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Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences RSS feed -- current issue1471-2962April 28, 2017Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences1364-503X<![CDATA[A new (multi-reference configuration interaction) potential energy surface for H2CO and preliminary studies of roaming]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160194?rss=1
We report a new global potential energy surface (PES) for H_{2}CO, based on precise fitting of roughly 67 000 MRCI/cc-pVTZ energies. This PES describes the global minimum, the cis- and trans-HCOH isomers, and barriers relevant to isomerization, formation of the molecular (H_{2}+CO) and radical (H+HCO) products, and the loose so-called roaming transition-state saddle point. The key features of the PES are reviewed and compared with a previous PES, denoted by PES04, based on five local fits that are ‘stitched’ together by switching functions (Zhang et al. 2004 J. Phys. Chem. A108, 8980–8986 (doi:10.1021/jp048339l)). Preliminary quasi-classical trajectory calculations are performed at the total energy of 36 233 cm^{–1} (103 kcal mol^{–1}), relative to the H_{2}CO global minimum, using the new PES, with a particular focus on roaming dynamics. When compared with the results from PES04, the new PES findings show similar rotational distributions, somewhat more roaming and substantially higher H_{2} vibrational excitation.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:20-07:00info:doi/10.1098/rsta.2016.0194hwp:master-id:roypta;rsta.2016.01942017-03-20ARTICLES37520922016019420160194Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160195?rss=1
We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC–DFTB) level of theory. The SCC–DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C_{2}H_{2} (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C_{2}H_{2} ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:20-07:00info:doi/10.1098/rsta.2016.0195hwp:master-id:roypta;rsta.2016.01952017-03-20ARTICLES37520922016019520160195Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[Gas-phase reactivity of [Ca(formamide)]2+ complex: an example of different dynamical behaviours]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160196?rss=1
In the present contribution, we have summarized our recent work on the comprehension of [Ca(formamide)]^{2+} complex gas-phase unimolecular dissociation. By using different theoretical approaches, we were able to revise the original (and typical for such kind of problems) understanding given in terms of stationary points on the potential energy surface, which did not provide a satisfactory explanation of the experimentally observed reactivity. In particular, we point out how non-statistical and non-intrinsic reaction coordinate mechanisms are of fundamental importance.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:20-07:00info:doi/10.1098/rsta.2016.0196hwp:master-id:roypta;rsta.2016.01962017-03-20ARTICLES37520922016019620160196Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[A global optimization perspective on molecular clusters]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160198?rss=1
Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points. In particular, global optimization methods are of major importance to search for the low-energy structures of molecular aggregates. We review the application of global optimization techniques to several molecular clusters; some new results are also reported. Emphasis is given to evolutionary algorithms and their application in the study of the microsolvation of alkali-metal and Ca^{2+} ions with various types of solvents.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:21-07:00info:doi/10.1098/rsta.2016.0198hwp:master-id:roypta;rsta.2016.01982017-03-20ARTICLES37520922016019820160198Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[Phase-space methods for the spin dynamics in condensed matter systems]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160199?rss=1
Using the phase-space formulation of quantum mechanics, we derive a four-component Wigner equation for a system composed of spin- fermions (typically, electrons) including the Zeeman effect and the spin–orbit coupling. This Wigner equation is coupled to the appropriate Maxwell equations to form a self-consistent mean-field model. A set of semiclassical Vlasov equations with spin effects is obtained by expanding the full quantum model to first order in the Planck constant. The corresponding hydrodynamic equations are derived by taking velocity moments of the phase-space distribution function. A simple closure relation is proposed to obtain a closed set of hydrodynamic equations.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:21-07:00info:doi/10.1098/rsta.2016.0199hwp:master-id:roypta;rsta.2016.01992017-03-20ARTICLES37520922016019920160199Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[Kinetics of low-temperature transitions and a reaction rate theory from non-equilibrium distributions]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160201?rss=1
