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Top 20 Most Read Articles
June 2011
The 20 articles with the most full-text downloads during the month, in descending order.
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J. Chem. Phys. 134, 244501 (2011); http://dx.doi.org/10.1063/1.3593064 (14 pages) Online Publication Date: 22 June 2011
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Studies on confined water are important not only from the viewpoint of scientific interest but also for the development of new nanoscale devices. In this work, we aimed to clarify the properties of confined water in the cylindrical pores of single-walled carbon nanotubes (SWCNTs) that had diameters in the range of 1.46 to 2.40 nm. A combination of x-ray diffraction (XRD), nuclear magnetic resonance, and electrical resistance measurements revealed that water inside SWCNTs with diameters between 1.68 and 2.40 nm undergoes a wet-dry type transition with the lowering of temperature; below the transition temperature Twd, water was ejected from the SWCNTs. Twd increased with increasing SWCNT diameter D. For the SWCNTs with D = 1.68, 2.00, 2.18, and 2.40 nm, Twd obtained by the XRD measurements were 218, 225, 236, and 237 K, respectively. We performed a systematic study on finite length SWCNT systems using classical molecular dynamics calculations to clarify the effect of open ends of the SWCNTs and water content on the water structure. It was found that ice structures that were formed at low temperatures were strongly affected by the bore diameter, a = D − σOC, where σOC is gap distance between the SWCNT and oxygen atom in water, and the number of water molecules in the system. In small pores (a < 1.02 nm), tubule ices or the so-called ice nanotubes (ice NTs) were formed irrespective of the water content. On the other hand, in larger pores (a > 1.10 nm) with small water content, filled water clusters were formed leaving some empty space in the SWCNT pore, which grew to fill the pore with increasing water content. For pores with sizes in between these two regimes (1.02 < a < 1.10 nm), tubule ice also appeared with small water content and grew with increasing water content. However, once the tubule ice filled the entire SWCNT pore, further increase in the water content resulted in encapsulation of the additional water molecules inside the tubule ice. Corresponding XRD measurements on SWCNTs with a mean diameter of 1.46 nm strongly suggested the presence of such a filled structure. |
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J. Chem. Phys. 134, 211101 (2011); http://dx.doi.org/10.1063/1.3598339 (4 pages) Online Publication Date: 1 June 2011
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The bond dissociation energy (D0) of the water dimer is determined by using state-to-state vibrational predissociation measurements following excitation of the bound OH stretch fundamental of the donor unit of the dimer. Velocity map imaging and resonance-enhanced multiphoton ionization (REMPI) are used to determine pair-correlated product velocity and translational energy distributions. H2O fragments are detected in the ground vibrational (000) and the first excited bending (010) states by 2 + 1 REMPI via the  1B1 (000) ←  1A1 (000 and 010) transitions. The fragments’ velocity and center-of-mass translational energy distributions are determined from images of selected rovibrational levels of H2O. An accurate value for D0 is obtained by fitting both the structure in the images and the maximum velocity of the fragments. This value, D0 = 1105 ± 10 cm−1 (13.2 ± 0.12 kJ/mol), is in excellent agreement with the recent theoretical value of D0 = 1103 ± 4 cm−1 (13.2 ± 0.05 kJ/mol) suggested as a benchmark by Shank et al. [J. Chem. Phys. 130, 144314 (2009)]. |
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Simulations of the confinement of ubiquitin in self-assembled reverse micelles J. Chem. Phys. 134, 225101 (2011); http://dx.doi.org/10.1063/1.3592712 (11 pages) Online Publication Date: 8 June 2011
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We describe the effects of confinement on the structure, hydration, and the internal dynamics of ubiquitin encapsulated in reverse micelles (RM). We performed molecular dynamics simulations of the encapsulation of ubiquitin into self-assembled protein/surfactant reverse micelles to study the positioning and interactions of the protein with the RM and found that ubiquitin binds to the RM interface at low salt concentrations. The same hydrophobic patch that is recognized by ubiquitin binding domains in vivo is found to make direct contact with the surfactant head groups, hydrophobic tails, and the iso-octane solvent. The fast backbone N-H relaxation dynamics show that the fluctuations of the protein encapsulated in the RM are reduced when compared to the protein in bulk. This reduction in fluctuations can be explained by the direct interactions of ubiquitin with the surfactant and by the reduced hydration environment within the RM. At high concentrations of excess salt, the protein does not bind strongly to the RM interface and the fast backbone dynamics are similar to that of the protein in bulk. Our simulations demonstrate that the confinement of protein can result in altered protein dynamics due to the interactions between the protein and the surfactant.
