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year-2005

Publications during 2005

Article Reference A density-functional approach to polarizable models: A Kim-Gordon response density interaction potential for molecular simulations
 
Article Reference A Recipe for the Computation of the Free Energy Barrier and the Lowest Free Energy Path of Concerted Reactions†
The recently introduced hills method (Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562) is a powerful tool to compute the multidimensional free energy surface of intrinsically concerted reactions. We have extended this method by focusing our attention on localizing the lowest free energy path that connects the stable reactant and product states. This path represents the most probable reaction mechanism, similar to the zero temperature intrinsic reaction coordinate, but also includes finite temperature effects. The transformation of the multidimensional problem to a one-dimensional reaction coordinate allows for accurate convergence of the free energy profile along the lowest free energy path using standard free energy methods. Here we apply the hills method, our lowest free energy path search algorithm, and umbrella sampling to the prototype SN2 reaction. The hills method replaces the in many cases difficult problem of finding a good reaction coordinate with choosing relatively simple collective variables, such as the bond lengths of the broken and formed chemical bonds. The second part of the paper presents a guide to using the hills method, in which we test and fine-tune the method for optimal accuracy and efficiency using the umbrella sampling results as a reference.
Article Reference A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical–molecular-mechanical calculations
 
Article Reference Ab Initio Design of High-k Dielectrics: LaxY1-xAlO3
We use calculations based on density-functional theory in the virtual crystal approximation for the design of high-k dielectrics, which could offer an alternative to silicon dioxide in complementary metal-oxide semiconductor devices. We show that aluminates LaxY1-xAlO3 alloys derived by mixing aluminum oxide with lanthanum and yttrium oxides have unique physical attributes for a possible application as gate dielectrics when stabilized in the rhombohedral perovskite structure, and which are lost in the orthorhombic modification. Stability arguments locate this interesting composition range as 0.2x0.4. Phase separation in microdomains is shown to have the tendency to further enhance the dielectric constant. We propose this as a novel family of high-k dielectrics deserving experimental exploration.
Article Reference Ab Initio Molecular Dynamics of Liquid 1,3-Dimethylimidazolium Chloride
Density-functional-based CarParrinello molecular dynamics (CPMD) simulations have been performed for the ionic liquid 1,3-dimethylimidazolium chloride, [dmim]Cl, at 438 K. The local structure of the liquid is described in terms of various partial radial distribution functions and anisotropic spatial distributions, which reveal a significant extent of hydrogen bonding. The cationanion distribution simulated with the BP86 functional is in qualitative agreement with the structural model derived from neutron diffraction data for the liquid, whereas the theoretical cationcation distribution shows less satisfactory accord. Population analyses indicate noticeable charge transfer from anions to cations, and specific CH...Cl hydrogen bonds are characterized in terms of donoracceptor interactions between lone pairs on Cl and antibonding sigma*CH orbitals.
Article Reference Ab Initio Molecular Dynamics Simulation of the Aqueous Ru2+/Ru3+ Redox Reaction: The Marcus Perspective†
A well-behaved (low spin) transition metal aqua ion, Ruaq2+, is used as a model system in an ab initio molecular dynamics study of a redox half reaction to which the Marcus theory of electron transfer is assumed to apply. Using constraint methods, we show that aqueous Ru2+ can be reversibly transformed to Ru3+ under the control of the classical solvent electrostatic potential as order parameter. The mean force is found to vary linearly with the order parameter in accordance with the Marcus theory. As can be expected for a half reaction, the slope in the oxidized and reduced states are asymmetric differing by approximately a factor of two. As a further test, we verify that the corresponding quadratic potential of mean force is in excellent agreement with the free energy profile obtained from the Gaussian distribution of potential fluctuations sampled from free (unconstrained) runs of the reduced and oxidized system. Similar to experimental electrochemical methods, our simulation scheme enables us to manipulate the effective thermodynamic driving force and align the free energy minima of product and reactant state. The activation energy and reaction entropy computed under these conditions are discussed and analyzed from the Marcus perspective.
Article Reference Ab initio molecular dynamics simulations of [beta]-d-glucose and [beta]-d-xylose degradation mechanisms in acidic aqueous solution
Ab initio molecular dynamics simulations were employed to investigate, with explicit solvent water molecules, [beta]-d-glucose and [beta]-d-xylose degradation mechanisms in acidic media. The rate-limiting step in sugar degradation was found to be protonation of the hydroxyl groups on the sugar ring. We found that the structure of water molecules plays a significant role in the acidic sugar degradation pathways. Firstly, a water molecule competes with the hydroxyl group on the sugar ring for protons. Secondly, water forms hydrogen bonds with the hydroxyl groups on the sugar rings, thus weakening the C-C and C-O bonds (each to a different degree). Note that the reaction pathways could be altered due to the change of relative stability of the C-C and C-O bonds. Thirdly, water molecules that are hydrogen-bonded to sugar hydroxyls could easily extract a proton from the reaction intermediate, terminating the reaction. Indeed, the sugar degradation pathway is complex due to multiple protonation probabilities and the surrounding water structure. Our experimental data support multiple sugar acidic degradation pathways.
Article Reference Ab Initio Molecular Dynamics Simulations of the Oxygen Reduction Reaction on a Pt(111) Surface in the Presence of Hydrated Hydronium (H3O)+(H2O)2: Direct or Series Pathway?
CarParrinello molecular dynamics simulations have been performed to investigate the oxygen reduction reaction (ORR) on a Pt(111) surface at 350 K. By progressive loading of (H3O)+(H2O)2,3 + e- into a simulation cell containing a Pt slab and O2 for the first reduction step, and either products or intermediate species for the subsequent reduction steps, the detailed mechanisms of the ORR are well illustrated via monitoring MD trajectories and analyzing KohnSham electronic energies. A proton transfer is found to be involved in the first reduction step; depending on the initial protonoxygen distance, on the degree of proton hydration, and on the surface charge, such transfer may take place either earlier or later than the O2 chemisorption, in all cases forming an adsorbed end-on complex HOO*. Decomposition of HOO* takes place with a rather small barrier, after a short lifetime of approximately 0.15 ps, yielding coadsorbed oxygen and hydroxyl (O* + HO*). Formation of the one-end adsorbed hydrogen peroxide, HOO*H, is observed via the reduction of HOO*, which suggests that the ORR may also proceed via HOO*H, i.e., a series pathway. However, HOO*H readily dissociates homolytically into two coadsorbed hydroxyls (HO* + HO*) rather than forming a dual adsorbed HOOH. Along the direct pathway, the reduction of HO* + O* yields two possible products, O* + H2O* and HO* + HO*. Of the three intermediates from the second electron-transfer step, HOO*H from the series pathway has the highest energy, followed by O* + H2O* and HO* + HO* from the direct pathway. It is therefore theoretically validated that the O2 reduction on a Pt surface may proceed via a parallel pathway, the direct and series occurring simultaneously, with the direct as the dominant step.
Article Reference Ab initio molecular dynamics study of glycine intramolecular proton transfer in water
 
