Nuclear quantum effect on the hydrogen-bonded structure of guanine�Ccytosine pair

The structure of Watson?CCrick type guanine?Ccytosine (G?CC) base pair has been studied by classical hybrid Monte Carlo (HMC) and quantum path integral hybrid Monte Carlo (PIHMC) simulations on the semiempirical PM6 potential energy surface. For the three NH?X hydrogen-bonded moieties, the intramolecular NH bonds are found systematically longer while the H?X distance shorter in the PIHMC simulation than in the HMC simulation. We found that the hydrogen bonded length N?X correlates with the H?X distance, but not with the NH distance. A correlation is also between the neighboring hydrogen bonds in the G?CC base pair.     

Rotational fluctuation of molecules in quantum clusters. I. Path integral hybrid Monte Carlo algorithm

In this paper, we present a path integral hybrid Monte Carlo (PIHMC) method for rotating molecules in quantum fluids. This is an extension of our PIHMC for correlated Bose fluids [S. Miura and J. Tanaka, J. Chem. Phys. 120, 2160 (2004)] to handle the molecular rotation quantum mechanically. A novel technique referred to be an effective potential of quantum rotation is introduced to incorporate the rotational degree of freedom in the path integral molecular dynamics or hybrid Monte Carlo algorithm. For a permutation move to satisfy Bose statistics, we devise a multilevel Metropolis method combined with a configurational-bias technique for efficiently sampling the permutation and the associated atomic coordinates. Then, we have applied the PIHMC to a helium-4 cluster doped with a carbonyl sulfide molecule. The effects of the quantum rotation on the solvation structure and energetics were examined. Translational and rotational fluctuations of the dopant in the superfluid cluster were also analyzed.     

Hybrid Monte Carlo implementation of the Fourier path integral algorithm

This paper formulates a hybrid Monte Carlo implementation of the Fourier path integral (FPI-HMC) approach with partial averaging. Such a hybrid Monte Carlo approach allows one to generate collective moves through configuration space using molecular dynamics while retaining the computational advantages associated with the Fourier path integral Monte Carlo method. In comparison with the earlier Metropolis Monte Carlo implementations of the FPI algorithm, the present HMC method is shown to be significantly more efficient for quantum Lennard-Jones solids and suggests that such algorithms may prove useful for efficient simulations of a range of atomic and molecular systems.     

The nature of base stacking: a Monte Carlo study

To elucidate the physical origin of the preference of nucleic acid bases for stacking over hydrogen bonding in water, Monte Carlo simulations were performed starting from Watson?CCrick structures of the adenine?Cthymine, adenine?Curacil and guanine?Ccytosine base pairs, as well as from the Hoogsteen adenine?Cthymine base pair, in clusters comprising 400 and 800 water molecules. The simulations employed a newly implemented Metropolis Monte Carlo algorithm based on the extended cluster approach. All simulations reached stacked structures, confirming that such structures are preferred over the hydrogen-bonded Watson?CCrick and Hoogsteen base pairs. The Monte Carlo simulations show the complete transition from hydrogen-bonded base pairs to stacked structures in the Monte Carlo framework. Analysis of the average energies shows that the preference of stacked over hydrogen-bonded structures is due to the increased water?Cbase interaction in these structures. This is corroborated by the increased number of water?Cbase hydrogen bonds in the stacked structures.     

Vibrational Dephasing in Ionic Liquids as a Signature of Hydrogen Bonding

Understanding both structure and dynamics is crucial for producing tailor‐made ionic liquids (ILs). We studied the vibrational and structural dynamics of medium versus weakly hydrogen‐bonded C?H groups of the imidazolium ring in ILs of the type [1‐alkyl‐3‐methylimidazolium][bis(trifluoromethanesulfonyl)imide] ([C_nmim][NTf₂]), with n=1, 2, and 8, by time‐resolved coherent anti‐Stokes Raman scattering (CARS) and quantum‐classical hybrid (QCH) simulations. From the time series of the CARS spectra, dephasing times were extracted by modeling the full nonlinear response. From the QCH calculations, pure dephasing times were obtained by analyzing the distribution of transition frequencies. Experiments and calculations reveal larger dephasing rates for the vibrational stretching modes of C(2)?H compared with the more weakly hydrogen‐bonded C(4,5)?H. This finding can be understood in terms of different H‐bonding motifs and the fast interconversion between them. Differences in population relaxation rates are attributed to Fermi resonance interactions.     

