Simulation of intramolecular hydrogen bond dynamics in manzamine A as a sensitive test for charge distribution quality

Subtle balance of inter- and intramolecular hydrogen bond strength in aqueous solutions often governs the structure and dynamics of molecular species used as potential drugs and in supramolecular applications. In silico molecular dynamics study of water solution of manzamine A has been performed with different atomic charges in order to investigate the influence of charge distribution choice on predicting qualitative and quantitative features of the simulated systems. Various well known charge schemes (MK-ESP, RESP, Mulliken, AMI-BCC, Gasteiger-Hückel, Gasteiger-Marsili, MMFF94, and Dynamic Electronegativity Relaxation - DENR) led to qualitatively different pictures of dynamic behavior of the intramolecular hydrogen bond. The reported calculation framework represents a relatively rare case where differences in charge distributions lead to noticeable differences in simulated properties, thus providing a useful test case for force field and charge distribution development, provided high quality experiments are conducted to use as references.     

Role of Surface Molecular Architecture and Energetics of Hydrogen Bonding Sites in Adsorption of Polymers and Surfactants

Hydrogen bonding is generally thought to be an ubiquitous adsorption mechanism, which often foils selective adsorption schemes. Through investigation of hydrogen bonding energy and its dependence on surface molecular architecture, it may be possible to develop new methodologies to control the adsorption of surfactants and polymeric flocculants, depressants, and dispersants used in particulate processing industries. A model system using St?ber silica spheres and polyethylene oxide, a polymer known for its ability to form hydrogen bonds, was examined. The effect of two different surface treatments of the silica particles, calcination and rehydroxylation, upon the adsorption of two polymer molecular weights was studied. The adsorption behavior was then linked to the respective surface structures via characterization of the surfaces using FTIR, NMR, and Raman techniques. In this paper role of hydrogen bonding sites and surface architecture on adsorption is discussed. Copyright 2000 Academic Press.     

Improving the convergence of closed and open path integral molecular dynamics via higher order Trotter factorization schemes

Higher order factorization schemes are developed for path integral molecular dynamics in order to improve the convergence of estimators for physical observables as a function of the Trotter number. The methods are based on the Takahashi-Imada and Susuki decompositions of the Boltzmann operator. The methods introduced improve the averages of the estimators by using the classical forces needed to carry out the dynamics to construct a posteriori weighting factors for standard path integral molecular dynamics. The new approaches are straightforward to implement in existing path integral codes and carry no significant overhead. The Suzuki higher order factorization was also used to improve the end-to-end distance estimator in open path integral molecular dynamics. The new schemes are tested in various model systems, including an ab initio path integral molecular dynamics calculation on the hydrogen molecule and a quantum water model. The proposed algorithms have potential utility for reducing the cost of path integral molecular dynamics calculations of bulk systems.     

Diversity of potential hydrogen bonds in cellulose I revealed by molecular dynamics simulation

We have performed molecular dynamics calculations using a revised version of the Gromos56A_carbo force field to understand the consequences of the different potential hydrogen bonding patterns on the structural stability and thermal behavior of the I_α and I_β forms of native cellulose. For each allomorph, we considered three patterns of hydrogen bonds: two patterns obtained from neutron diffraction data refinement and a regular mixture of the two. Upon annealing, the hydrogen bonding schemes of cellulose I_β, irrespective of the starting structure, re-arranged into the main hydrogen bond pattern experimentally observed (pattern A). On the other hand, the I_α structures, irrespective of the starting hydrogen bonding pattern, converged to a non-experimental structure where the adjacent chains are shifted along the chain direction by 0.12 nm in the hydrogen-bonded plane, and the hydroxymethyl group conformation alternates between gt and tg along the chain. The exotic structure in I_α might be a consequence of a deficiency in force field parameters and/or potential molecular arrangement in less crystalline cellulose.     

