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IEEE International Conference on Nano/Molecular Medicine and Engineering

作者： Zeina Salman Arun Nair Steve Tung Microelectronics and Photonics Graduate Program University of Arkansas Fayetteville Arkansas 72701 USA Department of Mechanical Engineering University of Arkansas Fayetteville Arkansas 72701 USA

ISBN: (纸本)9781467396738

Carbon based nanostructures such as graphene and carbon nanotubes have received widespread attention due to their unique mechanical and electronic properties. This paper describes a quantum mechanics based study of the electronic band structures and transport properties of one-dimensional (1D) carbon chains, the thinnest nanowires available in nature. The study is based on the application of density functional theory and non-equilibrium Green's function where maximally localized wannier functions and Landauer formalism are combined to compute the electronic band structures and quantum conductance of the 1D carbon chains. The simulation result indicates that the peak quantum conductance of 1D carbon chains is about five times smaller than that of carbon nanotubes. However, the quantum conductance is also a function of the length and chemical bonds of the carbon chains. When the carbon chains are mechanically strained at 3%, the quantum conductance is reduced by about 50%. This result suggests 1D carbon chains can provide ultra high-resolution electromechanical measurements of important biomolecules such as DNA.

关键词： Carbyne Chains First-principle simulation localized wannier functions Quantum Conductance

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Mechanism of the ethylene polymerization at very high pressure

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JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2008年第4期4卷 646-651页

作者： Mugnai, Martina Pagliai, Marco Cardini, Gianni Schettino, Vincenzo Univ Florence Dipartimento Chim Lab Spettroscopia Mol Sesto Fiorentino Italy European Lab Nonlinear Spect LENS Sesto Fiorentino Italy

The reaction of ethylene in condensed phases under high pressure has been investigated by ab initio molecular dynamics. Both disordered and crystalline samples have been simulated, and some insights on the reaction mechanism have been obtained. System size effects have been investigated for the disordered samples. A polymerization reaction occurs by an ionic, mechanism. In both the disordered and the crystal phases, the reaction products obtained (linear chains in the disordered systems and branched chains in the crystal) are in qualitative agreement with the experiments.

关键词： localized wannier functions PRINCIPLES MOLECULAR-DYNAMICS NATTA HETEROGENEOUS CATALYSIS 1ST PRINCIPLES CHEMICAL-REACTIONS SIMULATION DENSITY PROPENE

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Ab initio based polarizable force field parametrization

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JOURNAL OF CHEMICAL PHYSICS 2008年第18期128卷 184107-1-184107-4页

作者： Masia, Marco Univ Sassari Dipartimento Chim I-07100 Sassari Italy INSTM Unita Ric Sassari I-07100 Sassari Italy

Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by similar to 30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations. (C) 2008 American Institute of Physics.

关键词： localized wannier functions AQUEOUS SOLVATION SHELLS LIQUID-VAPOR INTERFACE MOLECULAR-DYNAMICS DIPOLE INTERACTION WATER-MOLECULES POINT-CHARGE SIMULATION DENSITY SPECTROSCOPY

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Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

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JOURNAL OF CHEMICAL PHYSICS 2007年第16期126卷 164501,1-16页

作者： Lee, Hee-Seung Tuckerman, Mark E. NYU Dept Chem New York NY 10003 USA NYU Courant Inst Math Sci New York NY 10003 USA

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A(2)/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become '' glassy '' as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential. (c) 2007 American Institute of Physics.

关键词： HYDROGEN-BOND DYNAMICS DENSITY-FUNCTIONAL THEORY ELECTRONIC-STRUCTURECALCULATIONS localized wannier functions 1ST PRINCIPLES SIMULATIONS CAR-PARRINELLO FORCE-FIELDS HEAVY-WATER COMPUTATIONAL APPROACH POTENTIAL functions

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Molecular properties investigation of a substituted aromatic Mannich base: Dynamic and static models

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JOURNAL OF CHEMICAL INFORMATION AND MODELING 2007年第3期47卷 818-831页

作者： Jezierska, Aneta Panek, Jaroslaw J. Filarowski, Aleksander Univ Wroclaw Inst Chem PL-50383 Wroclaw Poland

An analysis of the hydrogen bridge of a Mannich base-type compound [ 3,5,6-trimethyl-2( N,N-dimethylaminomethyl) phenol, TMM] was performed according to the Car-Parrinello molecular dynamics (CPMD) scheme. A classical treatment of nuclei coupled with a first-principle potential energy surface was obtained from molecular dynamics simulation. Dipole moment values were collected during CPMD trajectory acquisition and subsequently used for the data analysis. The vibrational features and the intramolecular hydrogen-bond properties in the gas phase and solid state of the TMM compound were analyzed on the basis of widely used approaches: Fourier transformation of the autocorrelation function of both the atomic velocities and dipole moments. In addition, the time evolution of the structural parameters related to the hydrogen bond was carried out. The optimally localized wannier functions served to describe the electronic structure of the Mannich base studied. The second part of the TMM compound study was performed in vacuo on the basis of density functional theory and second-order Moller-Plesset perturbation theory. The potential energy functions were used to solve the 1-D vibrational Schroedinger equation for the proton motion. This enabled a prediction of the anharmonic vibrational levels of the intramolecular hydrogen bond. The description of the electron density topology of the TMM molecule was carried out using the atoms in molecules theoretical framework. The computational results were further compared with the infrared spectra in the solid state.

