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Publications during 2007

Article Reference 2H Solid-State NMR of Mobile Protons: It Is Not Always the Simple Way
Article Reference A combined spectroscopic and theoretical approach to investigate structural properties of Co(ii)/Co(iii) tris-cysteinato complexes in aqueous medium
Physiological and toxicological effects of metallic ions depend on their speciation and on the structure of their associated bioligand complexes. In the field of chemical and/or nuclear toxicological studies, we are investigating cobalt complexes with biorelevant ligands such as amino acids or peptides. The aqueous reaction of cobalt dichloride with an excess of cysteine (Cys, C3H5NSO22-) in a basic medium under an anaerobic atmosphere and subsequent oxidation by O2, afforded the mononuclear complexes Co(ii):3Cys and Co(iii):3Cys, respectively. A combination of X-ray absorption spectroscopy (XAS) measurements and Car-Parrinello molecular dynamics (CPMD) simulations allowed us to assess structural features of the already explored Co(iii):3Cys complex. Inclusion of the temperature effects in the CPMD calculations gives an implicit access to disorder effects in the extended X-ray absorption fine structure (EXAFS) equation. The very good agreement between the measured and the simulated data showed the accuracy of these models provided by CPMD. The present investigation is completed by new UV-visible, X-ray absorption near edge structure (XANES) and electron paramagnetic resonance (EPR) data of Co(ii):3Cys. These data are consistent with a Co(ii) high-spin d7 complex in a distorted octahedral geometry. This work contributes to the knowledge of topics such as metal-bioligand interaction which is of major interest in the field of bioinorganic chemistry.
Article Reference A multi-scale ab initio theoretical study of the production of free radicals in swift ion tracks in liquid water
Using a multi-scale theoretical approach from first principles, we show that the production of HO2 radicals in liquid water can be understood from the initial Coulomb explosion of doubly ionized water molecules. Based on the separation of time scales, we used three different theoretical models, each one associated with a specific time scale. The initial [?]1 fs of water radiolysis is taken care of with a Monte Carlo code whose basic ingredients are cross-sections. These have been calculated in the present work using the continuum distorted wave eikonal initial state (CDW-EIS) model framework. Our calculated cross-sections nicely demonstrate that double ionization of water molecules is one major event compatible with the experimental HO2 molecular rate production. The subsequent tens of fs following the double ionization of one water molecule of the liquid medium have been described with microscopic ab initio Car-Parrinello molecular dynamics simulations. Dynamics shows that the water Coulomb explosion leads to the formation of two H3O+ ions and an atomic oxygen atom. The final stage of the Coulomb explosion (up to the ms timescale) has been modelled with a chemical Monte Carlo code, assessing that the production of HO2 results from the O + OH - HO2 reaction in the liquid phase.
Article Reference Ab initio computation of spectroscopic parameters as a tool for the structural elucidation of organic systems
Computation of spectroscopic parameters is rapidly evolving from a highly specialized research field into a versatile tool, capable of providing a crucial aid for the interpretation of experimental information. The present paper focuses on the application of computed spectroscopic parameters in organic chemistry, both in terms of assignment of observed transitions, and also in the more demanding task of discrimination among alternative structural hypotheses. The impact of dynamical and environmental effects, and some computational approaches that allow to properly take into account their influence on specific spectroscopic parameters, are also discussed based on some recent examples from the authors’ experience. Keywords: Spectroscopic parameters; UV; NMR; EPR; DFT; TD-DFT; PCM; Molecular dynamics
Article Reference Ab Initio Molecular Dynamics Study of Heterogeneous Nitric Acid Decomposition Reactions on Graphite Surfaces
The goal of the present work is to unravel the role of the soot surface on the decomposition of nitric acid as a possible renoxification process. We study the monomolecular and the bimolecular decomposition reactions of gas-phase nitric acid on a pristine and on a defective graphite surface as a simple model of the interactions occurring on the surface of atmospheric soot particles. The metadynamics method is employed to reproduce the atomistic details of the reaction paths for both monomolecular and bimolecular processes. Several different intermediate states, which are encountered along the reactive trajectory, are analyzed, and the role of the surface in catalyzing the reactions is discussed.
Article Reference Ab initio Molecular Dynamics Study of the Hydrolysis Reaction of Diborane.
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Article Reference Ab initio simulation of a gadolinium-based magnetic resonance imaging contrast agent in aqueous solution
Article Reference Ab Initio Static and Molecular Dynamics Study of 4-Styrylpyridine
We report an in-depth theoretical study of 4-styrylpyridine in its singlet S0 ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree-Fock (HF), second-order Moeller-Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post-HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis-trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car-Parrinello molecular dynamics simulations were also performed at 50, 150, and 300K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within 1 ps during the simulation carried out at 150K on this isomer.
Article Reference Annularly Fused Hexapyrrolohexaazacoronenes: An Extended pi System with Multiple Interior Nitrogen Atoms Displays Stable Oxidation States
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Article Reference Anomalous Behavior of the Dielectric Constant of Hafnium Silicates: A First Principles Study
Article Reference Are Isolated Nucleic Acid Bases Really Planar? A Car-Parrinello Molecular Dynamics Study
CarParrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carried out. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PW methods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-plane deformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling of conformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine, cytosine, guanine, and adenine has been investigated by using the ab initio CarParrinello molecular dynamics method. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanar effective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to a minimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring does not exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chair conformations are the most populated.