Quantum chemistry beyond Born–Oppenheimer approximation on a quantum computer: A simulated phase estimation study

We present an efficient quantum algorithm for beyond‐Born–Oppenheimer molecular energy computations. Our approach combines the quantum full configuration interaction method with the nuclear orbital plus molecular orbital method. We give the details of the algorithm and demonstrate its performance by classical simulations. Two isotopomers of the hydrogen molecule (H₂, HT) were chosen as representative examples and calculations of the lowest rotationless vibrational transition energies were simulated. © 2016 Wiley Periodicals, Inc.     

Car-Parrinello simulation of an O-H stretching envelope and potential of mean force of an intramolecular hydrogen bonded system: application to a Mannich base in solid state and in vacuum

Car-Parrinello molecular dynamics (CPMD) study was performed for an anharmonic system-an intramolecularly hydrogen bonded Mannich-base-type compound, 4,5-dimethyl-2(N,N-dimethylaminemethyl)phenol, to investigate the vibrational spectrum associated with the O-H stretching. Calculations were carried out for the solid state and for an isolated molecule. The classical CPMD simulation was performed and then the proton potential snapshots were extracted from the trajectory. The vibrational Schrodinger equation for the snapshots was solved numerically, and the (O-H) envelope was calculated as a superposition of the 0-->1 transitions. The potential of mean force for the proton stretching mode was calculated from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling, nuclear quantum effects, and effects of the environment. Perspectives for application of the presented methodology in the computational support of biocatalysis are given in the study.     

Path integral hybrid Monte Carlo algorithm for correlated Bose fluids

Path integral hybrid Monte Carlo (PIHMC) algorithm for strongly correlated Bose fluids has been developed. This is an extended version of our previous method [S. Miura and S. Okazaki, Chem. Phys. Lett. 308, 115 (1999)] applied to a model system consisting of noninteracting bosons. Our PIHMC method for the correlated Bose fluids is constituted of two trial moves to sample path-variables describing system coordinates along imaginary time and a permutation of particle labels giving a boundary condition with respect to imaginary time. The path-variables for a given permutation are generated by a hybrid Monte Carlo method based on path integral molecular dynamics techniques. Equations of motion for the path-variables are formulated on the basis of a collective coordinate representation of the path, staging variables, to enhance the sampling efficiency. The permutation sampling to satisfy Bose-Einstein statistics is performed using the multilevel Metropolis method developed by Ceperley and Pollock [Phys. Rev. Lett. 56, 351 (1986)]. Our PIHMC method has successfully been applied to liquid helium-4 at a state point where the system is in a superfluid phase. Parameters determining the sampling efficiency are optimized in such a way that correlation among successive PIHMC steps is minimized.     

Solid‐State NMR investigations of anhydrous proton‐conducting acid–base poly(acrylic acid)– poly(4‐vinyl pyridine) polymer blend system: A study of hydrogen bonding and proton conduction

NMR studies of the structure and dynamics of a system composed of the acidic polymer poly(acrylic acid) (PAA) and the basic polymer poly(4‐vinyl pyridine) (P4VP) are presented. This system aims at the application of anhydrous proton‐conducting membranes that can be used at elevated temperatures at which the proton conduction of hydrated membranes breaks down. The ¹H NMR measurements have been preformed under fast magic angle spinning (MAS) conditions to achieve sufficient resolution and the applied ¹H NMR methods vary from simple ¹H MAS to double‐quantum filtered methods and two‐dimensional ¹H double‐quantum spectroscopy. The dynamic behavior of the systems has been investigated via variable temperature ¹H MAS NMR. ¹³C cross‐polarization MAS NMR provides additional aspects of dynamic and structural features to complete the picture. Different types of acidic protons have been identified in the studied PAA‐P4VP systems that are nonhydrogen‐bonded free acidic protons, hydrogen‐bonded dicarboxylic dimers, and protons forming hydrogen bonds between carboxylic protons and ring nitrogens. The conversion of dimer structures in dried PAA to free carboxylic acid groups is accomplished at temperatures above 380 K. However, the stability of hydrogen‐bonding strongly depends on the hydration level of the polymer systems. The effect of hydration becomes less apparent in the complexes. An inverse proportionality between hydrogen‐bonding strength and proton conduction in the PAA‐P4VP acid–base polymer blend systems was established. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 138–155, 2009     

