Liquid-liquid extraction: A graphical method for equilibrium stage calculations for quaternary systems

Ruiz Beviá, F., Prats Rico, D. and Marcilla Gomis, A.F., 1984. Liquid-liquid extraction: a graphical method for equilibrium stage calculations for quaternary systems. Fluid Phase Equilibria, 15: 257-265.A very simple graphical method for stage calculations has been developed for quaternary systems. The calculation method is based on the equilibrium representation method proposed by Ruiz and Prats (1983a), and requires only two graphs for solution of the material balances. The method is based completely on experimental data and does not require any simplifying hypotheses.     

A classical dynamics method for H2 diffraction from metal surfaces

We present a discretization method that allows one to interpret measurements on diffraction of diatomic molecules from solid surfaces using six-dimensional (6D) classical trajectory calculations. It has been applied to the D2NiAl(110) and H2Pd(111) systems (which are models for activated and nonactivated dissociative chemisorption, respectively) using realistic potential energy surfaces obtained from first principles. Comparisons with experimental results and 6D quantum dynamical calculations show that, in general, the method is able to predict the relative intensity of the most important diffraction peaks. We therefore conclude that classical mechanics can be an efficient guide for experimentalists in the search for the most significant diffraction channels.     

Dimensional scaling treatment with relativistic corrections for stable multiply charged atomic ions in high-frequency super-intense laser fields

We present a theoretical framework which describes multiply charged atomic ions, their stability within super-intense laser fields, and also lay corrections to the systems due to relativistic effects. Dimensional scaling calculations with relativistic corrections for systems: H, H(-), H(2 -), He, He(-), He(2 -), He(3 -) within super-intense laser fields were completed. Also completed were three-dimensional self consistent field calculations to verify the dimensionally scaled quantities. With the aforementioned methods the system's ability to stably bind "additional" electrons through the development of multiple isolated regions of high potential energy leading to nodes of high electron density is shown. These nodes are spaced far enough from each other to minimize the electronic repulsion of the electrons, while still providing adequate enough attraction so as to bind the excess electrons into orbitals. We have found that even with relativistic considerations these species are stably bound within the field. It was also found that performing the dimensional scaling calculations for systems within the confines of laser fields to be a much simpler and more cost-effective method than the supporting D = 3 SCF method. The dimensional scaling method is general and can be extended to include relativistic corrections to describe the stability of simple molecular systems in super-intense laser fields.     

The three-dimensional nonadiabatic dynamics calculation of DH(2)(+) and HD(2)(+) systems by using the trajectory surface hopping method based on the Zhu-Nakamura theory

A theoretical investigation on the nonadiabatic processes of the full three-dimensional D(+)+H(2) and H(+)+D(2) reaction systems has been performed by using trajectory surface hopping (TSH) method based on the Zhu-Nakamura (ZN) theory. This ZN-TSH method refers to not only classically allowed hops but also classically forbidden hops. The potential energy surface constructed by Kamisaka et al. is employed in the calculation. A new iterative method is proposed to yield the two-dimensional seam surface from the topography of the adiabatic potential surfaces, in which the inconvenience of directly solving the first-order partial differential equation is avoided. The cross sections of these two systems are calculated for three competing channels of the reactive charge transfer, the nonreactive charge transfer, and the reactive noncharge transfer, for ground rovibrational state of H(2) or D(2). Also, this study provides reaction probabilities of these three processes for the total angular momentum J=0 and ground initial vibrational state of H(2) or D(2). The calculated results from ZN-TSH method are in good agreement with the exact quantum calculations and the experimental measurements.     

A study of simplified molecular models in phase equilibrium prediction

Monfort, J.P. and Rojas R., M.D.L., 1978. A study of simplified molecular models in phase equilibrium prediction. Fluid Phase Equilibria, 2: 181–198.The accuracy of three molecular models of solution (Wilson, UNIQUAC and NRTL) is tested for 34 binary systems and 9 ternary systems. The aim of this paper is to attempt some evaluation of these models. Vapor-liquid calculations show a slight superiority of the UNIQUAC equation in the representation of experimental data, while liquid-liquid calculations using a method of determination of binary energetic parameters from mutual solubility data show a better prediction with the NRTL equation.     