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The role of attractive forces in viscous liquids J. Chem. Phys. 134, 214503 (2011); http://dx.doi.org/10.1063/1.3592709 (12 pages) Online Publication Date: 1 June 2011
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We present evidence from computer simulation that the slowdown of relaxation of a standard Lennard-Jones glass-forming liquid and that of its reduction to a model with truncated pair potentials without attractive tails are quantitatively and qualitatively different in the viscous regime. The pair structure of the two models is however very similar. This finding, which appears to contradict the common view that the physics of dense liquids is dominated by the steep repulsive forces between atoms, is characterized in detail, and its consequences are explored. Beyond the role of attractive forces themselves, a key aspect in explaining the differences in the dynamical behavior of the two models is the truncation of the interaction potentials beyond a cutoff at typical interatomic distance. This leads us to question the ability of the jamming scenario to describe the physics of glass-forming liquids and polymers.
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The nature of electron correlation in a dissociating bond J. Chem. Phys. 134, 224103 (2011); http://dx.doi.org/10.1063/1.3599937 (5 pages) Online Publication Date: 10 June 2011
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We have constructed the unrestricted Hartree-Fock (UHF), restricted Hartree-Fock (RHF), and full configuration interaction (FCI) position and momentum intracules and holes for H⋅⋅⋅H at bond lengths R from 1 to 10 bohrs. We trace the recently discovered inversion of the UHF position hole at intermediate R to over-localization of the spin-orbitals, and support this by a correlation energy component analysis. The RHF and UHF momentum holes are found to be more complicated; however their features are explained through decomposition of electron correlation effects. The UHF momentum hole is also found to invert and exhibits interesting behavior at large R. The RHF (but not UHF) and FCI momentum intracules exhibit Young-type interference patterns related to recent double photoionization experiments. Our analyses yield the most comprehensive picture to date of the behavior of the electrons during homolytic bond fission.
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Communication: Non-adiabatic coupling and resonances in the F + H2 reaction at low energies J. Chem. Phys. 134, 231101 (2011); http://dx.doi.org/10.1063/1.3603453 (4 pages) Online Publication Date: 16 June 2011
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Quantum reactive scattering calculations on accurate potential energy surfaces predict that at energies below ∼5 meV, the reaction of F atoms with H2 is dominated by the Born-Oppenheimer (BO) forbidden reaction of the spin-orbit excited F(2P1/2) atom. This non-BO dominance is amplified by low-energy resonances corresponding to quasi-bound states of the HF(v = 3, j = 3) + H product channel. Neglect of non-adiabatic coupling between the electronic states of the F atom leads to a qualitatively incorrect picture of the reaction dynamics at low energy.
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Adsorption of organic molecules on the TiO2(011) surface: STM study J. Chem. Phys. 134, 224701 (2011); http://dx.doi.org/10.1063/1.3593403 (17 pages) Online Publication Date: 8 June 2011
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High resolution scanning tunneling microscopy has been applied to investigate adsorption and self-assembly of large organic molecules on the TiO2(011) surface. The (011) face of the rutile titania has been rarely examined in this context. With respect to possible industrial applications of rutile, quite often in a powder form, knowledge on behavior of organic molecules on that face is required. In the presented study we fill in the gap and report on experiments focused on the self-assembly of organic nanostructures on the TiO2(011) surface. We use three different kinds of organic molecules of potential interest in various applications, namely, PTCDA and CuPc representing flat, planar stacking species, and Violet Landers specially designed for new applications in molecular electronics. In order to reach a complete picture of molecular behavior, extended studies with different surface coverage ranging from single molecule up to 2 monolayer (ML) thick films are performed. Our results show that the adsorption behavior is significantly different from previously observed for widely used metallic templates. Creation of highly ordered molecular lines, quasi-ordered wetting layers, controlled geometrical reorientation upon thermal treatment, existence of specific adsorption geometries, and prospects for tip-induced molecule ordering and manipulation provide better understanding and add new phenomena to the knowledge on the (011) face of rutile titania. |
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J. Chem. Phys. 132, 154104 (2010); http://dx.doi.org/10.1063/1.3382344 (19 pages) Online Publication Date: 16 April 2010
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The method of dispersion correction as an add-on to standard Kohn–Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%–40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C6 coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.
