scholarly journals On the Importance of Considering Multinuclear Metal Sites in Homogeneous Catalysis Modeling

2021 ◽  
Author(s):  
Akinobu Matsuzawa ◽  
Jeremy N. Harvey ◽  
Fahmi Himo
Keyword(s):  
Free Energy ◽  
Homogeneous Catalysis ◽  
Catalytic Reaction ◽  
Reaction Mechanisms ◽  
A Priori ◽  
Short Review ◽  
Computational Studies ◽  
Metal Precursor ◽  
Careful Exploration ◽  
Better Than

AbstractIn this short review, we provide an account of a number of computational studies of catalytic reaction mechanisms carried out in our groups. We focus in particular on studies in which we came to realize during the course of the investigation that the active catalytic species was a bimetallic complex, rather a monometallic one as previously assumed. In some cases, this realization was in part prompted by experimental observations, but careful exploration based on computation of the speciation of the metal precursor also provided a powerful guide: it is often possible to predict that bimetallic species (intermediates or transition states) lie lower in free energy than a priori competitive monometallic species. In this sense, we argue that in organometallic catalysis, the rule whereby “two is better than one” turns out to be relevant much more often than one might expect.

Automated Assessment of Binding Affinity via Alchemical Free Energy Calculations

2020 ◽  
Author(s):  
Maximilian Kuhn ◽  
Stuart Firth-Clark ◽  
Paolo Tosco ◽  
Antonia S. J. S. Mey ◽  
Mark Mackey ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Structures ◽  
Free Energy Calculations ◽  
Distinct Advantage ◽  
Binding Affinities ◽  
Structure Based Drug Design ◽  
Energy Calculations ◽  
Kendall’S Τ ◽  
Experimental Values ◽  
Better Than

Free energy calculations have seen increased usage in structure-based drug design. Despite the rising interest, automation of the complex calculations and subsequent analysis of their results are still hampered by the restricted choice of available tools. In this work, an application for automated setup and processing of free energy calculations is presented. Several sanity checks for assessing the reliability of the calculations were implemented, constituting a distinct advantage over existing open-source tools. The underlying workflow is built on top of the software Sire, SOMD, BioSimSpace and OpenMM and uses the AMBER14SB and GAFF2.1 force fields. It was validated on two datasets originally composed by Schrödinger, consisting of 14 protein structures and 220 ligands. Predicted binding affinities were in good agreement with experimental values. For the larger dataset the average correlation coefficient Rp was 0.70 ± 0.05 and average Kendall’s τ was 0.53 ± 0.05 which is broadly comparable to or better than previously reported results using other methods. <br>

From Isovist to Spatial Perception: Wayfinding in Historic Quarter

2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Chih-Hung Chen ◽  
Ting-Ju Lin ◽  
Chih-Yu Chen
Keyword(s):  
Social Interactions ◽  
Spatial Perception ◽  
Publishing House ◽  
A Priori ◽  
Relative Area ◽  
Social Stimuli ◽  
Historical District ◽  
International Publishing ◽  
A Priori Analysis ◽  
Better Than

Based on the assumption that human behaviours are mainly affected by physical and animate environments, this empirical research takes the changeful and complex historical district in Tainan to observe wayfinding behaviours. An a priori analysis of the isovist fields is conducted to identify spatial characteristics. Three measures, the relative area, convexity, and circularity, are applied to scrutinize the possible stopping points, change of speed, and route choices. Accordingly, an experiment is carried out to observe spatial behaviours and different influences of social stimuli. Results show that social interactions afford groups and pairs to perform better than individual observers in wayfinding.© 2016. The Authors. Published for AMER ABRA by e-International Publishing House, Ltd., UK. Peer–review under responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians) and cE-Bs (Centre for Environment-Behaviour Studies, Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, MalaysiaKeywords: wayfinding; isovist; spatial perception and social stimuli; historic quarter

scholarly journals Recent advances in understanding oxygen evolution reaction mechanisms over iridium oxide

2021 ◽  
Author(s):  
Takahiro Naito ◽  
Tatsuya Shinagawa ◽  
Takeshi Nishimoto ◽  
Kazuhiro Takanabe
Keyword(s):  
Reaction Mechanism ◽  
Oxygen Evolution ◽  
Oxygen Evolution Reaction ◽  
Reaction Mechanisms ◽  
State Of The Art ◽  
Iridium Oxide ◽  
The State ◽  
Computational Studies ◽  
Recent Advances ◽  
Iridium Oxides

Recent spectroscopic and computational studies concerning the oxygen evolution reaction over iridium oxides are reviewed to provide the state-of-the-art understanding of its reaction mechanism.

scholarly journals Antiviral Resistance against Viral Mutation: Praxis and Policy for SARS-CoV-2

