Active-space coupled-cluster methods through connected quadruple excitations

Coupled-cluster methods that include just a subset of all connected triple, quadruple, or both excitation amplitudes, according to the ansatz of and Adamowicz co-workers [Int. Rev. Phys. Chem. 12, 339 (1993); J. Chem. Phys. 99, 1875 (1993); 100, 5792 (1994)] and Piecuch et al. [J. Chem. Phys. 110, 6103 (1999)], have been implemented into parallel execution programs. They are applicable to closed- and open-shell species and they take advantage of real Abelian point-group symmetry. A symbol manipulation program has been invoked to automate the implementation. These methods have been applied to the singlet-triplet separations of five triatomic hydrides (CH2, NH2+, SiH2, PH2+, and AsH2+) with consideration of scalar relativistic effects. They have been shown to be remarkably effective with errors arising from the use of a very small subset of higher-order excitations being no more than a few tenths of 1 kcal/mol.     

On the effects of ion-wall chemical association on the electric double layer: a density functional approach for the restricted primitive model at a charged wall

We describe a density functional theory for the restricted primitive model of ionic fluid at a charged wall with active sites to which ions can bond. The theory is an extension of our recent approach [Pizio et al., J. Chem. Phys. 121, 11957 (2004)] and is focused in the effects of specific adsorption of ions on the wall, besides the electrostatic phenomena. In order to solve the problem, we use the first-order thermodynamic perturbation theory of chemical association developed by Wertheim [J. Chem. Phys. 87, 7323 (1987)]. The microscopic structure of the electric double layer and the amount of adsorbed charge are investigated. Also, the temperature dependence of capacitance is analyzed. The capacitance depends on the kind of ions that form associative bonds with the surface sites and is determined by a net charge acting on the diffuse layer. The shape of the temperature dependence of capacitance essentially depends on the association energy and the density of bonding sites.     

Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion

The Crooks equation [Eq. (10) in J. Stat. Phys. 90, 1481 (1998)] relates the work done on a system during a nonequilibrium transformation to the free energy difference between the final and the initial state of the transformation. Recently, the authors have derived the Crooks equation for systems in the canonical ensemble thermostatted by the Nose-Hoover or Nose-Hoover chain method [P. Procacci et al., J. Chem. Phys. 125, 164101 (2006)]. That proof is essentially based on the fluctuation theorem by Evans and Searles [Adv. Phys. 51, 1529 (2002)] and on the equations of motion. Following an analogous approach, the authors derive here the Crooks equation in the context of molecular dynamics simulations of systems in the isothermal-isobaric (NPT) ensemble, whose dynamics is regulated by the Martyna-Tobias-Klein algorithm [J. Chem. Phys. 101, 4177 (1994)]. Their present derivation of the Crooks equation correlates to the demonstration of the Jarzynski identity for NPT systems recently proposed by Cuendet [J. Chem. Phys. 125, 144109 (2006)].     

Pair-correlated speed distributions for the OH+CH4/CD4 reactions: Further remarks on their classical trajectory calculations in a quantum spirit

Ten years ago, Liu and co-workers measured pair-correlated speed distributions for OH+CH₄/CD₄ reactions by means of velocity map imaging (VMI) techniques at a collision energy of ∼10 kcal/mol [B. Zhang, W. Shiu, J. J. Lin and K. Liu, J. Chem. Phys 122, 131102 (2005); B. Zhang, W. Shiu and K. Liu, J. Phys. Chem. A 109, 8989 (2005)]. Recently, two of us could semi-quantitatively reproduce these measurements by performing full-dimensional quasi-classical trajectory calculations in a quantum spirit on an ab-initio potential energy surface of their own [J. Espinosa-Garcia and J. C. Corchado, Theor. Chem. Acc. (2015) 134: 6; J. Phys. Chem. B 120, 1446 (2016)]. The goal of the present work is to show that these results can be significantly improved by adding a few more constraints in order to better comply with the restrictions imposed by VMI. Overall, the level of agreement between theory and experiment is remarkable owing to the large dimensionality of the reactions under scrutiny. This is an encouraging result considering the computational challenges of quantum scattering calculations for such large processes.     

