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At least 1,135 records · Page 63Linked to original sources
PubMed2005

Structure and dynamics of solvated Sn(II) in aqueous solution: an ab initio QM/MM MD approach.

Structural and dynamical properties of the hydrated Sn(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at double-zeta HF quantum mechanical level. The results indicate Sn(II)aq to be a rather peculiar, if not unique, case of a hydrated ion: four of its eight first-shell ligands do not take place in the otherwise frequent ligand-exchange processes, forming an approximately tetrahedral cage around the ion. The remaining ligands, however, exchange at a rate that is rather comparable to monovalent than divalent ions. This very surprising behavior of ligand exchange not yet observed in any previous simulation of over 30 hydrated metal ions is consistently confirmed by vibrational spectra, bond lengths, and a detailed analysis of the trajectories of the simulation.

Computer Simulation↗
PubMed2000

Electronic portal imaging with an avalanche-multiplication-based video camera.

The aim of this study is to investigate the degree to which the imaging quality of an existing (video-based) electronic portal imaging device (EPID) system may be improved by using an avalanche-multiplication-based video camera (called the avalanche-gain method). Due to avalanche multiplication in the target of the video camera tube, the new camera can be made up to several hundred times more sensitive than a camera using a conventional video (e.g., Saticon) tube. As a result, the camera noise which limits the performance of current video-based EPIDs should be overwhelmed and made negligible. The detective quantum efficiency (DQE) of an EPID using the avalanche-gain method has been measured with 6 MV and 18 MV beams obtained using a linear accelerator. It is shown that the camera noise is indeed much smaller than quantum noise and that the DQE of the system is significantly increased compared to conventional video-based EPIDs. Variation of DQE of the avalanche-gain video portal system with a change of demagnification was also investigated. It has been shown that the improvement of optical coupling has less effect in this system than that in a conventional video-based EPID system.

Humans↗
PubMed2006

A theoretical study of phenolic compounds with antioxidant properties.

Quantum chemical calculations at the DFT/B3LYP, HF, and AM1 and PM3 semiempirical levels were employed to calculate a set of molecular properties for 41 phenol compounds with antioxidant activity. The significant molecular descriptors related to the compounds were the vertical ionization potentials (IPvs) and the charge on oxygen atom 7. The IPv has been calculated using Koopman's theorem IPv=-epsilon(HOMO(DFT)), IPv=-epsilon(HOMO(HF)) and as the difference of energy calculations for the corresponding cation and for the neutral form IPv(E(cation)-E(neutral)) obtained with the DFT/B3LYP method. The best model obtained showed not only the statistical significance but also predictive ability.

Antioxidants↗
PubMed2006

Transition-state characterization of the ammonia ionization process in aqueous solution via the free-energy gradient method.

For the ionization process of ammonia in aqueous solution, the transition-state (TS) structure was fully optimized for the first time on the free-energy surface (FES) by applying the free-energy gradient (FEG) method combined with a hybrid quantum mechanical and molecular mechanical molecular dynamics (QM/MM-MD) method. In aqueous solution, the ionization process was found to proceed by way of a clear TS (R(N1-H5) = 1.512 A), which does not exist in the gas phase. The free-energy (FE) of activation for ionization obtained was 14.7 kcal/mol, within the classical approximation, via the QM/MM-MD FEG method, and is found to be in good agreement with 9.57 kcal/mol estimated from the TS theory using the experimental value of the rate constant. Apart from the dynamic correction, it is indicated that the theoretical value would be improved to be 10.28 kcal/mol if the electronic-state calculation could be executed at the B3LYP/6-31G(d) level of theory.

Ammonia↗
PubMed2003

Time-dependent density-functional approach for biological chromophores: the case of the green fluorescent protein.

We performed first-principles calculations of the optical response of the green fluorescent protein (GFP) within a combined quantum-mechanical molecular-mechanics and time-dependent density-functional theory approach. The computed spectra are in excellent agreement with experiments assuming the presence of two, protonated and deprotonated, forms of the photoreceptor in a approximately 4:1 ratio, which supports the conformation model of photodynamics in GFP. Furthermore, we discuss charge transfer, isomerization, and environment effects. The present approach allows for systematic studies of excited-state electron-ion dynamics in biological systems.