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J. Chem. Phys. 134, 214501 (2011); http://dx.doi.org/10.1063/1.3594115 (7 pages) Online Publication Date: 1 June 2011
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We investigate atomistic mechanisms governing hydrogen release and uptake processes in ammonia borane (AB) within the framework of the density functional theory. In order to determine the most favorable pathways for the thermal inter-conversion between AB and polyaminoborane plus H2, we calculate potential energy surfaces for the corresponding reactions. We explore the possibility of enclosing AB in narrow carbon nanotubes to limit the formation of undesirable side-products such as the cyclic compound borazine, which hinder subsequent rehydrogenation of the system. We also explore the effects of nanoconfinement on the possible rehydrogenation pathways of AB and suggest the use of photoexcitation as a means to achieve dehydrogenation of AB at low temperatures.
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The nature of singlet excitons in oligoacene molecular crystals J. Chem. Phys. 134, 204703 (2011); http://dx.doi.org/10.1063/1.3590871 (11 pages) Online Publication Date: 26 May 2011
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A theory for polarized absorption in crystalline oligoacenes is presented, which includes Frenkel exciton coupling, the coupling between Frenkel and charge-transfer (CT) excitons, and the coupling of all neutral and ionic excited states to the dominant ring-breathing vibrational mode. For tetracene, spectra calculated using all Frenkel couplings among the five lowest energy molecular singlet states predict a Davydov splitting (DS) of the lowest energy (0–0) vibronic band of only −32 cm−1, far smaller than the measured value of 631 cm−1 and of the wrong sign—a negative sign indicating that the polarizations of the lower and upper Davydov components are reversed from experiment. Inclusion of Frenkel-CT coupling dramatically improves the agreement with experiment, yielding a 0–0 DS of 601 cm−1 and a nearly quantitative reproduction of the relative spectral intensities of the 0–n vibronic components. Our analysis also shows that CT mixing increases with the size of the oligoacenes. We discuss the implications of these results on exciton dissociation and transport. |
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J. Chem. Phys. 53, 1126 (1970); http://dx.doi.org/10.1063/1.1674108 (5 pages) Online Publication Date: 18 September 2003
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Raman spectra are reported from single crystals of graphite and other graphite materials. Single crystals of graphite show one single line at 1575 cm−1. For the other materials like stress‐annealed pyrolitic graphite, commercial graphites, activated charcoal, lampblack, and vitreous carbon another line is detected at 1355 cm−1. The Raman intensity of this band is inversely proportional to the crystallite size and is caused by a breakdown of the k‐selection rule. The intensity of this band allows an estimate of the crystallite size in the surface layer of any carbon sample. Two in‐plane force constants are calculated from the frequencies. |
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Construction of CASCI-type wave functions for very large active spaces J. Chem. Phys. 134, 224101 (2011); http://dx.doi.org/10.1063/1.3596482 (13 pages) Online Publication Date: 8 June 2011
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We present a procedure to construct a configuration-interaction expansion containing arbitrary excitations from an underlying full-configuration-interaction-type wave function defined for a very large active space. Our procedure is based on the density-matrix renormalization group (DMRG) algorithm that provides the necessary information in terms of the eigenstates of the reduced density matrices to calculate the coefficient of any basis state in the many-particle Hilbert space. Since the dimension of the Hilbert space scales binomially with the size of the active space, a sophisticated Monte Carlo sampling routine is employed. This sampling algorithm can also construct such configuration-interaction-type wave functions from any other type of tensor network states. The configuration-interaction information obtained serves several purposes. It yields a qualitatively correct description of the molecule's electronic structure, it allows us to analyze DMRG wave functions converged for the same molecular system but with different parameter sets (e.g., different numbers of active-system (block) states), and it can be considered a balanced reference for the application of a subsequent standard multi-reference configuration-interaction method.
