Highly accurate potential-energy and dipole moment surfaces for vibrational state calculations of methane

Full-dimensional ab initio potential-energy surface (PES) and dipole moment surface are constructed for a methane molecule at the CCSD(T)/cc-pVTZ and MP2/cc-pVTZ levels of theory, respectively, by the modified Shepard interpolation method based on the fourth-order Taylor expansion [MSI(4th)]. The reference points for the interpolation have been set in the coupling region of CH symmetric and antisymmetric stretching modes so as to reproduce the vibrational energy levels related to CH stretching vibrations. The vibrational configuration-interaction calculations have been performed to obtain the energy levels and the absorption intensities up to 9000 cm(-1) with the use of MSI(4th)-PES. The calculated fundamental frequencies and low-lying vibrational energy levels show that MSI(4th) is superior to the widely employed quartic force field, giving a better agreement with the experimental values. The absorption bands of overtones as well as combination bands, which are caused by purely anharmonic effects, have been obtained up to 9000 cm(-1). Strongly coupled states with visible intensity have been found in the 6500-9000 cm(-1) region where the experimental data are still lacking.     

Multi-reference-state perturbation theory for computation of potential-energy surfaces

The implementation of multi-reference-state Rayleigh-Schrödinger perturbation theory for the evaluation of potential-energy surfaces is reviewed. The organization of the computation and the basic algorithms are outlined. A major difficulty is the quadratic increase in computing sources as the reference space is expanded. Truncating the space of nonreference determinants is suggested as a solution for the problem. The method applies a numerical cutoff criterion for the weights of the first-order wave function. The truncation reduces the computing time significantly with negligible sacrifice in the quality of the results.This paper was presented at the international conference on The Impact of Supercomputers on Chemistry, held at the University of London, London, UK, 13–16 April 1987     

F+OH reactive collisions on new excited 3A" and 3A' potential-energy surfaces

Global three-dimensional adiabatic potential-energy surfaces for the excited 2(3)A" and 1(3)A' triplet states of OHF are obtained to study the F(2P)+OH(2pi)-->O(3P)+HF(1sigma+) reaction. Highly accurate ab initio calculations are obtained for the two excited electronic states and fitted to analytical functions with small deviations. The reaction dynamics is studied using a wave-packet treatment within a centrifugal sudden approach, which is justified by the linear transition state of the two electronic states studied. The reaction efficiency presents a marked preference for perpendicular orientation of the initial relative velocity vector and the angular momentum of the OH reagent, consistent in the body-fixed frame used with an initial collinear geometry which facilitates the access to the transition state. It is also found that the reaction cross section presents a rather high threshold so that, in an adiabatic picture, the two excited triplet states do not contribute to the rate constant at room temperature. Thus, only the lowest triplet state leads to reaction under these conditions and the simulated rate constants are too low as compared with the experimental ones. Such disagreement is likely to be due to nonadiabatic transitions occurring at the conical intersections near the transition state for this reaction.     

Ab initio potential-energy surfaces for complex, multichannel systems using modified novelty sampling and feedforward neural networks

A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.     

A new diabatic molecular representation for triplet-triplet transitions in He+-He collisions

A “frozen-orbital” diabatic basis has been constructed for an impact parameter treatment of collisions of He⁺ with metastable He(2³S) at 1000 eV laboratory ion energy. Except for the two highest states used, the diabatic states correlate very well with the separated-atom energies, and the Σ-Π rotational couplings deviate little from the proper asymptotic behaviour (≈R^?2). Cross sections and transition probabilities are presented for some elastic and inelastic channels.     

A new ab initio potential energy surface for the NeCO complex with the vibrational coordinate dependence

A new high quality three-dimensional potential energy surface for the Ne-CO van der Waals complex is developed using the CCSD(T) method and avqz∕avqz+33221 basis set. The ab initio calculation is performed in a total of 1365 configurations with supermolecule method. There is a single global minimum located in a nearly T-shaped geometry. The global minimum energy is -49.4090 cm(-1) at R(e)=6.40a(0) and θ(e)=82.5(°) for V(00). Using the three-dimensional potential energy surface, we have calculated bound rovibrational energy levels up to J = 10 including the Coriolis coupling terms. Compared with the experimental transition frequencies, the theoretical results are in good agreement with the experimental results.     

