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Faraday Discussions

R D Astumian
Molecular machines use external energy to drive transport, to do mechanical, osmotic, or electrical work on the environment, and to form structure. In this paper the fundamental difference between the design principles necessary for a molecular machine to use light or external modulation of thermodynamic parameters as an energy source vs. the design principle for using an exergonic chemical reaction as a fuel will be explored. The key difference is that for catalytically-driven motors microscopic reversibility must hold arbitrarily far from equilibrium...
October 21, 2016: Faraday Discussions
Richard M Crooks
This article provides a summary of the Faraday Discussion on single entity electrochemistry held in York, U.K., in early September, 2016. The introduction provides some context for thinking about electrochemical studies of single entities. The next four sections follow the themes of the meeting as they relate to single-entity electrochemistry: (1) nanoparticles, nanotubes, and nanowires; (2) nanopores and nanofluidics; (3) complex surfaces and reactions at the nanoscale; and (4) molecular electroanalysis. Each paper presented at the Discussion is summarized, and some personal thoughts as to the significance of the findings, the technical advances that made the experiments possible, and common themes between articles are interspersed...
October 20, 2016: Faraday Discussions
Nancy Makri
The quantum-classical path integral (QCPI) offers a rigorous methodology for simulating quantum mechanical processes in condensed-phase environments treated in full atomistic detail. This paper describes the implementation of QCPI on system-bath models, which are frequently employed in studying the dynamics of reactive processes. The QCPI methodology incorporates all effects associated with stimulated phonon absorption and emission as its crudest limit, thus can (in some regimes) converge faster than influence functional-based path integral methods specifically designed for system-bath Hamiltonians...
October 19, 2016: Faraday Discussions
Pablo M Piaggi, Omar Valsson, Michele Parrinello
We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular dynamics simulations. Therefore we use a recently developed enhanced sampling method [Valsson and Parrinello, Phys. Rev. Lett.113, 090601 (2014)] based on the variational determination of a bias potential. We differ from previous applications of this method in that the bias is constructed on the basis of the physical model provided by the classical theory of nucleation...
October 18, 2016: Faraday Discussions
Timothy J H Hele, Nandini Ananth
We derive an exact quantum propagator for nonadiabatic dynamics in multi-state systems using the mapping variable representation, where classical-like Cartesian variables are used to represent both continuous nuclear degrees of freedom and discrete electronic states. The resulting Liouvillian is a Moyal series that, when suitably approximated, can allow for the use of classical dynamics to efficiently model large systems. We demonstrate that different truncations of the exact Liouvillian lead to existing approximate semiclassical and mixed quantum-classical methods and we derive an associated error term for each method...
October 18, 2016: Faraday Discussions
Samuel Beaulieu, Antoine Comby, Baptiste Fabre, Dominique Descamps, Amélie Ferré, Gustavo Garcia, Romain Géneaux, Francois Légaré, Laurent Nahon, Stéphane Petit, Thierry Ruchon, Bernard Pons, Valérie Blanchet, Yann Mairesse
Measuring the ultrafast dynamics of chiral molecules in the gas phase has been a long standing and challenging quest of molecular physics. The main limitation to reach that goal has been the lack of highly sensitive chiroptical measurement. By enabling chiral discrimination with up to several 10% of sensitivity, photoelectron circular dichroism (PECD) offers a solution to this issue. However, tracking ultrafast processes requires measuring PECD with ultrashort light pulses. Here we compare the PECD obtained with different light sources, from the extreme ultraviolet to the mid-infrared range, leading to different ionization regimes: single-photon, resonance-enhanced multiphoton, above-threshold and tunnel ionization...
October 18, 2016: Faraday Discussions
Giacomo Di Gesù, Tony Lelièvre, Dorian Le Peutrec, Boris Nectoux
We are interested in the connection between a metastable continuous state space Markov process (satisfying e.g. the Langevin or overdamped Langevin equation) and a jump Markov process in a discrete state space. More precisely, we use the notion of quasi-stationary distribution within a metastable state for the continuous state space Markov process to parametrize the exit event from the state. This approach is useful to analyze and justify methods which use the jump Markov process underlying a metastable dynamics as a support to efficiently sample the state-to-state dynamics (accelerated dynamics techniques)...
October 14, 2016: Faraday Discussions
Jessica Ryan Duke, Nandini Ananth
We present a mean field ring polymer molecular dynamics method to calculate the rate of electron transfer (ET) in multi-state, multi-electron condensed-phase processes. Our approach involves calculating a transition state theory (TST) estimate to the rate using an exact path integral in discrete electronic states and continuous Cartesian nuclear coordinates. A dynamic recrossing correction to the TST rate is then obtained from real-time dynamics simulations using mean field ring polymer molecular dynamics. We employ two different reaction coordinates in our simulations and show that, despite the use of mean field dynamics, the use of an accurate dividing surface to compute TST rates allows us to achieve remarkable agreement with Fermi's golden rule rates for nonadiabatic ET in the normal regime of Marcus theory...
October 14, 2016: Faraday Discussions
Mike O'Connor, Emanuele Paci, Simon McIntosh-Smith, David R Glowacki
The past decade has seen the development of a new class of rare event methods in which molecular configuration space is divided into a set of boundaries/interfaces, and then short trajectories are run between boundaries. For all these methods, an important concern is how to generate boundaries. In this paper, we outline an algorithm for adaptively generating boundaries along a free energy surface in multi-dimensional collective variable (CV) space, building on the boxed molecular dynamics (BXD) rare event algorithm...