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A novel interpretation of reduced density matrix and cumulant for electronic structure theories J. Chem. Phys. 134, 214109 (2011); http://dx.doi.org/10.1063/1.3596948 (9 pages) Online Publication Date: 2 June 2011
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We propose a novel interpretation of the reduced density matrix (RDM) and its cumulant that combines linear and exponential parametrizations of the wavefunction. Any n-particle RDM can be written as a weighted average of “configuration interaction” amplitudes. The corresponding n-particle cumulant is represented in terms of two types of contributions: “connected” (statistical averages of substitution amplitudes) and “disconnected” (cross-correlations of substitution amplitudes). A diagonal element of n-RDM represents the average occupation number of the orbital n-tuple. The diagonal elements of 2- and 3-cumulants take particularly elegant forms in the natural spin-orbital basis: they represent the covariances (correlated fluctuations) of the occupation numbers of the orbital pair and triples, respectively. Thus, the diagonal elements of the cumulants quantify the correlation between the orbital occupation numbers. Our interpretation is used to examine the weak to strong correlation transition in the “two electrons in two orbitals” problem.
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Poisson–Boltzmann–Nernst–Planck model J. Chem. Phys. 134, 194101 (2011); http://dx.doi.org/10.1063/1.3581031 (17 pages) Online Publication Date: 16 May 2011
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The Poisson–Nernst–Planck (PNP) model is based on a mean-field approximation of ion interactions and continuum descriptions of concentration and electrostatic potential. It provides qualitative explanation and increasingly quantitative predictions of experimental measurements for the ion transport problems in many areas such as semiconductor devices, nanofluidic systems, and biological systems, despite many limitations. While the PNP model gives a good prediction of the ion transport phenomenon for chemical, physical, and biological systems, the number of equations to be solved and the number of diffusion coefficient profiles to be determined for the calculation directly depend on the number of ion species in the system, since each ion species corresponds to one Nernst–Planck equation and one position-dependent diffusion coefficient profile. In a complex system with multiple ion species, the PNP can be computationally expensive and parameter demanding, as experimental measurements of diffusion coefficient profiles are generally quite limited for most confined regions such as ion channels, nanostructures and nanopores. We propose an alternative model to reduce number of Nernst–Planck equations to be solved in complex chemical and biological systems with multiple ion species by substituting Nernst–Planck equations with Boltzmann distributions of ion concentrations. As such, we solve the coupled Poisson–Boltzmann and Nernst–Planck (PBNP) equations, instead of the PNP equations. The proposed PBNP equations are derived from a total energy functional by using the variational principle. We design a number of computational techniques, including the Dirichlet to Neumann mapping, the matched interface and boundary, and relaxation based iterative procedure, to ensure efficient solution of the proposed PBNP equations. Two protein molecules, cytochrome c551 and Gramicidin A, are employed to validate the proposed model under a wide range of bulk ion concentrations and external voltages. Extensive numerical experiments show that there is an excellent consistency between the results predicted from the present PBNP model and those obtained from the PNP model in terms of the electrostatic potentials, ion concentration profiles, and current–voltage (I–V) curves. The present PBNP model is further validated by a comparison with experimental measurements of I–V curves under various ion bulk concentrations. Numerical experiments indicate that the proposed PBNP model is more efficient than the original PNP model in terms of simulation time.
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J. Chem. Phys. 134, 224102 (2011); http://dx.doi.org/10.1063/1.3598471 (13 pages) Online Publication Date: 10 June 2011
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We report a general implementation of alternative formulations of single-reference coupled cluster theory (extended, unitary, and variational) with arbitrary-order truncation of the cluster operator. These methods are applied to compute the energy of Ne and the equilibrium properties of HF and C2. Potential energy curves for the dissociation of HF and the BeH2 model computed with the extended, variational, and unitary coupled cluster approaches are compared to those obtained from the multireference coupled cluster approach of Mukherjee et al. [J. Chem. Phys. 110, 6171 (1999)] and the internally contracted multireference coupled cluster approach [F. A. Evangelista and J. Gauss, J. Chem. Phys. 134, 114102 (2011)10.1063/1.3559149]. In the case of Ne, HF, and C2, the alternative coupled cluster approaches yield almost identical bond length, harmonic vibrational frequency, and anharmonic constant, which are more accurate than those from traditional coupled cluster theory. For potential energy curves, the alternative coupled cluster methods are found to be more accurate than traditional coupled cluster theory, but are three to ten times less accurate than multireference coupled cluster approaches. The most challenging benchmark, the BeH2 model, highlights the strong dependence of the alternative coupled cluster theories on the choice of the Fermi vacuum. When evaluated by the accuracy to cost ratio, the alternative coupled cluster methods are not competitive with respect to traditional CC theory, in other words, the simplest theory is found to be the most effective one.