A fast and accurate algorithm for QTAIM integration in solids

A new algorithm is presented for the calculation of atomic properties, in the sense of the quantum theory of atoms in molecules. This new method, named QTREE , applies to solid‐state densities and allows the computation of the atomic properties of all the atoms in the crystal in seconds to minutes. The basis of the method is the recursive subdivision of a symmetry‐reduced wedge of the Wigner‐Seitz cell, which in turn is expressed as a union of tetrahedra, plus the use of β‐spheres to improve the performance. A considerable speedup is thus achieved compared with traditional quadrature‐based schemes, justified by the poor performance of the latter because of the particular features of atomic basins in solids. QTREE can use both analytical or interpolated densities, calculates all the atomic properties available, and converges to the correct values in the limit of infinite precision. Several gradient path tracing and integration techniques are tested. Basin volumes and charges for a selected set of 11 crystals are determined as a test of the new method. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

A configuration-interaction-oriented implementation of the complex coordinate method

An implementation of the complex coordinate method is demonstrated that exploits a new technique for obtaining the matrix representation of the complex dilated Hamiltonian. The purpose is to make the complex coordinate method applicable together with standard numerical ab initio codes designed for large-scale calculations on many-electron atoms and/or molecules. No complex intergrals have to be calculated, and no changes of the standard codes are required even in the common case where the kinetic and potential energy components are not stored separately. Instead, two standard (real) CI calculations are used to generate the dilated (complex) CI matrix representation. The performance of the procedure is demonstrated in the context of the GAMESS program and applied to obtain the resonant structure of the Bethe surface pertinent to the absorption spectrum of the helium atom. © 1993 John Wiley & Sons, Inc.     

Electronic energy-transfer rate constants for geometrical isomers of a bichromophoric macrocyclic complex

The rate of electronic energy transfer (EET) between a naphthalene donor and an anthracene acceptor in [ZnL(3)](ClO(4))(2) and [ZnL(4)](ClO(4))(2) was determined by time-resolved fluorescence measurements, where L(3) and L(4) are the geometrical isomers of 6-[(anthracen-9-ylmethyl)amino]-trans-6,13-dimethyl-1,4,8,11-tetraazacyclotetradecane-13-amine (L(2)), substituted with either a naphthalen-1-ylmethyl or naphthalen-2-ylmethyl donor, respectively. The energy-transfer rate constant, k(EET), was determined to be (0.92 +/- 0.02) x 10(9) s(-1) for the naphthalen-1-ylmethyl-substituted isomer, while that for the naphthalen-2-ylmethyl-substituted isomer is somewhat faster, with k(EET) = (1.31 +/- 0.01) x 10(9) s(-1). The solid-state structure of [ZnL(3)Cl]ClO(4) has been determined, and using molecular modeling calculations, the likely distributions of solution conformations in CH(3)CN have been evaluated for both complexes. The calculated conformational distributions in the common trans-III N-based isomeric form gave F?rster EET rate constants that account for the differences observed and are in excellent agreement with the experimental values. It is shown that the full range of conformers must be considered to accurately reproduce the observed EET kinetics.     

A new method for predicting conduction anesthesia

A new method for predicting conduction anesthesia has been suggested. The method is based on calculation of theP matrix probabilities of interatomic contacts for each molecule of the compounds considered. TheP matrix enables one to evaluate the main tendencies of atoms and atomic groups to interact in biochemical sorption on the nerve fiber surface. The minimum effective concentrations calculated for 25 compounds are in good agreement with the experimental data. The correlation coefficient between the experimental and calculated values is 0.98 when the standard deviation is 0.1 mmol L⁻¹. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1781–1784, October, 1997.     

