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year-2008

Publications during 2008

Article Reference A first principle study of terahertz (THz) spectra of acephate
Using first principles calculations based on the density functional method we have studied THz spectra of molecular and solid forms of acephate. The computations are preformed using different functionals for both isolated-molecule as well as solid-state periodic system. The computed infrared spectra are compared with experimental data using FTIR techniques and terahertz time-domain spectroscopy (THz-TDS) over a wide range of frequencies method. While isolated-molecule calculations of the harmonic frequencies were found to be deficient to reproduce the experimental spectrum, the same calculations performed in the solid-state have achieved better agreement with observed THz spectral characters. Detailed normal mode analyses have been carried out for both molecular and solid-state calculations. Our results show that the normal modes at low frequencies not only correspond to the inter-molecular vibrations but also arise due to the coupling between inter- and intra-molecular motions, as well as due to the formation of the hydrogen bonds between molecules in the crystal. Moreover Car-Parrinello molecular dynamics is used to obtain dipole-active vibrations at room temperature, thus revealing non-negligible temperature effects due to anharmonicity.
Article Reference A multi-technique approach to predicting the molecular structure of cuprizone in the gas phase and in the crystalline state
Cuprizone (oxalic acid bis(cyclohexylidene hydrazide)) is a potent neurotoxin that is known to induce the destruction of the myelinic sheath which covers the cells of the central nervous system (CNS). The mechanism of action has not yet been elucidated due to lack of structural information. We have performed an ab initio prediction of the molecular structure by high-level quantum chemical methods, leading to two possible conformers of a nearly identical energy: A, for which an analysis of the electron density distribution shows more propensity for intermolecular bonding, and B, with stronger intramolecular liaison. Having obtained suitable single crystals, we report a detailed study of the crystal and molecular structure, which reveals that the molecular and crystal centers of symmetry coincide, and that the actual conformer is A, as expected, and in agreement with the ab initio prediction. Further information is gained by optimization of the crystal structure by Car-Parrinello molecular dynamics, yielding good agreement with observation. Infrared and Raman spectra show mutual exclusion, suggesting a centrosymmetric molecule with carbonylic bonds in trans configuration; moreover, vibrational frequencies calculated ab initio also show excellent agreement with observations. We thus present a multi-technique approach to the prediction and interpretation of various aspects of the complex interplay between intra- and intermolecular forces.
Article Reference Ab Initio Molecular Dynamics Study of Mg2+ and Ca2+ Ions in Liquid Methanol
Ab initio CarParrinello molecular dynamics simulations have been performed in order to investigate the solvation properties of Mg2+ and Ca2+ in fully deuterated methanol solution to better understand polarization effects induced by the ions. Charge transfer and dipole moment calculations have been performed to give more detailed insight on the role of the electronic reorganization and its effect on the first solvation shell stability. The perturbation of the methanol H-bond network has been investigated.
Article Reference Ab initio study of dispersion of optic-like modes in a molten salt: Effect of ion polarization
Longitudinal and transverse dynamics of molten NaCl beyond the hydrodynamic region is studied by generalized collective modes (GCM) analysis of relevant time correlation functions obtained in ab initio molecular dynamics. A comparison with results of rigid-ion treatment of collective dynamics in the molten salt is made. A reduction of the long-wavelength gap between longitudinal and transverse optic-like excitations due to polarization effects is discussed. We propose an analysis, based on analytical expressions for ‘bare’ propagating collective excitations, that are a generalization of Takeno–Goda formulae for the case of binary disordered system at arbitrary wavenumber.
Article Reference Atomic wavefunction initialization in ab initio molecular dynamics using distributed Lanczos
We present a distributed scheme for initialization from atomic wavefunctions in ab initio molecular dynamics simulations. Good initial guesses for approximate wavefunctions are very important in order to enable practical simulations with thousands of atoms. The new scheme is based on a distributed implementation of the Lanczos algorithm for very large dense eigenproblems. We show that the massively parallel BG/L (Blue Gene/L) supercomputer with its very fast separate network for collective communications is an ideal platform for the parallel Lanczos algorithm. We have implemented the new scheme in the popular plane-wave code CPMD. We showcase the applicability of the distributed initialization by a series of examples on a family of Silicon super cells ranging from 512 to 2048 atoms. Keywords: Ab initio molecular dynamics; Lanczos; Large scale parallelization; BG/L supercomputer
Article Reference Conformational Behavior of Cinchonidine Revisited: A Combined Theoretical and Experimental Study
Conformational space of cinchonidine has been explored by means of ab initio potential and free energy surfaces, and the temperature-induced changes of conformational populations were studied by a combined NOESY-DFT analysis. The DFT-derived potential energy surface investigation identified four new conformers. Among them, Closed(7) is substantially relevant to fully understand the conformational behavior. The energy surfaces gave access to the favored transformation pathways at different temperatures (280-320 K). They also revealed the reasons for the negligible presence of energetically stable conformers and explained the experimentally observed temperature dependence of the populations.
Article Reference Copper binding sites in the C-terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study
We present a hybrid QM/MM Car-Parrinello molecular dynamics study of the copper-loaded C-terminal domain of the mouse prion protein. By means of a statistical analysis of copper coordination in known protein structures, we localized the protein regions with the highest propensity for copper ion binding. The identified candidate structures were subsequently refined via QM/MM simulations. Their EPR characteristics were computed to make contact with the experimental data and to probe the sensitivity to structural and chemical changes. Overall best agreement with the experimental EPR data (Van Doorslaer et al., J Phys Chem B 2001; 105: 1631-1639) and the information currently available in the literature is observed for a binding site involving H187. Moreover, a reinterpretation of the experimental proton hyperfine couplings was possible in the light of the present computational findings. Proteins 2008. 2007 Wiley-Liss, Inc.
Article Reference Hydrogen-Bonding Interactions in Cinchonidine-2-Methyl-2-Hexenoic Acid Complexes: A Combined Spectroscopic and Theoretical Study
Molecular interactions between cinchonidine (CD) and 2-methyl-2-hexenoic acid (MHA) have been studied by means of NMR, ATR-IR MES, DFT, and ab initio molecular dynamics. These interactions are of particular interest due to their pivotal role in the chiral induction occurring in the heterogeneous catalytic asymmetric hydrogenation of α,β-unsaturated acids. The population density of the Open(3) conformer of CD, the most populated one at room temperature in apolar solvents, considerably increased to a maximum by addition of MHA to CD in toluene. The CD−MHA complex showed prominent symmetric and asymmetric carboxylate stretching vibrations in the regions of 1350−1410 and 1520−1580 cm −1, respectively. DFT calculations revealed that these vibrational frequencies are expected to significantly shift depending on the chemical surrounding of MHA, that is, the hydrogen bond network. Earlier postulated 1:1 binding between CD and MHA was considered unlikely; instead, a dynamic equilibrium involving the MHA monomer and dimer, the 1:3 and possibly 1:2 CD−MHA complexes, were rationalized. Stable CD−MHA structures suggested by DFT calculations are the “1:3, halfN, cyclic” and the “1:3, halfN, cyclic tilted” complexes, where three MHA molecules are connected in wire by hydrogen bonding, two having direct interaction with CD. The confinement of CD’s torsional motions in the complexes, leading to a slightly distorted Open(3) conformer via specific hydrogen-bonding interactions, was clearly reproduced by ab initio molecular dynamics, and the stable and flexible nature of the interaction was verified. Theoretical IR spectra of the complexes reproduced the characteristic vibrational frequencies of the complexes observed experimentally, supporting the stability of the 1:3 and implying the possibility of even higher molecular weight CD−MHA complexes.
Article Reference Inelastic neutron scattering, Raman, vibrational analysis with anharmonic corrections, and scaled quantum mechanical force field for polycrystalline l-alanine
A scaled quantum mechanical harmonic force field (SQMFF) corrected for anharmonicity is obtained for the 23 K l-alanine crystal structure using van der Waals corrected periodic boundary condition density functional theory (DFT) calculations with the PBE functional. Scale factors are obtained with comparisons to inelastic neutron scattering (INS), Raman, and FT-IR spectra of polycrystalline l-alanine at 15-23 K. Calculated frequencies for all 153 normal modes differ from observed frequencies with a standard deviation of 6 wavenumbers. Non-bonded external k = 0 lattice modes are included, but assignments to these modes are presently ambiguous. The extension of SQMFF methodology to lattice modes is new, as are the procedures used here for providing corrections for anharmonicity and van der Waals interactions in DFT calculations on crystals. First principles Born-Oppenheimer molecular dynamics (BOMD) calculations are performed on the l-alanine crystal structure at a series of classical temperatures ranging from 23 K to 600 K. Corrections for zero-point energy (ZPE) are estimated by finding the classical temperature that reproduces the mean square displacements (MSDs) measured from the diffraction data at 23 K. External k = 0 lattice motions are weakly coupled to bonded internal modes.
Article Reference Metal-Carbon Nanotube Contacts: The Link between Schottky Barrier and Chemical Bonding
 
