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year-1999

Publications during 1999

Article Reference A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields
 
Article Reference Ab initio molecular dynamics studies of a synthetic biomimetic model of galactose oxidase
 
Article Reference Ab Initio Molecular Dynamics Study of Crystalline Nitric Acid Trihydrate
Ab initio based Car-Parrinello molecular dynamics calculations (CPMD) have been used to investigate the properties of crystalline nitric acid trihydrate (NAT) at 195 K. The crystal unit cell consists of four formula units of NAT and nominally contains the ions NO3- and H3O+ plus H2O molecules. Reversible proton-transfer events were observed between unique H3O+ and neighboring H2O pairs, which occur throughout the crystal. Full proton transfer to form a new neighboring H3O+ molecule was a rare event. The motion of this mobile proton was associated with hyperextension of the covalent oxygenhydrogen of H3O+, whose stretch frequency was observed in corresponding power spectra. Calculations showed that a classical free energy of 3.3 kBT was required for the proton to reach the center of the oxygenoxygen pair. Crystalline NAT was further characterized by calculated equilibrium averages, structural properties, and vibrational spectra.
Article Reference Ab initio molecular-dynamics simulation of K[sup +] solvation in water
 
Article Reference Ab Initio Simulation of Rotational Dynamics of Solvated Ammonium Ion in Water
We have performed an ab initio molecular dynamics simulation of the rotational dynamics of NH4+ ion in water. This work was motivated by the experimental evidence that the solvated NH4+ rotates rather fast, despite the expected formation of strong hydrogen bonds with water. We find that NH4+ is on average coordinated with five water molecules. Four water molecules form a long-lived tetrahedral cage around the ion, each molecule being hydrogen-bonded with one proton of NH4+. The fifth water molecule is much more mobile and occasionally exchanges with one of the four molecules in the tetrahedral cage. The hydrogen bonding of NH4+ with water is strong enough to prevent the free rotation of the ion, which instead tumbles in a sequence of discontinuous rotational jumps associated with the exchange of two water molecules in the tetrahedral cage. The simulated rotational dynamics is consistent with nuclear magnetic resonance data and encourages the use of ab initio simulations to describe the solvation of ions in water.
Article Reference Ab initio study of boron doping in tetrahedral amorphous carbon
We present an ab initio study of the effects of boron incorporation in tetrahedral amorphous carbon using Car-Parrinello molecular dynamics. Samples of tetrahedral amorphous carbon at a density of 2.9g/cm3 with different boron contents (1.6\% and 3.2\%) have been generated by quenching from the liquid phase. We found that boron is mainly threefold coordinated and does not affect the fraction of fourfold coordinated carbon atoms, in agreement with experimental findings. Moreover, boron incorporation in highly stressed three-membered rings induces the opening of the ring which might provide a possible mechanism of the stress release observed experimentally upon boron doping. An analysis of the electronic properties reveals that boron does not induce shallow acceptor levels in the gap in any of the cases studied.
Article Reference Ab initio study of structural and electronic properties of yttria-stabilized cubic zirconia
Ab initio calculations have been performed on the structural and electronic properties of pure zirconia and yttria-stabilized cubic zirconia (YSZ). We use the local-density approximation to the exchange and correlation energy functional. We expand the Kohn-Sham orbitals in plane waves and use norm-conserving fully separable pseudopotentials. We find, in agreement with experiments that the most stable phase at zero temperature and pressure is the monoclinic baddelyte structure which transforms under pressure in the brookite orthorhombic phase. We then study the properties of the YSZ cubic phase using a supercell of 96 atoms. This is a defective structure where oxygen vacancies and yttrium substitutional impurities play a major role. The pattern of relaxation around the defects is consistent with the most recent scattering data, as well as their relative interaction which leads to a next-nearest-neighbor attraction between vacancy and yttrium. The analysis of the electronic properties show that single occupied color centers F+ are only marginally stable and decay into neutral, doubly occupied F centers and empty (doubly charged) vacancies. Therefore, we found that the F+ center in YSZ is a negative Hubbard-U site.
Article Reference An ab initio molecular dynamics study of the S[sub N]2 reaction Cl[sup −]+CH[sub 3]Br→CH[sub 3]Cl+Br[sup −]
 