Decomposing total IR spectra of aqueous systems into solute and solvent contributions: a computational approach using maximally localized Wannier orbitals

The theoretical principles underpinning the calculation of infrared spectra for condensed-phase systems in the context of ab initio molecular dynamics have been recently developed in literature. At present, most ab initio molecular dynamics calculations are restricted to relatively small systems and short simulation times. In this paper we devise a method that allows well-converged results for infrared spectra from ab initio molecular dynamics simulations using small systems and short trajectories characteristic of simulations typically performed in practice. We demonstrate the utility of our approach by computing the imaginary part of the dielectric constant epsilon"(omega) for H2O and D2O in solid and liquid phases and show that it compares well with experimental data. We further demonstrate that maximally localized Wannier orbitals can be used to separate the individual contributions of different molecular species to the linear spectrum of complex systems. The new spectral decomposition method is shown to be useful in present-day ab initio molecular dynamics calculations to compute the magnitude of the "continuous absorption" generated by excess protons in aqueous solutions with good accuracy even when other species present in the solutions absorb strongly in the same frequency window.     

Molecular simulation of the reversible mechanical unfolding of proteins

In this work we have combined a Wang-Landau sampling scheme [F. Wang and D. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with an expanded ensemble formalism to yield a simple and powerful method for computing potentials of mean force. The new method is implemented to investigate the mechanical deformation of proteins. Comparisons are made with analytical results for simple model systems such as harmonic springs and Rouse chains. The method is then illustrated on a model 15-residue alanine molecule in an implicit solvent. Results for mechanical unfolding of this oligopeptide are compared to those of steered molecular dynamics calculations.     

Understanding the Photocatalytic Properties of Pt/CeOx/TiO2: Structural Effects on Electronic and Optical Properties

Ceria-titania interfaces play a crucial role in different chemical processes but are especially promising for the photocatalytic splitting of water using light in the visible wavelength region when Pt is added to the system. However, the complexity of this hierarchical structure hampers the study of the origin of its outstanding properties. In this article, the structural, electronic and optoelectronic properties of CeO₂/TiO₂ systems containing 1D, 2D, and 3D particles of ceria are analyzed by means of density functional calculations. Adsorption sites and vacancy effects have been studied to model Pt adsorption. Density of states calculations and absorption spectra simulations explain the behavior of these systems. Finally, these models are used for the screening of other metals that can be combined with this heterostructure to potentially find more efficient water splitting photocatalysts.     

Crystallographic and Dynamic Aspects of Solid‐State NMR Calibration Compounds: Towards ab Initio NMR Crystallography

The excellent results of dispersion‐corrected density functional theory (DFT‐D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT‐D calculations is a target, especially for the field of molecular NMR crystallography. Four ¹³C ss‐NMR calibration compounds are investigated by single‐crystal X‐ray diffraction, molecular dynamics and DFT‐D calculations. The crystal structure of 3‐methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated ¹³C chemical shifts of these compounds are in excellent agreement with experiment, with a root‐mean‐square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT‐D chemical shift calculation improves the accuracy of calculated chemical shifts.     

Monge-Ampere grids and the multidimensional mapped Fourier method

The efficiency of a numerical method can be greatly improved by combining it with coordinate transformations tailored to a given problem. This is the basis for the mapped Fourier methods. However, obtaining "good" coordinate transformations is a major obstacle for this approach in multidimensions. Here, we calculate coordinate transformations based on solving the Monge-Ampere equation. These transformations are combined in the mapped Fourier method and applied to Schrodinger's equation in multidimensions. Dramatic improvements in accuracy compared to the standard Fourier method were observed in eigenvalue calculations for two-dimensional systems. This work indicates that the Monge-Ampere equation may serve as a useful tool for constructing efficient representations for problems in computational quantum mechanics and other fields.     