Article Reference Modelling room temperature ionic liquids
Room temperature ionic liquids (IL) composed of organic cations and inorganic anions are already being utilized for wide-ranging applications in chemistry. Complementary to experiments, computational modelling has provided reliable details into the nature of their interactions. The intra- and intermolecular structures, dynamic and transport behaviour and morphologies of these novel liquids have also been explored using simulations. The current status of molecular modelling studies is presented along with the prognosis for future work in this area.
Article Reference Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure
Azole-bridged diplatinum compounds are promising new anticancer drugs designed to induce small distortions upon DNA alkylation, able to circumvent resistance problems of existing platinum drugs. Hybrid quantum classical (QM/MM) molecular dynamics (MD) simulations of different azole-bridged platinum drugs have recently revealed the nature of the local deformations at the DNA binding site. However, the description of global slow converging rearrangements cannot be addressed by QM/MM MD due to the short time scale accessible. Extensive classical MD simulations are therefore mandatory to describe accurately the structural distortions in the DNA double helix. This issue is now addressed by developing a new set of accurate force field parameters of the platinated moiety via a recently proposed force matching procedure of the classical forces to ab initio forces obtained from QM/MM trajectories. The accuracy of our force field parameters is validated by comparison of structural properties from classical MD and hybrid QM/MM simulations. The structural characteristics of the Pt-lesion are well reproduced during classical MD compared with QM/MM simulations and available experimental data. The global distortions in the DNA duplex upon binding of dinuclear Pt-compounds are very small and rather opposite to those induced by cisplatin. Thus, the force match approach significantly extends the potentialities of molecular simulations in the study of anticancer drugs and of the interactions with their biological targets. � 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Article Reference Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism
 
