Showing papers in "Journal of Chemical Physics in 2000"

A climbing image nudged elastic band method for finding saddle points and minimum energy paths

Abstract: A modification of the nudged elastic band method for finding minimum energy paths is presented. One of the images is made to climb up along the elastic band to converge rigorously on the highest saddle point. Also, variable spring constants are used to increase the density of images near the top of the energy barrier to get an improved estimate of the reaction coordinate near the saddle point. Applications to CH4 dissociative adsorption on Ir~111! and H2 on Si~100! using plane wave based density functional theory are presented. © 2000 American Institute of Physics. @S0021-9606~00!71246-3#

From molecules to solids with the DMol3 approach

Abstract: Recent extensions of the DMol3 local orbital density functional method for band structure calculations of insulating and metallic solids are described. Furthermore the method for calculating semilocal pseudopotential matrix elements and basis functions are detailed together with other unpublished parts of the methodology pertaining to gradient functionals and local orbital basis sets. The method is applied to calculations of the enthalpy of formation of a set of molecules and solids. We find that the present numerical localized basis sets yield improved results as compared to previous results for the same functionals. Enthalpies for the formation of H, N, O, F, Cl, and C, Si, S atoms from the thermodynamic reference states are calculated at the same level of theory. It is found that the performance in predicting molecular enthalpies of formation is markedly improved for the Perdew–Burke–Ernzerhof [Phys. Rev. Lett. 77, 3865 (1996)] functional.

Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points

Abstract: An improved way of estimating the local tangent in the nudged elastic band method for finding minimum energy paths is presented. In systems where the force along the minimum energy path is large compared to the restoring force perpendicular to the path and when many images of the system are included in the elastic band, kinks can develop and prevent the band from converging to the minimum energy path. We show how the kinks arise and present an improved way of estimating the local tangent which solves the problem. The task of finding an accurate energy and configuration for the saddle point is also discussed and examples given where a complementary method, the dimer method, is used to efficiently converge to the saddle point. Both methods only require the first derivative of the energy and can, therefore, easily be applied in plane wave based density-functional theory calculations. Examples are given from studies of the exchange diffusion mechanism in a Si crystal, Al addimer formation on the Al(100) surfa...

A reactive potential for hydrocarbons with intermolecular interactions

Abstract: A potential function is presented that can be used to model both chemical reactions and intermolecular interactions in condensed-phase hydrocarbon systems such as liquids, graphite, and polymers. This potential is derived from a well-known dissociable hydrocarbon force field, the reactive empirical bond-order potential. The extensions include an adaptive treatment of the nonbonded and dihedral-angle interactions, which still allows for covalent bonding interactions. Torsional potentials are introduced via a novel interaction potential that does not require a fixed hybridization state. The resulting model is intended as a first step towards a transferable, empirical potential capable of simulating chemical reactions in a variety of environments. The current implementation has been validated against structural and energetic properties of both gaseous and liquid hydrocarbons, and is expected to prove useful in simulations of hydrocarbon liquids, thin films, and other saturated hydrocarbon systems.

A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

Abstract: The ability of simple potential functions to reproduce accurately the density of liquid water from −37 to 100 °C at 1 to 10 000 atm has been further explored. The result is the five-site TIP5P model, which yields significantly improved results; the average error in the density over the 100° temperature range from −37.5 to 62.5 °C at 1 atm is only 0.006 g cm−3. Classical Monte Carlo statistical mechanics calculations have been performed to optimize the parameters, especially the position of the negative charges along the lone-pair directions. Initial calculations with 216 molecules in the NPT ensemble at 1 atm focused on finding a model that reproduced the shape of the liquid density curve as a function of temperature. Calculations performed for 512 molecules with the final TIP5P model demonstrate that the density maximum near 4 °C at 1 atm is reproduced, while high-quality structural and thermodynamic results are maintained. Attainment of high precision for the low-temperature runs required sampling for more than 1 billion Monte Carlo configurations. In addition, the dielectric constant was computed from the response to an applied electric field; the result is 81.5±1.5 at 25 °C and the experimental curve is mirrored from 0–100 °C at 1 atm. The TIP5P model is also found to perform well as a function of pressure; the density of liquid water at 25 °C is reproduced with an average error of ∼2% over the range from 1 to 10 000 atm, and the shift of the temperature of maximum density to lower temperature with increasing pressure is also obtained.

