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PubMed2005

Long-range electrostatic interactions in hybrid quantum and molecular mechanical dynamics using a lattice summation approach.

A method based on a lattice summation technique for treating long-range electrostatic interactions in hybrid quantum mechanics/molecular mechanics simulations is presented in this article. The quantum subsystem is studied at the semiempirical level, whereas the solvent is described by a two-body potential of molecular mechanics. Molecular dynamics simulations of a (quantum) chloride ion in (classical) water have been performed to test this technique. It is observed that the application of the lattice summations to solvent-solvent interactions as well as on solute-solvent ones has a significant effect on solvation energy and diffusion coefficient. Moreover, two schemes for the computation of the long-range contribution to the electrostatic interaction energy are investigated. The first one replaces the exact charge distribution of the quantum solute by a Mulliken charge distribution. The long-range electrostatic interactions are then calculated for this charge distribution that interacts with the solvent molecule charges. The second one is more accurate and involves a modified Fock operator containing long-range electron-charge interactions. It is shown here that both schemes lead to similar results, the method using Mulliken charges for the evaluation of long-range interactions being, however, much more computationally efficient.

Journal Article↗
PubMedDate not supplied

Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase.

The reaction pathway for the aromatic 3-hydroxylation of p-hydroxybenzoate by the reactive C4a-hydroperoxyflavin cofactor intermediate in p-hydroxybenzoate hydroxylase (PHBH) has been investigated by a combined quantum mechanical and molecular mechanical (QM/MM) method. A structural model for the C4a-hydroperoxyflavin intermediate in the PHBH reaction cycle was built on the basis of the crystal structure coordinates of the enzyme-substrate complex. A reaction pathway for the subsequent hydroxylation step was calculated by imposing a reaction coordinate that involves cleavage of the peroxide oxygen-oxygen bond and formation of the carbon-oxygen bond between the C3 atom of the substrate and the distal oxygen of the peroxide moiety of the cofactor. The geometric changes and the Mulliken charge distributions along the calculated reaction pathway are in line with an electrophilic aromatic substitution type of mechanism. The energy barrier of the calculated reaction is considerably lower when the substrate hydroxyl moiety is deprotonated, in comparison with the barrier found with a protonated hydroxyl moiety. This effect of the protonation state of the substrate on the calculated energy barrier supports experimental observations that deprotonation is required for hydroxylation of the substrate. A notable event in the calculated reaction pathway is a lengthening of the peroxide oxygen-oxygen bond at an intermediate stage. Further analysis of the reaction pathway indicates that this oxygen-oxygen bond elongation is accompanied by an increase in electrophilic reactivity on the distal oxygen of the peroxide moiety, which may assist the C-O bond formation in the reaction of the C4a-hydroperoxyflavin intermediate with the substrate. Analysis of the effect of individual active site residues on the reaction reveals a specific transition state stabilization by the backbone carbonyl moiety of Pro293. The crystal water 717 appears to drive the hydroxylation step through a stabilizing hydrogen bond interaction to the proximal oxygen of the C4a-hydroperoxyflavin intermediate, which increases in strength as the hydroperoxyflavin cofactor converts to the anionic (deprotonated) hydroxyflavin.

4-Hydroxybenzoate-3-Monooxygenase↗
PubMed2006

Multipole-multimode Floquet theory of rotational resonance width experiments: 13C-13C distance measurements in uniformly labeled solids.

A formal description of zero-quantum (ZQ) NMR processes using multipole-multimode Floquet theory is proposed for studying polarization transfer in magic angle spinning experiments. Specifically, we investigate the factors affecting the accuracy and precision of 13C-13C distance measurements that are based on ZQ-magnetization exchange processes in rotational resonance width experiments. With suitable examples drawn from measurements in N-acetyl-[U-13C,15N]-L-valine-L-leucine, we substantiate our approach and propose methods for improving the accuracy and reliability of such 13C-13C distance measurements in uniformly 13C, 15N-labeled solids. In addition, the theoretical model presented in this article provides a more general framework for describing relaxation phenomena involving multiple decay rate constants in zero-quantum processes.

Carbon Isotopes↗
PubMed2003

A three dimensional (3-D) physical model of ribosome movement in protein synthesis.