2021 ◽  
Vol 9 (1) ◽  
pp. 81-89
Author(s):  
Robert Penner
Keyword(s):  
Free Energy ◽  
Vaccine Development ◽  
A Priori ◽  
Structural Data ◽  
Medical Sciences ◽  
Spike Glycoprotein ◽  
Mutagenic Potential ◽  
Viral Mutation ◽  
Novel Method ◽  
Antiviral Targets

Abstract Tools developed by Moderna, BioNTech/Pfizer, and Oxford/Astrazeneca, among others, provide universal solutions to previously problematic aspects of drug or vaccine delivery, uptake and toxicity, portending new tools across the medical sciences. A novel method is presented based on estimating protein backbone free energy via geometry to predict effective antiviral targets, antigens and vaccine cargos that are resistant to viral mutation. This method is reviewed and reformulated in light of the recent proliferation of structural data on the SARS-CoV-2 spike glycoprotein and its mutations in multiple lineages. Key findings include: collections of mutagenic residues reoccur across strains, suggesting cooperative convergent evolution; most mutagenic residues do not participate in backbone hydrogen bonds; metastability of the glyco-protein limits the change of free energy through mutation thereby constraining selective pressure; and there are mRNA or virus-vector cargos targeting low free energy peptides proximal to conserved high free energy peptides providing specific recipes for vaccines with greater specificity than the full-spike approach. These results serve to limit peptides in the spike glycoprotein with high mutagenic potential and thereby provide a priori constraints on viral and attendant vaccine evolution. Scientific and regulatory challenges to nucleic acid therapeutic and vaccine development and deployment are finally discussed.

scholarly journals Sensorimotor priors in nonstationary environments

2013 ◽  
Vol 109 (5) ◽  
pp. 1259-1267 ◽  
Author(s):  
Devika Narain ◽  
Robert J. van Beers ◽  
Jeroen B. J. Smeets ◽  
Eli Brenner
Keyword(s):  
Environmental Variables ◽  
A Priori ◽  
Past Research ◽  
Systematic Change ◽  
Recent Experience ◽  
Environmental Variance ◽  
Adaptive Models ◽  
Priori Information ◽  
Human Nervous System ◽  
Better Than

In the course of its interaction with the world, the human nervous system must constantly estimate various variables in the surrounding environment. Past research indicates that environmental variables may be represented as probabilistic distributions of a priori information (priors). Priors for environmental variables that do not change much over time have been widely studied. Little is known, however, about how priors develop in environments with nonstationary statistics. We examine whether humans change their reliance on the prior based on recent changes in environmental variance. Through experimentation, we obtain an online estimate of the human sensorimotor prior (prediction) and then compare it to similar online predictions made by various nonadaptive and adaptive models. Simulations show that models that rapidly adapt to nonstationary components in the environments predict the stimuli better than models that do not take the changing statistics of the environment into consideration. We found that adaptive models best predict participants' responses in most cases. However, we find no support for the idea that this is a consequence of increased reliance on recent experience just after the occurrence of a systematic change in the environment.

Combining Experimental and Computational Studies to Understand and Predict Reactivities of Relevance to Homogeneous Catalysis

2014 ◽  
Vol 20 (50) ◽  
pp. 16432-16441 ◽  
Author(s):  
Althea S.-K. Tsang ◽  
Italo A. Sanhueza ◽  
Franziska Schoenebeck
Keyword(s):  
Homogeneous Catalysis ◽  
Computational Studies

scholarly journals Revisiting Catalytic Cycles: A Broader View Through the Energy Span Model

2020 ◽  
Author(s):  
Diego Garay-Ruiz ◽  
Carles Bo
Keyword(s):  
Catalytic Reaction ◽  
Reaction Mechanisms ◽  
Computational Study ◽  
Reaction Network ◽  
Co2 Hydrogenation ◽  
Level Of Detail ◽  
Reaction Pathways ◽  
Catalytic Systems ◽  
Computational Code ◽  
Catalytic Cycles

<div><div><div><p>The computational study of catalytic processes allows discovering really intricate and detailed reaction mechanisms that involve many species and transformations. This increasing level of detail can even result detrimental when drawing conclusions from the computed mechanism, as many co-existing reaction pathways can be in close com- petence. Here we present a reaction network-based implementation of the energy span model in the form of a computational code, gTOFfee, capable of dealing with any user-specified reaction network. This approach, compared to microkinetic simulations, enables a much easier and straightforward analysis of the performance of any catalytic reaction network. In this communication, we will go through the foundations and appli- cability of the underlying model, and will tackle the application to two relevant catalytic systems: homogeneous Co-mediated propene hydroformylation and heterogeneous CO2 hydrogenation over Cu(111).</p></div></div></div>

In Situ Investigations of Catalysts and Catalytic Reaction Mechanisms

2000 ◽  
pp. 99-123
Author(s):  
E. G. Derouane ◽  
S. B. Derouane-Abd Hamid ◽  
I. I. Ivanova ◽  
H. He ◽  
J. C. Vedrine
Keyword(s):  
Catalytic Reaction ◽  
Reaction Mechanisms
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