Overtone spectroscopy of H2D+ and D2H+ using laser induced reactions

The method of laser induced reaction is used to obtain high-resolution IR spectra of H2D+ and D2H+ in collision with n-H2 at a nominal temperature of 17 K. For this purpose three cw-laser systems have been coupled to a 22-pole ion trap apparatus, two commercial diode laser systems in the ranges of 6100-6600 cm(-1) and 6760-7300 cm(-1), respectively, and a high-power optical parametric oscillator tunable in the range of 2600-3200 cm(-1). In total, 27 new overtone and combination transitions have been detected for H2D+ and D2H+, as well as a weak line in the nu1 vibrational band of H2D+ (2(20)<--1(01)) at 3164.118 cm(-1). The line positions are compared to high accuracy ab initio calculations, showing small but mode-dependent differences, being largest for three vibrational quanta in the nu2 symmetric bending of H2D+. Within the experimental accuracy, the relative values of the ab initio predicted Einstein B coefficients are confirmed.     

A full-dimensional coupled-surface study of the photodissociation dynamics of ammonia using the multiconfiguration time-dependent Hartree method

Full-dimensional quantum mechanical computations are carried out to investigate the photodissociation dynamics of A? state NH(3) and ND(3) using the multiconfiguration time-dependent Hartree (MCTDH) method with recently developed coupled ab initio potential energy surfaces (PESs) [Z. H. Li, R. Valero, and D. G. Truhlar, Theor. Chim. Acc. 118, 9 (2007)]. To use the MCTDH method efficiently the PESs are represented as based on the high-dimensional model representation. The A? ← X? absorption spectra for both isotopomers were calculated for the zeroth vibrational state of the ground electronic state. With a view to treating larger systems, Jacobi coordinates are used. Computations on the coupled PES are carried out for two-, three-, five-, and six-dimensional model systems to understand the validity of reduced-dimensional calculations. In addition to the fully coupled calculations, the effect of nonadiabatic coupling on absorption spectra is shown by propagating the initial wavepacket only in the A? electronic state. The calculated absorption spectra are shown to be in good agreement with available theoretical and experimental observations. Comparisons with calculations using Radau and valence coordinates show the effect of including the symmetry of the system explicitly. Finally, branching ratios for loss of a hydrogen atom via the two available channels are calculated. These predict that the nonadiabatic product increases with the dimension of the calculations and confirm the importance of the full-dimensional calculations.     

Effect of Coriolis coupling in chemical reaction dynamics

It is essential to evaluate the role of Coriolis coupling effect in molecular reaction dynamics. Here we consider Coriolis coupling effect in quantum reactive scattering calculations in the context of both adiabaticity and nonadiabaticity, with particular emphasis on examining the role of Coriolis coupling effect in reaction dynamics of triatomic molecular systems. We present the results of our own calculations by the time-dependent quantum wave packet approach for H + D2 and F(2P3/2,2P1/2) + H2 as well as for the ion-molecule collisions of He + H2 +, D(-) + H2, H(-) + D2, and D+ + H2, after reviewing in detail other related research efforts on this issue.     

Quantum chemistry in solution by combining 3D integral equation theory with a cluster embedding approach

Free energy changes associated with chemical reactions in solution are treated by integral equation theory in the form of the 3D reference interaction site model (RISM) in combination with quantum-chemical calculations via an embedded cluster approach (EC-RISM). The electronic structure of the solute is computed self-consistently with the solvent structure by mapping the charge distribution of the solvent onto a set of discrete background point charges that are added to the molecular Hamiltonian. The EC-RISM procedure yields chemical accuracy in free energy predictions for several benchmark systems without adjusting empirical parameters. We apply the method to the standard reaction free energy for the gauche-trans equilibrium of 1,2-dichloroethane in water and to pKa shift calculations for trifluoroacetic acid/acetic acid and 4-nitroaniline/aniline in water.     

