The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.
Proxima is a molecular perception library designed with a double purpose: to be used with immersive molecular viewers (thus providing any required feature not supported by third party libraries) and to be integrated in workflow managers thus providing the functionalities needed for the first steps of molecular modeling studies. It thus stands at the boundary between visualization and computation. The purpose of the present article is to provide a general introduction to the first release of Proxima, describe its most significant features, and highlight its performance by means of some case studies. The current version of Proxima is available for evaluation purposes at .
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. K E Y W O R D S atom diatom reactions, immersive virtual reality, potential energy surface, ring puckering motions 1 | INTRODUCTION As well known, rigorous simulations of molecular processes should be based on the solution of the Schrödinger equation for the wavefunction of the involved nuclei and electrons, which is usually cast in its nonrelativistic time-independent form with a Hamiltonian including a kinetic term for the electronsT e , a kinetic term for the nucleiT N , and an interaction-potential term V (r, R), with r and R being the set of spatial coordinates of electrons and nuclei, respectively.This equation is seldom solved as is, due to the associated mathematical difficulties and computational cost. More commonly, on the grounds that the nuclei are much heavier than the electrons, the Born-Oppenheimer approximation [1] is adopted and the problem is broken down in two separate problems, one for the motion of the electrons at a given nuclear geometry:T
Many non-cardiovascular drugs can prolong the QT interval of the electrocardiogram (ECG); this is an accessory property not necessary for their pharmacological action and generally linked to the block of the potassium HERG channels and delayed cardiac repolarization. The QT prolongation can lead to a dangerous tachyarrhythmia, called torsade de pointes, and potentially to fatal ventricular fibrillation. The experimental approaches, aimed at an early identification of this undesidered property, often require sophisticated and expensive equipment or the use of superior animal species (dog, primates) that cannot be employed easily for ethical and/or economic reasons. This work aimed to study drug-induced QT prolongation in anaesthetized guinea-pigs and to evaluate the reliability of such an experimental approach to obtain a satisfying predictive parameter of the torsadogenicity of drugs in humans. Seven drugs that were torsadogenic in humans (astemizole, cisapride, haloperidol, quinidine, sotalol, terfenadine and thioridazine) and two that were non-torsadogenic (chlorprotixene and diazepam) were administered i.v. to guinea-pigs under pentobarbital anaesthesia. The ECGs were recorded by four electrodes inserted in the subcutaneous layer of the limbs. Both RR and QT intervals were measured in Leads II and III and then the correct QT values were calculated by Bazett and Fridericia algorithms (QTcB and QTcF, respectively). All the drugs, with the exception of chlorprotixene and diazepam, produced a dose-dependent prolongation of the QT and RR intervals and a significant increase of QTcB and QTcF values. It can be concluded that this method represents a rapid and low-cost procedure to evaluate the cardiac safety pro fi le in the preliminary screening of a high number of drugs or drug candidates.
An integrated environment for the analysis of chemical bonding based on immersive virtual reality is presented. Using a multiscreen stereoscopic projection system, researchers are cast into the world of atoms and molecules, where they can visualize at a human scale the electron charge rearrangement (computed via state-of-the-art quantum-chemical methods) occurring on bond formation throughout the molecular region. Thanks to specifically designed features, such a virtual laboratory couples the immediacy of an immersive experience with a powerful, recently developed method yielding quantitative, spatially detailed pictures of the several charge flows involved in the formation of a chemical bond. By means of two case studies on organometallic complexes, we show how familiar concepts in coordination chemistry, such as donation and back-donation charge flows, can be effectively identified and quantified to predict experimental observables.
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