Structural and Spectral characterization, Topological study and activity prediction of antiviral (E)-5-(diethylamino)-2-((3,5-dinitrophenylimino)methyl)phenol against SARS-CoV-2 Main Protease

The (E)-5-(diethylamino)-2-((3,5-dinitrophenylimino)methyl)phenol was deliberated by Ultraviolet-Visible (UV-Vis) and Fourier Transform Infrared (FT-IR) spectroscopy techniques. Hirshfeld surface analysis was performed to analyze the contribution of intermolecular contacts in crystal structure of the studied Schiff base ligand. The plots of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and the electrostatic potential (ESP) were used to research the nucleophilic and electrophilic attack sites for the Schiff base ligand. According to the ESP analysis, the electrophilic reactivity was mainly found in nitro and hydroxy groups attached to phenyl rings, while the nucleophilic attack was more concentrated on hydrogen atoms. Major contributions from molecular orbitals to the electronic transitions computed according to the time-dependent DFT (TD-DFT) method were investigated using chloroform as a solvent. The topological parameters; electron density, Laplacian of electron density, kinetic energy, electron potential energy density, total electron energy density, ellipticity, hydrogen bond energy at the bond critical points have been evaluated. The compound was docked into the severe acute respiratory syndrome coronavirus 2, including a 3-chymotrypsin-like protease receptor's active site with the PDB ID 6LU7. The Schiff base ligand exhibited a good activity against coronavirus main protease receptor with 6LU7 protein as compared with Chloroquine, Favipiravir, and Remdesivir with −4.68 kcal/mol value of the binding energy.

Insights from the Interfaces of Corona Viral Proteins: Homomers Versus Heteromers

The outbreak of COVID-19 and its mutant variants has become a life-threatening and fatal viral disease to mankind. Several studies have been carried out to identify an effective receptor against coronavirus using clinically driven samples distinguished as hematological, immunological and biochemical biomarkers. Simultaneously, protein interfaces are being researched to understand the structural and functional mechanism of action. Therefore, we characterized and examined the interfaces of corona viral proteins using a dataset consisting of 366 homomeric and 199 heteromeric protein interfaces. The interfaces were analyzed using six parameters including interface area, interface size, van der Waal, hydrogen bond, electrostatic and total stabilizing energies. We observed the interfaces of corona viral proteins (homomer and heteromer) to be alike. Therefore, we clustered the interfaces based on the percent contribution of vdW towards total stabilizing energy as vdW energy dominant (≥60%) and vdW energy subdominant (<60%). We found 91% of interfaces to have vdW energy in dominance with large interface size [146±29 (homomer) and 122±29 (heteromer)] and interface area [1690±683 (homomer) and 1306±355 (heteromer)]. However, we also observed 9% of interfaces to have vdW energy in sub-dominance with small interface size [60±12 (homomer) and 41±20 (heteromer)] and interface area [472±174 (homomer) and 310±199 (heteromer)]. We noticed the interface area of large interfaces to be four-fold more when compared to small interfaces in homomer and heteromer. It was interesting to observe that the small interfaces of homomers to be rich in electrostatics (r2=0.50) destitute of hydrogen bond energy (r2=0.04). However, the heteromeric interfaces were equally pronounced with hydrogen bond (r2=0.70) and electrostatic (r2=0.61) energies. Hence, our earlier findings stating that the small protein interfaces are rich in electrostatic energy remaintrue with the homomeric interfaces of corona viral proteins whereas not in heteromeric interfaces.

Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy

Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.

A theoretical insight in interactions of some chemical compounds as mTOR inhibitors

Background A series of known Food and Drug Administration (FDA) approved anticancer drugs were collected from the literature and docked against mTOR receptor which has been identified in present time as a target for therapeutic anticancer agents. The compounds binding affinity were calculated after minimising the interaction within the binding pockets’ of the mTOR (4JT6) receptor. Results The result shows that PF-04691502 ligand best inhibited mTOR while occupying the Adenosine triphosphate (ATP)-binding site on the receptor. PF-04691502 had the best binding affinity with a reported value of − 39.261 kcal/mol, and a hydrogen bond energy contribution of − 8.326 kcal/mol. Polamid529 is also found to have a good binding affinity of − 36.75 kcal/mol with the receptor, but was less significant than that calculated for the reference or standard inhibitor (X6K) used (− 37.862 kcal/mol). Further analysis revealed that Palomid529 formed a more stable complex with the receptor than torin2 and X6K due to the significant hydrogen bond contributions it adds to its overall binding score. Conclusion PF-04691502 ligand was identified as the best inhibitor due to its high binding affinity for mTOR and should be considered as the best alternative to the reference inhibitor X6K.

Mechanism and Characteristics of CH4/CO2/H2O Adsorption in Lignite Molecules

Adsorption characteristics of coalbed methane (CBM) are significant to investigate the absorption of coal, shale, and porous media. In particular, adsorption characteristics of CH4, CO2, and H2O play an important role in predicting CBM output and geologic sequestration potentials of CO2 in research fields of CO2-enhanced CBM recovery (CO2-ECBM) and sequestration of CO2. In this work, adsorption characteristics of CH4, CO2, and H2O in lignite molecules were simulated through the grand canonical Monte Carlo (GCMC) method and molecular dynamics (MD) method. Research results demonstrated that given the same temperature and pressure, the ultimate adsorption capacity of lignite per unit to H2O is the highest, followed by those of CO2 and CH4 successively. All isothermal adsorption curves conform to the “I-type” characteristics. In the saturated molecular configuration, gas molecules show different distribution patterns at two sides of the lignite molecule chain. Lignite has typical physical adsorption to CH4 and CO2, with adsorption energy provided by nonbonding energy. However, lignite has both physical adsorption and chemical adsorption to H2O, with adsorption energy provided by both nonbonding energy and hydrogen bond energy. High temperature is against adsorption of CH4, CO2, and H2O. Temperature might inhibit adsorption of gas molecules. Research conclusions lay foundations for the exploitation and development of CBM and relevant studies on sequestration of CO2.