October 14, 2016: Faraday Discussions
Alexander V Soudackov, Sharon Hammes-Schiffer
A general theory has been developed for proton-coupled electron transfer (PCET), which is vital to a wide range of chemical and biological processes. This theory describes PCET reactions in terms of nonadiabatic transitions between reactant and product electron-proton vibronic states and includes the effects of thermal fluctuations of the solvent or protein environment, as well as the proton donor-acceptor motion. Within the framework of this general PCET theory, a series of analytical rate constant expressions has been derived for PCET reactions in well-defined regimes...
October 13, 2016: Faraday Discussions
Jeremy O Richardson
Semiclassical instanton theory is used to study the quantum effects of tunnelling and delocalization in molecular systems. An analysis of the approximations involved in the method is presented based on a recent first-principles derivation of instanton rate theory [J. Chem. Phys., 2016, 144, 114106]. It is known that the standard instanton method is unable to accurately compute thermal rates near the crossover temperature. The causes of this problem are identified and an improved method is proposed, whereby an instanton approximation to the microcanonical rate is defined and integrated numerically to obtain a thermal rate at any temperature...
October 12, 2016: Faraday Discussions
Jonny Proppe, Tamara Husch, Gregor N Simm, Markus Reiher
For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided...
October 12, 2016: Faraday Discussions
Adithya Vijaykumar, Peter G Bolhuis, Pieter Rein Ten Wolde
Intrinsic rate constants play a dominant role in the theory of diffusion-influenced reactions, but usually as abstract quantities that are implicitly assumed to be known. However, recently it has become clear that modeling complex processes requires explicit knowledge of these intrinsic rates. In this paper we provide microscopic expressions for the intrinsic rate constants for association and dissociation processes of isotropically interacting particles and illustrate how these rates can be computed efficiently using rare event simulations techniques...
October 11, 2016: Faraday Discussions
Jorge R Espinosa, Pablo Sampedro, Chantal Valeriani, Carlos Vega, Eduardo Sanz
We present a new simulation method for the calculation of crystal nucleation rates by computer simulation. The method is based on the use of molds to induce crystallization in state points where nucleation is a rare event. The mold is a cluster of potential energy wells placed in the lattice positions of the solid. The method has two distinct steps. In the first one the probability per unit volume of forming a sub-critical crystal cluster in the fluid is computed by means of thermodynamic integration. The thermodynamic route consists in gradually switching on an attractive interaction between the wells and the fluid particles...
October 11, 2016: Faraday Discussions
Wei Zhang, Carsten Hartmann, Christof Schütte
In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature...
October 10, 2016: Faraday Discussions
Yixian Wang, Xiaonan Shan, Nongjian Tao
Electrochemistry studies charge transfer and related processes at various microscopic structures (atomic steps, islands, pits and kinks on electrodes), and mesoscopic materials (nanoparticles, nanowires, viruses, vesicles and cells) made by nature and humans, involving ions and molecules. The traditional approach measures averaged electrochemical quantities of a large ensemble of these individual entities, including the microstructures, mesoscopic materials, ions and molecules. There is a need to develop tools to study single entities because a real system is usually heterogeneous, e...
October 10, 2016: Faraday Discussions
Ralf Banisch, Eric Vanden-Eijnden
A computational procedure is proposed to generate directly loop-erased transition paths in the context of non-equilibrium reactions, i.e. reactions that occur in systems whose dynamics is not in detailed balance. The procedure builds on results from Transition Path Theory (TPT), and it avoids altogether the need to generate reactive trajectories, either by brute-force calculations or using importance sampling schemes such as Transition Path Sampling (TPS). This is computationally advantageous since these reactive trajectories can themselves be very long and intricate in complex reactions...
October 10, 2016: Faraday Discussions
Joshua S Kretchmer, Thomas F Miller Iii
We investigate the performance of the recently developed kinetically-constrained ring polymer molecular dynamics (KC-RPMD) method for the description of model condensed-phase electron transfer (ET) reactions in which solvent and donor-acceptor dynamics play an important role. Comparison of KC-RPMD with results from Golden-Rule rate theories and numerically exact quantum dynamics calculations demonstrates that KC-RPMD accurately captures the combination of electronic- and nuclear-dynamical effects throughout the Marcus (intermediate solvent friction) and Zusman (large solvent friction) regimes of ET...
October 7, 2016: Faraday Discussions
Reuven Ianconescu, Eli Pollak
Kramers' turnover theory, based on the dynamics of the collective unstable normal mode (also known as PGH theory), is extended to the motion of a particle on a periodic potential interacting bilinearly with a dissipative harmonic bath. This is achieved by considering the small parameter of the problem to be the deviation of the collective bath mode from its value along the reaction coordinate, defined by the unstable normal mode. With this change, the effective potential along the unstable normal mode remains periodic, albeit with a renormalized mass, or equivalently a renormalized lattice length...
October 7, 2016: Faraday Discussions
Ambuj Tiwari, Bernd Ensing
Outer sphere electron transfer between two ions in aqueous solution is a rare event on the time scale of first principles molecular dynamics simulations. We have used transition path sampling to generate an ensemble of reactive trajectories of the self-exchange reaction between a pair of Ru(2+) and Ru(3+) ions in water. To distinguish between the reactant and product states, we use as an order parameter the position of the maximally localised Wannier center associated with the transferring electron. This allows us to align the trajectories with respect to the moment of barrier crossing and compute statistical averages over the path ensemble...
October 5, 2016: Faraday Discussions
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