On the extent of intramolecular hydrogen bonding in gas-phase and hydrated 1,2-ethanediol

We investigate the quantum dynamical nature of hydrogen bonding in 1,2-ethanediol and monohydrated 1,2-ethanediol using different levels of ab initio theory. Global full-dimensional potential energy surfaces were constructed from PW91/cc-pVDZ, B3LYP/cc-pVDZ, and MP2/cc-pVDZ ab initio data for gas-phase and monohydrated 1,2-ethanediol, using a modified Shepard interpolation scheme. Zero-point energies and nuclear vibrational wave functions were calculated on these surfaces using the quantum diffusion Monte Carlo algorithm. The nature of intra- and intermolecular hydrogen bonding in these molecules was investigated by considering a ground-state nuclear vibrational wavefunction with reduced complete nuclear permutation and inversion (CNPI) symmetry. Separate wavefunction histograms were determined from the ground-state nuclear vibrational wavefunction by projection into bondlength coordinates. The O-H and O-O wavefunction histograms and vibrationally averaged distances were then used to probe the extent of intra- and intermolecular hydrogen bonding. From these data, we conclude that gas-phase ethanediol may possess a weak hydrogen bond, with a relatively short O-O distance but no detectable proton delocalization. Monohydrated ethanediol was found to exhibit no intramolecular hydrogen bonding but instead possessed two intermolecular hydrogen bonds, indicated by both shortening of the O-O distance and significant proton delocalization. The degree of proton delocalization and shortening of the vibrationally averaged O-O distance was found to be dependent on the ab initio method used to generate the potential energy surface (PES) data set.     

Quantum effects on adsorption and diffusion of hydrogen and deuterium in microporous materials

Monte Carlo and molecular dynamics simulations and neutron scattering experiments are used to study the adsorption and diffusion of hydrogen and deuterium in zeolite Rho in the temperature range of 30-150 K. In the molecular simulations, quantum effects are incorporated via the Feynman-Hibbs variational approach. We suggest a new set of potential parameters for hydrogen, which can be used when Feynman-Hibbs variational approach is used for quantum corrections. The dynamic properties obtained from molecular dynamics simulations are in excellent agreement with the experimental results and show significant quantum effects on the transport at very low temperature. The molecular dynamics simulation results show that the quantum effect is very sensitive to pore dimensions and under suitable conditions can lead to a reverse kinetic molecular sieving with deuterium diffusing faster than hydrogen.     

Thermodynamics of hydrogen adsorption in slit-like carbon nanopores at 77 K. Classical versus path-integral Monte Carlo simulations

Hydrogen in slit-like carbon nanopores at 77 K represents a quantum fluid in strong confinement. We have used path-integral grand canonical Monte Carlo and classical grand canonical Monte Carlo simulations for the investigation of the "quantumness" of hydrogen at 77 K adsorbed in slit-like carbon nanopores up to 1 MPa. We find that classical simulations overpredict the hydrogen uptake in carbon nanopores due to neglect of the quantum delocalization. Such disagreement of both simulation methods depends on the slit-like carbon pore size. However, the differences between the final uptakes of hydrogen computed from both classical and quantum simulations are not large due to a similar effective size of quantum/classical hydrogen molecules in carbon nanospaces. For both types of molecular simulations, the volumetric density of stored energy in optimal carbon nanopores exceeds 6.4 MJ dm(-3) (i.e., 45 kg m(-3); Department of Energy target for 2010). In contrast to the hydrogen adsorption isotherms, we found a large reduction of isosteric enthalpy of adsorption computed from the quantum Feynman's path-integral simulations in comparison to the classical values at 77 K and pressures up to 1 MPa. Depression of the quantum isosteric enthalpy of adsorption depends on the slit-like carbon pore size. For the narrow pores (pore width H in [0.59-0.7] nm), the reduction of the quantum isosteric enthalpy of adsorption at zero coverage is around 50% in comparison to the classical one. We observed new phenomena called, by us, the quantum confinement-inducing polymer shrinking. In carbon nanospaces, the quantum cyclic polymers shrink, in comparison to its bulk-phase counterpart, due to a strong confinement effect. At considered storage conditions, this complex phenomenon depends on the size of the slit-like carbon nanopore and the density of hydrogen volumetric energy. For the smallest nanopores and a low density of hydrogen volumetric energy, the reduction of the polymer effective size is the highest, whereas an increase of the pore size and the density of hydrogen volumetric energy causes the polymer swelling up to a value slightly below the one computed from the bulk phase. Quantum confinement-inducing polymer shrinking is of great importance for realizing the potential of quantum molecular sieves.     

