Classical probability matrix: Prediction of quantum-state distributions by a moment analysis of classical trajectories

A new method is presented for extracting approximate quantum mechanical state-to-state transition probabilities from the results of classical trajectory calculations. The method recognizes quantum discreteness by dealing with the quantum mechanical probability matrix, but all dynamical quantities are evaluated by classical mechanics. It is illustrated by application to the linear atom-diatom collision (vibrational excitation); it is capable of treating both classically allowed and classically forbidden processes.     

Solvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection

End-point methods such as linear interaction energy (LIE) analysis, molecular mechanics generalized Born solvent-accessible surface (MM/GBSA), and solvent interaction energy (SIE) analysis have become popular techniques to calculate the free energy associated with protein-ligand binding. Such methods typically use molecular dynamics (MD) simulations to generate an ensemble of protein structures that encompasses the bound and unbound states. The energy evaluation method (LIE, MM/GBSA, or SIE) is subsequently used to calculate the energy of each member of the ensemble, thus providing an estimate of the average free energy difference between the bound and unbound states. The workflow requiring both MD simulation and energy calculation for each frame and each trajectory proves to be computationally expensive. In an attempt to reduce the high computational cost associated with end-point methods, we study several methods by which frames may be intelligently selected from the MD simulation including clustering and address the question of how the number of selected frames influences the accuracy of the SIE calculations.     

The method of Gaussian weighted trajectories. V. On the 1GB procedure for polyatomic processes

In recent years, many chemical reactions have been studied by means of the quasiclassical trajectory (QCT) method within the Gaussian binning (GB) procedure. The latter consists of "quantizing" the final vibrational actions in Bohr spirit by putting strong emphasis on the trajectories reaching the products with vibrational actions close to integer values. A major drawback of this procedure is that if N is the number of product vibrational modes, the amount of trajectories necessary to converge the calculations is ～10(N)×larger than with the standard QCT method. Applying it to polyatomic processes is thus problematic. In a recent paper, however, Czako? and Bowman propose to quantize the total vibrational energy instead of the vibrational actions [G. Czako? and J. M. Bowman, J. Chem. Phys. 131, 244302 (2009)], a procedure called 1GB here. The calculations are then only ～10 times more time consuming than with the standard QCT method, allowing thereby for considerable numerical saving. In this paper, we propose some theoretical arguments supporting the 1GB procedure and check its validity on model test cases as well as the prototype four-atom reaction OH+D(2)→HOD+D.     

Evaluation of the charge penetration energy between non-orthogonal molecular orbitals using the Spherical Gaussian Overlap approximation

An overlap dependent formula for evaluating the charge penetration energy between non-orthogonal molecular orbitals is derived using the Spherical Gaussian Overlap approximation. When combined with an accurate multipole representation of the electrostatic energy, such as in the effective fragment potential method, ab initio electrostatic energies are generally reproduced to within 0.2 kcal/mol for a variety of molecular dimers and basis sets. The only larger error is for the DMSO dimer, where the electrostatic energy is overestimated by 0.7 kcal/mol.     

Translational energy disposal in molecular collisions: The transfer of momentum constraint

A Franck—Condon type argument, which requires the least transfer of momenta to the nuclei during a collision is outlined and applied to the analysis of translational energy disposal and its dependence on the initial translational energy. Using the maximal entropy procedure of information theory we are able to proceed directly from the assumed (model) constraint to the product state distribution.     

Ionizing collisions of potassium atoms with molecules: Excitation energy of the product molecular ion

For processes of the type K + M

K⁺ + M^? at eV collision energies, measurements are reported of the population of excited states of the product negative ions. For M = Br₂ and SF₆ only a small excitation (0.5 – 3 eV) is found. For M = O₂, the products can be excited up to higher energies (? 5 eV); this is ascribed to a second electronic channel of the process.     

Investigating the impact of operating parameters on molecular weight distributions using functional regression

Molecular weight distributions (MWDs) are inherently functional observations in which differential weight fraction is expressed as a function of chain length. Conventional approaches for analyzing and predicting MWDs include discretization and treatment as multi-response estimation problems, characterization using moments, and detailed mechanistic modeling to predict fractions for each chain length. However, these approaches can be sensitive to loss of information, complexity and problem conditioning. An alternative is to treat the MWDs as functional observations, and to use techniques from Functional Data Analysis (FDA), notably functional regression. The objective of this paper is to develop and apply empirical modeling techniques based on functional regression for investigating the impact of operating parameters on MWDs.     