In this study, we propose new concepts of Active Potential Energy Well, Specificity and Non-Specificity of the wells. We perform these concepts to establish a 3-D physical model and to elucidate how a complete functional ribosome traps an aminoacyl tRNA, and how it moves along the mRNA template in the elongation of protein synthesis. In our model, we first introduce concepts of reduced mass and relative coordinates of a two objects system. Then we simplify a ribosome movement along mRNA in protein synthesis. We also introduce concepts of active objects and active controls in this study. Our model is based on quantum mechanics, thermal dynamics and the published biochemical data.

Cell Movement↗
PubMed2005

Dynamic nuclear polarization and nuclear magnetic resonance in the vicinity of edge states of a 2DES in GaAs quantum wells.

Nuclear magnetic resonance is detected via the in-plane conductivity of a two-dimensional electron system at unity Landau level filling factor in the regime of the quantum Hall effect in narrow and wide quantum wells. The NMR is spatially selective to nuclei with a coupling to electrons in the current carrying edge states at the perimeter of the 2DES. Interpretation of the electron-nuclear double resonance signals is facilitated by numerical simulations. A new RF swept method for conductivity-detected NMR is introduced which offers more efficient signal averaging. The method is applied to the study of electric quadrupole interactions, weakly allowed overtone transitions, and evaluation of the extent of electron wave function delocalization in the wide quantum well.

Algorithms↗
PubMed1998

Calculations of proton-binding thermodynamics in proteins.

Computational models of proton binding can range from the chemically complex and statistically simple (as in the quantum calculations) to the chemically simple and statistically complex. Much progress has been made in the multiple-site titration problem. Calculations have improved with the inclusion of more flexibility in regard to both the geometry of the proton binding and the larger scale protein motions associated with titration. This article concentrated on the principles of current calculations, but did not attempt to survey their quantitative performance. This is (1) because such comparisons are given in the cited papers and (2) because continued developments in understanding conformational flexibility and interaction energies will be needed to develop robust methods with strong predictive power. Nevertheless, the advances achieved over the past few years should not be underestimated: serious calculations of protonation behavior and its coupling to conformational change can now be confidently pursued against a backdrop of increasing understanding of the strengths and limitations of such models. It is hoped that such theoretical advances will also spur renewed experimental interest in measuring both overall titration curves and individual pKa values or pKa shifts. Exploration of the shapes of individual titration curves (as measured by Hill coefficients and other parameters) would also be useful in assessing the accuracy of computations and in drawing connections to functional behavior.

Hemoglobins↗
PubMed2005

Self-consistent solution of two-dimensional poisson and Schrödinger wave equations for nanoscale MOSFET approaching ballistic limit.

A numerical solution of the potential distribution of two-dimensional Poisson equation and Schrödinger wave equation under a set of boundary conditions has been obtained for a deep submicron and nanoscale MOSFET. The output characteristics can be found out by simply solving the two-dimensional Poisson equation under specific boundary conditions governed by the physics of the device. The channel potential profile has been presented. It is seen that the classical model underestimates the channel voltage and hence the longitudinal electric field in the channel as compared to that obtained through the quantum mechanical approach. For the purpose of validation, the results obtained on the basis of our model have been compared and contrasted with reported experimental result.

Computer Simulation↗
PubMed2005

Energy levels in self-assembled quantum arbitrarily shaped dots.

A model to determine the electronic structure of self-assembled quantum arbitrarily shaped dots is applied. This model is based principally on constant effective mass and constant potentials of the barrier and quantum dot material. An analysis of the different parameters of this model is done and compared with those which take into account the variation of confining potentials, bands, and effective masses due to strain. The results are compared with several spectra reported in literature. By considering the symmetry, the computational cost is reduced with respect to other methods in literature. In addition, this model is not limited by the geometry of the quantum dot.

Journal Article↗
PubMed2005

Matrix isolation and computational study of the photochemistry of p-azidoaniline.

The photochemistry of p-azidoaniline was studied in argon matrices in the absence and presence of oxygen. With the help of quantum chemical calculations we were able to characterize the triplet p-aminophenylnitrene as well as the cis- and trans-p-aminophenylnitroso oxides. It was found that the latter two isomers can be interconverted by selective irradiation and that they are ultimately converted into p-nitroaniline. Although restricted wavefunctions of the nitroso oxides are unstable, CASSCF calculations turned up no evidence for the claimed diradical character of these compounds. Also we found no evidence for dioxaziridines as intermediates of the conversion of the nitroso oxides to p-nitroaniline.

Aniline Compounds↗
PubMed2002

Simulation of the strong interaction.

