Simulation of slow-motion CW EPR spectrum using stochastic Liouville equation for an electron spin coupled to two nuclei with arbitrary spins: matrix elements of the Liouville superoperator

An algorithm is developed that extends the well known nitroxide slow-motional continuous wave electron paramagnetic resonance (EPR) simulation technique developed originally by Meirovitch et al. [E. Meirovitch, D. Inger, E. Inger, G. Moro, J.H. Freed, J. Chem. Phys. 77 (1982) 3915-3938], and implemented by Schneider and Freed [D.J. Schneider, J.H. Freed, Calculating slow motional magnetic resonance spectra: a user's guide, in: Biological Magnetic Resonance, vol. 6, Plenum Publishing Corporation, 1989]. This paper deals with the more general case of coupling of one electron spin to two nuclear spins. A complete listing of the matrix elements of the Liouville superoperator for this extension has been included. This advance has been successfully tested by reproducing the observed spectral lineshapes of a solution of the novel radical Mes(*)(CH(3))P-PMes(*) [Mes(*)=2,4,6 (tBu)(3)C(2)H(2)] in tetrahydrofuran (THF), in which the radical is undergoing slow tumbling, with the coupling of one electron spin to two physically and magnetically inequivalent phosphorus ((31)P) nuclei.     

A case study of the MSA approach to quantized polarizable media

The mean spherical approximation (MSA) has proved to be a very general and flexible method to analyze equilibrium statistical mechanical systems. In this note we test its accuracy against a simple one-dimensional model, i.e., a lattice gas of polarizable molecules where the internal degree of freedom is treated as quantized harmonic oscillators which interact via harmonic forces. This model can be solved exactly. We find a very good agreement between the MSA and exact solutions.2 The corresponding classical problem of polarizable particles was first solved in a mean spherical approximation (MSA) by M. Wertheim [J. Chem. Phys. 26:1425 (1973)]. He considered the model with nonfluctuating dipole moments. Later L. Pratt [Mol. Phys. 40:347 (1980)] and J. S. Høye and G. Stell [J. Chem. Phys. 73:461 (1980)] solved the corresponding classical problem in the MSA for particles with fluctuating dipole moments.     

Anomaly in the stability limit of liquid 3He

We propose that the liquid-gas spinodal line of 3He reaches a minimum at 0.4 K. This feature is supported by our cavitation measurements. We also show that it is consistent with extrapolations of sound-velocity measurements. Speedy [J. Phys. Chem. 86, 3002 (1982)] previously proposed this peculiar behavior for the spinodal of water and related it to a change in sign of the expansion coefficient alpha, i.e., a line of density maxima. 3He exhibits such a line at positive pressure. We consider its extrapolation to negative pressure. Our discussion raises fundamental questions about the sign of alpha in a Fermi liquid along its spinodal.     

A quasi-classical trajectory study of the Cl + H<Subscript>2</Subscript> (D<Subscript>2</Subscript>) reaction on a new BW3 potential energy surface

Molecular reaction dynamics of Cl + H₂ (D₂) has been studied on the latest analytical potential energy surface called BW3 using the Monte Carlo quasi-classical trajectory method. Excitation functions, differential cross sections and angular distributions of HCl and DCl products have been calculated. The excitation functions of the Cl (²P_3/2) + n-H₂ and Cl(²P_3/2) + n-D₂ reactions are also studied. The results are compared with those of quasi-classical trajectory [M. Alagia et al.: Phys. Chem. Chem. Phys. 2 (2000); F. J. Aoiz et al.: J. Phys. Chem. 100 (1996)], quantum mechanical (QM) calculations [F. J. Aoiz et al.:J. Chem. Phys. 115 (2001)] and experimental data [S. H. Lee et al.: J. Chem. Phys. 110 (1999); F. Dong et al.: J. Chem. Phys. 115 (2001)]. Discussions are given to some new results.     

Reaction rate theory: what it was, where is it today, and where is it going?