A theoretical characterization of the photoisomerization channels of 1,2-cyclononadienes on both singlet and triplet potential-energy surfaces

The ground-, (1)(pipi*)-, and (3)(pipi*)-state potential-energy surfaces of 1,2-cyclononadiene and isomeric C(9)H(14) species, as well as 1-methyl-1,2-cyclononadiene and isomeric C(10)H(16) species were all mapped using CASSCF and the 6-31G(d) basis set. Theoretical results were found to be in good agreement with the available experimental observations for both 1,2-cyclononadiene and 1-methyl-1,2-cyclononadiene isomerization reactions under singlet and triplet direct or sensitized irradiation. Extremely efficient decay occurs from the first singlet excited state to the ground state through at least three different conical intersections (surface crossings). The first of these crossing points is accessed by a one-bond ring closure. From this conical intersection point (CI-A or CI-C), some possible subsequent ground-state reaction paths have been identified: 1) intramolecular C--H bond insertion to form the bicyclic photoproduct and 2) intramolecular C--H bond insertion to form tricyclic photoproducts. An excited state [1,3]-sigmatropic shift leads to the second conical intersection (CI-B or CI-E), which can give a three-bond cyclononyne species. Besides these, in the singlet photochemical reactions of 1-methyl-1,2-cyclononadiene, excited-state, one allenic C--H bond insertion leads to a third conical intersection (CI-D). Possible ground-state reaction pathways from this structure lead to the formation of a diene photoproduct or to transannular insertion photoproducts. Moreover, in the case of triplet 1,2-cyclononadiene and 1-methyl-1,2-cyclononadiene photoisomerization reactions, both chemical reactions will adopt a 1,3-biradical (T(1)/S(0)-1, T(1)/S(0)-2, and T(1)/S(0)-3), which may undergo intersystem crossings leading to the formation of tricyclic or bicyclic photoproducts. The results obtained allow a number of predictions to be made.     

Ir-laser-induced changes in the uv absorption spectrum of ozone. A new technique for vibrational energy-transfer studies

Gaseous ozone has been vibrationally excited using single pulses from an 1R laser operating on the 9.5 μm band ofCO₂· and transient changes in UV absorption in the region of the Hartley continuum have been observed. These changes have been temporally resolved at 310 nm in pure O₃ and in binary mixures of O₃ with He· Ar, Xe, H₂· N₂· O₂, CO₂ and SF₆, and rate constants for the decay of transient absorption obtained. These rate constants are compared with those measured for deactivation of vibrationally cxcited O₃ using IR excited fluorescence and IR-enhanced reaction techniques.     

Interpolating moving least-squares methods for fitting potential-energy surfaces: further improvement of efficiency via cutoff strategies

In standard applications of interpolating moving least squares (IMLS) for fitting a potential-energy surface (PES), all available ab initio points are used. Because remote ab initio points negligibly influence IMLS accuracy and increase IMLS time-to-solution, we present two methods to locally restrict the number of points included in a particular fit. The fixed radius cutoff (FRC) method includes ab initio points within a hypersphere of fixed radius. The density adaptive cutoff (DAC) method includes points within a hypersphere of variable radius depending on the point density. We test these methods by fitting a six-dimensional analytical PES for hydrogen peroxide. Both methods reduce the IMLS time-to-solution by about an order of magnitude relative to that when no cutoff method is used. The DAC method is more robust and efficient than the FRC method.     

Fast and accurate methods for predicting short-range constraints in protein models

Protein modeling tools utilize many kinds of structural information that may be predicted from amino acid sequence of a target protein or obtained from experiments. Such data provide geometrical constraints in a modeling process. The main aim is to generate the best possible consensus structure. The quality of models strictly depends on the imposed conditions. In this work we present an algorithm, which predicts short-range distances between Cα atoms as well as a set of short structural fragments that possibly share structural similarity with a query sequence. The only input of the method is a query sequence profile. The algorithm searches for short protein fragments with high sequence similarity. As a result a statistics of distances observed in the similar fragments is returned. The method can be used also as a scoring function or a short-range knowledge-based potential based on the computed statistics.     