A complete basis set model chemistry. VII. Use of the minimum population localization method

Abstract: It is shown that localization is necessary to preserve size consistency in nonlinear extrapolations of molecular energies. We demonstrate that the unphysical behavior of Mulliken populations obtained from extended basis set wave functions can lead to incomplete localization of orbitals by the Pipek–Mezey population localization method, and introduce a modification to correct this problem. The new localization procedure, called minimum population localization, is incorporated into the CBS-QB3 and the new CBS-4M model chemistries, and their performance is assessed on the G2/97 test set. The errors found for CBS-QB3 are comparable with those for the G3 and G3(MP2) (mean absolute deviation of 1.10, 0.94, and 1.21 kcal/mol, respectively, on the G2/97 test set). The CBS-4M is less accurate than the other models (mean absolute deviation of 3.26 kcal/mol on the G2/97 test set), but can be applied to much larger systems. The modified localization method resolves several problem cases found with CBS-4 and improves the reliability of CBS-QB3.

The chemical Langevin equation

Abstract: The stochastic dynamical behavior of a well-stirred mixture of N molecular species that chemically interact through M reaction channels is accurately described by the chemical master equation. It is shown here that, whenever two explicit dynamical conditions are satisfied, the microphysical premise from which the chemical master equation is derived leads directly to an approximate time-evolution equation of the Langevin type. This chemical Langevin equation is the same as one studied earlier by Kurtz, in contradistinction to some other earlier proposed forms that assume a deterministic macroscopic evolution law. The novel aspect of the present analysis is that it shows that the accuracy of the equation depends on the satisfaction of certain specific conditions that can change from moment to moment, rather than on a static system size parameter. The derivation affords a new perspective on the origin and magnitude of noise in a chemically reacting system. It also clarifies the connection between the stochas...

CC2 excitation energy calculations on large molecules using the resolution of the identity approximation

Abstract: A new implementation of the approximate coupled cluster singles and doubles method CC2 is reported, which is suitable for large scale integral-direct calculations. It employs the resolution of the identity (RI) approximation for two-electron integrals to reduce the CPU time needed for calculation and I/O of these integrals. We use a partitioned form of the CC2 equations which eliminates the need to store double excitation cluster amplitudes. In combination with the RI approximation this formulation of the CC2 equations leads to a reduced scaling of memory and disk space requirements with the number of correlated electrons (n) and basis functions (N) to, respectively, O(N2) and O(nN2), compared to O(n2N2) in previous implementations. The reduced CPU, memory and disk space requirements make it possible to perform CC2 calculations with accurate basis sets on large molecules, which would not be accessible with conventional implementations of the CC2 method. We present an application to vertical excitation ene...

Small-core multiconfiguration-Dirac–Hartree–Fock-adjusted pseudopotentials for post-d main group elements: Application to PbH and PbO

Abstract: Relativistic pseudopotentials (PPs) of the energy-consistent variety have been generated for the post-d group 13–15 elements, by adjustment to multiconfiguration Dirac–Hartree–Fock data based on the Dirac–Coulomb–Breit Hamiltonian. The outer-core (n−1)spd shells are explicitly treated together with the nsp valence shell, with these PPs, and the implications of the small-core choice are discussed by comparison to a corresponding large-core PP, in the case of Pb. Results from valence ab initio one- and two-component calculations using both PPs are presented for the fine-structure splitting of the ns2np2 ground-state configuration of the Pb atom, and for spectroscopic constants of PbH (X 2Π1/2, 2Π3/2) and PbO (X 1Σ+). In addition, a combination of small-core and large-core PPs has been explored in spin-free-state shifted calculations for the above molecules.