Anions↗
PubMed2003

Quantum mechanical study of stereoselectivity in the oxazaborolidine-catalyzed reduction of acetophenone.

Chiral oxazaborolidines, known as CBS catalysts after the work of Corey, Bakshi and Shibata, are used for the stereoselective reduction of prochiral ketones to secondary chiral alcohols. Due to their relative low cost, ease of use, and high selectivity, their popularity has remarkably grown in the last 15 years. Oxazaborolidine-catalyzed reductions have been much studied, both experimentally and computationally, by means of semiempirical methods. Though, a more accurate high level quantum mechanical study on the complete system, capable of elucidating reliably the origins of stereoselectivity, is still lacking. Therefore, the acetophenone (PhMK) reduction with Corey's oxazaborolidine has been modeled for the first time with ab initio and DFT-B3LYP calculations on the complete system as well as with AM1. Calculations on the complexation of BH(3) to CBS, which can occur only in a cis fashion with respect to the hydrogen on the stereogenic C-4 carbon atom, have allowed us to confirm the great rigidity of Corey's catalyst, possibly determining its excellent enantioselectivity. Acetophenone-CBS-BH(3) complexes were characterized at various levels of theory, and it was found that the picture obtained depends heavily on the method adopted. A computational strategy for identifying the hydride transfer transition states of the competing pathways was developed and tested, using a model system for which the transition state geometry was already known. The application of the TS search method to the reduction of acetophenone allowed the characterization of the TS's for the competing pathways in this reaction, making it possible to predict with good quantitative accuracy the stereochemical outcome of the reaction at all the levels of theory adopted. The characterization of the intermediate oxazadiboretane products confirmed that the highly exothermic hydride transfer provides the thermodynamical drive for the reaction.

Journal Article↗
PubMed2007

Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies.

A free energy perturbation (FEP) method was developed that uses ab initio quantum mechanics (QM) for treating the solute molecules and molecular mechanics (MM) for treating the surroundings. Like our earlier results using AM1 semi empirical QMs, the ab initio QM/MM-based FEP method was shown to accurately calculate relative solvation free energies for a diverse set of small molecules that differ significantly in structure, aromaticity, hydrogen bonding potential, and electron density. Accuracy was similar to or better than conventional FEP methods. The QM/MM-based methods eliminate the need for time-consuming development of MM force field parameters, which are frequently required for drug-like molecules containing structural motifs not adequately described by MM. Future automation of the method and parallelization of the code for Linux 128/256/512 clusters is expected to enhance the speed and increase its use for drug design and lead optimization.

Computer Simulation↗
PubMed2003

Structure and dynamics of metal ions in solution: QM/MM molecular dynamics simulations of Mn(2+) and V(2+).

Structural and dynamical properties of the transition metal ions V(2+) and Mn(2+) in aqueous solution, resulting from combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations have been compared. The necessity of polarization functions on the ligand's oxygen for a satisfactory description of such ions in aqueous solution is shown using V(2+) as test case. Radial distribution functions, coordination number distributions, and several angle distributions were pursued for a detailed structural comparison of the first hydration shells. Dynamical properties, such as the librational and vibrational motions of water molecules were evaluated by means of velocity autocorrelation functions. Approximative normal coordinate analyses were employed to calculate the rotational frequencies and vibrational motions around the three principal axes. The very low exchange rates for the first shell water exchanges only allow an investigation of the water exchange processes in the second shell, which take place within the picosecond range.

Cations, Divalent↗
PubMed2005

Quantum-chemical study of CHCl3-SO2 association.

CHCl(3)-SO(2) association is studied by high-level quantum-chemical calculations of stationary points of the dimer electronic potential-energy hypersurface, including correlated second-order Moller-Plesset and CCSD(T) calculations with basis sets up to 6-311++G(d,p). During geometry optimization, frequency, and energy calculations, a self-written computer code embedding the GAMESS ab initio program suite applies counterpoise correction of the basis set superposition error. A CH...O hydrogen-bonded complex (DeltaE(0)=-8.73 kJmol) with a 2.4 A intermolecular H...O distance and two very weak van der Waals complexes (DeltaE(0)=-3.78 and -2.94 kJmol) are located on the counterpoise-corrected potential-energy surface. The intermolecular interactions are characterized by Kitaura-Morokuma interaction energy decompositions and Mulliken electron population analyses. The unusual hydrogen bond is distinguished by a CH-bond contraction, a pronounced enhancement of the IR intensity and a shift to higher frequency ("blueshift") of the CH-stretching vibration compared to the CHCl(3) monomer. Spectroscopy and association in liquid solution is also discussed; our results provide an alternative explanation for features in the CH-stretching vibration spectrum of chloroform dissolved in liquid sulfur dioxide which have been attributed previously to an intermolecular Fermi resonance.