Adsorption at the liquid-vapor surface of a binary liquid mixture

In a binary liquid mixture, the component possessing the lowest surface tension preferentially adsorbs at the liquid-vapor surface. In the past this adsorption behavior has been extensively investigated for critical binary liquid mixtures near the mixture's critical temperature T(c). In this fluctuation-dominated regime the adsorption is described by a universal function of the dimensionless depth zxi where xi is the bulk correlation length. Fewer studies have quantitatively examined adsorption for off-critical mixtures because, in this case, one must carefully account for both the bulk and surface crossover from the fluctuation-dominated regime (close to T(c)) to the mean-field dominated regime (far from T(c)). In this paper we compare extensive liquid-vapor ellipsometric adsorption measurements for the mixture aniline+cyclohexane at a variety of critical and noncritical compositions with the crossover theory of Kiselev and co-workers [J. Chem. Phys. 112, 3370 (2000)].     

Diffusion in linear porous media with periodic entropy barriers: A tube formed by contacting spheres

The problem of transport in quasi-one-dimensional periodic structures has been studied recently by several groups [D. Reguera et al., Phys. Rev. Lett.96, 130603 (2006); P. S. Burada et al., Phys. Rev. E75, 051111 (2007); B. Q. Ai and L. G. Liu, ibid.74, 051114 (2006); B. Q. Ai et al., ibid.75, 061126 (2007); B. Q. Ai and L. G. Liu, J. Chem. Phys.126, 204706 (2007); 128, 024706 (2008); E. Yariv and K. D. Dorfman, Phys. Fluids19, 037101 (2007); N. Laachi et al., Europhys. Lett.80, 50009 (2007); A. M. Berezhkovskii et al., J. Chem. Phys.118, 7146 (2003); 119, 6991 (2003)]. Using the concept of "entropy barrier" [R. Zwanzig, J. Phys. Chem.96, 3926 (1992)] one can classify such structures based on the height of the entropy barrier. Structures with high barriers are formed by chambers, which are weakly connected with each other because they are connected by small apertures. To escape from such a chamber a diffusing particle has to climb a high entropy barrier to find an exit that takes a lot of time [I. V. Grigoriev et al., J. Chem. Phys.116, 9574 (2002)]. As a consequence, the particle intrachamber lifetime tau(esc) is much larger than its intrachamber equilibration time, tau(rel), tau(esc)>tau(rel). When the aperture is not small enough, the intrachamber escape and relaxation times are of the same order and the hierarchy fails. This is the case of low entropy barriers. Transport in this case is analyzed in the works of Schmid and co-workers, Liu and co-workers, and Dorfman and co-workers, while the work of Berezhkovskii et al. is devoted to diffusion in the case of high entropy barriers.     

Observation of a transition in the water-nanoparticle formation process at 167 K

Rapid-scan Fourier transform infrared spectroscopy of the vapor/solid formation process of water nanoparticles in the 180-140 K temperature range at thermal-equilibrium conditions is reported. At 167 K a transition in the formation process was observed: the particle volume quintuples and the particle formation time triples within a temperature interval of +/-0.4 K caused by the temperature control. The authors interpret this behavior by an abrupt change in the nucleation rate of the H2O monomers in He buffer gas kept at 167 K and 200 mbar. A size and shape analysis of the particles during the formation process was carried out by application of the discrete dipole approximation method which delivers excellent accordance between experimental and calculated mid-IR spectra. Compared to other compact shapes (cube, prolate ellipsoid, and hexagonal prism) the ideal spherical shape fits the experimental spectra best. A distinct change in shape by particle conversion or agglomeration could be excluded to be involved in the formation process. As a possible explanation of the observed phenomenon, a transition from vapor/liquid/solid to vapor/solid nucleation with decreasing temperature is considered which was recently theoretically predicted by van Dongen and co-workers [J. Chem. Phys. 117, 5647 (2002); private communication; J. Chem. Phys. 120, 6314 (2004)].     

Trajectory dynamics study of the Ar + CH4 dissociation reaction at high temperatures: the importance of zero-point-energy effects

Large-scale classical trajectory calculations have been performed to study the reaction Ar + CH4--> CH3 +H + Ar in the temperature range 2500 < or = T/K < or = 4500. The potential energy surface used for ArCH4 is the sum of the nonbonding pairwise potentials of Hase and collaborators (J. Chem. Phys. 2001, 114, 535) that models the intermolecular interaction and the CH4 intramolecular potential of Duchovic et al. (J. Phys. Chem. 1984, 88, 1339), which has been modified to account for the H-H repulsion at small bending angles. The thermal rate coefficient has been calculated, and the zero-point energy (ZPE) of the CH3 product molecule has been taken into account in the analysis of the results; also, two approaches have been applied for discarding predissociative trajectories. In both cases, good agreement is observed between the experimental and trajectory results after imposing the ZPE of CH3. The energy-transfer parameters have also been obtained from trajectory calculations and compared with available values estimated from experiment using the master equation formalism; in general, the agreement is good.     