This article surveys the empirical information which originated both by laboratory experiments and by computational simulations, and expands previous understanding of the rates of chemical processes in the low-temperature range, where deviations from linearity of Arrhenius plots were revealed. The phenomenological two-parameter Arrhenius equation requires improvement for applications where interpolation or extrapolations are demanded in various areas of modern science. Based on Tolman's theorem, the dependence of the reciprocal of the apparent activation energy as a function of reciprocal absolute temperature permits the introduction of a deviation parameter d covering uniformly a variety of rate processes, from those where quantum mechanical tunnelling is significant and d < 0, to those where d > 0, corresponding to the Pareto–Tsallis statistical weights: these generalize the Boltzmann–Gibbs weight, which is recovered for d = 0. It is shown here how the weights arise, relaxing the thermodynamic equilibrium limit, either for a binomial distribution if d > 0 or for a negative binomial distribution if d < 0, formally corresponding to Fermion-like or Boson-like statistics, respectively. The current status of the phenomenology is illustrated emphasizing case studies; specifically (i) the super-Arrhenius kinetics, where transport phenomena accelerate processes as the temperature increases; (ii) the sub-Arrhenius kinetics, where quantum mechanical tunnelling propitiates low-temperature reactivity; (iii) the anti-Arrhenius kinetics, where processes with no energetic obstacles are rate-limited by molecular reorientation requirements. Particular attention is given for case (i) to the treatment of diffusion and viscosity, for case (ii) to formulation of a transition rate theory for chemical kinetics including quantum mechanical tunnelling, and for case (iii) to the stereodirectional specificity of the dynamics of reactions strongly hindered by the increase of temperature.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:21-07:00info:doi/10.1098/rsta.2016.0201hwp:master-id:roypta;rsta.2016.02012017-03-20ARTICLES37520922016020120160201Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[Insights into the deactivation of 5-bromouracil after ultraviolet excitation]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160202?rss=1
5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright * state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C–Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the ^{1}n_{O}* and ^{3}* states.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:21-07:00info:doi/10.1098/rsta.2016.0202hwp:master-id:roypta;rsta.2016.02022017-03-20ARTICLES37520922016020220160202Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[Perspective: chemical dynamics simulations of non-statistical reaction dynamics]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160204?rss=1
Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:21-07:00info:doi/10.1098/rsta.2016.0204hwp:master-id:roypta;rsta.2016.02042017-03-20ARTICLES37520922016020420160204Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[A velocity-map imaging study of methyl non-resonant multiphoton ionization from the photodissociation of CH3I in the A-band]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160205?rss=1
Chemical reaction dynamics and, particularly, photodissociation in the gas phase are generally studied using pump–probe schemes where a first laser pulse induces the process under study and a second one detects the produced fragments. Providing an efficient detection of ro-vibrationally state-selected photofragments, the resonance enhanced multiphoton ionization (REMPI) technique is, without question, the most popular approach used for the probe step, while non-resonant multiphoton ionization (NRMPI) detection of the products is scarce. The main goal of this work is to test the sensitivity of the NRMPI technique to fragment vibrational distributions arising from molecular photodissociation processes. We revisit the well-known process of methyl iodide photodissociation in the A-band at around 280 nm, using the velocity-map imaging technique in conjunction with NRMPI of the methyl fragment. The detection wavelength, carefully selected to avoid any REMPI transition, was scanned between 325 and 335 nm seeking correlations between the different observables—the product vibrational, translational and angular distributions—and the excitation wavelength of the probe laser pulse. The experimental results have been discussed on the base of quantum dynamics calculations of photofragment vibrational populations carried out on available ab initio potential-energy surfaces using a four-dimensional model.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:21-07:00info:doi/10.1098/rsta.2016.0205hwp:master-id:roypta;rsta.2016.02052017-03-20ARTICLES37520922016020520160205Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20160206?rss=1
The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at ‘hotspots’ that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH_{3} does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:21-07:00info:doi/10.1098/rsta.2016.0206hwp:master-id:roypta;rsta.2016.02062017-03-20ARTICLES37520922016020620160206Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase<![CDATA[Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces]]>
http://rsta.royalsocietypublishing.org/cgi/content/short/375/2092/20170035?rss=1
In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces ‘on the fly’ has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.

This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.

]]>2017-03-20T00:05:21-07:00info:doi/10.1098/rsta.2017.0035hwp:master-id:roypta;rsta.2017.00352017-03-20INTRODUCTION37520922017003520170035Theme issue [ldquo ]Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces[rdquo ] compiled and edited by Riccardo Spezia, Emilio Marti[acute ]nez-Nun[tilde ]ez, Saulo Vazquez and William L. Hase