Multidimensional replica-exchange method for free-energy calculations

Abstract: We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.

Multireference perturbation theory for large restricted and selected active space reference wave functions

Abstract: A multireference second-order perturbation theory (MRPT2) has been developed which allows the use of reference wave functions with large active spaces and arbitrary configuration selection. Internally contracted configurations are used as a basis for all configuration subspaces of the first-order wave function for which the overlap matrix depends only on the second-order density matrix of the reference function. Some other subspaces which would require the third- or fourth-order density matrices are left uncontracted. This removes bottlenecks of the complete active space second order pertubation theory (CASPT2) caused by the need to construct and diagonalize large overlap matrices. Preliminary applications of the new method for 1,2-dihydronaphthalene (DHN) and free base porphin are presented in which the effect of applying occupancy restrictions in the reference wave function (restricted active space second-order perturbation theory, RASPT2) and reference configuration selection (general MRPT2) on electro...

Scanning near-field optical microscopy with aperture probes: Fundamentals and applications

Abstract: In this review we describe fundamentals of scanning near-field optical microscopy with aperture probes. After the discussion of instrumentation and probe fabrication, aspects of light propagation in metal-coated, tapered optical fibers are considered. This includes transmission properties and field distributions in the vicinity of subwavelength apertures. Furthermore, the near-field optical image formation mechanism is analyzed with special emphasis on potential sources of artifacts. To underline the prospects of the technique, selected applications including amplitude and phase contrast imaging, fluorescence imaging, and Raman spectroscopy, as well as near-field optical desorption, are presented. These examples demonstrate that scanning near-field optical microscopy is no longer an exotic method but has matured into a valuable tool.

Assessment of Gaussian-3 and density functional theories for a larger experimental test set

Abstract: The G2/97 test set [J. Chem. Phys. 106, 1063 (1997)] for assessing quantum chemical methods used to predict thermochemical data is expanded to include 75 additional enthalpies of formation of larger molecules. This new set, referred to as the G3/99 test set, includes enthalpies of formation, ionization potentials, electron affinities, and proton affinities in the G2/97 set and 75 new enthalpies of formation. The total number of energies in the G3/99 set is 376. Overall, G3 theory has a mean absolute deviation of 1.07 kcal/mol for the G3/99 test set and does about as well for the new hydrocarbons and substituted hydrocarbons as it does for those in the G2/97 test. However, G3 theory has large deviations for several of the new nonhydrogen systems in the G3/99 test set such as SF6 and PF5. Part of the source of error is traced to the inadequate geometries used in G3 theory for these molecules. Other variations of G3 theory are also assessed such as G3(MP2), G3(MP3), and the versions of G3 theory using scaled...

Nonexponential “blinking” kinetics of single CdSe quantum dots: A universal power law behavior

Abstract: Single molecule confocal microscopy is used to study fluorescence intermittency of individual ZnS overcoated CdSe quantum dots (QDs) excited at 488 nm The confocal apparatus permits the distribution of “on” and “off” times (ie, periods of sustained fluorescence emission and darkness) to be measured over an unprecedentedly large dynamic range (109) of probability densities, with nonexponential behavior in τoff over a 105 range in time scales In dramatic contrast, these same τoff distributions in all QDs are described with remarkable simplicity over this 109-fold dynamic range by a simple inverse power law, ie, P(τoff)∝1/τoff1+α Such inverse power law behavior is a clear signature of distributed kinetics, such as predicted for (i) an exponential distribution of trap depths or (ii) a distribution of tunneling distances between QD core/interface states This has important statistical implications for all previous studies of fluorescence intermittency in semiconductor QDs and may have broader implications for other systems such as single polymer molecules

