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Publications during 2006

Article Reference (Amidomethyl)dimethylsilanol hydrohalides: Synthesis, NMR and IR studies. Characteristic features of the electronic structure from high-resolution X-ray study and quantum chemical calculation
(C,O)-chelate silanol hydrohalides RC(O)NHCH2SiMe2OH · HHal (2a,b and 5b), and their precursors, (C,O)-chelate chlorosilanes RC(O)NHCH2SiMe2Cl (6a,b) and disiloxanes [RC(O)NHCH2SiMe2]2O (8a,b) (R = Me (a), Ph (b); Hal = Cl (2), Br (5)), were obtained by several routes. The original scheme of hydrolysis of the above chlorides was discussed in detail. X-ray analysis has shown that the silanol hydrohalogenides PhC(O)NHCH2SiMe2OH · HX (2b and 5b) in the crystal exist in the form of cation-anion pairs [PhC(O)NHCH2SiMe2(OH2)]+ · X- (14b · Cl- and 14b · Br-) assembled by H-bonds in a 3D framework. The Si atom in the cation has a trigonal bipyramidal configuration with the oxygen atom of the carbonyl group and protonated hydroxyl exo-substituent in axial positions. The endocyclic Si-O bonds are equal with an average of 1.905 A while the exocyclic Si-O bonds are 1.979 and 2.009 A, for Hal = Cl and Br, respectively. Quantum chemical calculations have shown that the cation [PhC(O)NHCH2SiMe2(OH2)]+ (14b) is stable only in the crystal. Based on a high-resolution X-ray study and a quantum chemical calculation, it was found that the chemical bonding pattern in the OSiO axial fragment of the cation 14b corresponds to a three-centred four electron interaction. The cation 14b should be considered as a silylium cation stabilized by coordinated H2O molecules rather than a silyloxonium ion.
Article Reference [sup 17]O nuclear quadrupole coupling constants of water bound to a metal ion: A gadolinium(III) case study
Article Reference A comparative theoretical study of dipeptide solvation in water
Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged �-�NH3+ and �-�CO2- side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd). � 2006 Wiley Periodicals, Inc. J Comput Chem 27:672-684, 2006
Article Reference A Coupled Car-Parrinello Molecular Dynamics and EXAFS Data Analysis Investigation of Aqueous Co2+
We have studied the microscopic solvation structure of Co2+ in liquid water by means of density functional theory (DFT)-based CarParrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co2+water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. CarParrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co2+ in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from CarParrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co2+ solvation properties obtained using first-principle simulations.
Article Reference A density functional theory based study of the microscopic structure and dynamics of aqueous HCl solutions
The aqueous solvation of hydrochloric acid is studied using density functional theory based molecular dynamics simulations at two concentrations. The large simulation boxes that we use allow us to investigate larger-scale structures such as the water-bridged chloride ion network. We find a strong concentration dependence for almost all structural and dynamical properties. Excess protons are mostly present both as Eigen and Zundel structures, either as a direct hydronium-chloride contact-ion pair or a solvent-separated ion pair. Increasing the concentration has a detrimental effect on the natural hydrogen bonded network of water molecules. This effect is visible in our studies as a decrease in the persistence time of the solvation shells around the chloride ions. Also the number of proton hops, determined by a new and well defined identification procedure, suffers from the breakdown of the natural hydrogen bond network.
Article Reference A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures
Density functional molecular dynamics simulations using a QM/MM approach are used to get insight into the binding modes of formic acid in catalase. Two ligand binding sites are found, named A and B, in agreement with recent high resolution structures of catalase with bound formic acid. In addition, the calculations show that the His56 residue is protonated and the ligand is present as a formate anion. The lowest energy minimum structure (A) corresponds to the ligand interacting with both the heme iron and the catalytic residues (His56 and Asn129). The second minimum energy structure (B) corresponds to the situation in which the ligand interacts solely with the catalytic residues. A mechanism for the process of formic acid binding in catalase is suggested.
Article Reference Ab Initio Finite-Temperature Electronic Absorption Spectrum of Formamide
A combination of CarParrinello molecular dynamics (CPMD) and high-level ab initio quantum chemical calculations has been used to calculate the electronic absorption spectrum of formamide at finite temperatures. Thermally broadened spectra have been obtained by averaging over a large number of single-point multireference configuration interaction excitation energies calculated for geometries sampled from a CPMD simulation. Electronic excitation spectra of possible contaminants ammonia and formamidic acid have also been computed. Ammonia exhibits a strong peak in the shoulder region of the experimental formamide spectrum at 6.5 eV, and formamidic acid has a strong absorption above 7.5 eV. The calculations reproduce the shape of the experimental absorption spectrum, in particular, the low-energy shoulder of the main peak, and demonstrate how finite-temperature electronic absorption spectra can be computed from first principles.