Polarizable and flexible model for ethanol

A polarizable, flexible model for ethanol is obtained based on an extensive series of B3LYP/6-311++G(d,p) calculations and molecular dynamics simulations. The ethanol model includes electric-field dependence in both the atomic charges and the intramolecular degrees of freedom. Field-dependent intramolecular potentials have been attempted only once previously, for OH and HH stretches in water [P. Cicu et al., J. Chem. Phys. 112, 8267 (2000)]. The torsional potential involving the hydrogen-bonding hydrogen in ethanol is found to be particularly field sensitive. The methodology for developing field-dependent potentials can be readily generalized to other molecules and is discussed in detail. Molecular dynamics simulations of bulk ethanol are performed and the results are assessed based on comparisons with the self-diffusion coefficient [N. Karger et al., J. Chem. Phys. 93, 3437 (1990)], dielectric constant [J. T. Kindt and C. A. Schmuttenmaer, J. Phys. Chem. 100, 10373 (1996)], enthalpy of vaporization [R. C. Wilhoit and B. J. Zwolinski, J. Phys. Chem. Ref. Data, Suppl. 2, 2 (1973)], and experimental interatomic distributions [C. J. Benmore and Y. L. Loh, J. Chem. Phys. 112, 5877 (2000)]. The simultaneous variation of the atomic charges and the intramolecular potentials requires modified equations of motion and a multiple time step algorithm has been implemented to solve these equations. The article concludes with a discussion of the bulk structure and properties with an emphasis on the hydrogen bonding network.     

An ab initio investigation of the O(3P)-H2(1sigma(g)+) van der Waals well

We report an ab initio study of the van der Waals region of the O(3P)-H2 potential energy surface based on RCCSD(T) calculations with an aug-cc-pVQZ basis supplemented by bond functions. In addition, an open-shell implementation of symmetry-adapted perturbation theory (SAPT) is used to corroborate the RCCSD(T) calculations and to investigate the relative magnitudes of the various contributions to the van der Waals interaction. We also investigate the effect of the spin-orbit coupling on the position and depth of the van der Waals well. We predict the van der Waals minimum to occur in perpendicular geometry, and located at a closer distance than a secondary well in colinear geometry. The potentials obtained in the present study confirm the previous calculations of Alexander [M. H. Alexander, J. Chem. Phys., 1998, 108, 4467], but disagree with the earlier work of Harding and co-workers [Z. Li, V. A. Apkarian and L. B. Harding, J. Chem. Phys., 1997, 106, 942] as well as with recently refitted surfaces of Brand?o and coworkers [J. Brand?o, C. Mogo and B. C. Silva, J. Chem. Phys., 2004, 121, 8861]. Inclusion of spin-orbit coupling reduces the depth of the van der Waals minimum without causing a change in its position.     

Hybrid one-electron/many-electron methods for ionized states of molecular clusters

To describe singly-ionized states of molecular clusters we devised an effective Hamiltonian approach that combines (1) accurate monomer ionization potentials from many-electron wave functions with (2) polarization shifts and (3) effective monomer couplings obtained from a simple one-electron approach (the superposition-of-fragment-states (SFS) method [Valeev et al., J. Am. Chem. Soc., 2006, 128, 9882]). The accuracy of the intermolecular coupling parameters evaluated with SFS Hartree-Fock (HF) and Density-Functional-Theory (DFT) variants was evaluated for several weakly-bound dimers and compared against the state-of-the-art equation-of-motion ionization-potential coupled-cluster singles and doubles (EOM-IP-CCSD) data of Krylov and co-workers. The SFS-HF method produces coupling integrals accurate to a few percent, whereas SFS-DFT predictions are substantially worse. A hybrid approach combining SFS-HF couplings and shifts with EOM-IP-CCSD ionization potentials of monomers (denoted as SFS-EOM-IP-CCSD) was applied to ionized states of two conformers of a benzene dimer and ten representative DNA base pairs. The 16 considered SFS-EOM-IP-CCSD ionization potentials of the benzene dimer differed from the reference EOM-IP-CCSD IPs of Krylov and co-workers [Pieniazek et al., J. Chem. Phys. 2007, 127, 044317; Bravaya et al., Phys. Chem. Chem. Phys. 2010, 12, 2261] by less than 0.1 eV on average, and at most by 0.2 eV. For the DNA base pairs the mean absolute (median) deviation of the SFS-EOM-IP-CCSD IPs was 0.27 (0.23) eV; several deviations for non-Koopmans states were as large as 0.9 eV. The SFS-EOM-IP-CCSD method can be readily applied to large molecular clusters with computational effort scaling cubically with the size of the cluster.     