Article Reference Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching
We introduce a novel procedure to parametrize biomolecular force fields. We perform finite-temperature quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, with the fragment or moiety that has to be parametrized being included in the QM region. By applying a force-matching algorithm, we derive a force field designed in order to reproduce the steric, electrostatic, and dynamic properties of the QM subsystem. The force field determined in this manner has an accuracy that is comparable to the one of the reference QM/MM calculation, but at a greatly reduced computational cost. This allows calculating quantities that would be prohibitive within a QM/MM approach, such as thermodynamic averages involving slow motions of a protein. The method is tested on three different systems in aqueous solution: dihydrogenphosphate, glycylalanine dipeptide, and a nitrosyldicarbonyl complex of technetium(I). Molecular dynamics simulations with the optimized force field show overall excellent performance in reproducing properties such as structures and dipole moments of the solutes as well as their solvation pattern.
Article Reference Basis Set Superposition Error along the Free-Energy Surface of the Water Dimer
In this article we review the behavior of static plane wave basis set calculations in comparison to Gaussian basis set calculations. This was done in the framework of density functional theory for description of hydrogen bonds with the water dimer as an example. Furthermore we carried out molecular dynamics simulations enforcing the self-dissociation reaction of the water dimer to study the influence of the basis set onto the reaction. Not surprisingly, we find strongly varying results of the calculated forces for a chosen cutoff along the reaction coordinates. The basis set superposition errors of the dimer interaction energy are analyzed along the free-energy surface, i.e., along the trajectories. Based on the analysis along the trajectories a qualitative and quantitative estimate depending on the particular point of the free-energy surface can be provided. Namely, at the intermolecular O...H distance close to the equilibrium geometry the errors are smaller than at shorter O...H distances. However, the distribution at the equilibrium distance is more unsymmetrical than the distribution at short distances. It is wider, and the standard deviation is larger than at shorter distances where the basis set superposition error is larger.
Article Reference C 1s core-level photoemission spectra of stilbene on Si(100)2 x 1 surface from first-principles calculations
Article Reference Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the chloroacetic acid dimer system
Article Reference Car-Parrinello Molecular Dynamics Study of Anharmonic Systems: A Mannich Base in Solution
A CarParrinello molecular dynamics study was performed for 4,5-dimethyl-2-(N,N-dimethylaminomethyl)phenol, a Mannich base, to investigate the vibrational properties in solution of its intramolecular hydrogen bond. The dynamic behavior of this hydrogen-bonded system was investigated using an explicit solvent model. Addition of a nonpolar solvent permitted inclusion of delicate environmental effects on the strongly anharmonic system which was studied from first principles. Molecular dynamics and a posteriori quantization of the OH motion were applied to reproduce the vibrational features of the OH stretching mode. Consistent application of CarParrinello dynamics based on the density functional theory with subsequent solution of the vibrational Schrodinger equation for the OH stretching motion offers an effective method for strongly anharmonic systems, and this is supported by the comparison of the results with experimental spectra. As a further element of the intramolecular hydrogen bond study, the effects of deuteration were taken into account and a successful application of the OH stretching mode quantization technique to the liquid phase is demonstrated. This provides a valuable computational methodology for investigations incorporating nuclear quantum effects in the liquid phase and enzyme active centers and can be used to investigate numerous systems that are not readily susceptible to experimental analysis.
Article Reference Car-Parrinello simulation of an O-H stretching envelope and potential of mean force of an intramolecular hydrogen bonded system: Application to a Mannich base in solid state and in vacuum
Article Reference Carbocation-pi interaction with Car-Parrinello molecular dynamics: Ab initio molecular dynamics investigation of complex of methyl cation with benzene
Cation-pi interaction plays an important role as a general noncovalent binding force in a wide range of systems. To examine the more stable state of carbocation-pi complex, we have carried out Car-Parrinello molecular dynamics (CPMD) simulations of six models. These results are proved to be reliable from the comparison with those of investigations by ab initio calculations. Charge transfer and molecular orbital interaction are discussed to depict the interaction modes of different models. From our CPMD studies without restraints, the methyl group moves toward the side of the benzene forming a stable pi-complex. However, if the methyl group is maintained above benzene, the inter-conversions among different models of complex, which are determined from ab initio optimization, are observed; and distances between the carbon of methyl group and the center of benzene range from 2.67 A to 3.61 A. Our results provide a dynamic process concerning the motion of methyl group above the benzene ring. To examine more stable state of carbocation-pi complex, six models of benzene-methyl cation system are studied by Car-Parrinello molecular dynamics simulation, showing that inter-conversions among different models of complex are possible for the carbocation-pi interaction. Thus, a dynamic relationship among the different models is first constructed in our studies.
Article Reference Carboranes: chemical concepts derived from the AIM study of the experimental and theoretical electron density distribution functions
On the basis of high-resolution X-ray diffraction studies as well as quantum-chemical calculations of five carborane derivatives the peculiarities of electron density distribution functions have been analyzed. The data obtained permitted a deeper insight into the nature of unusual properties of the C-C bond in o-carborane and investigating intermolecular HH interactions in crystal. It was shown that such an approach allows estimating the values of lattice energy for the crystals of carboranes.
Article Reference Charge transfer mechanism in a PolydGpdCp fiber and in wet DNA
Recently there has been great interest in the conducting properties of DNA because of their potential applications to nanotechnology and their role in protecting the molecule from oxidative damage. Unfortunately, experiments have provided very contradictory results. Using state of the art ab-initio simulation we investigated the hole localization and transfer in both a laboratory realizable polydGpCp wet Z-DNA molecule and in a fully solvated B-DNA. Keywords: Density functional calculations; DNA damage; Electron transfer; Molecular dynamics; Nucleobases
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