Hyperhomogeneity of hydrogen-disordered ice and its origin: the residual entropy compatible with the disparity in hydrogen bond energy

The residual entropy is one of the most crucial properties for the existence of a large number of ice polymorphs. The residual entropy has been estimated by Pauling assuming that there is no large difference between the hydrogen bond energies in ice. This simple model accurately predicts the entropy change of the phase transition between a hydrogen-disordered ice phase and its hydrogen-ordered counterpart. This fact is, however, incompatible with another fact that the difference in the pair interaction energies involved in hydrogen bonds in an ice phase can be larger than the thermal energy of a few kJ/mol. Here we propose a mechanism that reconciles them by considering the equality of the binding energy in each molecule rather than the pair interaction energy of the proximate pair. The topological feature of ice, called the ice rules, allows us to replace the interactions of a water molecule with the other individual molecules by that with the collections of the dipoles represented by directed cycles consisting of O-H vectors. This resummation reveals that molecular environments in ice are extremely homogeneous thereby providing a solid basis for Pauling's model.

Computational studies of ionic liquids as co-catalyst for CO2 electrochemical reduction to produce syngas using COSMO-RS

Transforming carbon dioxide (CO2) into value-added products through electrochemical reduction reaction (CO2ERR) is a promising technique due to its potential advantages using renewable energy. The main challenge is to find a stable catalytic system that could minimize the reaction overpotential with high faradaic efficiency and high current density. Ionic liquids (ILs) as electrolyte in CO2ERR have attracted attention due to the advantages of their unique properties in enhancing catalytic efficiency. For better performance, a systematic understanding of the role of ILs as electrocatalyst is needed. Therefore, this paper aims to correlate the performance of ILs as co-catalyst in (CO2ERR) with the lowest unoccupied molecular orbital (LUMO) energy level and the interaction energy as predicted by quantum chemical calculation using Conductor like Screening Model for Real Solvents (COSMO-RS) and Turbomole. The results show strong linearity (R2=0.98) between hydrogen bond energy (HB) and LUMO values. It is demonstrated that as HB increases, the LUMO value decreases, and the catalytic activity for CO2ERR also increases. This result allows further understanding on the correlation between the molecular structure and the catalytic activity for CO2ERR. It can serve as a priori prediction to aid in the design of new effective catalysts.

Hydrogen bonding systems in birch bark

Произведено сравнение систем водородных связей во внешнем и внутреннем слоях березовой бересты, в сравнении с водородными связями в высококачественной бумаге и в образце выделенной из древесины целлюлозы. Интервал исследуемых частот от 3000 до 3700 см-1, ограничен областью поглощения гидроксильными ОН-группами, частоты которых наиболее чувствительны к возникновению Н-связей. Для оценки параметров Н-связей проводилась деконволюция полос поглощения ОН-групп гауссовыми компонентами. Для корректного выделения поглощения гидроксильными группамипервоначально деконволюции подвергается весь фрагмент, включающий в себя полосы поглощения как метиленовым, так и гидроксильными группами. В дальнейшем анализировались только параметры контуров деконволюции, относящейся к гидроксильным группам. Принималось, что каждый компонент деконволюции может быть ассоциирован с определенным типом водородной связи. Определялся сдвиг частот компонентов деконволюции относительно собственной частоты колебаний изолированной гидроксильной группы, не охваченной по этой причине водородной связью. Для определения энергии водородных связей использовались литературные данные по корреляции энергии водородной связи с частотным сдвигом. Относительная плотность водородных связей оценивалась по отношению площадей контуров деконволюции. A comparison was made of the hydrogen bond systems in the outer and inner layer of birch bark, as well as a comparison of high-quality paper with a sample of pure pulp. The range of frequencies under study from 3000 to 3700 cm-1 is limited by the absorption region by hydroxyl OH groups, the frequencies of which are most sensitive to the occurrence of H bonds. To estimate the parameters of H-bonds, the absorption bands of OH groups were deconvolved by Gaussian components. In order to correctly isolate the absorption by hydroxyl groups, the entire fragment, whichincludes absorption bands of both methylene and hydroxyl groups, is initially deconvolved. In the future, only the parameters of the deconvolution contours related to hydroxyl groups were analyzed. It was assumed that each component of deconvolution can be associated with a certain type of hydrogen bond. The frequency shift of the components of the deconvolution was determined relative to the natural frequency of vibrations of the isolated hydroxyl group, which is therefore not covered by a hydrogen bond. To determine the energy of hydrogen bonds, we used literature data on the correlation of the hydrogen bond energy with a frequency shift. The relative density of hydrogen bonds was estimated by the ratio of the area of the contours of deconvolution.

Intramolecular Hydrogen Bond Energy and Its Decomposition—O–H∙∙∙O Interactions

The method to calculate the energy of intramolecular hydrogen bond is proposed and tested for a sample of malonaldehyde and its fluorine derivatives; the corresponding calculations were performed at the ωB97XD/aug-cc-pVTZ level. This method based on relationships found for related intermolecular hydrogen bonds is compared with other approaches which may be applied to estimate the intramolecular hydrogen bond energy. Particularly, methods based on the comparison of the system that contains the intramolecular hydrogen bond compared with corresponding conformations where such interaction does not occur are discussed. The function-based energy decomposition analysis, FB-EDA, of the intramolecular hydrogen bonds is also proposed here.