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Publications during 2003

Article Reference A hybrid TDDFT/MM investigation of the optical properties of aminocoumarins in water and acetonitrile solution
We present a hybrid time-dependent density functional/molecular mechanics (TDDFT/MM) simulation study on the optical properties of aminocoumarins in gas phase and solution. As solvation is described through a molecular approach, the effects due to the inhomogeneities of the electric field of the solvent molecules are fully included. We focus on the ground state and first excited singlet state properties of C151, C35 and C153, three aminocoumarins for which a homogeneous set of experimental data is available. Our approach is able to give quantitative information on the redshifts in water and acetonitrile, two solvents which show different H-bonding properties. In addition, it is able to quantify the effects of chemical substituents, such as the spectral redshift due to the increased alkylation at the amino position.
Article Reference A molecular dynamics study of the behavior of sodium in low albite
The structural features of albite (atomic coordinates and distances, thermal displacements) at 25 and 1040 degreesC, obtained by Molecular Dynamic simulations following the Car-Parrinello approach, were favorably compared with those obtained by single-crystal diffraction experiments. Starting from this basis, it was shown that the marked anisotropy of electron density distribution about the positions of the sodium atoms is due to a time average of highly anisotropic thermal vibrations, and not to a space average of multiple positions occupied by Na. Although the large displacement of Na from its center of gravity results in great variations over time of the individual Na-O distances of the sodium coordination polyhedron, the average distance remains approximately constant, reaching its minimum variation when the 9 nearest O atoms are considered, thus supporting a true 9-coordination of sodium.
Article Reference A Wavefunction-Based Criterion for the Detection of Intermolecular Interactions in Molecular Dynamics Simulations
The availability of quantum mechanical wave functions in molecular dynamics simulations for example in those of the CarParrinello type offers the ability to analyze intermolecular interactions of a system in terms of quantum chemical descriptors. We demonstrate how standard population analyses can be utilized for a semiquantitative analysis of intermolecular interactions. The approach is therefore of particular value for the study of those systems for which geometric criteria and predefined interaction potentials have not yet been obtained. This is demonstrated for a DMSOwater mixture, for which the population-analysis criterion provides a simple measure for different interaction types, e.g., between wateroxygen and methylhydrogen atoms. In the case of a polypeptide, it is shown that the wave-function-based criterion provides insight into hydrogen bonding of the CO groups with a hydrogen atom attached to a carbon atom from the peptide's backbone.
Article Reference Ab Initio Molecular Dynamics Computation of the Infrared Spectrum of Aqueous Uracil
Recent progress in the development of ab initio molecular dynamics methods for the computation of infrared absorption spectra in condensed molecular systems is reviewed and illustrated by a detailed account of an application to aqueous uracil. Similar to classical force field simulations, the spectrum is obtained as the Fourier transform of the polarization time autocorrelation function. The density functional methodology for the computation of electronic polarization in periodic supercells is briefly outlined, and also the effect of quantum corrections is discussed. The spectral patterns obtained for the model system in the 20001000 cm-1 domain are in good agreement with experiment. Comparing to the low-temperature vacuum spectrum computed by similar time-dependent methods, we found that the narrow amide bending band in a vacuum is spread out over a 500 cm-1 wide interval in solution with a substantially blue-shifted high-frequency end. The highest increase in frequency was found for N1H1 bending. The red shift and broadening of CO stretching bands is, in comparison, a much smaller effect.
Article Reference Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states
Article Reference Ab initio molecular dynamics study of aqueous solvation of ethanol and ethylene
Article Reference Ab initio molecular dynamics study of liquid methanol
Article Reference Ab Initio Molecular Dynamics Study of the Hydration of a Sodium Smectite Clay
Ab Initio molecular dynamics simulations have been performed to study the hydration of a sodium smectite clay. Water molecules are intercalated as a double layer in the interlayer spacing of this swelling clay mineral. The solvent structure was found to be very similar to predictions by a previous Monte Carlo study based on classical pair potentials (Boek, E. S.; Coveney, P. V.; Skipper, N. T. J. Am. Chem. Soc. 1995, 117, 12608). This lends support to our observations regarding the dynamics of the water molecules. First, the water shows a strong preference to form a hydrogen-bonded network between the solvent molecules. The hydrogen bonds to the aluminosilicate surface are only weak and short-lived. Second, the solvent displays liquidlike relaxation dynamics. Our results suggest that, because of the two-surface geometry in clays, intercalated water is prevented from freezing and should be considered in terms of a confined liquid. This is consistent with recent QENS experiments. Finally, we have calculated the power spectra for both hydrated and dehydrated clay from a Fourier transform of the MD trajectories. The calculated spectra are compared with experimental FTIR spectra.