Mathematical modeling of kinetic behavior of the hydrogen electrode in carbonate melts under non-steady-state conditions: An analysis of various reaction schemes

An extended analysis of the kinetic behavior exhibited by the hydrogen electrode in a molten carbonate electrolyte is performed by a method of mathematical modeling of relaxation processes as applied to chronoamperometric and coulostatic experiments. A set of differential equations with corresponding initial and boundary conditions, which fixes the balance of charge and substance at the electrode/electrolyte interface, is presented for several particular versions of reaction schemes and the method used for bringing the system out of equilibrium. Numerical calculations are performed and their results are compared with the experimental time dependences of the current and overvoltage obtained in chronoamperometric and coulostatic conditions, respectively. As a result, possible intervals of variations in the kinetic, adsorption, and transport parameters of the system are evaluated. The deviations of their values when using different investigation procedures and different electrode materials (gold, nickel) are discussed. To differentiate assorted reaction schemes as applied to a real electrode process of the anodic oxidation of hydrogen in a carbonate electrolyte it is necessary to expand the base of experimental material to be analyzed and the circle of procedures to be used for investigation.     

Quantum corrections to classical time-correlation functions: hydrogen bonding and anharmonic floppy modes

Several simple quantum correction factors for classical line shapes, connecting dipole autocorrelation functions to infrared spectra, are compared to exact quantum data in both the frequency and time domain. In addition, the performance of the centroid molecular dynamics approach to line shapes and time-correlation functions is compared to that of these a posteriori correction schemes. The focus is on a tunable model that is able to describe typical hydrogen bonding scenarios covering continuously phenomena from tunneling via low-barrier hydrogen bonds to centered hydrogen bonds with an emphasis on floppy modes and anharmonicities. For these classes of problems, the so-called "harmonic approximation" is found to perform best in most cases, being, however, outperformed by explicit centroid molecular dynamics calculations. In addition, a theoretical analysis of quantum correction factors is carried out within the framework of the fluctuation-dissipation theorem. It can be shown that the harmonic approximation not only restores the detailed balance condition like all other correction factors, but that it is the only one that also satisfies the fluctuation-dissipation theorem. Based on this analysis, it is proposed that quantum corrections of response functions in general should be based on the underlying Kubo-transformed correlation functions.     

Accuracy of basis-set extrapolation schemes for DFT-RPA correlation energies in molecular calculations

We construct a reference benchmark set for atomic and molecular random phase approximation (RPA) correlation energies in a density functional theory framework at the complete basis-set limit. This set is used to evaluate the accuracy of some popular extrapolation schemes for RPA all-electron molecular calculations. The results indicate that for absolute energies, accurate results, clearly outperforming raw data, are achievable with two-point extrapolation schemes based on quintuple- and sextuple-zeta basis sets. Moreover, we show that results in good agreement with the benchmark can also be obtained by using a semiempirical extrapolation procedure based on quadruple- and quintuple-zeta basis sets. Finally, we analyze the performance of different extrapolation schemes for atomization energies.     

Die Elektronenstoßfragmentierung von Alkoxy-methylsilylaminen

Electron impact fragmentation of alkoxy-methyl-silylamines The mass spectra of five alkoxy-methyl-N-(butyl-n)-silylamines and of five alkoxy-methyl-N-phenyl-silylamines have been recorded and the fragmentation schemes are presented. The rearrangement involving hydrogen migration to an even-electron siliconium centre is common for the N-(butyl-n) derivatives. For the N-phenyl derivatives the high stability of the molecular ion and also of the other odd-electron ions is striking. A new rearrangement of the aniline group bounded to silicon is proposed.     

Dipole and quadrupole moments of molecules in crystals: a novel approach based on integration over Hirshfeld surfaces

Elegant expressions are derived for the computation of dipole and quadrupole moments of molecules using the electrostatic potential and electric field evaluated on an oriented molecular surface. These expressions are implemented for Hirshfeld surfaces, applied to various molecular crystals, and compared with the results from the quantum theory of atoms in molecules. The effect of intermolecular interactions is also explored by examining the differences between electrostatic moments derived from a periodic Hartree-Fock electron density and an electron density resulting from a superposition of noninteracting molecules. The enhancement of the dipole moment for hydrogen bonded molecular crystals is typically 30%-40% and shown to be largely independent of the partitioning scheme. Dipole moments calculated from Hirshfeld surfaces systematically underestimate those from zero-flux surfaces, a result attributed to the translation of the Hirshfeld surface relative to the zero-flux surfaces for these molecules. For acetylene and benzene, the differences between a crystal calculation and the sum of noninteracting molecules are small, and both partitioning schemes yield quadrupole and second moment results in close agreement.     