Article Reference Ab initio molecular dynamics: Plane waves vs. local basis: The role of energy cutoff on the convergence of molecular properties
For ab initio molecular dynamics the choice of basis sets (plane waves - PW or localized atomic orbitals - LAO) used is not a trivial issue, since inaccurate results can arise and the extent of these errors are not easily detected. The advantages of each are illustrated for (HF)n clusters. Good agreement with experiment is obtained with LAO while, for the PW approach, electronic energies and IR frequencies are very slowly converging as functions of the cutoff parameter. Basic geometrical parameters oscillate as the cutoff parameter grows, thus it is necessary to properly describe the electronic structure before attempting to include subtler effects.
Article Reference Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited
 
Article Reference Ab initio resonant Raman spectra of diamond-like carbons
Raman spectroscopy is a standard tool for the characterisation of carbon materials, from graphite to diamond-like carbon and carbon nanotubes. An important factor is the dependence of the Raman spectra on excitation energy, which is due to resonant processes. Here, we calculate the resonant Raman spectra of tetrahedral amorphous carbon. This is done by a tight-binding method, using an approach different from Placzek's approximation, which allows calculation of Raman intensities also in resonant conditions. The calculated spectra confirm that the G peak arises from chains of sp2 bonded atoms and that it correlates with the atomic and electronic structure of the samples. The calculated dispersion of the G peak position with excitation energy follows the experimental observations. Our ab initio calculations also show that the sp3 phase can only be seen by using UV excitation above 4 eV, confirming the assignment of the T peak at ˊ1060 cm-1, seen only in UV Raman measurements, to C-C sp3 vibrations.
Article Reference Ab initio simulation of photoinduced transformation of small rings in amorphous silica
We have studied the photoinduced transformation of small rings (three membered) in amorphous silica by Car-Parrinello simulations. The process of ring opening leading to the formation of a couple of paramagnetic centers, namely an E′ and a nonbridging-oxygen hole center (NBOHC), has been proposed experimentally to occur in silica exposed to F2 laser irradiation (at 7.9 eV ). By using a scheme for the simulation of rare events in ab initio molecular dynamics [M. Iannuzzi, A. Laio, and M. Parrinello, Phys. Rev. Lett. 90, 238303 (2003)], we have identified a transformation path for the opening of a three-membered ring induced by a self-trapped triplet exciton, the migration of NBOHC and formation of a couple of stable E′ and NBOHC paramagnetic defects.
Article Reference Adsorption of Water Molecules on Flat and Stepped Nickel Surfaces from First Principles
We present an ab initio density functional study of the adsorption of a series of water oligomers (molecule, dimer and trimer) on nickel surfaces with and without step defects. We investigate the preferred adsorption geometries and adsorption energies and analyze the binding mechanisms by means of electronic density difference maps. Special attention is devoted to the incremental adsorption process, i.e., the way additional molecules attaches to an already adsorbed water. In agreement with recent findings, we show that the first water molecule is bound to the surface with an energy of about 0.20.4 eV, i.e., with up to twice the strength of a hydrogen bond. In contrast to this, subsequent water molecules increase the total adsorption energy by typically 0.5 eV. However, electron density difference considerations indicate that this additional attraction is not due to the interaction of the new molecule with the surface but mediated by the first water molecule. The interaction of the additional molecule with the surface appears even to be repulsive. We discuss the implications of these findings for the wetting properties of transition metal surfaces.
Article Reference Anomalous temperature dependence of nuclear quadrupole interactions in strongly hydrogen-bonded systems from first principles
 