A brief history is presented, outlining the development of rate theory during the past century. Starting from Arrhenius [Z. Phys. Chem. 4, 226 (1889)], we follow especially the formulation of transition state theory by Wigner [Z. Phys. Chem. Abt. B 19, 203 (1932)] and Eyring [J. Chem. Phys. 3, 107 (1935)]. Transition state theory (TST) made it possible to obtain quick estimates for reaction rates for a broad variety of processes even during the days when sophisticated computers were not available. Arrhenius' suggestion that a transition state exists which is intermediate between reactants and products was central to the development of rate theory. Although Wigner gave an abstract definition of the transition state as a surface of minimal unidirectional flux, it took almost half of a century until the transition state was precisely defined by Pechukas [Dynamics of Molecular Collisions B, edited by W. H. Miller (Plenum, New York, 1976)], but even this only in the realm of classical mechanics. Eyring, considered by many to be the father of TST, never resolved the question as to the definition of the activation energy for which Arrhenius became famous. In 1978, Chandler [J. Chem. Phys. 68, 2959 (1978)] finally showed that especially when considering condensed phases, the activation energy is a free energy, it is the barrier height in the potential of mean force felt by the reacting system. Parallel to the development of rate theory in the chemistry community, Kramers published in 1940 [Physica (Amsterdam) 7, 284 (1940)] a seminal paper on the relation between Einstein's theory of Brownian motion [Einstein, Ann. Phys. 17, 549 (1905)] and rate theory. Kramers' paper provided a solution for the effect of friction on reaction rates but left us also with some challenges. He could not derive a uniform expression for the rate, valid for all values of the friction coefficient, known as the Kramers turnover problem. He also did not establish the connection between his approach and the TST developed by the chemistry community. For many years, Kramers' theory was considered as providing a dynamic correction to the thermodynamic TST. Both of these questions were resolved in the 1980s when Pollak [J. Chem. Phys. 85, 865 (1986)] showed that Kramers' expression in the moderate to strong friction regime could be derived from TST, provided that the bath, which is the source of the friction, is handled at the same level as the system which is observed. This then led to the Mel'nikov-Pollak-Grabert-Hanggi [Mel'nikov and Meshkov, J. Chem. Phys. 85, 1018 (1986); Pollak, Grabert, and Hanggi, ibid. 91, 4073 (1989)] solution of the turnover problem posed by Kramers. Although classical rate theory reached a high level of maturity, its quantum analog leaves the theorist with serious challenges to this very day. As noted by Wigner [Trans. Faraday Soc. 34, 29 (1938)], TST is an inherently classical theory. A definite quantum TST has not been formulated to date although some very useful approximate quantum rate theories have been invented. The successes and challenges facing quantum rate theory are outlined. An open problem which is being investigated intensively is rate theory away from equilibrium. TST is no longer valid and cannot even serve as a conceptual guide for understanding the critical factors which determine rates away from equilibrium. The nonequilibrium quantum theory is even less well developed than the classical, and suffers from the fact that even today, we do not know how to solve the real time quantum dynamics for systems with "many" degrees of freedom.     

基于级联方程的量子耗散半经典方法

We present a semiclassical (SC) approach for quantum dissipative dynamics, constructed on basis of the hierarchical-equation-of-motion (HEOM) formalism. The dynamical components considered in the developed SC-HEOM are wavepackets'' phase-space moments of not only the primary reduced system density operator but also the auxiliary density operators (ADOs) of HEOM. It is a highly numerically efficient method, meanwhile taking into account the high-order effects of system-bath couplings. The SC-HEOM methodology is exemplified in this work on the hierarchical quantum master equation[J. Chem. Phys. 131, 214111 (2009)] and numerically demonstrated on linear spectra of anharmonic oscillators.     

理解随机过程分子动力学中的真实/虚拟动力学

Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed for the Langevin equation[J. Chem. Phys. 147, 184104 (2017)] in principle exists in other types of stochastic thermostats as well. The recommended "middle" scheme[J. Chem. Phys. 147, 034109 (2017)] of the Andersen thermostat is investigated as an example. As shown by both analytic and numerical results, while the real and virtual dynamics cases approach the same plateau of the characteristic correlation time in the high collision frequency limit, the accuracy and efficiency of sampling are relatively insensitive to the value of the collision frequency in a broad range. After we compare the behaviors of the Andersen thermostat to those of Langevin dynamics, a heuristic schematic representation is proposed for understanding efficient stochastic thermostatting processes with molecular dynamics.     

