An old challenge in rate theory is the formulation of a quantum thermodynamic rates which gives accurate estimates but does not demand any real time propagation. In this paper we attempt to answer by extending an idea suggested Voth, Chandler and Miller [J. Phys. Chem. 93, 7009 (1989)]. A new expression for derived replacing exact dependent dynamics with analytically known parabolic barrier utilizing symmetrized thermal flux operator. The barrier, leads derivation rather than ansatz phase...

The exact quantum expression for the thermal rate of reaction is trace a product two operators. It may therefore be written exactly as phase space integral over Wigner representations are projection operator onto product’s space, which difficult to compute, and symmetrized flux operator, can computed using Monte Carlo methods. A transition state theory was presented recently, in replaced by its parabolic barrier limit. Alternatively, classical Both approximations give thermodynamic estimates...

Adenosine-5′-triphosphate (ATP) hydrolysis represents a most important reaction in biology. Despite extensive research efforts, the mechanism for ATP aqueous solution still remains under debate. Previous theoretical studies often predefined coordinates to characterize water with Mg2+ by evaluating free energy profiles through these preassumed paths. In present work, nudged elastic band method is applied identify minimum path calculated hybrid quantum mechanics and molecular approach. Along...

A centroid molecular dynamics (CMD) approach [J. Chem. Phys. 1999 111, 2357; 2371] is developed to study nonadiabatic in condensed phases, as represented by the spin-boson model. The CMD variables for both electronic and nuclear degrees of freedom are defined on basis concept a quasi-density operator. initial distribution system investigated not at thermal equilibrium, operator therefore constructed using mixed Wigner representation. approximation employed motion variables, set equations...

We use quantum mechanical and molecular (QM/MM) simulations to study ATP hydrolysis catalyzed by the maltose transporter. This protein is a prototypical member of large family that consists ATP-binding cassette (ABC) transporters. The ABC proteins catalyze perform variety biological functions. Despite extensive research efforts, precise mechanism enzymes remains elusive. In this work, reaction pathway for in transporter evaluated using QM/MM implementation nudged elastic band method without...

ATP-binding cassette (ABC) exporters pump various substrates across the cell membrane by alternating between inward-facing (IF) and outward-facing (OF) conformations of transmembrane domains (TMDs). However, structural determinants conformational transition their functional roles are not fully understood. In this study, we carried out coarse-grained molecular dynamics (CG-MD) simulations with umbrella sampling for multidrug transporter P-glycoprotein from Caenorhabditis elegans in presence...

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disorder characterized by progressive destruction of lung tissues and airway obstruction. COPD currently the third leading cause death worldwide there no curative treatment available so far. Cigarette smoke (CS) major risk factor for COPD. Yet, only relatively small percentage smokers develop disease, showing that susceptibility varies significantly among smokers. As smoking cessation can prevent in some smokers, quitting...

Numerically exact solutions for the quantum rate of potential barrier crossing in dissipative systems are only possible highly idealized systems. It is, therefore, interest to develop approximate theories more general applicability. In this paper we formulate a mixed classical thermodynamical theory The consists two parts. evaluation thermal flux and computation classically evolved product projection operator. Since dividing surface is perpendicular unstable normal mode system, reformulate...

The spliceosome catalyzes nuclear pre-mRNA splicing via formation of an intron lariat and is arguably the most complex macromolecular machine in eukaryotic cells. Intron a conservative feature reaction for both spliceosomal group II introns. Despite importance splicing, atomic-level understanding mechanism remains elusive. In this work, quantum mechanics molecular method with thermodynamic integration used to calculate free-energy profile along pathway. results demonstrate that catalytic...

The recently formulated quantum transition state theory (QTST) in which the projection operator is approximated by its parabolic barrier limit and symmetrized thermal flux evaluated numerically exactly, applied to collinear hydrogen exchange reaction. results are found bound exact from above for temperatures ranging T = 200 K 1000 K. QTST rate almost at high temperature a factor of 3.7 greater than K, where there extensive tunneling. Contour plots reactive reveal that accounts well “corner...

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The recently formulated mixed quantum classical rate theory (MQCLT) is implemented for a model system with two degrees of freedom. In MQCLT, one must compute the Wigner representation symmetrized thermal flux operator. This phase space distribution then multiplied by reaction probability to obtain rate. major computational difficulty multidimensional Fourier transform necessary obtaining distribution. reintroduces sign problem when attempting estimate MQCLT using Monte Carlo methods. Two...

A recently formulated quantum transition state theory is applied to scattering over an Eckart barrier coupled bilinearly a harmonic mode. Results are compared with the numerically exact and centroid density method computations of McRae et al. [J. Chem. Phys. 97, 7392 (1992)]. We find that comparable accuracy approximation for all parameter ranges studied.

As a critical sensor protein, NLRP3 detects cellular perturbation caused by diverse exogenous and endogenous stimuli. activation requires domain rotation within the NEK7-bound monomer assembly. However, detailed molecular mechanism for assembly remains elusive, particularly in terms of dynamics energetics. In this work, all-atom (MD) simulations are executed to describe large-amplitude closed-to-open conformational transitions along rotational pathway. From MD trajectories, computed...

Similar structures having similar activities is a dogma for identifying new functional molecules. However, it not rare that minor structural change can cause significant activity change. Methods to measure the molecular similarity be classified into two categories of overall three-dimensional shape based methods and local substructure methods. The former states relation between activity, represented by conventional algorithms. latter match Practically, molecules with depends on contributions...

ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding molecular mechanism remains elusive. As these large-scale conformational movements are global collective, we have previously performed coarse-grained dynamics simulations potential mean force along transition pathway [J. Phys. Chem. B 119, 1295 (2015)]. However,...