Internal proton transfer and H2 rotations in the H5(+) cluster: a marked influence on its thermal equilibrium state

Classical and path integral Monte Carlo (CMC, PIMC) "on the fly" calculations are carried out to investigate anharmonic quantum effects on the thermal equilibrium structure of the H5(+) cluster. The idea to follow in our computations is based on using a combination of the above-mentioned nuclear classical and quantum statistical methods, and first-principles density functional (DFT) electronic structure calculations. The interaction energies are computed within the DFT framework using the B3(H) hybrid functional, specially designed for hydrogen-only systems. The global minimum of the potential is predicted to be a nonplanar configuration of C(2v) symmetry, while the next three low-lying stationary points on the surface correspond to extremely low-energy barriers for the internal proton transfer and to the rotation of the H2 molecules, around the C2 axis of H5(+), connecting the symmetric C(2v) minima in the planar and nonplanar orientations. On the basis of full-dimensional converged PIMC calculations, results on the quantum vibrational zero-point energy (ZPE) and state of H5(+) are reported at a low temperature of 10 K, and the influence of the above-mentioned topological features of the surface on its probability distributions is clearly demonstrated.     

Including quantum subsystem character within classical equilibrium simulations

A mixed quantum/classical density matrix approximation is derived. The density matrix makes use of quantum subsystem vibrational wave functions. The diagonal of the density matrix can be used as an equilibrium distribution in Monte Carlo simulations. The approximate distribution compares well with the path integral distribution for a model system. Since it includes quantum subsystem information, it performs much better than the quadratic Feynman-Hibbs distribution. These types of distributions can aid in including quantum vibrational information in otherwise classical simulations.     

Hydrogen storage in porous structures of adamantane‐based nitrogen‐heterocyclic ring with diamond‐like structure

Using the density functional theory and molecular mechanics methods, we calculated the binding energy and parameters about the primitive cell designed by us with the adamantane and the nitrogen heterocyclic ring, the vibrational frequencies about the small complexes. Grand canonical Monte Carlo simulations were performed to predict the capacities for the hydrogen storage and adsorption isotherms. The results show the positive effects of bigger specific surface area and pore volume on hydrogen storage and isosteric heat. The gravimetric hydrogen uptake of adamantane‐based nitrogen‐heterocyclic ring of quaterpyridyl can reach 9.02 wt % at room temperature and 100 bar. But the volumetric H₂ capacities of the four materials are low at T = 298 K because of weak interaction between the materials and H₂ molecule. © 2014 Wiley Periodicals, Inc.     

Influence of Ions on Aqueous Acid–Base Reactions

We study the effects of bromide salts on the rate and mechanism of the aqueous proton/deuteron‐transfer reaction between the photoacid 8‐hydroxy‐1,3,6‐pyrenetrisulfonic acid (HPTS) and the base acetate. The proton/deuteron release is triggered by exciting HPTS with 400 nm femtosecond laser pulses. Probing the electronic and vibrational resonances of the photoacid, the conjugate photobase, the hydrated proton/deuteron and the accepting base with femtosecond visible and mid‐infrared pulses monitors the proton transfer. Two reaction channels are identified: 1) direct long‐range proton transfer over hydrogen‐bonded water bridges that connect the acid and base and 2) acid dissociation to produce fully solvated protons followed by proton scavenging from solution by acetate. We observe that the addition of salt affects the long‐range reaction pathway, and reduces both the rate at which protons are released to solution by HPTS and the rate at which solvated protons are scavenged from solution by acetate. We study the dependence of these effects on the nature and concentration of the dissolved salt.     

