Dynamics of the concerted triple proton transfer in cyclic water trimer using the multiconfiguration molecular mechanics algorithm

Cyclic water clusters are important molecular species to understand the nature of hydrogen bonded networks. Theoretical studies for the dynamics of triple proton transfer in the cyclic water trimer were performed. The potential energy surface (PES) of triple proton transfer is generated by the multiconfiguration molecular mechanics (MCMM) algorithm. We have used the MP2/6-31G(d,p) level for high-level ab initio data (energies, gradients, and Hessians), which are used in the Shepard interpolation. Eight high-level reference points were added step by step, including two points for the critical configurations of the large curvature tunneling paths. The more high-level points are used, the better the potential energy surfaces become. The rate constant and kinetic isotope effect (KIE) for the triple proton transfer at 300 K, which have been calculated by the canonical variational transition-state theory with microcanonical optimized multidimensional semiclassical tunneling approximation, are 1.6 x 10(-3) s(-1) and 230, respectively. Tunneling is very important not only for the triple proton transfer but also for the triple deuterium transfer. The MCMM results show good agreement with those from the direct ab initio dynamics calculations.     

Calculation of intramolecular force fields from second-derivative tensors

A practical procedure (FUERZA) to obtain internal force constants from Cartesian second derivatives (Hessians) is presented and discussed. It allows a systematic analysis of pair atomic interactions in a molecular system, and it is fully invariant to the choice of internal coordinates of the molecule. Force constants for bonds or for any pair of atoms in general are defined by means of the eigenanalysis of their pair interaction matrix. Force constants for the angles are obtained from their corresponding two-pair interaction matrices of the two bonds or distances forming the angle, and the dihedral force constants are similarly obtained using their corresponding three-pair interaction matrices. © 1996 John Wiley & Sons, Inc.     

Full-dimensional analytical ab initio potential energy surface of the ground state of HOI

Extensive ab initio calculations using a complete active space second-order perturbation theory wavefunction, including scalar and spin-orbit relativistic effects with a quadruple-zeta quality basis set were used to construct an analytical potential energy surface (PES) of the ground state of the [H, O, I] system. A total of 5344 points were fit to a three-dimensional function of the internuclear distances, with a global root-mean-square error of 1.26 kcal mol(-1). The resulting PES describes accurately the main features of this system: the HOI and HIO isomers, the transition state between them, and all dissociation asymptotes. After a small adjustment, using a scaling factor on the internal coordinates of HOI, the frequencies calculated in this work agree with the experimental data available within 10 cm(-1).     

Calculation of the cartesian components of average internuclear displacements in CO2 and CS2 from the force fields in natural curvilinear internal coordinates

The Cartesian components of average internuclear distances for bonded atom pairs in CO₂ and CS₂ were calculated by a perturbation heory of second-order in a large temperature interval from spectroscopic force fields expanded in a power series of natural curvilinear internal coordinates. It is shown that the harmonic pattern of the linear term <ΔZ> makes a significant contribution to the average internuclear distance. The temperature dependence of average distance parameters under various definitions was estimated and discussed.     

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.     

Estimating the hessian for gradient-type geometry optimizations

Optimization methods that use gradients require initial estimates of the Hessian or second derivative matrix; the more accurate the estimate, the more rapid the convergence. For geometry optimization, an approximate Hessian or force constant matrix is constructed from a simple valence force field that takes into account the inherent connectivity and flexibility of the molecule. Empirical rules are used to estimate the diagonal force constants for a set of redundant internal coordinates consisting of all stretches, bends, torsions and out-of-plane deformations involving bonded atoms. The force constants are transformed from the redundant internal coordinates to Cartesian coordinates, and then from Cartesian coordinates to the non-redundant internal coordinates used in the specification of the geometry and optimization. This method is especially suitable for cyclic molecules. Problems associated with the choice of internal coordinates for geometry optimization are also discussed.Fellow of the Alfred P. Sloan Foundation, 1981–83     

Effects of non-uniform electric fields on the convergence behavior of energy expansions

The influence of electric field gradients on the radius of convergence of the energy expansion is investigated using an analysis based on N-variable rational approximation for the power series. The influence of the field gradient on the energy of LiH in a one-dimensional electric field is found to be greatest at small internuclear distances. The radius of convergence is smallest at large internuclear distances. The implications of these results for finite field and test charge calculations are discussed.     