Article Reference QM/MM lineshape simulation of the hydrogen-bonded uracil NH stretching vibration of the adenine:uracil base pair in CDCl3
A hybrid Car-Parrinello QM/MM molecular dynamics simulation has been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. The resulting trajectory is analyzed putting emphasis on the N-H...N hydrogen bond geometry. Using an empirical correlation between the N...N-distance and the fundamental NH-stretching frequency, the time-dependence of this energy gap along the trajectory is obtained. From the gap-correlation function we determine the infrared absorption spectrum using lineshape theory in combination with a multimode oscillator model. The obtained average transition frequency and the width of the spectrum are in reasonable agreement with recent experimental data.
Article Reference Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods
Mechanistic studies on the hydrolytic dehalogenation catalyzed by haloalkane dehalogenases are of importance for environmental and industrial applications. Here, Car-Parrinello (CP) and ONIOM hybrid quantum-mechanical/molecular mechanics (QM/MM) are used investigate the second reaction step of the catalytic cycle, which comprises a general base-catalyzed hydrolysis of an ester intermediate (EI) to alcohol and free enzyme. We focus on the enzyme LinB from Sphingomonas paucimobilis UT26, for which the X-ray structure at atomic resolution is available. In agreement with previous proposals, our calculations suggest that a histidine residue (His272), polarized by glutamate (Glu132), acts as a base, accepting a proton from the catalytic water molecule and transferring it to an alcoholate ion. The reaction proceeds through a metastable tetrahedral intermediate, which shows an easily reversed reaction to the EI. In the formation of the products, the protonated aspartic acid (Asp108) can easily adopt conformation of the relaxed state found in the free enzyme. The overall free energy barrier of the reaction calculated by potential of the mean force integration using CP-QM/MM calculations is equal to 19.5 ± 2 kcal · mol−1. The lowering of the energy barrier of catalyzed reaction with respect to the water reaction is caused by strong stabilization of the reaction intermediate and transition state and their preorganization by electrostatic field of the enzyme. Proteins 2008. © 2007 Wiley-Liss, Inc.
Article Reference The binding domain of the HMGB1 inhibitor carbenoxolone: Theory and experiment
We present a combined computational and experimental study of the interaction of the Box A of the HMGB1 protein and carbenoxolone, an inhibitor of its pro-inflammatory activity. The computational approach consists of classical molecular dynamics (MD) simulations based on the GROMOS force field with quantum-refined (QRFF) atomic charges for the ligand. Experimental data consist of fluorescence intensities, chemical shift displacements, saturation transfer differences and intermolecular Nuclear Overhauser Enhancement signals. Good agreement is found between observations and the conformation of the ligand-protein complex resulting from QRFF-MD. In contrast, simple docking procedures and MD based on the unrefined force field provide models inconsistent with experiment. The ligand-protein binding is dominated by non-directional interactions.
Article Reference The hydration of glucose: the local configurations in sugar-water hydrogen bonds
The hydration of a simple sugar is an essential model for understanding interactions between hydrophilic groups and interfacial water molecules. Here I perform first-principles molecular dynamics simulations on a glucose-water system and investigate how individual hydroxyl groups are locally hydrated. I demonstrate that the hydroxyl groups are less hydrated and more incompatible with a locally tetrahedral network of hydrogen bonds than previously thought. The results suggest that the hydroxyl groups form roughly two hydrogen bonds. Further, I find that the local hydration of the hydroxyl groups is sensitively affected by seemingly small variations in the local electronic structure and bond polarity of the groups. My findings offer insight into an atomic-level understanding of sugar-water interactions.
Article Reference Ultrafast transformation of graphite to diamond: An ab initio study of graphite under shock compression
 
Article Reference X-ray Diffraction and Computation Yield the Structure of Alkanethiols on Gold(111)
The structure of self-assembled monolayers (SAMs) of long-chain alkyl sulfides on gold(111) has been resolved by density functional theory-based molecular dynamics simulations and grazing incidence x-ray diffraction for hexanethiol and methylthiol. The analysis of molecular dynamics trajectories and the relative energies of possible SAM structures suggest a competition between SAM ordering, driven by the lateral van der Waals interaction between alkyl chains, and disordering of interfacial Au atoms, driven by the sulfur-gold interaction. We found that the sulfur atoms of the molecules bind at two distinct surface sites, and that the first gold surface layer contains gold atom vacancies (which are partially redistributed over different sites) as well as gold adatoms that are laterally bound to two sulfur atoms.
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