Article Reference Ab Initio Molecular Dynamics of Protonated Dialanine and Comparison to Infrared Multiphoton Dissociation Experiments
Finite temperature CarParrinello molecular dynamics simulations are performed for the protonated dialanine peptide in vacuo, in relation to infrared multiphoton dissociation experiments. The simulations emphasize the flexibility of the different torsional angles at room temperature and the dynamical exchange between different conformers which were previously identified as stable at 0 K. A proton transfer occurring spontaneously at the N-terminal side is also observed and characterized. The theoretical infrared absorption spectrum is computed from the dipole time correlation function, and, in contrast to traditional static electronic structure calculations, it accounts directly for anharmonic and finite temperature effects. The comparison to the experimental infrared multiphoton dissociation spectrum turns out very good in terms of both band positions and band shapes. It does help the identification of a predominant conformer and the attribution of the different bands. The synergy shown between the experimental and theoretical approaches opens the door to the study of the vibrational properties of complex and floppy biomolecules in the gas phase at finite temperature.
Article Reference Ab Initio Molecular Dynamics Simulation of NO Reactivity on the CaO(001) Surface
Ab initio molecular dynamics (MD) is used to investigate NO reaction processes on the (001) surface of CaO. A novel path is proposed for the first steps of nitrogen oxides reactivity catalyzed by the CaO surface. The mechanism consists of the formation of anionic dimers, adsorbing on the surface cations, at the expense of oxidized NO species adsorbed on surface anions. The complete charge-transfer process takes place in two steps, producing first monovalent anionic dimers (NO)2- and, later on, divalent anionic dimers (NO)22-. These redox processes cause spin quenching and are observed in the short time scale of the ab initio MD simulation at 300 K. The results presented provide a rationalization of a recent electron spin resonance (ESR) investigation indicating that the spectroscopy is silent to most of the nitrogen oxide species adsorbed on CaO powders, despite deposition of paramagnetic NO molecules at room temperature.
Article Reference Ab Initio Molecular Dynamics Simulation of the Structure and Proton Transport Dynamics of Methanol−Water Solutions†
Ab initio molecular dynamics simulations are employed to study the structural and proton transport properties of methanolwater mixtures. Structural characteristics analyzed at two different methanol mole fractions (XM = 0.25 and XM = 0.5) reveal enhanced structuring of water as the methanol mole fraction increases in agreement with recent neutron diffraction experiments. The simulations reveal the existence of separate hydrogen-bonded water and methanol networks, also in agreement with the neutron diffraction data. The addition of a single proton to the XM = 0.5 mixture leads to an anomalous structural or Grotthuss-type diffusion mechanism of the charge defect in which water-to-water, methanol-to-water, and water-to-methanol proton transfer reactions play the dominant role with methanol-to-methanol transfers being much less significant. Unlike in bulk water, where coordination number fluctuations drive the proton transport process, suppression of the coordination number of waters in the first solvation shell of the defect diminish the importance of coordination number fluctuations as a driving force in the structural diffusion process. The charge defect is found to reside preferentially at the interface between water and methanol networks. The length of the ab initio molecular dynamics run (120 ps), allowed the diffusion constant of the charge defect to be computed, yielding a value of D = 4.2 10-5 cm2/s when deuterium masses are assigned to all protons in the system. The relation of this value to excess proton diffusion in bulk water is discussed. Finally, a kinetic theory is introduced to identify the relevant time scales in the proton transfer/transport process.
Article Reference Ab Initio Molecular Dynamics Study of Heterogeneous Oxidation of Graphite by Means of Gas-Phase Nitric Acids
The interaction between gas-phase nitric acid and the graphite surface is taken as a simple model of interactions occurring at the surface of atmospheric soot particles. In particular, we study the heterogeneous processes that lead to the dissociation of the nitric acid and the production of nitrous acid. The atomistic details of the reaction mechanisms are reproduced by use of the new metadynamics method. The binding interactions of the HNO3 molecule and its fragments with the graphite surface are calculated, and the role of the surface in catalyzing the reaction is taken into account. From the reactive trajectory generated by the metadynamics, it is seen that the path goes through several different intermediate states. We analyze in detail the electronic structures and spin density distributions of the relevant products and report on the mechanisms and the main features of the transition regions relative to all the activated processes observed.
Article Reference Ab initio molecular dynamics study of the hydration of the formohydroxamate anion
We apply ab initio molecular dynamics (AIMD) to study the hydration structures and electronic properties of the formohydroxamate anion in liquid water. We consider the cis- nitrogen-deprotonated, cis- oxygen-deprotonated, and trans- oxygen-deprotonated formohydroxamate tautomers. They form an average of 6.3, 6.9, and 6.0 hydrogen bonds with water molecules, respectively. The predicted pair correlation functions and time dependence of the hydration numbers suggest that water is highly structured around the nominally negatively charged oxime oxygen in O-deprotonated tautomers but significantly less so around the nitrogen atom in the N-deprotonated species. Wannier function analysis suggests that, in the O-deprotonated anions, the negative charge is concentrated on the oxime oxygen, while in the N-deprotonated case, it is partially delocalized between the nitrogen and the adjoining oxime oxygen atom.
