An extension of the grid empowered molecular simulator to quantum reactive scattering

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.

Full Dimensional Potential Energy Function and Calculation of State-Specific Properties of the CO+N2 Inelastic Processes Within an Open Molecular Science Cloud Perspective

A full dimensional Potential Energy Surface (PES) of the CO + N₂ system has been generated by extending an approach already reported in the literature and applied to N₂-N₂ (Cappelletti et al., 2008), CO₂-CO₂ (Bartolomei et al., 2012), and CO₂-N₂ (Lombardi et al., 2016b) systems. The generation procedure leverages at the same time experimental measurements and high-level ab initio electronic structure calculations. The procedure adopts an analytic formulation of the PES accounting for the dependence of the electrostatic and non-electrostatic components of the intermolecular interaction on the deformation of the monomers. In particular, the CO and N₂ molecular multipole moments and electronic polarizabilities, the basic physical properties controlling the behavior at intermediate and long-range distances of the interaction components, were made to depend on relevant internal coordinates. The formulated PES exhibits substantial advantages when used for structural and dynamical calculations. This makes it also well suited for reuse in Open Molecular Science Cloud services.

Chirality in molecular collision dynamics

Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.

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.

The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations

The MoSGrid portal offers an approach to carry out high-quality molecular simulations on distributed compute infrastructures to scientists with all kinds of background and experience levels. A user-friendly Web interface guarantees the ease-of-use of modern chemical simulation applications well established in the field. The usage of well-defined workflows annotated with metadata largely improves the reproducibility of simulations in the sense of good lab practice. The MoSGrid science gateway supports applications in the domains quantum chemistry (QC), molecular dynamics (MD), and docking. This paper presents the open-source MoSGrid architecture as well as lessons learned from its design.