Quantum mechanical model for the dissociative adsorption of diatomic molecules on metal surfaces

A quantum mechanical nonadiabatic theory of dissociative adsorption of diatomic molecules X2 on metal surface is presented. The following reaction coordinates are used to construct crossing diabatic potential energy surfaces (PES): the distance y between the atoms of the X2 molecule, the distance x of the X2 molecular axis from the surface, the set of coordinates describing possible displacements of metal atoms under adsorption. Expression for the rate constant is derived using the model potentials describing vibrations along these coordinates. The calculated dependency of the rate constant W on the reaction heat DeltaE is compared with that in classical approximation. It is shown that quantum effects lead to a weaker dependence of W on DeltaE as compared to that for classical one.     

Multi-component molecular orbital theory for electrons and nuclei including many-body effect with full configuration interaction treatment: isotope effects on hydrogen molecules

A multi-component molecular orbital (MC_MO) theory is developed for a combined quantum system of electrons and nuclei with the full configuration interaction (CI) scheme of Cartesian Gaussian-type functions. The technique of graphical unitary group approach (GUGA) is modified to obtain the CI matrix elements for many kinds of quantum particles efficiently. The optimum basis sets for quantum nuclei are proposed with the fully variational procedure. The average internuclear distances, dipole polarizabilities, and nuclear vibrational excitation energies for isotopic hydrogen molecules calculated with optimized basis sets are found to adequately reproduce the corresponding experimental values.     

An algorithm to find minimum free-energy paths using umbrella integration

The calculation of free-energy barriers by umbrella sampling and many other methods is hampered by the necessity for an a priori choice of the reaction coordinate along which to sample. We avoid this problem by providing a method to search for saddle points on the free-energy surface in many coordinates. The necessary gradients and Hessians of the free energy are obtained by multidimensional umbrella integration. We construct the minimum free-energy path by following the gradient down to minima on the free-energy surface. The change of free energy along the path is obtained by integrating out all coordinates orthogonal to the path. While we expect the method to be applicable to large systems, we test it on the alanine dipeptide in vacuum. The minima, transition states, and free-energy barriers agree well with those obtained previously with other methods.     

On a possible mechanism for Ar 4 + fragmentation

The full potential energy surface (PES) for the collinear Ar ₄ ⁺ cluster as a function of the three internuclear distances is computed at the post-Hartree-Fock level using Density Functional Theory (DFT) methods to treat dynamic correlation effects. The behaviour of the overall configuration energy minima as the central Ar ₂ ⁺ bond stretches is analysed as a function of the fragmentation coordinates of the wing atoms. The coupling between the stretching coordinate and the fragmentation coordinates is also analysed over the whole PES. The calculations suggest that large vibrational energy content in the core dimer ion causes localization of the coupling with either wing atoms which could in turn favour energetically the sequential fragmentation, while Ar ₄ ⁺ with a vibrationally cold core markedly lowers any energy barrier to fragment in a concerted fashion. Such suggestions provide further useful information for what has been found in some of the experimental studies on this ionic system (and on larger ionized argon clusters) and underline the possible role which the internal vibrational energy content of the ionic cluster can play in the fragmentation.     

The impact of approximate VSCF schemes and curvilinear coordinates on the anharmonic vibrational frequencies of formamide and thioformamide

The accuracy of the vibrational self-consistent field (VSCF) method for the computation of anharmonic vibrational frequencies in the infrared (IR) spectrum of formamide and thioformamide is investigated. The importance of triple potentials in the commonly used hierarchical expansion of the potential energy surface (PES) is studied in detail. The PES is expanded in terms of Cartesian as well as internal coordinate normal mode displacements. It is found that triples play an important role when using rectilinear coordinates. A VSCF computation based on rectilinear displacements exhibits serious shortcomings which are only remedied by a large vibrational configuration interaction (VCI) treatment including triple potentials. These limitations are partially removed when using curvilinear coordinates. The merits and disadvantages of either type of displacements for the generation of the PES are discussed.     