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Density‐functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 98, 5648 (1993); http://dx.doi.org/10.1063/1.464913 (5 pages)
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Despite the remarkable thermochemical accuracy of Kohn–Sham density‐functional theories with gradient corrections for exchange‐correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact‐exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange‐correlation functional containing local‐spin‐density, gradient, and exact‐exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first‐ and second‐row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol. |
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J. Chem. Phys. 134, 224104 (2011); http://dx.doi.org/10.1063/1.3599045 (5 pages) Online Publication Date: 13 June 2011
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A review of the literature on the calculation of electrostatic potentials, fields, and field gradients in systems consisting of charges and dipoles using the Ewald summation technique is presented. Discrepancies between the previous formulas are highlighted, and an error in the derivation of the reciprocal contributions to the electrostatic field and field gradient is corrected. The new formulas for the field and field gradient are shown to exhibit a termwise identity with the ones for the electrostatic energy.
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First principles semiclassical calculations of vibrational eigenfunctions J. Chem. Phys. 134, 234103 (2011); http://dx.doi.org/10.1063/1.3599469 (12 pages) Online Publication Date: 17 June 2011
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Vibrational eigenfunctions are calculated on-the-fly using semiclassical methods in conjunction with ab initio density functional theory classical trajectories. Various semiclassical approximations based on the time-dependent representation of the eigenfunctions are tested on an analytical potential describing the chemisorption of CO on Cu(100). Then, first principles semiclassical vibrational eigenfunctions are calculated for the CO2 molecule and its accuracy evaluated. The multiple coherent states initial value representations semiclassical method recently developed by us has shown with only six ab initio trajectories to evaluate eigenvalues and eigenfunctions at the accuracy level of thousands trajectory semiclassical initial value representation simulations.
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Communication: Atomic and molecular Rydbergs from water J. Chem. Phys. 134, 201101 (2011); http://dx.doi.org/10.1063/1.3593199 (4 pages) Online Publication Date: 23 May 2011
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We report the formation of energetic neutral Rydberg hydrogen atoms and transient Rydberg molecular ions, [(H2O)q+]☆ in ion-impact dissociation of isolated water molecules. The kinetic energy spectra of the neutral Rydberg H atoms are determined from the complete study of (H⋆, H+, O+) dissociation channel. This channel of water dissociation is suggested as a possible additional source of the energetic neutrals detected in upper atmospheres of extra solar planets, and of slow electrons which are known to play a major role in radiation induced damage to living cells.
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Molecular dynamics simulation of the dielectric constant of water: The effect of bond flexibility J. Chem. Phys. 134, 234501 (2011); http://dx.doi.org/10.1063/1.3600337 (6 pages) Online Publication Date: 15 June 2011
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The role of bond flexibility on the dielectric constant of water is investigated via molecular dynamics simulations using a flexible intermolecular potential SPC/Fw [Y. Wu, H. L. Tepper, and G. A. Voth, J. Chem. Phys. 128, 024503 (2006)]. Dielectric constants and densities are reported for the liquid phase at temperatures of 298.15 K and 473.15 K and the supercritical phase at 673.15 K for pressures between 0.1 MPa and 200 MPa. Comparison with both experimental data and other rigid bond intermolecular potentials indicates that introducing bond flexibility significantly improves the prediction of both dielectric constants and pressure–temperature–density behavior. In some cases, the predicted densities and dielectric constants almost exactly coincide with experimental data. The results are analyzed in terms of dipole moments, quadrupole moments, and equilibrium bond angles and lengths. It appears that bond flexibility allows the molecular dipole and quadrupole moment to change with the thermodynamic state point, and thereby mimic the change of the intermolecular interactions in response to the local environment. |
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