Unimolecular rovibrational bound and resonance states for large angular momentum: J=20 calculations for HO2

We explore the calculation of unimolecular bound states and resonances for deep-well species at large angular momentum using a Chebychev filter diagonalization scheme incorporating doubling of the autocorrelation function as presented recently by Neumaier and Mandelshtam [Phys. Rev. Lett. 86, 5031 (2001)]. The method has been employed to compute the challenging J=20 bound and resonance states for the HO2 system. The methodology has firstly been tested for J=2 in comparison with previous calculations, and then extended to J=20 using a parallel computing strategy. The quantum J-specific unimolecular dissociation rates for HO2-->H+O2 in the energy range from 2.114 to 2.596 eV have been reported for the first time, and comparisons with the results of Troe and co-workers [J. Chem. Phys. 113, 11019 (2000) Phys. Chem. Chem. Phys. 2, 631 (2000)] from statistical adiabatic channel method/classical trajectory calculations have been made. For most of the energies, the reported statistical adiabatic channel method/classical trajectory rate constants agree well with the average of the fluctuating quantum-mechanical rates. Near the dissociation threshold, quantum rates fluctuate more severely, but their average is still in agreement with the statistical adiabatic channel method/classical trajectory results.     

A global 12-dimensional ab initio potential energy surface and dynamical studies for the SiH4+H-->SiH3+H2 reaction

A global 12-dimensional ab initio interpolated potential energy surface (PES) for the SiH(4)+H-->SiH(3)+H(2) reaction is presented. The ab initio calculations are based on the unrestricted quadratic configuration interaction treatment with all single and double excitations together with the cc-pVTZ basis set, and the modified Shepard interpolation method of Collins and co-workers [K. C. Thompson et al., J. Chem. Phys. 108, 8302 (1998); M. A. Collins, Theor. Chem. Acc. 108, 313 (2002); R. P. A. Bettens and M. A. Collins, J. Chem. Phys. 111, 816 (1999)] is applied. Using this PES, classical trajectory and variational transition state theory calculations have been carried out, and the computed rate constants are in good agreement with the available experimental data.     

Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations

The generalized Crooks theorem (GCT) for deterministic non-Hamiltonian molecular dynamics simulations [Phys. Rev. E 75, 050101 (2007)] connects the probabilities of nonequilibrium realizations switching the system between two thermodynamic states, to the partition functions of these states. In comparison to the "classical" Crooks nonequilibrium work theorem [J. Stat. Phys. 90, 1481 (1998)], which deals with realizations involving only mechanical work, the GCT also accounts for additional work resulting from changes of the intensive and extensive thermodynamic variables of the system. In this article we present a numerical verification of the GCT using a Lennard-Jones fluid model where two particles are subject to a time-dependent external potential. Moreover, in order to switch the system between different thermodynamic states, the temperature and the pressure (or volume), which are controlled through the Martyna-Tobias-Klein equations of motion [J. Chem. Phys. 101, 4177 (1994)], are also varied externally. The free energy difference between states characterized by different distances of the target particles is evaluated using both a standard methodology (pair radial distribution functions) and the GCT. In order to exploit the various options provided by the GCT approach, i.e., the possibility of temperature/pressure/volume changes during the realizations, the free energy difference is recovered via arbitrary thermodynamic cycles. In all tests, the GCT is quantitatively verified.     

Local response dispersion method. II. Generalized multicenter interactions

Recently introduced local response dispersion method [T. Sato and H. Nakai, J. Chem. Phys. 131, 224104 (2009)], which is a first-principles alternative to empirical dispersion corrections in density functional theory, is implemented with generalized multicenter interactions involving both atomic and atomic pair polarizabilities. The generalization improves the asymptote of intermolecular interactions, reducing the mean absolute percentage error from about 30% to 6% in the molecular C(6) coefficients of more than 1000 dimers, compared to experimental values. The method is also applied to calculations of potential energy curves of molecules in the S22 database [P. Jure?ka et al., Phys. Chem. Chem. Phys. 8, 1985 (2006)]. The calculated potential energy curves are in a good agreement with reliable benchmarks recently published by Molnar et al. [J. Chem. Phys. 131, 065102 (2009)]. These improvements are achieved at the price of increasing complexity in the implementation, but without losing the computational efficiency of the previous two-center (atom-atom) formulation. A set of different truncations of two-center and three- or four-center interactions is shown to be optimal in the cost-performance balance.     