Article Reference Ab Initio Molecular Dynamics Study of the Keto-Enol Tautomerism of Acetone in Solution
We have studied the keto-enol interconversion of acetone to understand the mechanism of tautomerism relevant to numerous organic and biochemical processes. Applying the ab initio metadynamics method, we simulated the keto-enol isomerism both in the gas phase and in the presence of water. For the gas-phase intramolecular mechanism we show that no other hydrogen-transfer reactions can compete with the simple keto-enol tautomerism. We obtain an intermolecular mechanism and remarkable participation of water when acetone is solvated by neutral water. The simulations reveal that C deprotonation is the kinetic bottleneck of the keto-enol transformation, in agreement with experimental observations. The most interesting finding is the formation of short H-bonded chains of water molecules that provide the route for proton transfer from the carbon to the oxygen atom of acetone. The mechanistic picture that emerged from the present study involves proton migration and emphasizes the importance of active solvent participation in tautomeric interconversion.
Article Reference Ab initio rigid water: Effect on water structure, ion hydration, and thermodynamics
We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ([similar]8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 [Angstrom] longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.
Article Reference Ab initio Simulation of the Grafting of Phenylacetylene on Hydrogenated Surfaces of Crystalline Silicon Catalyzed by a Lewis Acid
CarParrinello simulations have been carried out to identify the grafting mechanism of phenylacetylene, a prototypical alkyne, on the hydrogenated surfaces of crystalline silicon, catalyzed by a Lewis acid (AlCl3). To this purpose, we have made use of a new technique, metadynamics, devised recently to deal with complex chemical reactions in first principles simulations. The reaction mechanism, leading to a styrenyl-terminated surface, turns out to be equivalent to the corresponding gas-phase hydrosilylation reaction by silanes that we have identified in a previous work. The activation energies for the surface reactions (0.43, 0.42, 0.35 eV, for HSi(111), HSi(100)2 1, and HSi(100)1 1, respectively) are very close to that of the corresponding gas-phase reaction (0.37 eV). The estimated activation free energy at room temperature is sufficiently low for the grafting reaction to be viable at normal conditions and at low coverage on the crystalline silicon surfaces, as already well documented to occur on the surface of porous silicon. However, the conformation of the transition state shadows a large area of the surface, which might contribute to making the grafting process self-limiting.
Article Reference AB INITIO Simulations of Desorption and Reactivity of Glycine at a Water-Pyrite Interface at “Iron-Sulfur World” Prebiotic Conditions
Abstract Glycine at the interface of a pyrite surface (001) FeS2, and bulk water at high pressure and temperature conditions relevant to the “iron-sulfur world” scenario of the origin of life is investigated by theoretical means. Car-Parrinello molecular dynamics is used in order to study the desorption process of the zwitterionic form of this amino acid using two different adsorption modes, where either only one or both oxygens of the carboxylate group are anchored to surface iron atoms. It is found that the formation of stabilizing hydrogen bonds plays a key role in the detachment process, leading to longer retention times for the bidentate adsorption mode. In addition, the chemical reactivity of this heterogeneous system is probed by calculating the Fukui functions as site-specific reactivity indices. The most prominent targets for both nucleophilic and electrophilic reactions to occur are surface atoms, whereas the reactivity of glycine is only slightly affected upon anchoring.
Article Reference Acidity of Uranyl(VI) Hydrate Studied with First-Principles Molecular Dynamics Simulations
No Abstract
Article Reference Adsorption of alanine on a Ni(111) surface: A multiscale modeling oriented density functional study
Article Reference An ab Initio Molecular Dynamics and Density Functional Theory Study of the Formation of Phosphate Chains from Metathiophosphates
Reaction between two MeSPO2 molecules to yield a diphosphate chain followed by the extension to longer phosphates.
Article Reference Angular-dependent interatomic potential for tantalum
A new angular-dependent semi-empirical interatomic potential suitable for atomistic simulations of plastic deformation, fracture and related processes in body-centered cubic Ta has been constructed by fitting to experimental properties and a first-principles database generated in this work. The potential reasonably reproduces a variety of properties of Ta, including elastic constants, thermal expansion, high-pressure behavior, the vacancy formation and migration energies, surface energies, gamma surfaces on the 1 1 0 and 2 1 1 planes, energy along the twinning and anti-twinning deformation paths, structure of the 2 1 1 twin boundary and energies of alternate crystal structures of Ta. The potential is applied to calculate the core structure of the 1/2 1 1 1 screw dislocation and the critical resolved shear stress as a function of the angle between the 2 1 1 slip plane and the maximum-stress plane. The results are in good agreement with previous first-principles calculations and experimentally known mechanical behavior of body-centered cubic metals.
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