Algorithms↗
PubMed2006

Reliable electron affinities of perfluorocyclopropane and perfluorocyclobutane from convergent ab initio computations.

To resolve discrepancies concerning the magnitude of the electron affinities of perfluorocyclopropane and perfluorocyclobutane, quantum chemical calculations have been carried out with the MP2 and CCSD(T) methods in conjunction with augmented correlation consistent basis sets (aug-cc-pVX Z, X = D, T, Q). Though no experimental values have been found for perfluorocyclopropane, we estimate its electron affinity to be 0.17 eV (0.00 eV without zero-point vibrational energy corrections). In addition, determination of the electron affinity of perfluorocyclobutane (0.61 and 0.44 eV with and without zero-point vibrational energy corrections, respectively) is in good agreement with experimental values reported by Miller and co-workers (0.63 +/- 0.05 eV). This study also demonstrates that the widely prescribed B3LYP/DZP++ model chemistry for computing electron affinities does not correctly describe these systems.

Journal Article↗
PubMed2006

Force-field parametrization of retro-inverso modified residues: development of torsional and electrostatic parameters.

Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined.

Amino Acids↗
PubMed2006

Molecular dynamics simulations of electron-alkali cation pairs in bulk water.

The structural, dynamic, and thermodynamic properties of an excess electron interacting with an alkali cation (Na+, K+, Li+) in bulk water were investigated by means of a mixed quantum-classical molecular dynamics simulation technique. This study includes a reparametrization of the electron-cation pseudopotentials. The free energy calculations for all three systems show that a contact electron-cation pair can be observed, which is either as stable as the dissociated pair (Li+) or more stable by only a few kT (Na+, K+). Given that the dissociation barrier is also quite small, we suggest that the average cation-electron distance in the experiments at room temperature will not depend on this free energy profile but rather on the minimization of the Coulombic repulsive interaction between like charges in the solvent medium. This enables us to compare the present molecular dynamics simulations with the spectroscopic data obtained for different ionic strengths. The overall trend of the UV-vis hydrated absorption spectra, namely, the shift toward shorter wavelengths at high ionic strengths, is fairly well reproduced. This confirms our hypothesis of statistical distribution of the cations and solvated electrons.

Cations↗
PubMed2005

Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results.

This chapter discusses methods for modeling electronic polarization in proteins and protein-ligand complexes. Two different approaches are considered: explicit incorporation of polarization into a molecular mechanics force field and the use of mixed quantum mechanics/molecular mechanics methods to model polarization in a restricted region of the protein or protein-ligand complex. A brief description is provided of the computational methodology and parameterization protocols and then results from two preliminary studies are presented. The first study employs quantum mechanics/molecular mechanics (QM/MM) methods to improve the accuracy of protein-ligand docking; here, incorporation of polarization is shown to dramatically improve the robustness of the accuracy of structural prediction of the protein-ligand docking by enabling qualitative improvement in the selection of the correct hydrogen bonding patterns of the docked ligand. The second study discusses a 2-ns simulation of bovine pancreatic trypsin inhibitor (BPTI) in water using a variety of fixed charge and polarizable models for both the protein and the solvent, analyzing observed root mean square deviations (RMSD), intraprotein hydrogen bonding, and water structure and dynamics. All of these efforts are in a relatively early stage of development, the results are encouraging in that stable methods have been developed, and significant effects of polarization are seen and (in the case of the QM/MM-based docking) improvements have been validated as compared to experiment. With regard to accuracy and robustness of full simulations, a great deal more work needs to be done to quantitate and improve the present models.

Animals↗
PubMed2004

Quantum and classical studies of the O(3P) + H2(v = 0-3,j = 0) --> OH + H reaction using benchmark potential surfaces.