Photofragment angular momentum distribution beyond the axial recoil approximation: the role of molecular axis rotation

We present the quantum-mechanical expressions for the recoil angle dependence of the photofragment multipole moments which explicitly treat the role of molecular axis rotation on the electronic angular momentum polarization of the fragments. The paper generalizes the result of Siebbeles et al. [J. Chem. Phys. 100, 3610 (1994)] to the case of dissociation of rotating molecules. The electronic wave function of the molecule was used in the adiabatic body-frame representation. The obtained rigorous expressions for the fragment state multipoles have been explicitly derived from the scattering wave-function formalism and then simplified using the quasiclassical approximation in the high-J limit. Possible radial and Coriolis nonadiabatic interactions have been taken into consideration. It is shown that the rotation of the molecular axis is described by a number of rotation factors which depend on the rank of the incident-photon polarization matrix, on the dissociation mechanism, and on the classical angle of rotation of the molecular axis gamma.     

Conversion of kinetic energy to internal energy in the 2-pentanone molecular ion at threshold in low-energy collisions with helium target atoms

Values of the threshold kinetic energy for formation of m/z 58 and m/z 43 from 2-pentanone molecular ion after collisional activation (CA) with He were studied in a hybrid tandem quadrupole system. These values indicate that the fraction of kinetic energy converted to internal energy and available for fragmentation is 0.14–0.25. Onset of conversion to internal energy through an electronically excited state was observed at 2.0 eV. Uses of He and heavier gases as collision gases in low-energy CA are projected to differ, He being used to screen classes of compounds and heavier gases to provide more complete structural information for ions.     

Molecular structure calculations: a unified quantum mechanical description of electrons and nuclei using explicitly correlated Gaussian functions and the global vector representation

We elaborate on the theory for the variational solution of the Schro?dinger equation of small atomic and molecular systems without relying on the Born-Oppenheimer paradigm. The all-particle Schro?dinger equation is solved in a numerical procedure using the variational principle, Cartesian coordinates, parameterized explicitly correlated Gaussian functions with polynomial prefactors, and the global vector representation. As a result, non-relativistic energy levels and wave functions of few-particle systems can be obtained for various angular momentum, parity, and spin quantum numbers. A stochastic variational optimization of the basis function parameters facilitates the calculation of accurate energies and wave functions for the ground and some excited rotational-(vibrational-)electronic states of H(2) (+) and H(2), three bound states of the positronium molecule, Ps(2), and the ground and two excited states of the (7)Li atom.     

Estimating the Gibbs energy of hydration from molecular dynamics trajectories obtained by integral equations of the theory of liquids in the RISM approximation

A method of integral equations of the theory of liquids in the reference interaction site model (RISM) approximation is used to estimate the Gibbs energy averaged over equilibrium trajectories computed by molecular mechanics. Peptide oxytocin is selected as the object of interest. The Gibbs energy is calculated using all chemical potential formulas introduced in the RISM approach for the excess chemical potential of solvation and is compared with estimates by the generalized Born model. Some formulas are shown to give the wrong sign of Gibbs energy changes when peptide passes from the gas phase into water environment; the other formulas give overestimated Gibbs energy changes with the right sign. Note that allowance for the repulsive correction in the approximate analytical expressions for the Gibbs energy derived by thermodynamic perturbation theory is not a remedy.     

Distributed basis sets of s-type Gaussian functions for molecular electronic structure calculations: Applications of the Gaussian cell model to one-electron polycentric linear molecular systems

A particular formulation of the distributed Gaussian basis-set approach, the extended Gaussian cell model, is applied to the simplest polycentric molecule, the linear H₃²⁺ ion. Calculations of the total energy using two extensions of the original Gaussian cell model are described and results are reported for the ground state and the first excited state. A comparison with recently reported finite element calculations is made for a number of nuclear geometries. © 1996 John Wiley & Sons, Inc.     