Temperature-accelerated dynamics for simulation of infrequent events

Abstract: We present a method for accelerating dynamic simulations of activated processes in solids. By raising the temperature, but allowing only those events that should occur at the original temperature, the time scale of a simulation is extended by orders of magnitude compared to ordinary molecular dynamics, while preserving the correct dynamics at the original temperature. The main assumption behind the method is harmonic transition state theory. Importantly, the method does not require any prior knowledge about the transition mechanisms. As an example, the method is applied to a study of surface diffusion, where concerted processes play a key role. In the example, times of hours are achieved at a temperature of 150 K.

Molecular calculations of excitation energies and (hyper)polarizabilities with a statistical average of orbital model exchange-correlation potentials

Abstract: An approximate Kohn–Sham exchange-correlation potential νxcSAOP is developed with the method of statistical averaging of (model) orbital potentials (SAOP) and is applied to the calculation of excitation energies as well as of static and frequency-dependent multipole polarizabilities and hyperpolarizabilities within time-dependent density functional theory (TDDFT). νxcSAOP provides high quality results for all calculated response properties and a substantial improvement upon the local density approximation (LDA) and the van Leeuwen–Baerends (LB) potentials for the prototype molecules CO, N2, CH2O, and C2H4. For the first three molecules and the lower excitations of the C2H4 the average error of the vertical excitation energies calculated with νxcSAOP approaches the benchmark accuracy of 0.1 eV for the electronic spectra.

Resolving the hydrogen bond dynamics conundrum

Abstract: This paper analyzes dynamic properties of hydrogen bonds in liquid water. We use molecular dynamics simulation to calculate different probability densities that govern the time evolution of the formation and rupture of hydrogen bonds. We provide analytical connections between these functions. Excellent agreement with our simulation results is observed. We prove transition state theory rate constant to be identical to the inverse of the associated mean first passage time (hydrogen bond lifetime). Hence, the analysis establishes its Arrhenius temperature dependence. We give the explicit relation between reactive flux correlation function for the relaxation dynamics of hydrogen bonds, and their first passage time probability densities. All the different observations in the existing literature, associated with various estimates of hydrogen bonding times in liquid water that are affected (or not affected) by particular bond criteria, as well as by different definitions of hydrogen bond lifetimes applied in sim...

Cooling of large molecules below 1 K and He clusters formation

Abstract: We present here the design details of a high-pressure pulsed valve that generates intense supersonic jets. The measured rotational contours of Aniline indicate that temperatures lower than 0.5 K can be achieved before the formation of clusters with the He carrier gas. The spectral shifts and vibronic structure of Anthracene–Hen clusters (n=1–6) are showing some surprising features.

Extended corresponding-states behavior for particles with variable range attractions

Abstract: We propose an extension of the law of corresponding states that can be applied to systems—such as colloidal suspensions—that have widely different ranges of attractive interactions. We argue that the “reduced” second virial coefficient is a convenient parameter to quantify the effective range of attraction. Knowledge of the pair-potential alone allows one to estimate the relative location of the liquid–vapor and solid–fluid coexistence curves.

Solute molecular dynamics in a mesoscale solvent

Abstract: A hybrid molecular dynamics (MD) algorithm which combines a full MD description of solute–solute and solute–solvent interactions with a mesoscale treatment of solvent-solvent interactions is developed. The solvent dynamics is modeled on a mesoscale level by coarse graining the system into cells and updating the velocities of the solvent molecules by multiparticle collisions within each cell. The solvent dynamics is such that the correct hydrodynamic equations are obtained in the macroscopic limit and a Boltzmann distribution of velocities is established in equilibrium. Discrete-time versions of the hydrodynamic equations and Green–Kubo autocorrelation functions are derived. Between the discrete-time solvent–solvent collisions the system evolves by the classical equations of motion. The hybrid MD scheme is illustrated by an application to the Brownian motion of a nanocolloidal particle in the mesoscale solvent and concentrated nanocolloidal suspensions.

Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface

Abstract: A new practical approach to studying enzyme reactions by combining ab initio QM/MM calculations with free energy perturbation is presented An efficient iterative optimization procedure has been developed to determine optimized structures and minimum energy paths for a system with thousands of atoms on the ab initio QM/MM potential: the small QM sub-system is optimized using a quasi-Newton minimizer in redundant internal coordinates with ab initio QM/MM calculations, while the large MM sub-system is minimized by the truncated Newton method in Cartesian coordinates with only molecular mechanical calculations The above two optimization procedures are performed iteratively until they converge With the determined minimum energy paths, free energy perturbation calculations are carried out to determine the change in free energy along the reaction coordinate Critical to the success of the iterative optimization procedure and the free energy calculations is the smooth connection between the QM and MM regions p

What can x-ray scattering tell us about the radial distribution functions of water?

Abstract: We present an analysis of the Advanced Light Source (ALS) x-ray scattering experiment on pure liquid water at ambient temperature and pressure described in the preceding article. The present study discusses the extraction of radial distribution functions from the x-ray scattering of molecular fluids. It is proposed that the atomic scattering factors used to model water be modified to include the changes in the intramolecular electron distribution caused by chemical bonding effects. Based on this analysis we present a gOO(r) for water consistent with our recent experimental data gathered at the ALS, which differs in some aspects from the gOO(r) reported by other x-ray and neutron scattering experiments. Our gOO(r) exhibits a taller and sharper first peak, and systematic shifts in all peak positions to smaller r. Based on experimental uncertainties, we discuss what features of gOO(r) should be reproduced by classical simulations of nonpolarizable and polarizable water models, as well as ab initio simulations of water, at ambient conditions. We directly compare many water models and simulations to the present data, and discuss possible improvements in both classical and ab initio simulation approaches in the future.

The method of moments of coupled-cluster equations and the renormalized CCSD[T], CCSD(T), CCSD(TQ), and CCSDT(Q) approaches

Abstract: This paper is the first in a series of papers on the new approach to the many-electron correlation problem, termed the method of moments of coupled-cluster equations (MMCC). A hierarchy of MMCC approximations, including the renormalized and completely renormalized CCSD[T], CCSD(T), CCSD(TQ), and CCSDT(Q) methods, which can be viewed as generalizations of the well-known perturbative coupled-cluster CCSD[T], CCSD(T), CCSD(TQf), and CCSDT(Qf) schemes, is introduced. In this initial study, an emphasis is placed on the ability of the MMCC approach to describe bond breaking and large effects due to connected triples and quadruples by modifying the standard noniterative CC approaches, such as the popular CCSD(T) method. The performance of selected MMCC approaches, including the renormalized and completely renormalized CCSD[T], CCSD(T), and CCSD(TQ) schemes, is illustrated by the results of pilot calculations for the HF and H2O molecules.

Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions

Abstract: We have implemented classical Ewald and particle-mesh Ewald (PME) based treatments of fixed and induced point dipoles into the sander molecular dynamics (MD) module of AMBER 6. During MD the induced dipoles can be propagated along with the atomic positions either by iteration to self-consistency at each time step, or by a Car–Parrinello (CP) technique using an extended Lagrangian formalism. In this paper we present the derivation of the new algorithms and compare the various options with respect to accuracy, efficiency, and effect on calculated properties of a polarizable water model. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in large macromolecular systems.

Solvent effect on vertical electronic transitions by the polarizable continuum model

Abstract: A recent extension of the polarizable continuum solvation model (PCM) to excited electronic states is applied to the study of solvent effects on electronic transitions, accounting for both electrostatic and nonelectrostatic solute–solvent interactions. A general formalism for nonequilibrium electrostatic solvation is developed, applicable to all PCM versions, and a recent procedure for the quantum-mechanical computation of dispersion and repulsion solute–solvent interactions is implemented and used for the first time in this context. The procedure is applied to the study of the n→π* transition of acetone in aqueous and nonaqueous solvents: nonequilibrium effects are very important in polar environments; also, the inclusion of dispersion and repulsion is mandatory to obtain the correct trend of the solvatochromic shifts. The effect of adding some explicit solvent molecules is also analyzed.