A molecular dynamics investigation of dynamical heterogeneity in supercooled water

We investigate the presence of dynamical heterogeneity in supercooled water with molecular dynamics simulations using the new water model proposed by Mahoney and Jorgensen [M.W. Mahoney, W.L. Jorgensen J. Chem. Phys. 112, 8910 (2000)]. Prompted by recent theoretical results [J.P. Garrahan, D. Chandler, Phys. Rev. Lett. 89, 35704 (2002)] we study the dynamical aggregation of the least and the most mobile molecules. We find dynamical heterogeneity in supercooled water and string-like dynamics for the most mobile molecules. We also find the dynamical aggregation of the least mobile molecules. The two kinds of dynamical aggregation appear however to be very different. Characteristic times are different and evolve differently. String-like motions appear only for the most mobile molecules, a result predicted by the facilitation theory. The aggregation of the least mobile molecules is more organized than the bulk while the opposite is observed for the most mobile molecules.     

The vicinity of an equilibrium three-phase contact line using density-functional theory: density profiles normal to the fluid interface

The paper by Nold et al. [Phys. Fluids 26 (7), 072001 (2014)] examined density profiles and the micro-scale structure of an equilibrium three-phase (liquid–vapour–solid) contact line in the immediate vicinity of the wall using elements from the statistical mechanics of classical fluids, namely density-functional theory. The present research note, building on the above work, further contributes to our understanding of the nanoscale structure of a contact line by quantifying the strong dependence of the liquid–vapour density profile on the normal distance to the interface, when compared to the dependence on the vertical distance to the substrate. A recent study by Benet et al. [J. Phys. Chem. C 118 (38), 22079 (2014)] has shown that this could explain the emergence of a film-height-dependent surface tension close to the wall, with implications for the Frumkin–Derjaguin theory.     

The calculation of active Raman modes of α-quartz crystal via density functional theory based on B3LYP Hamiltonian in 6–311+G(2d) basis set?

We obtained an approximation of the force field of ??-quartz crystal using a new idea of applying density functional theory [J Purton, R Jones, C R A Catlow and M Leslie, Phys. Chem. Minerals 19, 392 (1993)]. Our calculations were based on B3LYP Hamiltonian [A N Lazarev and A P Mirgorodsky, Phys. Chem. Minerals 18, 231 (1991)] in 6?311+G(2d) basis set for H₁₆Si₇O₆ cluster and included a unit cell of the lattice. The advantage of our method is the increase in the speed of calculations and the better adaption of simulation results with the experimental data.     

Diffusion-mediated reactions with a time-dependent absorption rate

Diffusion-mediated reactions models are particularly useful for the characterization of physical, chemical, and biological problems. In this paper we present a theoretical study of the absorption probability density, survival probability, and reaction rate for diffusion-mediated reactions models with a time-dependent finite absorption rate (an extension of a model usually referred to as the "imperfect trap model"). The results are obtained by means of the formalism of continuous time random walk on a lattice and considering a general reaction dynamics upon encounter of the reactives. First jump probability densities are included to take initial conditions into account. Previous results presented by Collins and Kimball [J. Colloid. Sci. 4, 425 (1949)] and Noyes [J. Chem. Phys. 22, 1349 (1954)] are reobtained for the particular case of a time-independent absorptivity. Short and long time behaviors are analyzed resulting, in particular, in that the long time behavior of the absorption probability density exhibits the same time dependence as the first passage time density. The results obtained are illustrated by considering a one-dimensional model with consequent discussion.     

The bulk modulus and its pressure derivative for 18 metals

Volume compression data of Vaidya and Kennedy [J. Phys. Chem. Solids31, 2329 (1970)] have been used to recalculate the isothermal bulk moduli and their pressure derivatives and to compare various equations of state.     

Interplay between time-temperature transformation and the liquid-liquid phase transition in water

We study the new water model proposed by Mahoney and Jorgensen [J. Chem. Phys. 112, 8910 (2000)], which is closer to real water than previously proposed classical pairwise additive potentials. We simulate the model in a wide range of deeply supercooled states and find (i) the existence of a nonmonotonic "nose-shaped" temperature of maximum density line and a nonreentrant spinodal, (ii) the presence of a low-temperature phase transition, (iii) the free evolution of bulk water to ice, and (iv) the time-temperature-transformation curves at different densities.     

