conjunction with its large polarizability, dominates each molecule's SERS signal with the strong presence of its ring modes in all samples. These results are important for understanding SERS of protein molecules.

Strong-field ionization of sputtered molecules for biomolecular imaging

January 2009


32 Reads

Photoionization of molecules sputtered from molecular thin films has been achieved using high field 125 fs pulses in the mid-IR spectral range. Using several model systems, we show that it is possible to significantly reduce molecular fragmentation induced by the laser field by increasing the photoionization wavelength. By examining the photoionization spectra as a function of wavelength, it is apparent that the photoionization mechanism is changing from a non-adiabatic multi-electron excitation process to a process that involves tunnel ionization. The results of these observations are discussed in terms of their significance for bioimaging with focused ion beams and mass-spectrometry.

Solvation of Biomolecules by the Soft Sticky Dipole-Quadrupole-Octupole Water Model

February 2010


30 Reads

The soft sticky dipole-quadrupole-octupole (SSDQO) potential energy function represents a water molecule by a single site with a van der Waals sphere and point multipoles. Previously, SSDQO was shown to give good properties for liquid water and solvation of simple ions and is faster than three point models. Here, SSDQO is assessed for solvating biologically relevant molecules having a multi-site, partial charge description. Monte Carlo simulations of ethanol, benzene, and N-methylacetamide in SSDQO with SPC/E moments showed the water structure was as good as in SPC/E. Thus, SSDQO is potentially useful for simulations of biological macromolecules in aqueous solution.

Suppressed Blinking in Single Quantum Dots (QDs) Immobilized Near Silver Island Films (SIFs)

November 2007


46 Reads

In this report, we use single-molecule spectroscopic method to study emission behaviors of streptavidin conjugated quantum dots immobilized on biotinylated-BSA (bovine serum albumin) monolayer near non-continuous rough silver nanostructure. We observed greatly reduced blinking and enhanced emission fluorescence of quantum dots next to silver island films.

Numerical Poisson-Boltzmann Model for Continuum Membrane Systems

January 2013


42 Reads

Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.

Progress and Challenges for the Bottom-Up Synthesis of Carbon Nanotubes with Discrete Chirality

July 2010


70 Reads

Carbon nanotubes (CNTs) have emerged as some of the most promising materials for the technologies of the future. One of the most significant limitations to furthering the understanding and application of these fascinating systems is the lack of atomic-level structural control in their syntheses. Current synthetic methods produce mixtures of structures with varying physical properties. In this article, we describe the potential advantages, recent advances, and challenges that lie ahead for the bottom-up organic synthesis of homogeneous carbon nanotubes with well-defined structures.

New calculations on the ion—molecule processes C2H+2 + H2 → C2H+3 + H and C2H+2 + H2 → C2H+4

February 1994


12 Reads

New high-level quantum chemical calculations have been undertaken to understand the rates and mechanisms of the reactive and associative channels for the reactants C2H2(+) + H2. The reactive channel, which produces C2H3(+) + H, has been shown to be slightly endothermic, confirming earlier calculations at a somewhat lower level and in agreement with some recent experimental work. The associative channel, leading to C2H4+, has been shown to proceed via a transition state with negative energy relative to the reactants, so that association is predicted to be efficient. This result is in conflict with an earlier theoretical study but in agreement with low-temperature experimental measurements.

Deuterium hyperfine structure in interstellar C3HD

June 1987


9 Reads

The deuterium nuclear quadrupole hyperfine structure of the transition 1(10)-1(01) of the ring molecule cyclopropenylidene-d1 (C3HD) has been observed in emission from interstellar molecular clouds. The narrowest linewidths (approximately 7 kHz) so far observed are in the cloud L1498. The derived D coupling constants Xzz = 186.9(1.4) kHz, eta=0.063(18) agree well with correlations based on other molecules.

A priori predictions of the rotational constants for HC13N, HC15N, C5O

July 1989


9 Reads

Ab initio molecular orbital theory is used to estimate the rotational constant for several carbon-chain molecules that are candidates for discovery in interstellar space. These estimated rotational constants can be used in laboratory or astronomical searches for the molecules. The rotational constant for HC13N is estimated to be 0.1073 +/- 0.0002 GHz and its dipole moment 5.4 D. The rotational constant for HC15N is estimated to be 0.0724 GHz, with a somewhat larger uncertainty. The rotational constant of C5O is estimated to be 1.360 +/- 2% GHz and its dipole moment 4.4. D.

Calculation of the Entropy of Lattice Polymer Models from Monte Carlo Trajectories

August 2005


92 Reads

While lattice models are used extensively for macromolecules (synthetic polymers proteins, etc), calculation of the absolute entropy, S, and the free energy, F, from a given Monte Carlo (MC) trajectory is not straightforward. Recently we have developed the hypothetical scanning MC (HSMC) method for calculating S and F of fluids. Here we extend HSMC to self-avoiding walks on a square lattice and discuss its wide applicability to complex polymer lattice models. HSMC is independent of existing techniques and thus constitutes an independent research tool; it provides rigorous upper and lower bounds for F, which can be obtained from a very small sample and even from a single chain conformation.

Carotenoid response to retinal excitation and photoisomerization dynamics in xanthorhodopsin

November 2011


43 Reads

We present a comparative study of xanthorhodopsin, a proton pump with the carotenoid salinixanthin serving as an antenna, and the closely related bacteriorhodopsin. Upon excitation of retinal, xanthorhodopsin exhibits a wavy transient absorption pattern in the region between 470 and 540 nm. We interpret this signal as due to electrochromic effect of the transient electric field of excited retinal on salinixanthin. The spectral shift decreases during the retinal dynamics through the ultrafast part of the photocycle. Differences in dynamics of bacteriorhodopsin and xanthorhodopsin are discussed.

Regioselectivity of Catechol O-Methyltransferase Confers Enhancement of Catalytic Activity

April 2011


24 Reads

Catechol O-methyltransferase (COMT) metabolizes catechol moieties by methylating a single hydroxyl group at the meta- or para- hydroxyl position. Hydrophobic amino acids near the active site of COMT influence the regioselectivity of this reaction. Our sequence analysis highlights their importance by showing that these residues are highly conserved throughout evolution. Reaction barriers calculated in the gas phase reveal a lower barrier during methylation at the meta- position, suggesting that the observed meta-regioselectivity of COMT can be attributed to the substrate itself, and that COMT has evolved residues to orient the substrate in a manner that increases the rate of catalysis.

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