Partial hessian fitting for determining force constant parameters in molecular mechanics

We present a new protocol for deriving force constant parameters that are used in molecular mechanics (MM) force fields to describe the bond‐stretching, angle‐bending, and dihedral terms. A 3 × 3 partial matrix is chosen from the MM Hessian matrix in Cartesian coordinates according to a simple rule and made as close as possible to the corresponding partial Hessian matrix computed using quantum mechanics (QM). This partial Hessian fitting (PHF) is done analytically and thus rapidly in a least‐squares sense, yielding force constant parameters as the output. We herein apply this approach to derive force constant parameters for the AMBER‐type energy expression. Test calculations on several different molecules show good performance of the PHF parameter sets in terms of how well they can reproduce QM‐calculated frequencies. When soft bonds are involved in the target molecule as in the case of secondary building units of metal‐organic frameworks, the MM‐optimized geometry sometimes deviates significantly from the QM‐optimized one. We show that this problem is rectified effectively by use of a simple procedure called Katachi that modifies the equilibrium bond distances and angles in bond‐stretching and angle‐bending terms. © 2016 Wiley Periodicals, Inc.     

Matrix elements for Ĵ2 and Ĵz operators over explicitly correlated Cartesian Gaussian functions

General formalism for evaluation of multiparticle integrals involving J?² and J?_z operators over explicitly correlated Cartesian Gaussian functions is presented. The integrals are expressed in terms of the general overlap integrals. An explicitly correlated Cartesian Gaussian function is a product of spherical orbital Gaussian functions, powers of the Cartesian coordinates of the particle, and exponential Gaussian factors, which depend on interparticular distances. This development is relevant to both adiabatic and nonadiabatic calculations of energy and properties of multiparticle systems. © 1995 John Wiley & Sons, Inc.     

Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs

The model of Regularized Quantum Mechanical Force Field (RQMFF) was applied to the joint treatment of ab initio and experimental vibrational data of the four primary nucleobases using a new algorithm based on the scaling procedure in Cartesian coordinates. The matrix of scaling factors in Cartesian coordinates for the considered molecules includes diagonal elements for all atoms of the molecule and off-diagonal elements for bonded atoms and for some non-bonded atoms (1–3 and some 1–4 interactions). The choice of the model is based on the results of the second-order perturbation analysis of the Fock matrix for uncoupled interactions using the Natural Bond Orbital (NBO) analysis. The scaling factors obtained within this model as a result of solving the inverse problem (regularized Cartesian scale factors) of adenine, cytosine, guanine, and thymine molecules were used to correct the Hessians of the canonical base pairs: adenine–thymine and cytosine–guanine. The proposed procedure is based on the block structure of the scaling matrix for molecular entities with non-covalent interactions, as in the case of DNA base pairs. It allows avoiding introducing internal coordinates (or coordinates of symmetry, local symmetry, etc.) when scaling the force field of a compound of a complex structure with non-covalent H-bonds.     

Global X2A′ potential energy surface of Li2H and quantum dynamics of H + Li2 (X1Σg+) → Li + LiH (X1Σ+) reaction

A global potential energy surface (PES) for the electronic ground state of Li₂H system is constructed over a large configuration space. About 30 000 ab initio energy points have been calculated by MRCI‐F12 method with aug‐cc‐pVTZ basis set. The neural network method is applied to fit the PES and the root mean square error of the current PES is only 1.296 meV. The reaction dynamics of the title reaction has been carried out by employing time‐dependent wave packet approach with second order split operator on the new PES. The reaction probability, integral cross section and thermal rate constant are obtained from the dynamics calculation. In most of the collision energy regions, the integral cross sections are in well agreement with the results reported by Gao et al. The rate constant calculated from the new PES increases in the temperature range of present investigation.     