Intramolecular association within the SAFT framework

A general theory for modelling intramolecular association within the SAFT framework is proposed. Sear and Jackson [Phys. Rev. E. 50 (1), 386 (1994)] and Ghonasgi and Chapman [J. Chem. Phys. 102 (6), 2585 (1995)] have previously extended SAFT to include intramolecular association for chains with two sites. We show that the resulting equations from the two approaches are equivalent, and use their work as a basis for developing a new general theory. The approach used by Ghonasgi and Chapman is based on mass balances and an infinite dilution result and provides the equations needed to determine the contribution to the Helmholtz free energy from association (inter- as well as intramolecularly) at equilibrium. Sear and Jackson rederived the contribution to the Helmholtz free energy from association from the theory by Wertheim [J. Stat. Phys. 42 (3–4), 459 (1986)] with inclusion of intramolecular association, and using this approach we obtain an expression for the Helmholtz free energy that is valid also at non-equilibrium states (with respect to hydrogen bonds), which is very useful when calculating derivatives.     

Fluorescence Spectroscopic Properties Analysed within the Extended Förster Theory with Application to Biomacromolecular Systems

The extended Förster theory (EFT) of electronic energy transport accounts for translational and rotational dynamics, which are neglected by the classical Förster theory (FT). EFT has been developed for electronic energy transfer within donor-acceptor pairs [Isaksson, et al, Phys. Chem. Chem. Phys., 9, 1941(2007)] and donor-donor pairs [Johansson, et al, J. Chem. Phys., 105, 10896 (1996); Norlin, et al, Phys. Chem. Chem. Phys., 10, 6962(2008)]. For donors that exhibit different or identical non-exponential fluorescence relaxation within a donor-donor pair, the process of reverberating energy migration is reversible to a higher or lower degree. Here the impact of the EFT has been studied with respect to its influence on fluorescence quantum yields, fluorescence lifetimes as well as depolarisation experiments. The FT predicts relative fluorescence quantum yields which usually agree with the EFT within experimental accuracy, however, substantial deviations occurs in the steady-state and in particular the time-resolved depolarisation data.     

Fractional-dimensional approach for biexcitons in GaAs/AlxGa1−xAs quantum wells

The energy of a biexciton in a GaAs/Al_xGa_1?xAs quantum well structure with finite barriers is investigated by using the geometrical model of two-dimensional biexcitons proposed by Singh et al. [J. Singh, D. Birkedal, V.G. Layssenko, J.M. Hvam, Phys. Rev. B 53 (1996) 15909; I.-K. Oh, J. Singh, Phys. Rev. B 60 (1999) 2528]. A fractional-dimensional approach is used to obtain the binding energy of the biexciton in both square quantum wells and parabolic quantum wells. Theoretical results show that the binding energy of a biexciton in a finite quantum well exhibits a maximum with increasing well width. The ratio of the binding energy of a biexciton to that of an exciton in a quantum well structure is found to be sensitive to the electron-to-hole mass ratio and larger than that in the three-dimensional system. The results agree fairly well with previous experimental results. The results of our approach are also compared with those of earlier theories.     

“Electron impact ionization of helium isoelectronic systems”

We show that the criticism [Eur. Phys. J. D 49, 167 (2008)] of our empirical formula for electron-impact ionization of atomic ions [J. Phys B. 33, 5025 (2000)] is unjustified.     

Numerical integration of projective Hamiltonian dynamics

Projective Hamiltonian dynamics [S. Melchionna, J. Chem. Phys. 121, 4534 (2004)] is an approach to reduce mode spreading in complex systems, thus improving the performances of Molecular Dynamics simulations. A numerical integration of the dynamics requires proper treatment of the non-separable form of the Hamiltonian. Due to its symplectic nature, the generalized leapfrog scheme is shown to provide robust and reliable numerical trajectories even in the case of stiff projective forces.     

Statistical mechanics of hydrogen bond networks

The static and dynamic properties of several hydrogen bond network models, based on thesquare ice model of Lieb [Phys. Rev.162, 162 (1967)] are studied. The two dimensionalsquare water (SW) model and the three-dimensioaalbrick water (BW) model were analyzed by means of Monte Carlo simulations. A simplified vesion of SW (simplified square water, SSW) can be solved exactly. All models yield similar thermodynamic results which can be derived-alternatively-from an independent bond approach due to Angell [J. Chem. Phys.75, 3698 (1971)]. We suggest the existence of a universality class of hydrogen bond networks that can be described by this theory, and which may include the liquid state of water. The mean lifetime of a hydrogen bond exhibits an Arrhenius temperature dependence. Comparison with experimental data on water provides an absolute time scale for the Monte Carlo simulations. The possible use of these models in simulations of protein-solvent systems is discussed.