Monte Carlo computation of ground‐state energy derivatives

Monte Carlo is a simple technique, which uses random numbers to compute ground‐state energies of small molecules (and quantum systems in general). The results always have a small statistical error, which poses a major obstacle when estimating properties defined as ground‐state‐energy derivatives (such as the molecule's geometry, its vibrational frequencies, polarizabilities, etc.). In this article, we present and demonstrate an approach that makes an accurate Monte–Carlo estimation of such derivatives possible. This is achieved by realizing that the simulation constitutes an autocorrelated stochastic process, whose proper analysis then enables us to estimate various energy derivatives as a combination of total correlation between readily computable quantities. The resulting procedure is a natural extension of the usual Monte Carlo algorithm for computing the ground‐state energy, with relatively small computational overhead. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials

The Dynamo module library has been developed for the simulation of molecular systems using hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials. Dynamo is not a program package but is a library of Fortran 90 modules that can be employed by those interested in writing their own programs for performing molecular simulations. The library supports a range of different types of molecular calculation including geometry optimizations, reaction‐path determinations and molecular dynamics and Monte Carlo simulations. This article outlines the general structure and capabilities of the library and describes in detail Dynamo's semiempirical QM/MM hybrid potential. Results are presented to indicate three particular aspects of this implementation—the handling of long‐range nonbonding interactions, the nature of the boundary between the quantum mechanical and molecular mechanical atoms and how to perform path‐integral hybrid‐potential molecular dynamics simulations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1088–1100, 2000     

Monte Carlo simulations of hydrogen adsorption in alkali-doped single-walled carbon nanotubes

Monte Carlo simulations and Widom's test particle insertion method have been used to calculate the solubility coefficients (S) and the adsorption equilibrium constants (K) in single-walled (10,10) armchair carbon nanotubes including single nanotubes, and nanotube bundles with various configurations with and without alkali dopants. The hydrogen adsorption isotherms at room temperature were predicted by following the Langmuir adsorption model using the calculated constants S and K. The simulation results were in good agreement with experimental data as well as the grand canonical Monte Carlo simulation results reported in the literature. The simulations of nanotube bundle configurations suggest that the gravimetric hydrogen adsorption increases with internanotube gap size. It may be attributed to favorable hydrogen-nanotube interactions outside the nanotubes. The effect of alkali doping on hydrogen adsorption was studied by incorporating K+ or Li+ ions into nanotube arrays using a Monte Carlo simulation. The results on hydrogen adsorption isotherms indicate hydrogen adsorption of 3.95 wt% for K-doping, and 4.21 wt% for Li-doping, in reasonable agreement with the experimental results obtained at 100 atm and room temperature.     

Multicanonical Monte Carlo calculation of the free‐energy map of the base–amino acid interaction

The specific interactions between base pairs and amino acids were studied by the multicanonical Monte Carlo method. We sampled numerous interaction configurations and side‐chain conformations of the amino acid by the multicanonical algorithm, and calculated the free energies of the interactions between an amino acid at given C_α positions and a fixed base pair. The contour maps of free energy derived from this calculation represent the preferred C_α position of the amino acid around the base, and these maps of various combinations of bases and amino acids can be used to quantify the specificity of intrinsic base–amino acid interactions. Similarly, enthalpy and entropy maps will provide further details of the specific interactions. We have also calculated the free‐energy map of the orientations of the C_α C_β bond vector, which indicates the preferential orientation of the amino acid against the base. We compared the results obtained by the multicanonical method with those of the exhaustive sampling and canonical Monte Carlo methods. The free‐energy map of the base–amino acid interaction obtained by the multicanonical simulation method was nearly identical to the accurate result derived from the exhaustive sampling method. This indicates that a single multicanonical Monte Carlo simulation can produce an accurate free‐energy map. Multicanonical Monte Carlo sampling produced free‐energy maps that were more accurate than those produced by canonical Monte Carlo sampling. Thus, the multicanonical Monte Carlo method can serve as a powerful tool for estimating the free‐energy landscape of base–amino acid interactions and for elucidating the mechanism by which amino acids of proteins recognize particular DNA base pairs. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 954–962, 2000