Article Reference Application of transition path sampling methods in catalysis: A new mechanism for CC bond formation in the methanol coupling reaction in chabazite
We describe the application of transition path sampling methods to the methanol coupling reaction in the zeolite chabazite; these methods have only been recently applied to complex chemical systems. Using these methods, we have found a new mechanism for the formation of the first CC bond. In our mechanism, the reaction, at 400[thin space]°C, proceeds via a two-step process: (1) the breaking of the CO bond of the chemisorbed methoxonium cation, followed by the transfer of a hydride ion from the remaining methanol molecule to the methyl cation, resulting in the formation of H2O, CH4, and CH2OH+ and (2) a simultaneous proton transfer from methane to water, and direct CC bond formation between the methyl anion and CH2OH+, resulting in the formation of ethanol. The CC bond forming process has the higher barrier, with an activation energy of about 100.49[thin space]kJ/mol.
Article Reference Aspects of Glycosidic Bond Formation in Aqueous Solution: Chemical Bonding and the Role of Water
A model of the specific acid-catalyzed glycosidic bond formation in liquid water at ambient conditions is studied based on constrained Car-Parrinello ab initio molecular dynamics. Specifically the reaction of alpha-D-glucopyranose and methanol is found to proceed by a DNAN mechanism. The DN step consists of a concerted protonation of the O1 hydroxyl leaving group; this process results in the breaking of the C1&bond;O1 bond, and oxocarbenium ion formation involving C1&dbond;O5. The second step, AN, is the formation of the C1&bond;Om glycosidic bond, deprotonation of the methanol hydroxyl group OmHm, and re-formation of the C1&bond;O5 single bond. A focus of this study is the analysis of the electronic structure during this condensed phase reaction relying on both Boys/Wannier localized orbitals and the electron localization function ELF. This analysis allows the clear elucidation of the chemical bonding features of the intermediate bracketed by the DN and AN steps, which is a non-solvent equilibrated oxocarbenium cation. Most interestingly, it is found that the oxygen in the pyranose ring becomes ldquodesolvatedrdquo upon double bond/oxocarbenium formation, whereas it is engaged in the hydrogen-bonded water network before and after this period. This demonstrates that hydrogen bonding and thus the aqueous solvent play an active role in this reaction implying that microsolvation studies in the gas phase, both theoretical and experimental, might lead to qualitatively different reaction mechanisms compared to solution.
Article Reference Atomic and Electronic Structures of Molecular Crystalline Cellulose Iβ: A First-Principles Investigation
A theoretical model based on the competition between hydrogen-bonding energy and strain energy was constructed to explain the size of native cellulose Ibeta. The cellodextrins in native crystalline cellulose Ialpha and Ibeta are unusually stable compared to other polysaccharides, not easily prone to hydrolysis even though they are only nanometers in diameter. The stability of crystalline cellulose Ibeta is most likely due to its greatly enhanced hydrogen-bonding (HB) network. We carried out ab initio calculations to determine the native crystalline cellulose Ibeta atomic and conformational structures. For crystalline cellulose, we found that every hydroxyl group in the cellulose structure is hydrogen bonded as both a donor and an acceptor. This agrees well with published X-ray and neutron diffraction data. We also determined the electronic structures and the energetics for one cellodextrin chain, one to four sheets of cellodextrins in cellulose, and the bulk cellulose Ibeta.
Article Reference Binding of Organometallic Ruthenium(II) and Osmium(II) Complexes to an Oligonucleotide: A Combined Mass Spectrometric and Theoretical Study†
The binding of ruthenium(II)arene and osmium(II)arene anticancer compounds with an oligonucleotide has been investigated by mass spectrometry, showing loss of the arene in some cases. DFT has been used to help rationalize these observations.
Article Reference Bonding in the Superionic Phase of Water
The predicted superionic phase of water is investigated via ab initio molecular dynamics at densities of 2.0–3.0 g/cc (34–115 GPa) along the 2000 K isotherm. We find that extremely rapid (superionic) diffusion of protons occurs in a fluid phase at pressures between 34 and 58 GPa. A transition to a stable body-centered cubic O lattice with superionic proton conductivity is observed between 70 and 75 GPa, a much higher pressure than suggested in prior work. We find that all molecular species at pressures greater than 75 GPa are too short lived to be classified as bound states. Up to 95 GPa, we find a solid superionic phase characterized by covalent O-H bonding. Above 95 GPa, a transient network phase is found characterized by symmetric O-H hydrogen bonding with nearly 50\% covalent character. In addition, we describe a metastable superionic phase with quenched O disorder.
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