The mechanical strength of a covalent bond calculated by density functional theory

Abstract: The rupture forces of covalent bonds in a polymer as a function of bond lifetime are calculated with an Arrhenius kinetics model based on high-level density functional theory calculations. Relaxed potential energy surface scans of small model molecules yield potential functions that account for the deformations and hybridizations caused by the application of force. Morse potentials chosen to exhibit the same well depth and maximum force are used as an analytic representation of an individual bond in an infinitely long one-dimensional polymer. Application of force deforms the potential, and the activation energy for the bond rupture event together with the frequency of an optical phonon in the one-dimensional polymer are the two Arrhenius parameters. Rupture forces of the bonds C–C, C–N, C–O, Si–C, Si–N, Si–O, and Si–Si are reported as a function of the lifetime of the bond.

Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach

Abstract: An energy decomposition scheme based on the block-localized wave function (BLW) method is proposed. The key of this scheme is the definition and the full optimization of the diabatic state wave function, where the charge transfer among interacting molecules is deactivated. The present energy decomposition (ED), BLW-ED, method is similar to the Morokuma decomposition scheme in definition of the energy terms, but differs in implementation and the computational algorithm. In addition, in the BLW-ED approach, the basis set superposition error is fully taken into account. The application of this scheme to the water dimer and the lithium cation–water clusters reveals that there is minimal charge transfer effect in hydrogen-bonded complexes. At the HF/aug-cc-PVTZ level, the electrostatic, polarization, and charge-transfer effects contribute 65%, 24%, and 11%, respectively, to the total bonding energy (−3.84 kcal/mol) in the water dimer. On the other hand, charge transfer effects are shown to be significant in Lewis acid–base complexes such as H3NSO3 and H3NBH3. In this work, the effect of basis sets used on the energy decomposition analysis is addressed and the results manifest that the present energy decomposition scheme is stable with a modest size of basis functions.

New generalized gradient approximation functionals

Abstract: New generalized gradient approximation (GGA) functionals are reported, using the expansion form of A. D. Becke, J. Chem. Phys. 107, 8554 (1997), with 15 linear parameters. Our original such GGA functional, called HCTH, was determined through a least squares refinement to data of 93 systems. Here, the data are extended to 120 systems and 147 systems, introducing electron and proton affinities, and weakly bound dimers to give the new functionals HCTH/120 and HCTH/147. HCTH/120 has already been shown to give high quality predictions for weakly bound systems. The functionals are applied in a comparative study of the addition reaction of water to formaldehyde and sulfur trioxide, respectively. Furthermore, the performance of the HCTH/120 functional in Car–Parrinello molecular dynamics simulations of liquid water is encouraging.

Low-order scaling local electron correlation methods. III. Linear scaling local perturbative triples correction (T)

Abstract: A new method for the perturbative calculation of the correlation energy due to connected triple excitations (T) in the framework of local coupled cluster theory is presented, for which all computational resources scale linearly with molecular size. One notable complication in the formalism for connected triples introduced by the local approach is the nondiagonality of the Fock matrix in the localized MO (LMO) and projected AO (PAO) basis, which leads to couplings between individual triples amplitudes via the internal–internal and external–external blocks of the Fock matrix, respectively. Further complications and couplings arise due to the nonorthogonality of the PAOs. While the couplings via the external–external block can easily be dealt with, this is more difficult for the internal–internal couplings. In a previous paper we already published preliminary results of an approximation of the method, which neglects these internal–internal couplings entirely and recovers about 97% of the total local triples ...