ABSTRACT
We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the dominant reaction pathways formalism, in which the quantum corrections to the classical overdamped Langevin dynamics are rigorously taken into account to order h(2). We first illustrate our approach in simple cases, and compare with the results of the instanton theory. Then we apply our method to study the C7(eq) â C7(ax) transition of alanine dipeptide. We find that the inclusion of quantum fluctuations can significantly modify the reaction mechanism for peptides. For example, the energy difference which is overcome along the most probable pathway is reduced by as much as 50%.
Subject(s)
Molecular Dynamics Simulation , Quantum Theory , Diffusion , Macromolecular Substances/chemistryABSTRACT
We introduce a framework to investigate ab initio the dynamics of rare thermally activated reactions, which cannot be studied using the existing techniques. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear degrees of freedom are coupled to a thermal bath, through a classical Langevin equation. This method is based on the path integral representation for the stochastic dynamics and yields the time evolution of both nuclear and electronic degrees of freedom, along the most probable reaction pathways, without spending computational time to explore metastable states. As a first illustrative application, we characterize the dominant pathway in the cyclobutene-->butadiene reaction, using the semiempirical Parametrized Model 3 (PM3) approach.
Subject(s)
Quantum Theory , Temperature , Algorithms , Models, ChemicalABSTRACT
The collective properties of water confined in the (10,10), (8,8) and (6,6) carbon nanotubes are studied by analysing the longitudinal-current autocorrelation function, calculated from computer-simulated trajectories. The corresponding spectra clearly show the presence of two excitations, but their behaviour is quite different from that observed in the case of bulk water. Instead of the strong positive dispersion of the hydrodynamic sound mode characteristic of bulk water (the fast-sound phenomenon), the sound dispersion relation of confined water is observed to flatten into a non-propagating mode, while a second excitation appears at a higher frequency. This behaviour is analysed in terms of the localized oscillation modes of the hydrogen-bond network.
Subject(s)
Computer Simulation , Nanotubes, Carbon/chemistry , Water/chemistry , Diffusion , Hydrogen Bonding , Models, Chemical , Monte Carlo Method , Spectrum AnalysisABSTRACT
We derive an efficient method for the insertion of structured particles in grand canonical Monte Carlo simulations of adsorption in very confining geometries. We extend this method to path integral simulations and use it to calculate the isotherm of adsorption of hydrogen isotopes in narrow carbon nanotubes (two-dimensional confinement) and slit pores (one-dimensional confinement) at the temperatures of 20 and 77 K, discussing its efficiency by comparison to the standard path integral grand canonical Monte Carlo algorithm. We use this algorithm to perform multicomponent simulations in order to calculate the hydrogen isotope selectivity for adsorption in narrow carbon nanotubes and slit pores at finite pressures. The algorithm described here can be applied to the study of adsorption of real oligomers and polymers in narrow pores and channels.
ABSTRACT
We develop a theoretical approach to the protein-folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps are removed, and simulating the entire reaction in atomistic details using existing computers becomes feasible. We discuss how to determine the most probable folding pathway, identify configurations representative of the transition state, and compute the most probable transition time. We perform an illustrative application of these ideas, studying the conformational evolution of alanine dipeptide, within an all-atom model based on the empiric GROMOS96 force field.
Subject(s)
Protein Folding , Proteins/chemistry , Biophysical Phenomena , Biophysics , Models, Molecular , Protein Conformation , Stochastic Processes , ThermodynamicsABSTRACT
Grand canonical Monte Carlo simulations of argon, hydrogen, and methane adsorption in four covalent organic frameworks are presented. Argon adsorption isotherms from computer simulations overestimate the amount adsorbed by 25% upon saturation, with respect to the available experiments at T = 87 K. Hydrogen adsorption isotherms show that these materials might attain a 30% increase for the uptake when compared with analogous simulations performed for metal organic frameworks at T = 77 K and T = 298 K. Methane adsorption isotherms give a strong indication that at least one material in this class, COF-102, could meet or exceed the Department of Energy's target of 180 cm3 (STP)/cm3 for P = 35 bar and room temperature. The origin of this large affinity for methane is investigated by analyzing the structure of the potential energy surface of interaction between the adsorbate and the adsorbent.
ABSTRACT
The authors report the structural and dynamical properties of water interacting with the surface of a lipid bilayer. Three regions have been identified, which show different dynamical regimes of water: a region of strong water-solute interaction, a transition region, and the bulk water region. The dynamics of the strong-interacting water is dominated by caging effects, as shown by the analysis of the self-intermediate scattering function, and by the disrupture of water's hydrogen bond network, while the smooth transition to bulk water is traced back to the roughness of the bilayer surface.
Subject(s)
Computer Simulation , Lipid Bilayers/chemistry , Models, Chemical , Water/chemistry , Lipid Bilayers/metabolism , Water/metabolismABSTRACT
We present an instantaneous normal mode analysis of liquid HF aimed at clarifying the origin of peculiar dynamical properties which are supposed to stem from the arrangement of molecules in a linear hydrogen-bonded network. The present study shows that this approach is a unique tool for the understanding of the spectral features revealed in the analysis of both single molecule and collective quantities. For the system under investigation, we demonstrate the relevance of hydrogen-bonding "stretching" and fast librational motion in the interpretation of these features.