Article Reference Ab initio molecular dynamics: basic concepts, current trends and novel applications
The field of ab initio molecular dynamics (AIMD), in which finite temperature molecular dynamics (MD) trajectories are generated with forces obtained from accurate 'on the fly' electronic structure calculations, is a rapidly evolving and growing technology that allows chemical processes in condensed phases to be studied in an accurate and unbiased way. This article is intended to present the basics of the AIMD method as well as to provide a broad survey of the state of the art of the field and showcase some of its capabilities. Beginning with a derivation of the method from the Born-Oppenheimer approximation, issues including the density functional representation of electronic structure, basis sets, calculation of observables and the Car-Parrinello extended Lagrangian algorithm are discussed. A number of example applications, including liquid structure and dynamics and aqueous proton transport, are presented in order to highlight some of the current capabilities of the approach. Finally, advanced topics such as inclusion of nuclear quantum effects, excited states and scaling issues are addressed.
Article Reference Ab initio simulation of H[sub 2]S adsorption on the (100) surface of pyrite
Article Reference Ab initio study of rearrangements between C60 fullerenes
Rearrangement mechanisms between different C60 fullerenes are characterised for all the local minima and transition states up to five steps away from the buckminsterfullerene global minimum. The electronic structure is treated using plane-wave density-functional theory, and combined with hybrid eigenvector-following techniques to obtain accurately converged transition states. Our results basically confirm the picture deduced in a previous study that employed tight-binding theory: the low energy region of the potential energy surface leads to efficient relaxation to buckminsterfullerene if the system has sufficient energy to overcome the high downhill barriers.
Article Reference Accurate First Principles Prediction of 17O NMR Parameters in SiO2: Assignment of the Zeolite Ferrierite Spectrum
17O NMR parameters, both the chemical shifts and the quadrupolar parameters, are calculated for SiO2 polymorphs using density functional theory with the generalized gradient-corrected PBE functional. The gauge including projector augmented wave (GIPAW) method (Pickard, C. J.; Mauri, F. Phys. Rev. B 2001, 63, 245101) ensures the reproduction of all electron results while using computationally efficient pseudopotentials. The use of plane-waves permits fully converged calculations to be performed on structures containing 144 atoms in the unit cell, without the need to resort to the cluster approximation. The calculated NMR parameters of cristobalite, quartz, coesite, and faujasite are in excellent agreement with experimental data. This demonstrates that density functional theory is able to reproduce with high accuracy the 17O NMR parameters in SiO2 systems. This precision is used to assign the spectrum of the zeolite ferrierite. The data calculated for SiO2 are used to confirm that no simple correlation between the chemical shift and Cq NMR parameters and SiOSi angle exists, emphasizing the importance of predictive theories in this field.
Article Reference An ab initio molecular dynamics study of the S[sub N]2 reaction F[sup -] + CH[sub 3]Cl – CH[sub 3]F + Cl[sup -]
Article Reference An Iab initio/I force field for the cofactors of bacterial photosynthesis
This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins. � 2002 Wiley Periodicals, Inc. J Comput Chem 24: 129-142, 2003
Article Reference ATP Hydrolysis in Water − A Density Functional Study
Adenosine 5`-triphosphate (ATP) is a basic energy carrier in cellular metabolism. As a high-energy intermediate, it provides a way to convert energy from one biochemical process to another via an environment-dependent hydrolysis reaction. Two paths for ATP hydrolysis in water with Mg2+ are studied here using the density functional method: an associative reaction involving a nucleophilic attack of one water molecule, and a dissociative reaction involving a scission of the terminal bridging PO bond. The latter has an activation energy of 35 kcal/mol, where 25 kcal/mol can be assigned to the PO bond breaking and 10 kcal/mol to the artificial stability of PO3- resulting from the small size and the short time scale of the simulation. The path and energy barrier (39 kcal/mol) of the less-favorable associative reaction suggest that it is possible only under conditions where the lytic water is already deprotonated to OH-. The Mg cation elongates the terminal bridging PO bond when forming a bidentate chelate with the two terminal phosphates. Additional constrained displacements of Mg2+ with respect to the nearest phosphate oxygens show that a direct electrophilic attack of Mg toward a bridging O is possible.