We present results of time-dependent quantum mechanics (TDQM) and quasiclassical trajectory (QCT) studies of the excitation function for O(3P) + H2(v = 0-3,j = 0) --> OH + H from threshold to 30 kcal/mol collision energy using benchmark potential energy surfaces [Rogers et al., J. Phys. Chem. A 104, 2308 (2000)]. For H2(v = 0) there is excellent agreement between quantum and classical results. The TDQM results show that the reactive threshold drops from 10 kcal/mol for v = 0 to 6 for v = 1, 5 for v = 2 and 4 for v = 3, suggesting a much slower increase in rate constant with vibrational excitation above v = 1 than below. For H2(v > 0), the classical results are larger than the quantum results by a factor approximately 2 near threshold, but the agreement monotonically improves until they are within approximately 10% near 30 kcal/mol collision energy. We believe these differences arise from stronger vibrational adiabaticity in the quantum dynamics, an effect examined before for this system at lower energies. We have also computed QCT OH(v',j') state-resolved cross sections and angular distributions. The QCT state-resolved OH(v') cross sections peak at the same vibrational quantum number as the H2 reagent. The OH rotational distributions are also quite hot and tend to cluster around high rotational quantum numbers. However, the dynamics seem to dictate a cutoff in the energy going into OH rotation indicating an angular momentum constraint. The state-resolved OH distributions were fit to probability functions based on conventional information theory extended to include an energy gap law for product vibrations.

Journal Article↗
PubMed1988

Quantum simulation of ferrocytochrome c.

The dramatic progress in the understanding of the dynamics of biomolecules has been largely fuelled by computer simulations based on the law of classical mechanics. However in some respects biomolecules are at the borders of the domain of applicability of classical mechanics. The role of quantum mechanical effects in biomolecular structure and function is therefore worth investigating. Here we present preliminary results from a quantum simulation of a protein and contrast them with results from full classical simulations. The most significant differences are found in motions of high frequency, such as bond stretching or the torsional oscillation of groups that bear hydrogen atoms. The amplitudes of such motions are significantly increased by the penetration of atoms into classically forbidden regions. These differences will directly influence the rates of such processes as proton and electron transfer.

Cytochrome c Group↗
PubMed2004

Polarization-transfer methods in solid-state magic-angle-spinning NMR: adiabatic CN pulse sequences.

An adiabatic double-quantum polarization-transfer experiment is described. It can be characterized as an adiabatic variant of the POST-C7 experiment. A continuous variation of the phase increment between pulses leads to the introduction of a fictitious Zeeman field that allows for an adiabatic passage through the recoupling condition. This results in a chemical-shift-offset-compensated adiabatic experiment, which leads to an efficient and broadbanded polarization transfer or to a double-quantum excitation. Similar variations of other C- or R-type experiments can be envisioned.

Carbon Isotopes↗
PubMed2002

Analysis of ice-binding sites in fish type II antifreeze protein by quantum mechanics.

Many organisms living in cold environments can survive subzero temperatures by producing antifreeze proteins (AFPs) or antifreeze glycoproteins. In this paper we investigate the ice-binding surface of type II AFP by quantum mechanical methods, which, to the best of our knowledge, represents the first time that molecular orbital computational approaches have been applied to AFPs. Molecular mechanical approaches, including molecular docking, energy minimization, and molecular dynamics simulation, were used to obtain optimal systems for subsequent quantum mechanical analysis. We selected 17 surface patches covering the entire surface of the type II AFP and evaluated the interaction energy between each of these patches and two different ice planes using semi-empirical quantum mechanical methods. We have demonstrated the weak orbital overlay phenomenon and the change of bond orders in ice. These results consistently indicate that a surface patch containing 19 residues (K37, L38, Y20, E22, Y21, I19, L57, T56, F53, M127, T128, F129, R17, C7, N6, P5, G10, Q1, and W11) is the most favorable ice-binding site for both a regular ice plane and an ice plane where water O atoms are randomly positioned. Furthermore, for the first time the computation results provide new insights into the weakening of the ice lattice upon AFP binding, which may well be a primary factor leading to AFP-induced ice growth inhibition.

Animals↗