In the Standard Model (SM) of particle physics, quarks are permanently confined by the strong interaction into bound states called hadrons. The values of some parameters, such as the quark masses and the strengths of the decays of one quark flavour into another, cannot be measured directly and must be deduced from experiments on hadrons. This requires calculations of the strong-interaction effects within the bound states, which are only possible using numerical simulations of quantum chromodynamics (QCD), the quantum field theory of the strong interaction. In conjunction with experimental data from B factories over the next few years, QCD simulations may provide clues to physics beyond the SM. The simulations are computationally intensive and, for the past 20 years, have exploited leading-edge computing technology. This continues today, with a project to develop a 10 Tflops computer for QCD costing less than 1 US dollar per Mflops.

Algorithms↗
PubMed2003

Finite-difference time-domain simulation of ultrashort pulse propagation incorporating quantum-mechanical response functions.

A semiclassical implementation of the finite-difference time-domain method is used to simulate coherent linear propagation of ultrashort mid-infrared pulses through optically dense samples of isotropically diluted liquid water. Bloch equations for the density matrix are used as a simple model of the O--H oscillator relaxation, and the algorithm is extended to other response functions. Sensitivity of the field to the form of the response function is demonstrated, and the results are compared with experimentally determined electric fields in the same media [Rev. Sci. Instrum. 73, 2227 (2002)].

Computer Simulation↗
PubMed2005

Scaled quantum chemical calculations and FTIR, FT-Raman spectral analysis of 3,4-diamino benzophenone.

The vibrational spectra of 3,4-diamino benzophenone (DABP) have been computed using B3LYP methodology and 6-31G* and 6-31G** basis sets. The solid phase FTIR and FT-Raman spectra were recorded in the region 4000-400 cm-1 and 3500-100 cm-1, respectively. A close agreement was achieved between the observed and calculated frequencies by employing normal coordinate calculations. The observed and simulated spectra were found to be well comparable.

Benzophenones↗
PubMed2002

The ab initio simulation of the Earth's core.

The Earth has a liquid outer and solid inner core. It is predominantly composed of Fe, alloyed with small amounts of light elements, such as S, O and Si. The detailed chemical and thermal structure of the core is poorly constrained, and it is difficult to perform experiments to establish the properties of core-forming phases at the pressures (ca. 300 GPa) and temperatures (ca. 5000-6000 K) to be found in the core. Here we present some major advances that have been made in using quantum mechanical methods to simulate the high-P/T properties of Fe alloys, which have been made possible by recent developments in high-performance computing. Specifically, we outline how we have calculated the Gibbs free energies of the crystalline and liquid forms of Fe alloys, and so conclude that the inner core of the Earth is composed of hexagonal close packed Fe containing ca. 8.5% S (or Si) and 0.2% O in equilibrium at 5600 K at the boundary between the inner and outer cores with a liquid Fe containing ca. 10% S (or Si) and 8% O.

Computer Simulation↗
PubMed2005

Vibrational energy relaxation rates via the linearized semiclassical approximation: applications to neat diatomic liquids and atomic-diatomic liquid mixtures.

We report the results obtained from the application of our previously proposed linearized semiclassical method for computing vibrational energy relaxation (VER) rates (J. Phys. Chem. A 2003, 107, 9059, 9070) to neat liquid oxygen, neat liquid nitrogen, and liquid mixtures of oxygen and argon. Our calculations are based on a semiclassical approximation for the quantum-mechanical force-force correlation function, which puts it in terms of the Wigner transforms of the force and the product of the Boltzmann operator and the force. The calculation of the multidimensional Wigner integrals is made feasible by the introduction of a local harmonic approximation. A systematic analysis has been performed of the temperature and mole-fraction dependences of the VER rate constant, as well as the relative contributions of centrifugal and potential forces, and of different types of quantum effects. The results were found to be in very good quantitative agreement with experiment, and they suggest that this semiclassical approximation can capture the quantum enhancement, by many orders of magnitude, of the experimentally observed VER rate constants over the corresponding classical predictions.

Algorithms↗
PubMed2005

Hybrid ab initio VB/MM method--a valence bond ride through classical landscapes.

The development of a new hybrid (QM/MM) method, where the QM part is treated by ab initio valence bond (VB) theory is presented. This VB/MM method has the advantages of empirical VB (EVB) methodology but does not rely on empirical parameterization for the quantum part. The method implements embedding of the quantum region of each diabatic state separately, by treating the electrostatic interactions between QM and MM regions classically. Additionally, it assumes that changes of the off diagonal matrix element due to different environments are such that the overall resonance integral does not change. These assumptions are discussed in detail and the validity of the method is shown to be successful in three different bond dissociation processes, where bond dissociation as well as solvation energies compare very well with the experimental data.

