A new universal force-field for the Li2S-P2S5 system

Lithium thiophosphate electrolyte is a promising material for application in all-solid-state batteries. Ab initio molecular dynamics (AIMD) simulations have been used to investigate the ion conduction mechanisms in single-crystalline and...

Estudio teórico de la síntesis de hemiacetales catalizada por ácidos de Lewis

Se llevó a cabo un estudio teórico de la síntesis de acetaldehído metilhemiacetal, benzaldehído metilhemiacetal, 4-metil benzaldehído metilhemiacetal y 4-nitro benzaldehído metilhemiacetal, comparando la reactividad de los aldehídos frente a la reacción con metanol, catalizada por iones metálicos: Zn2+; Co2+, Mn2+; Cu2+ y Ni2+, a través del análisis de los intermediarios de reacción correspondientes e indicando la influencia del anillo aromático y de los iones metálicos en la velocidad de dicha reacción. Las energías de activación y las de los intermediarios de reacción se calcularon con el método Universal Force Field (UFF). Los valores obtenidos se compararon con datos de la literatura. La obtención de hemiacetales, además de su utilidad dentro de la industria química, es una reacción usada frecuentemente en síntesis orgánica, al proporcionar un medio eficiente y económico para proteger el grupo carbonilo en un proceso sintético. El acetaldehído presentó la mayor reactividad frente a la reacción de síntesis de hemiacetales en todos los casos, el anillo aromático disminuyó la velocidad de reacción y el Zn2+ resultó ser el ion metálico más reactivo, reportando los valores más bajos de energía.

Identifying Therapeutic Compounds Targeting RNA-Dependent-RNA-Polymerase of Sars-Cov-2

<p>COVID-19 emerged as the biggest threat of this century for mankind and later it spread across the globe through human to human transmission. Scientists rushed to understand the structure and mechanism of the virus so that antiviral drugs or vaccines to control this disease can be developed. A key to stop the progression of the disease is to inhibit the replication mechanism of Sars-Cov-2. RNA-dependent-RNA polymerase protein also called RdRp protein is the engine of Sars-Cov-2 that replicates the virus using viral RNA when it gains entry into the human cell. Numerous drugs proposed for the treatment of COVID-19 such as Camostat Mesylate, Remdesivir, Famotidine, Hesperidin, etc. are under trial to analyze the aftermath of their medicinal use. Nature is enriched with compounds that have antiviral activities and can potentially play a pivotal role to inhibit this virus. This study focuses on the phytochemicals that have the potential to exhibit antiviral activities. A large number of compounds were screened and a cohort of most suitable ones are suggested via in-silico techniques which are used worldwide for drug discovery such as docking, binding analysis, Universal Force Field Analysis, Broyden-Fletcher-Goldfarb-Shanno (BFGS) Method, Molecular Dynamic Simulation, and Electrostatic Potential Calculation. The proposed compounds are naturally occurring substances with low toxicity, very few side effects, proven anti-pathogenic effects, and most importantly are easily available.</p>

Identifying Therapeutic Compounds Targeting RNA-Dependent-RNA-Polymerase of Sars-Cov-2

<p>COVID-19 emerged as the biggest threat of this century for mankind and later it spread across the globe through human to human transmission. Scientists rushed to understand the structure and mechanism of the virus so that antiviral drugs or vaccines to control this disease can be developed. A key to stop the progression of the disease is to inhibit the replication mechanism of Sars-Cov-2. RNA-dependent-RNA polymerase protein also called RdRp protein is the engine of Sars-Cov-2 that replicates the virus using viral RNA when it gains entry into the human cell. Numerous drugs proposed for the treatment of COVID-19 such as Camostat Mesylate, Remdesivir, Famotidine, Hesperidin, etc. are under trial to analyze the aftermath of their medicinal use. Nature is enriched with compounds that have antiviral activities and can potentially play a pivotal role to inhibit this virus. This study focuses on the phytochemicals that have the potential to exhibit antiviral activities. A large number of compounds were screened and a cohort of most suitable ones are suggested via in-silico techniques which are used worldwide for drug discovery such as docking, binding analysis, Universal Force Field Analysis, Broyden-Fletcher-Goldfarb-Shanno (BFGS) Method, Molecular Dynamic Simulation, and Electrostatic Potential Calculation. The proposed compounds are naturally occurring substances with low toxicity, very few side effects, proven anti-pathogenic effects, and most importantly are easily available.</p>

Identifying Therapeutic Compounds Targeting RNA-Dependent-RNA-Polymerase of Sars-Cov-2

<p>COVID-19 emerged as the biggest threat of this century for mankind and later it spread across the globe through human to human transmission. Scientists rushed to understand the structure and mechanism of the virus so that antiviral drugs or vaccines to control this disease can be developed. A key to stop the progression of the disease is to inhibit the replication mechanism of Sars-Cov-2. RNA-dependent-RNA polymerase protein also called RdRp protein is the engine of Sars-Cov-2 that replicates the virus using viral RNA when it gains entry into the human cell. Numerous drugs proposed for the treatment of COVID-19 such as Camostat Mesylate, Remdesivir, Famotidine, Hesperidin, etc. are under trial to analyze the aftermath of their medicinal use. Nature is enriched with compounds that have antiviral activities and can potentially play a pivotal role to inhibit this virus. This study focuses on the phytochemicals that have the potential to exhibit antiviral activities. A large number of compounds were screened and a cohort of most suitable ones are suggested via in-silico techniques which are used worldwide for drug discovery such as docking, binding analysis, Universal Force Field Analysis, Broyden-Fletcher-Goldfarb-Shanno (BFGS) Method, Molecular Dynamic Simulation, and Electrostatic Potential Calculation. The proposed compounds are naturally occurring substances with low toxicity, very few side effects, proven anti-pathogenic effects, and most importantly are easily available.</p>

Strong inhibition of M-Protease activity of Coronavirus by using PX-12 inhibitor based on ab initio ONIOM calculations

In this study, the interaction of seven potential inhibitors in complex with SARS-CoV-2’s M protease (Mpro) is modelled and optimized using ONIOM (Own N-layered Integrated molecular Orbital and molecular Mechanics; QM/MM) approach. Density functional theory is used for the small system and Universal Force Field is used for the rest of the molecule with ONIOM (m062x/6-311++G (d,p):UFF) model chemistry. The seven inhibitors that are used in this study are N3, ebselen, disulfiram, tideglusib, carmofur, shikonin and PX-12. The calculated interaction energy between the inhibitor and Mpro shows a strong inhibition of Mpro activity with N3, ebselen as well as PX-12 inhibitors. The two former inhibitors are previously reported as strong inhibitors; however, the strong inhibition effect of PX-12 has not been previously reported. The results of this study can provide useful insight into designing an effective inhibitor drug for SARS-nCoV, suggesting a better inhibition from PX-12 than ebselen.