The reorganization energy of electron transfer in nonpolar solvents: molecular level treatment of the solvent

The intermolecular electron transfer in a solute pair consisting of pyrene and dimethylaniline is investigated in a nonpolar solvent, n-hexane. The earlier elaborated approach [M. Tachiya, J. Phys Chem. 97, 5911 (1993)] is used; this method provides a physically relevant background for separating inertial and inertialess polarization responses for both nonpolarizable and polarizable molecular level simulations. The molecular-dynamics technique was implemented for obtaining the equilibrium ensemble of solvent configurations. The nonpolar solvent, n-hexane, was treated in terms of OPLS-AA parametrization. Solute Lennard-Jones parameters were taken from the same parametrization. Solute charge distributions of the initial and final states were determined using ab initio level [HF/6-31G(d,p)] quantum-chemical calculations. Configuration analysis was performed explicitly taking into account the anisotropic polarizability of n-hexane. It is shown that the Gaussian law well describes calculated distribution functions of the solvent coordinate, therefore, the rate constant of the ET reaction can be characterized by the reorganization energy. Evaluated values of the reorganization energies are in a range of 0.03-0.11 eV and significant contribution (more then 40% of magnitude) comes from anisotropic polarizability. Investigation of the reorganization energy lambda dependence on the solute pair separation distance d revealed unexpected behavior. The dependence has a very sharp peak at the distance d=7 A where solvent molecules are able to penetrate into the intermediate space between the solute pair. The reason for such behavior is clarified. This new effect has a purely molecular origin and cannot be described within conventional continuum solvent models.     

A combined freeze-and-cut strategy for the description of large molecular systems using a localized orbitals approach

A technique to reduce the computational effort in calculating ab initio energies using a localized orbitals approach is presented. By exploiting freeze strategy at the self-consistent field (SCF) level and a cut of the unneeded atomic orbitals, it is possible to perform a localized complete active space (CAS-SCF) calculation on a reduced system. This will open the possibility to perform ab initio treatments on very large molecular systems, provided that the chemically important phenomena happen in a localized zone of the molecule. Two test cases are discussed, to illustrate the performance of the method: the cis-trans interconversion curves for the (7Z)-13 ammoniotridec-7-enoate, which demonstrates the ability of the method to reproduce the interactions between charged groups; and the cisoid-transoid energy barrier for the aldehydic group in the C13 polyenal molecule.     

An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution

For the purpose to execute direct dynamics calculation in solution chemistry, we propose an optimum strategy for solution chemistry using semiempirical molecular orbital (MO) method with neglect of diatomic differential overlap (NDDO) approximation with specific solution reaction parameters (SSRP), i.e., the NDDO‐SSRP method. In this strategy, the empirical parameters of the semi‐empirical MO method were optimized individually for target molecule or ion by reference to the ab initio MO calculation data for many configurations on the potential energy surface near the reaction path. For demonstration, the NDDO‐SSRP method was applied to two molecules and two ions (OH^?, H₂O, NH₃, NH₄⁺) at their equilibrium states in aqueous solution, respectively. Accordingly, it was verified that both the potential energy surface and the charge distribution of these solutes in aqueous solution are dramatically improved to reproduce themselves accurately at ab initio MO calculation level. In conclusion, it is expected that the NDDO‐SSRP method should become quite useful for dynamic and statistical applications to chemical reaction systems in solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method

Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed.     

Numerical sensitivity of trajectories across conformational energy hypersurfaces from geometry optimized molecular orbital calculations: AM1, MNDO,and MINDO/3

The monocyclic β-lactam [[4(S)-methyl-2-oxo-1-azetidinyl]thia]acetic acid was studied by the semiempirical molecular orbital methods AM1, MNDO, and MINDO/3. Using the reaction coordinate option in the program MOPAC on VAX and Cray X-MP computers, the potential energy curve was calculated for rotation of the C2-N1-S-C torsional angle in the conformationally flexible side chain while optimizing all other geometrical variables in the molecule. The trajectory taken during geometry optimization was found to be sensitive to the computer, the program version, the convergence criteria, and the degree of code optimization used in the calculation. In order to reduce the likelihood of spurious results, conformational or reaction energy hypersurfaces need to be calculated with the more precise SCF convergence and minimization criteria available in programs for MINDO/3, MNDO, and AM1 calculations. The nitrogen in the model β-lactam antibiotic is predicted to invert periodically as the dihedral angle to the exocyclic N-substituent sweeps through 360°.