Algorithms↗
PubMed2001

Structure of the P700(+ )A1(-) radical pair intermediate in photosystem I by high time resolution multifrequency electron paramagnetic resonance: analysis of quantum beat oscillations.

The geometry of the secondary radical pair P700(+)A1(-), in photosystem I (PSI) from the deuterated and 15N-substituted cyanobacterium Synechococcus lividus, has been determined by high time resolution electron paramagnetic resonance (EPR), performed at three different microwave frequencies. Structural information is extracted from light-induced quantum beats observed in the transverse magnetization of P700(+)A1(-) at early times after laser excitation. A computer analysis of the two-dimensional Q-band experiment provides the orientation of the various magnetic tensors of with respect to a magnetic reference frame. The orientation of the cofactors of the primary donor in the g-tensor system of is then evaluated by analyzing time-dependent X-band EPR spectra, extracted from a two-dimensional data set. Finally, the cofactor arrangement of P700(+)A1(-) in the photosynthetic membrane is deduced from angular-dependent W-band spectra, observed for a magnetically aligned sample. Thus, the orientation of the g-tensor of P700(+) with respect to a chlorophyll based reference system could be determined. The angle between the g1(z) axis and the chlorophyll plane normal is found to be 29 +/- 7 degrees, while the g1(y) axis lies in the chlorophyll plane. In addition, a complete structural model for the reduced quinone acceptor, A1(-), is evaluated. In this model, the quinone plane of is found to be inclined by 68 +/- 7 degrees relative to the membrane plane, while the P700(+)-A1(-) axis makes an angle of 35 +/- 6 degrees with the membrane normal. All of these values refer to the charge separated state, observed at low temperatures, where forward electron transfer to the iron-sulfur centers is partially blocked. Preliminary room temperature studies of P700(+)A1(-), employing X-band quantum beat oscillations, indicate a different orientation of A1(-) in its binding pocket. A comparison with crystallographic data provides information on the electron-transfer pathway in PSI. It appears that quantum beats represent excellent structural probes for the short-lived intermediates in the primary energy conversion steps of photosynthesis.

Cell Membrane↗
PubMed2005

Quantum and dynamical effects of proton donor-acceptor vibrational motion in nonadiabatic proton-coupled electron transfer reactions.

This paper presents a general theoretical formulation for proton-coupled electron transfer (PCET) reactions. The solute is represented by a multistate valence bond model, and the active electrons and transferring proton(s) are treated quantum mechanically. This formulation enables the classical or quantum mechanical treatment of the proton donor-acceptor vibrational mode, as well as the dynamical treatment of the proton donor-acceptor mode and the solvent. Nonadiabatic rate expressions are presented for PCET reactions in a number of well-defined limits for both dielectric continuum and molecular representations of the environment. The dynamical rate expressions account for correlations between the fluctuations of the proton donor-acceptor distance and the nonadiabatic PCET coupling. The quantities in the rate expressions can be calculated with a dielectric continuum model or a molecular dynamics simulation of the full system. The significance of the quantum and dynamical effects of the proton donor-acceptor mode is illustrated with applications to model PCET systems.

Computer Simulation↗
PubMed2006

Multiple particle tracking in 3-D+t microscopy: method and application to the tracking of endocytosed quantum dots.

We propose a method to detect and track multiple moving biological spot-like particles showing different kinds of dynamics in image sequences acquired through multidimensional fluorescence microscopy. It enables the extraction and analysis of information such as number, position, speed, movement, and diffusion phases of, e.g., endosomal particles. The method consists of several stages. After a detection stage performed by a three-dimensional (3-D) undecimated wavelet transform, we compute, for each detected spot, several predictions of its future state in the next frame. This is accomplished thanks to an interacting multiple model (IMM) algorithm which includes several models corresponding to different biologically realistic movement types. Tracks are constructed, thereafter, by a data association algorithm based on the maximization of the likelihood of each IMM. The last stage consists of updating the IMM filters in order to compute final estimations for the present image and to improve predictions for the next image. The performances of the method are validated on synthetic image data and used to characterize the 3-D movement of endocytic vesicles containing quantum dots.

Algorithms↗