Ab initio calculations and vibrational energy level fits for the lower singlet potential-energy surfaces of C3

Ab initio multireference configuration interaction potential energy surfaces are computed for the eight lowest singlet surfaces of C(3). These reveal several important features, including several conical intersections in linear, nonlinear, and equilateral triangle geometries. These intersections are important because, particularly for the excited A (1)Pi(u) state, reasonable ab initio results could only be obtained by including nearby, near degenerate, (1)Sigma(u) (-) and (1)Delta(u) states that cross the A (1)Pi(u) state around 4500 cm(-1) above the equilibrium geometry, and a (1)Pi(g) state whose potential in turn crosses the other states about 2000 cm(-1) further up. These states are probably responsible for the complexity of the shorter wavelength UV absorption spectrum of C(3). The computed potential energy surface for the ground, X (1)Sigma(g) (+), state and for the lowest two excited singlet surfaces (which both correlate with the A (1)Pi(u) state in a collinear geometry) are fitted to analytic functional forms. Vibrational energy levels are calculated for both states, taking account of the Renner-Teller coupling in the excited A (1)Pi(u) state. The potential parameters for both states are then least-squares fitted to experimental data. The ground-state fit covers a range of approximately 8500 cm(-1) above the lowest level, and reproduces 100 observed vibrational levels with an average error of 2.8 cm(-1). The A (1)Pi(u) state surfaces cover a range of 3250 cm(-1) above the zero-point level, and reproduce the 44 observed levels in this range with an average error of 2.8 cm(-1).     

Temperature dependence of the ligand field strength in systems with modulated potential-energy surfaces. A suggestion for interpreting spectroscopic properties of metalloproteins

The structural and spectroscopic properties of physical systems having different potential-energy wells are strongly affected by temperature where energy barriers are comparable to the thermal energy. A theoretical analysis has been performed using an asymmetric double-well potential and, on the basis of the results obtained, an interpretation of the temperature-dependent properties of some real systems, such as the active sites in copper proteins, is proposed.     

Pendant bubble method for an accurate characterization of superhydrophobic surfaces

The commonly used sessile drop method for measuring contact angles and surface tension suffers from errors on superhydrophobic surfaces. This occurs from unavoidable experimental error in determining the vertical location of the liquid-solid-vapor interface due to a camera's finite pixel resolution, thereby necessitating the development and application of subpixel algorithms. We demonstrate here the advantage of a pendant bubble in decreasing the resulting error prior to the application of additional algorithms. For sessile drops to attain an equivalent accuracy, the pixel count would have to be increased by 2 orders of magnitude.     

Direct calculation of coupled diabatic potential-energy surfaces for ammonia and mapping of a four-dimensional conical intersection seam

We used multiconfiguration quasidegenerate perturbation theory and the fourfold-way direct diabatization scheme to calculate ab initio potential-energy surfaces at 3600 nuclear geometries of NH3. The calculations yield the adiabatic and diabatic potential-energy surfaces for the ground and first electronically excited singlet states and also the diabatic coupling surfaces. The diabatic surfaces and coupling were fitted analytically to functional forms to obtain a permutationally invariant 2 x 2 diabatic potential-energy matrix. An analytic representation of the adiabatic potential-energy surfaces is then obtained by diagonalizing the diabatic potential-energy matrix. The analytic representation of the surfaces gives an analytic representation of the four-dimensional conical intersection seam which is discussed in detail.     

A new method of accurate pKb determinations for some organic amines

The accurate pK_b determinations for some amines have been investigated using the combination of the extended clusters‐continuum model with the polarizable continuum solvation model. The formation of molecular clusters by means of the amines wrapped up with water molecules leads to the weakness of the mutual function between the polar solvents and the amines, and, hence, the accuracy of pK_b has been enhanced by using a coherent and well‐defined approach without external approximations or experimental data. The calculations are performed at the HF/6‐311++G(d, p) level and agreed well with experimental data because electron correlation effect cancels mutually in the calculated value of ΔG which is not an absolute value, but a relative value. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008