Homogeneous nucleation and growth in supersaturated zinc vapor investigated by molecular dynamics simulation

Homogeneous nucleation and growth of zinc from supersaturated vapor are investigated by nonequilibrium molecular dynamics simulations in the temperature range from 400 to 800 K and for a supersaturation ranging from log S=2 to 11. Argon is added to the vapor phase as carrier gas to remove the latent heat from the forming zinc clusters. A new parametrization of the embedded atom method for zinc is employed for the interaction potential model. The simulation data are analyzed with respect to the nucleation rates and the critical cluster sizes by two different methods, namely, the threshold method of Yasuoka and Matsumoto [J. Chem. Phys. 109, 8451 (1998)] and the mean first passage time method for nucleation by Wedekind et al. [J. Chem. Phys. 126, 134103 (2007)]. The nucleation rates obtained by these methods differ approximately by one order of magnitude. Classical nucleation theory fails to describe the simulation data as well as the experimental data. The size of the critical cluster obtained by the mean first passage time method is significantly larger than that obtained from the nucleation theorem.     

Coherent vibrational energy transfer along a peptide helix

To measure the transport of vibrational energy along a peptide helix, Hamm and co-workers [J. Phys. Chem. B 112, 9091 (2008)] performed time-resolved vibrational experiments, which showed that the energy transport rate increases by at least a factor of 4, when a localized C=O mode of the peptide instead of an attached chromophore is excited. This finding raises the question if coherent excitonic energy transfer between the C=O modes may be of importance for the overall energy transport in peptides. With this idea in mind, nonequilibrium molecular dynamics simulations as well as quantum-classical calculations are performed, which qualitatively reproduce the experimental findings. Moreover, the latter model (an exciton Hamiltonian whose matrix elements depend on the instantaneous positions of the peptide and solvent atoms) indeed exhibits the signatures of coherent quantum energy transport, at least within the first few picoseconds and at low temperatures. The origin of the observed decoherence, the absence of vibrational self-trapping, and the possibility of quantum interference between various transport paths are discussed in some detail.     

Statistical mechanical theory for steady state systems. VI. Variational principles

Several variational principles that have been proposed for nonequilibrium systems are analyzed. These include the principle of minimum rate of entropy production due to Prigogine [Introduction to Thermodynamics of Irreversible Processes (Interscience, New York, 1967)], the principle of maximum rate of entropy production, which is common on the internet and in the natural sciences, two principles of minimum dissipation due to Onsager [Phys. Rev. 37, 405 (1931)] and to Onsager and Machlup [Phys. Rev. 91, 1505 (1953)], and the principle of maximum second entropy due to Attard [J. Chem.. Phys. 122, 154101 (2005); Phys. Chem. Chem. Phys. 8, 3585 (2006)]. The approaches of Onsager and Attard are argued to be the only viable theories. These two are related, although their physical interpretation and mathematical approximations differ. A numerical comparison with computer simulation results indicates that Attard's expression is the only accurate theory. The implications for the Langevin and other stochastic differential equations are discussed.     

Argon nucleation in a cryogenic nucleation pulse chamber

Homogeneous nucleation of argon droplets has been measured with a newly designed cryogenic nucleation pulse chamber presented already in a previous paper [Fladerer and Strey, J. Chem. Phys. 124, 16 (2006)]. Here we present the first systematic nucleation onset data for argon measured in a temperature range from 42 to 58 K and for vapor pressures from 0.3 to 10 kPa. For these data we provide an analytical fit function. From the geometry of the optical detection system and the time of nucleation the experimental nucleation-rate range can be estimated. This allows a comparison of the data with the predictions of classical nucleation theory. We found 16-26 orders of magnitude difference between theory and experiment, and a too strong theoretical dependence of the nucleation rate on temperature. A comparison with the self-consistent theory of Girshick and Chiu [J. Chem. Phys. 93, 1273 (1990)] showed improved temperature dependence but still discrepancies of 11-17 orders of magnitude compared to experimental data. The thermodynamically consistent theory of Kashchiev [J. Chem. Phys. 118, 1837 (2003)] was found to agree rather well with experiment in respect to the temperature dependence and to predict rates about 5-7 orders of magnitude below the experimental ones. With the help of the Gibbs-Thomson equation we were able to evaluate the size of the critical nucleus to be 40-80 argon atoms.