Article Reference Benzoxazine Oligomers: Evidence for a Helical Structure from Solid-State NMR Spectroscopy and DFT-Based Dynamics and Chemical Shift Calculations
A combination of molecular modeling, DFT calculations, and advanced solid-state NMR experiments is used to elucidate the supramolecular structure of a series of benzoxazine oligomers. Intramolecular hydrogen bonds are characterized and identified as the driving forces for ring-shape and helical conformations of trimeric and tetrameric units. In fast MAS 1H NMR spectra, the resonances of the protons forming the hydrogen bonds can be assigned and used for validating and refining the structure by means of DFT-based geometry optimizations and 1H chemical-shift calculations. Also supporting these proposed structures are homonuclear 1H1H double-quantum NMR spectra, which identify the local protonproton proximities in each material. Additionally, quantitative 15N1H distance measurements obtained by analysis of dipolar spinning sideband patterns confirm the optimized geometry of the tetramer. These results clearly support the predicted helical geometry of the benzoxazine polymer. This geometry, in which the N...H...O and O...H...O hydrogen bonds are protected on the inside of the helix, can account for many of the exemplary chemical properties of the polybenzoxazine materials. The combination of advanced experimental solid-state NMR spectroscopy with computational geometry optimizations, total energy, and NMR spectra calculations is a powerful tool for structural analysis. Its results provide significantly more confidence than the individual measurements or calculations alone, in particular, because the microscopic structure of many disordered systems cannot be elucidated by means of conventional methods due to lack of long-range order.
Article Reference Branching Reactions in Polycarbonate: A Density Functional Study
Branching can have a dramatic effect on the properties of polymers, and bisphenol A polycarbonate (BPAPC) is no exception. We describe here the results of a density functional (DF) study of branching that can occur during transesterification reactions in BPAPC in the presence of catalysts. We find that sodium phenoxide (NaOPh) can lead to different branched products, because the Na ion can bond to different O atoms simultaneously. Tetraphenylphosphonium phenoxide, which can be used as an alternative catalyst to NaOPh in BPAPC synthesis, does not lead to branching, because steric hindrance prevents its active sites from approaching the O atoms.
Article Reference Car-Parrinello molecular dynamics on the SN2 reaction Cl-+CH3Br in water
The results of the analysis of ab initio molecular dynamics simulations of the transition state of a bimolecular nuclear substitution reaction in water are discussed and a lower limit for the life-time of the hydrogen bonded interactions between the halogens and the surrounding water molecules is estimated. A new function is introduced to compute a lower estimate of the H-bond life-time and compared with the results of the traditional one.
Article Reference Car-Parrinello Molecular Dynamics Study of the Rearrangement of the Valeramide Radical Cation
Car-Parrinello molecular dynamics (CPMD) studies of neutral (1) and ionized (1+.) valeramide are performed with the aim of providing a rationalization for the unusual temperature effect on the dissociation pattern of 1+. observed in mass spectrometric experiments. According to CPMD simulations of neutral valeramide 1 performed at approximately 500 K, the conformation with the fully relaxed carbon backbone predominates (96�\%). Conformational changes involving folding of the carbon backbone into conformers that would allow intramolecular H transfers are predicted not to take place spontaneously at this temperature because of the barrier heights associated with these transitions (3.5 and 6.9 kcal�mol-1), which cannot be overcome by thermal motion alone. For 1+., CPMD simulations performed at ≈300 K reveal a substantial stability of a conformation in which the carbon backbone is fully relaxed; no reaction is observed even after 7 ps. However, when conformers with already folded carbon-backbones are used as initial geometries in the CPMD simulations, the gamma-hydrogen migration (McLafferty rearrangement resulting in C3H6) is already completed within 2 ps. For this important process, the free activation energy associated with both a required conformational change and the subsequent H transfer equals 4.5 kcal�mol-1, while for the formally related delta-H shift (which eventually gives rise to the elimination of C2H4/C2H5.) it amounts to 7.0 kcal�mol-1. Since the barriers associated with conformational changes are energetically more demanding than those of the corresponding hydrogen transfers, 1+. is essentially trapped by conformational barriers and long-lived at ≈300 K. At elevated temperatures (500 K), the preferred reaction (within 7.3 ps) in the CPMD simulation corresponds to the McLafferty rearrangement. The estimated free activation energy associated with this process amounts to 2.5 kcal�mol-1, while the free activation energy for the delta-H transfer equals 4.4 kcal�mol-1. This relatively small free activation energy for the McLafferty rearrangement might cause dissociation of a substantial fraction of 1+. prior to the time-delayed mass selection, which would reduce the C3/C2 ratio in the experiments conducted with metastable ions that have a lifetime in the order of some mus at a source temperature of 500 K.
Article Reference Catalytic role of boron atoms in self-interstitial clustering in Si
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