A priori modeling of chemical reactions on computational grid platforms: Workflows and data models

A General User-Friendly Tool for Kinetic Calculations of Multi-Step Reactions within the Virtual Multifrequency Spectrometer Project

We discuss the implementation of a computer program for accurate calculation of the kinetics of chemical reactions integrated in the user-friendly, multi-purpose Virtual Multifrequency Spectrometer tool. The program is based on the ab initio modeling of the involved molecular species, the adoption of transition-state theory for each elementary step of the reaction, and the use of a master-equation approach accounting for the complete reaction scheme. Some features of the software are illustrated through examples including the interconversion reaction of hydroxyacetone and 2-hydroxypropanal and the production of HCN and HNC from vinyl cyanide.

Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality

The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.

Closer versus Long Range Interaction Effects on the Non-Arrhenius Behavior of Quasi-Resonant O2 + N2 Collisions

We report in this paper an investigation on energy transfer processes from vibration to vibration and/or translation in thermal and subthermal regimes for the O₂ + N₂ system performed using quantum-classical calculations on different empirical, semiempirical, and ab initio potential energy surfaces. In particular, the paper focuses on the rationalization of the non-Arrhenius behavior (inversion of the temperature dependence) of the quasi-resonant vibration-to-vibration energy transfer transition rate coefficients at threshold. To better understand the microscopic nature of the involved processes, we pushed the calculations to the detail of the related cross sections and analyzed the impact of the medium and long-range components of the interaction on them. Furthermore, the variation with temperature of the dependence of the quasi-resonant rate coefficient on the vibrational energy gap between initial and final vibrational states and the effectiveness of quantum-classical calculations to overcome the limitations of the purely classical treatments were also investigated. These treatments, handled in an open molecular science fashion by chaining data and competencies of the various laboratories using a grid empowered molecular simulator, have allowed a rationalization of the dependence of the computed rate coefficients in terms of the distortion of the O₂-N₂ configuration during the diatom-diatom collisions. A way of relating such distortions to a smooth and continuous progress variable, allowing a proper evolution from both long to closer range formulation of the interaction and from its entrance to exit channel (through the strong interaction region) relaxed graphical representations, is also discussed in the paper.

Enhanced Flexibility of the O2 + N2 Interaction and Its Effect on Collisional Vibrational Energy Exchange

Prompted by a comparison of measured and computed rate coefficients of Vibration-to-Vibration and Vibration-to-Translation energy transfer in O2 + N2 non-reactive collisions, extended semiclassical calculations of the related cross sections were performed to rationalize the role played by attractive and repulsive components of the interaction on two different potential energy surfaces. By exploiting the distributed concurrent scheme of the Grid Empowered Molecular Simulator we extended the computational work to quasiclassical techniques, investigated in this way more in detail the underlying microscopic mechanisms, singled out the interaction components facilitating the energy transfer, improved the formulation of the potential, and performed additional calculations that confirmed the effectiveness of the improvement introduced.

A high-level ab initio study of the N2 + N2 reaction channel

A new six-dimensional (6D) global potential energy surface (PES) is proposed for the full range description of the interaction of the N2(1Σg+)+N2(1Σg+) system governing collisional processes, including N atom exchange. The related potential energy values were determined using high-level ab initio methods. The calculations were performed at a coupled-cluster with single and double and perturbative triple excitations level of theory in order to have a first full range picture of the PES. Subsequently, in order to accurately describe the stretching of the bonds of the two interacting N2 molecules by releasing the constraints of being considered as rigid rotors, for the same molecular geometries higher level of theory multi reference calculations were performed. Out of the calculated values a 6D 4-atoms global PES was produced for use in dynamical calculations. The ab initio calculations were made possible by the combined use of High Throughput Computing and High Performance Computing techniques within the frame of a computing grid empowered molecular simulator.

Cooperative modelling and design on the computing grid: data, flux and knowledge interoperability

The fast interconnections of the presently available distributed platforms allow scientists to target highly complex problems by chaining software developed and maintained by experts of the relevant fields. A pillar of such cooperative endeavor in molecular and materials science and technologies is the so-called grid empowered molecular simulator that combines the expertise of molecular science theorists (electronic structure and nuclei dynamics) and experimentalists in order to build and validate ab initio models. This line has prompted an unprecedented level of data format standardization procedures, the bridging of high throughput and high performance platforms, the assemblage of ad hoc designed virtual experiments. In addition this approach has prompted the design and development of tools allowing the evaluation of the quality of the cooperative effort produced by the members of a given research community as well as its rewards to such effort through a credit economy is reported.