Probing the range of applicability of structure‐ and energy‐adjusted QM/MM link bonds

The hydrogen‐capping method is one of the most popular and widely used coupling‐schemes for quantum mechanics/molecular mechanics (QM/MM)‐molecular dynamics simulations of macromolecular systems. This is mostly due to the fact that it is fairly convenient to implement and parametrize, thus providing an excellent compromise between accuracy and computational effort. In this work, a viable and straight‐forward approach to optimize the placing of the link atom on a suitable distance ratio between the frontier atoms is discussed. To further increase the accuracy, instead of global parameters for all amino acids, different parameter sets for each type of amino acid are derived. The dependency of the link bond parameters on the chemical environment and the used QM‐method is probed to assess the range of applicability of the parametrization. Suitable sets of parameters for RI‐MP2, B3LYP, (RI)‐B3LYP‐D3, and RI‐BLYP‐D3 at triple‐zeta level for all relevant proteinogenic amino acids are presented. Furthermore, the scope and range of the perturbation, stemming from the introduction of link bonds is evaluated through application of the presented QM/MM scheme in calculations of the active site of 15S‐lipoxygenase. © 2015 Wiley Periodicals, Inc.     

A new optimization technique for artificial neural networks applied to prediction of force constants of large molecules

An artificial neural network (ANN) method for the prediction of force constants of chemical bonds in large, polyatomic molecules was developed. The force constant information evaluated is to be used for generating accurate estimates of the Hessian used in Newton-Raphson-type ab initio molecular structure optimization schemes. Different network topologies as well as a training procedure based on simulated annealing are evaluated. The results show that an ANN can be designed and trained to provide force constant information within a 1.5 to 5% error band even if the range of the force constants evaluated is very large (from triple bonds to hydrogen bridges). © 1995 by John Wiley & Sons, Inc.     

Lie groups and unitary transformations in ligand field theory

Unitary transformations are performed with respect to three Lie group chains in quasispin schemes that are involved in the study of three different calculation schemes in ligand field theory. The unitary transformations hold true for either molecular or atomic orbitals being taken as the starting point. As a result, unitary transformations with respect to matrix elements are accomplished as well.     

Molecular Dynamics Simulations of Cellulose Oligomers: Conformational Analysis

Summary: The results of classical molecular simulations of cellulose oligomers are presented here. The conformations of the chains in the high temperature melt, room temperature quenched melt and gas phase are compared with respect to various geometrical parameters including square end‐to‐end distances, glycosidic link torsion correlations, ring puckering and hydrogen bonding. The cellulose oligomer melts were relaxed at 800 K with molecular dynamics, and then cooled down in three different ways to obtain dense amorphous systems at 500 K and at room temperature. The sample resulting from the quench (step) shows too much similarity with the melt at 800 K. The two other cooling schemes (ramp, 2ramps) give very similar results for all quantities investigated. The relevance of previous single molecule calculations with respect to the dense amorphous systems is called into question. Comparisons between the chains in the dense systems and those in the gas phase reveal that, even for these relatively short stiff chains, differences exist in the preferred conformations. At high temperatures, where both systems are in equilibrium, the distribution of square end‐to‐end distances are both fairly smooth, but the gas phase clearly prefers more compact conformations. At 300 K, the differences are exacerbated as the equilibrium distribution for the gas phase shows a high proportion of folded conformers, whereas the nonequilibrium quenched systems necessarily retain the extended envelope of the higher temperature. Differences are also evident in the puckering, the rotation of the hydroxymethyl groups and the pattern of hydrogen bonds.

The probability density distribution for the square end‐to‐end distance for octaose in the gas phase (light line) and in the dense phase (dark line) at 300 K.     

Radical yields in the radiolysis of cyclic compounds

The radiolytic decomposition of simple cyclic organic liquids mainly occurs by the breakage of a carbon–hydrogen bond giving the molecular radical and a hydrogen atom. Although the mechanism may be similar, very different yields are found for various six member rings such as cyclohexane, benzene, and pyridine. Experiments using iodine-scavenging techniques give both molecular radical and H atom yields directly and allow an examination of their correlation with each other in different condensed phase cyclic organics.     