Article Reference An Excited State Density Functional Theory Study of the Rhodopsin Chromophore
Using a recently developed scheme for performing, within density functional theory, molecular dynamics and geometry optimization for fairly large systems in the first excited singlet state, we have studied the structure and energy changes that the rhodopsin chromophore undergoes during the photoisomerization from 11-cis to all-trans. We discuss the effects of relevant parts of the protein environment close to the chromophore on the isomerization barrier and on the chromophore structure.
Article Reference Analysis of the Dissociation of H2O in Water Using First-Principles Molecular Dynamics
We have analyzed the structural, electronic, and dynamic properties along the reaction path of the dissociation of an H2O molecule in bulk water. There are four stages to the dissociation process, the last step being effected by a separation of hydroxyl and hydronium ions by two solvation shells. Structural as well as electronic data bear out this interpretation. In addition, by analyzing the electron localization function (ELF) around the oxygen in the hydroxyl ion, the question of why this species is most often 4-fold coordinated is addressed. The explanation arising from ELF is that unpaired electrons are symmetrically localized in a ring-shape around the O atom leading to the possibility of a planar solvation shell as observed in ab initio simulations. Finally, a dynamic analysis gives an indication of the femtosecond time-scale of the solvent response.
Article Reference Broensted acid sites in gmelinite
 
Article Reference Carbon Structures Containing Negatively Curved Sheets
 
Article Reference CH5+: The Cheshire Cat Smiles
 
Article Reference Density functional study of carbon clusters C[sub 2n] (2≤n≤16). I. Structure and bonding in the neutral clusters
 
Article Reference Density Functional Study of Polycarbonate. 2. Crystalline Analogs, Cyclic Oligomers, and Their Fragments
Density functional studies have been performed for the crystalline forms of the cyclic dimer and tetramer of bisphenol A polycarbonate (BPAPC), as well as for the isolated structural units and their fragments (including carbonic acid, benzene, phenol, monophenyl carbonate, and BPA). There are no adjustable parameters in the calculation, and the optimized structures agree well with the results of X-ray diffraction analyses where available. Calculated vibration frequencies are compared with experimental data and with earlier calculations. Ring-opening of the cyclic oligomers is an important polymerization technique, and the cyclic tetramer provides an interesting model for future calculations of reactions between polymer segments and additional molecules.
Article Reference Density-functional study of hydration of ammonium in water clusters
 
Article Reference Dimethyl Phosphate: Stereoelectronic versus Environmental Effects
Structure and bonding of dimethyl phosphate (DMP) in vacuo and in the crystal phase is investigated using density functional theory calculations with gradient corrections for the exchange-correlation functional. Calculated structural properties agree well with experiment and previous high-level ab initio results. Analysis of the chemical bonding in terms of localized Wannier orbitals allows us to compare stereoelectronic effects to those of the environment. It is found that the latter play a much more critical role for the conformational flexibility of DMP.
Article Reference Dipolar host/guest interactions and geometrical confinement at the basis of the stability of one-dimensional ice in zeolite bikitaite
 
Article Reference Dynamical Host/Guest Interactions in Zeolites: Framework Isotope Effects on Proton Transfer Studied by Car−Parrinello Molecular Dynamics
Zeolites are microporous crystals of technological relevance, as they are used in many area as industrial catalysts, and the understanding of their behavior at the molecular level is of major interest. Differences in shape and compositions of the host crystals affect the reactivity of chemicals adsorbed in the pores of these materials, showing that host/guest interactions play a specific role. We report a CarParrinello study of sodium hydroxo sodalite dihydrate Na8[Al6Si6O24](OH)2.2H2O for the undoped crystal (28Si) and the one doped with 30Si. It is shown that differences in the relaxations of the framework atom oscillations, due to isotopic exchange, affect the relaxation of a proton transfer inside the zeolitic cage. The present results give an indication of dynamical coupling between one proton dynamics and its host crystalline matrix, which is effective only in the case of weak bonds.
Article Reference Evolution of Fragments Formed at the Rupture of a Knotted Alkane Molecule
Common experience tells us that a knot significantly weakens the polymer strand in which it is tied, which, in turn, leads to more facile chain rupture under tensile loading. Using first-principles molecular dynamics calculations we describe the dynamical evolution of the radicals that form after chain rupture of a single knotted alkane molecule in its very early stages of life. They are able to recombine, to form cyclic alkanes, and to undergo disproportionation phenomena with nearby chain segments. The breaking of a single knotted polymer chain under mechanical loading is thus predicted to reveal phenomena falling in the domain of ultrafast spectroscopy.
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