An efficient route to thermal rate constants in reduced dimensional quantum scattering simulations: applications to the abstraction of hydrogen from alkanes

We present an efficient approach to the determination of two-dimensional potential energy surfaces for use in quantum reactive scattering simulations. Our method involves first determining the minimum energy path (MEP) for the reaction by means of an ab initio intrinsic reaction coordinate calculation. This one-dimensional potential is then corrected to take into account the zero point energies of the spectator modes. These are determined from Hessians in curvilinear coordinates after projecting out the modes to be explicitly treated in quantum scattering calculations. The final (1+1)-dimensional potential is constructed by harmonic expansion about each point along the MEP before transforming the whole surface to hyperspherical coordinates for use in the two-dimensional scattering simulations. This new method is applied to H-atom abstraction from methane, ethane and propane. For the latter, both reactive channels (producing i-C(3)H(7) or n-C(3)H(7)) are investigated. For all reactions, electronic structure calculations are performed using an efficient, explicitly correlated, coupled cluster methodology (CCSD(T)-F12). Calculated thermal rate constants are compared to experimental and previous theoretical results.     

A ground state potential energy surface for H2 using Monte Carlo methods

Using variational Monte Carlo and a simple explicitly correlated wave function we have computed the Born-Oppenheimer energy of the H2 ground state (X 1Sigmag+) at 24 internuclear distances. We have also calculated the diagonal correction to the Born-Oppenheimer approximation and the lowest-order relativistic corrections at each distance using variational Monte Carlo techniques. The nonadiabatic values are evaluated from numerical derivatives of the wave function with respect to the nuclear coordinates. With this potential energy surface we have computed several of the lowest vibrational-rotational energies for this system. Our results are in good agreement with the best values found in the literature.     

Using a family of dividing surfaces normal to the minimum energy path for quantum instanton rate constants

One of the outstanding issues in the quantum instanton (QI) theory (or any transition-state-type theory) for thermal rate constants of chemical reactions is the choice of an appropriate "dividing surface" (DS) that separates reactants and products. (In the general version of the QI theory, there are actually two dividing surfaces involved.) This paper shows one simple and general way for choosing DSs for use in QI theory, namely, using the family of (hyper) planes normal to the minimum energy path on the potential energy surface at various distances s along it. Here the reaction coordinate is not one of the dynamical coordinates of the system (which will in general be the Cartesian coordinates of the atoms), but rather simply a parameter which specifies the DS. It is also shown how this idea can be implemented for an N atom system in three-dimensional space in a way that preserves overall translational and rotational invariance. Numerical application to a simple system (the collinear H+H(2) reaction) is presented to illustrate the procedure.     

Calculating rate constants with updated Hessians using variational transition state theory with multidimensional tunneling

Variational transition state theory with multidimensional tunneling (VTST/MT) has been used for calculating the rate constants of reactions. The updated Hessians have been used to reduce the computational costs for both geometry optimization and trajectory following procedures. In this paper, updated Hessians are used to reduce the computational costs while calculating the rate constants applying VTST/MT. Although we found that directly applying the updated Hessians will not generate good vibrational frequencies along the minimum energy path (MEP), however, we can either re-compute the full Hessian matrices at fixed intervals or calculate the Block Hessians, which is constructed by numerical one-side difference for the Hessian elements in the "critical" region and Bofill updating scheme for the rest of the Hessian elements. Due to the numerical instability of the Bofill update method near the saddle point region, we have suggested a simple strategy in which we follow the MEP until certain percentage of the classical barrier height from the barrier top with full Hessians computed and then performing rate constant calculation with the extended MEP using Block Hessians. This strategy results a mean unsigned percentage deviation (MUPD) around 10% with full Hessians computed till the point with 80% classical barrier height for four studied reactions. This proposed strategy is attractive not only it can be implemented as an automatic procedure but also speeds up the VTST/MT calculation via embarrassingly parallelization to a personal computer cluster.