Efficiency and accuracy of the elongation method as applied to the electronic structures of large systems

Current state of development of the elongation method originally proposed by Imamura is presented. Recent progress in methodology, including geometry optimization and employment of the fast multiple method, is highlighted. The accuracy and efficiency of the elongation method as compared to exact canonical Hartree-Fock and Kohn-Sham approaches are discussed. Potential applications are illustrated by wide range of calculations for model systems. The elongation calculations are demonstrated to be much more efficient compared to the conventional ones with high accuracy maintained. The elongation CPU time is shown by the model calculations as linear or sub-linear scaling for quasi-one-dimensional systems. Future work of development into post-Hartree-Fock methodologies are pointed out.     

Fully optimized implementation of the cluster-in-molecule local correlation approach for electron correlation calculations of large systems

A fully optimized implementation of the cluster-in-molecule (CIM) local correlation method for faster and more accurate electron correlation calculations of large systems is reported. The speedup comes from the new procedure of constructing virtual localized molecular orbitals of clusters. In the new procedure, Boughton–Pulay projection method is employed instead of a much more expensive Boys localization procedure. In addition, basis set superposition error correction for binding energy calculations and parallelized electron correlation calculations of clusters are now implemented. Benchmark calculations and illustrative applications at the Møller–Plesset perturbation theory, coupled cluster singles and doubles (CCSD), and CCSD with perturbative triples correction levels show that this newly optimized CIM approach is a reliable theoretical tool for electron correlation calculations of various large chemical systems. © 2018 Wiley Periodicals, Inc.     

Theoretical characterization of intermolecular vibrational states through the multi-configuration time dependent Hartree approach: the He2,3ICl clusters

Benchmark, full-dimensional calculations on the ground and excited vibrational states for the tetra-, and penta-atomic weakly bound He(2,3)ICl complexes are reported. The representation of the potential energy surfaces includes three-body HeICl potentials parameterized to coupled-cluster singles, doubles, and perturbative triples ab initio data. These terms are important in accurately describing the interactions of such highly floppy systems. The corresponding 6D/9D computations are performed with the multi-configuration time dependent Hartree method, using natural potential fits, and a mode combination scheme to optimize the computational effort in the improved relaxation calculations. For these complexes several low-lying vibrational states are computed, and their binding energies and radial/angular probability density distributions are obtained. We found various isomers which are assigned to different structural models related with combinations of the triatomic isomers, like linear, T-shaped, and antilinear ones. Comparison of these results with recent experimental data is presented, and the quantitative deviations found with respect to the experiment are discussed.     

Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling

Potential of mean force (PMF) calculations provide a reliable method for determination of the absolute binding free energies for protein-ligand systems. The common method used for this purpose -- umbrella sampling with weighted histogram analysis -- is computationally very laborious, which limits its applications. Recently, a much simpler alternative for PMF calculations has become available, namely, using Jarzynski's equality in steered molecular dynamics simulations. So far, there have been a few comparisons of the two methods and mostly in simple systems that do not reflect the complexities of protein-ligand systems. Here, we use both methods to calculate the PMF for ion permeation and ligand binding to ion channels. Comparison of results indicate that Jarzynski's method suffers from relaxation problems in complex systems and would require much longer simulation times to yield reliable PMFs for protein-ligand systems.     

PBFC-PI量子动力学方法及应用

对多原子体系的量子动力学计算非常重要, 然而, 对含六原子以上的分子体系进行精确量子动力学计算仍具挑战性. 面向过程的基函数定制(PBFC)-并行迭代(PI)方法是一种高效的量子动力学方法, 已应用于对含九原子的丙二醛异构体系的氢迁移速率的精确量子计算. 本综述首先阐明了PBFC的基本思想, 之后重点回顾了PBFC-PI方法的具体内容、 该方法与其它方法的结合及其应用方面的新进展. 应用这些方法实现了对单氢迁移、 协同双氢迁移和分步双氢迁移3种类型基准体系的大规模并行计算, 有助于获得对氢迁移过程的新认识.