关键词： INTRAMOLECULAR HYDROGEN-BONDS localized wannier functions DENSITY-FUNCTIONAL THEORY AB-INITIO BETA-THIOSEMICARBAZONES BASIS-SETS 3D QSAR SIMULATIONS WATER SYSTEMS

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The vibrational frequencies of forsterite Mg₂SiO₄:: an all-electron ab initio study with the CRYSTAL code

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PHYSICS AND CHEMISTRY OF MINERALS 2006年第6期33卷 383-393页

作者： Noel, Y. Catti, M. D'Arco, Ph. Dovesi, R. Univ Turin IFM Dipartimento Chim I-10125 Turin Italy Univ Paris 06 UMR 7160 Lab PMMP F-75005 Paris France CNRS UMR 7160 Lab PMMP F-75005 Paris France Univ Milano Bicocca Dipartimento Sci Mat I-20125 Milan Italy Ctr Excellence NIS I-10125 Turin Italy

The vibrational spectrum of Mg2SiO4 olivine was calculated at the Gamma point by using the periodic ab initio CRYSTAL program. An all electron localized Gaussian-type basis set and the B3LYP Hamiltonian were employed. The full set of frequencies (35 IR active, 36 Raman active, 10 "silent" modes) was computed and compared to experimental data from different sources (four for IR and four for Raman). A generally good agreement is observed with experiment (the mean absolute difference ranging from 7 to 10 cm(-1) for the various sets), when some of the experimental frequencies, whose attribution is uncertain or appears to be affected by large errors, are not taken into account. A small number of observed peaks are not consistent with calculated frequencies, and a few theoretical peaks do not correspond to measured values. The implications are discussed in detail. The full set of modes are characterized using different tools, namely isotopic substitution, direct inspection of the eigenvectors and graphical representation, so as to obtain a consistent mode assignment.

关键词： QUANTUM-MECHANICAL CALCULATION localized wannier functions HARTREE-FOCKGRADIENTS FE-MG OLIVINES PERIODIC-SYSTEMS SINGLE-CRYSTAL LATTICE-DYNAMICS INFRARED-SPECTROSCOPY HIGH-PRESSURE IMPLEMENTATION

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The construction and application of a fully flexible computer simulation model for lithium oxide

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JOURNAL OF PHYSICS-CONDENSED MATTER 2004年第27期16卷 S2795-S2810页

作者： Wilson, M Jahn, S Madden, PA UCL Dept Chem London WC1H 0AJ England Univ Oxford Phys & Theoret Chem Lab Oxford OX1 3QZ England

An aspherical ion model (AIM) is constructed for lithium oxide, Li(2)O. The model incorporates both many-body polarization and short-range ion distortion effects. A procedure for extracting the required model parameters by fitting to results from a series of electronic structure calculations is described. The model is tested with respect to both static and dynamic properties. The experimentally observed Cauchy violation in the elastic constants and phonon frequencies are well reproduced as is the onset temperature for superionic behaviour in the Li(+) sublattice. The system is shown to display a peak in the heat capacity as a function of temperature. The correlated and uncorrelated ion dynamics are studied and the origin of the respective solid- and liquid-state Haven ratios is rationalized.

关键词： INITIO MOLECULAR-DYNAMICS localized wannier functions ALKALINE-EARTHOXIDES AB-INITIO IONIC SYSTEMS QUADRUPOLE POLARIZATION INTERATOMIC POTENTIALS PREMELTINGTRANSITION ELASTIC PROPERTIES CRYSTAL-STRUCTURE

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Interatomic surfaces in condensed systems: A quantum-classical analysis

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INTERNATIONAL JOURNAL OF MODERN PHYSICS B 2000年第7期14卷 771-781页

作者： Delle Site, L Queens Univ Belfast Sch Math & Phys Atomist Simulat Grp Belfast BT7 1NN Antrim North Ireland Queens Univ Belfast Sch Math & Phys Irish Ctr Colloid Sci Belfast BT7 1NN Antrim North Ireland

We analyze the concept of interatomic surface in condensed systems whose properties are calculated with an ab initio approach. Two different criteria for defining such a surface are considered: a classical criterion known as "Bader criterion" and a quantum criterion based on the quantum dynamical behavior of the electrons. Next the classical and quantum approach are combined to obtain a general definition of interatomic surface which is valid from both quantum and classical point of view. The two criteria are presented in the form of partial differential equations and their basic properties are discussed. The relevance of the theory analyzed for a practical implementation in molecular modeling is also discussed.

关键词： localized wannier functions First principles Water-molecules Triangulations Dipole Phase Water Molecule triangulation Valid quanta molecular model Electrons dipoles Phase

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