Density functional theory study of hydrogen bonding in ionic molecular materials

Crystal structures are usually described in geometric terms. However, it is the energetics of intermolecular interactions that determine the chemical and physical properties of molecular materials.(1) In this paper, we use density functional theory (DFT) in combination with numerical basis sets to analyze the hydrogen bonding interactions in a family of novel ionic molecular materials. We find that the calculated binding energies are consistent with those of other ionic hydrogen bonded systems. We also examine electron density distributions for the systems of interest to gain insight into the nature of the hydrogen bonding interaction and investigate the effects of different aspects of the crystal field on the geometry of the hydrogen bond.     

Hydrogen bond lifetime for water in classic and quantum molecular dynamics

The lifetime of hydrogen bonds in water at T = 298 K and p = 0.1 MPa is computed by means of classic molecular dynamics with eight different potentials of pair lifetime interaction and Car-Parinello molecular dynamics. The results obtained using various computational techniques for hydrogen bond life-times are compared. It is shown that they can differ from one another by several times. The dependence for the hydrogen bond lifetime computed in our numerical experiment upon the method of its determination is found.     

Hydrogen bonding of methanol in supercritical CO2: comparison between 1H NMR spectroscopic data and molecular simulation results

Molecular dynamics simulation results on hydrogen bonding in mixtures of methanol with CO2 at supercritical, liquid-like conditions are compared to 1H NMR spectroscopic data that have recently become available. The molecular models are parametrized using vapor-liquid equilibrium data only, which they reliably describe. A new molecular model for methanol of Lennard-Jones plus point charge type is presented. This molecular methanol model is investigated in terms of its capability to yield hydrogen-bonding statistics. Simple assumptions are made regarding the assignment of NMR chemical shifts to the different types of hydrogen-bonded species. Only two state-independent parameters are fitted to the large NMR data set on the basis of hydrogen-bonding statistics from molecular simulations. Excellent agreement between the molecular simulation results and the NMR data is found. This shows that the molecular models of the simple type studied here cannot only describe thermodynamic properties but also structural effects of hydrogen bonding in solutions.     

Dynamics of Atomic and Molecular Hydrogen Elimination from Hydrocarbons at VUV Excitation

Elimination of atomic hydrogen (H) and molecular hydrogen (H₂) are important elementary chemical processes in photochemistry and combustion chemistry. Recently, unique and sensitive detection techniques for atomic and molecular hydrogen detection were developed in our laboratory. Using the advanced molecular beam methods, we have studied the photodissociation of a few typical hydrocarbons at 157 nm excitation, especially their atomic and molecular hydrogen elimination processes. In this report, we will briefly describe the results from photodissociation of propane, ethylene, propyne and methanol at 157 nm excitation. These molecules represent different classes of hydrocarbons such as alkane, alkene, alkyne and alcohol. Through careful studies on differently deuterated compounds, clear pictures of selective atomic and molecular hydrogen elimination processes can be constructed for all of the above compounds. These results will help us to understand the dissociation dynamics of the small hydrocarbon molecules.     

Structure and dynamics of the aqueous liquid-vapor interface: a comprehensive particle-based simulation study

This research addresses a comprehensive particle-based simulation study of the structural, dynamic, and electronic properties of the liquid-vapor interface of water utilizing both ab initio (based on density functional theory) and empirical (fixed charge and polarizable) models. Numerous properties such as interfacial width, hydrogen bond populations, dipole moments, and correlation times will be characterized with identical schemes to draw useful conclusions on the strengths and weakness of the proposed models for interfacial water. Our findings indicate that all models considered in this study yield similar results for the radial distribution functions, hydrogen bond populations, and orientational relaxation times. Significant differences in the models appear when examining both the dipole moments and surface relaxation near the aqueous liquid-vapor interface. Here, the ab initio interaction potential predicts a significant decrease in the molecular dipole moment and expansion in the oxygen-oxygen distance as one approaches the interface in accordance with recent experiments. All classical polarizable interaction potentials show a less dramatic drop in the molecular dipole moment, and all empirical interaction potentials studied yield an oxygen-oxygen contraction as the interface is approached.