Journal of Computational Chemistry

doi: 10.1002/jcc.26274pmid: N/A

Yuan, Fang; Yang, Zhifang; Zhang, Xiaoying; Tong, Cuiyan; Gahungu, Godefroid; Li, Wenliang; Zhang, Jingping

doi: 10.1002/jcc.26510pmid: 33713464

The effects of functional groups (including OH, OCH3, NH2, CH2NH2, COOH, SO3H, OCO(CH2)2COOH(E‐COOH), and (CH2)4COOH(c‐COOH)) in 3D covalent organic frameworks (3D‐COFs) on CO2 adsorption and separation are investigated by grand canonical Monte Carlo (GCMC) simulations and density functional theory calculations. The results indicate that interaction between CO2 and the framework is the main factor for determining CO2 uptakes at low pressure, while pore size becomes the decisive factor at high pressure. The binding energy of CO2 with functionalized linker is correlated to CO2 uptake at 0.3 bar and 298 K on 3D‐COF‐1, suggesting functional groups play a key role in CO2 capture in microporous 3D‐COFs. Moreover, CO2 selectivity over CH4, N2, and H2 can be significantly enhanced by functionalization, where CH2NH2, COOH, SO3H, and E‐COOH enhance CO2 adsorption more effectively at 1 bar. Among them, SO3H is the most promising functional group in 3D‐COFs for CO2 separation.

Sixto‐López, Yudibeth; Martínez‐Archundia, Marlet

doi: 10.1002/jcc.26512pmid: 33713492

SARS‐CoV and SARS‐CoV‐2 belong to the subfamily Coronaviridae and infect humans, they are constituted by four structural proteins: Spike glycoprotein (S), membrane (M), envelope (E) and nucleocapsid (N), and nonstructural proteins, such as Nsp15 protein which is exclusively present on nidoviruses and is absent in other RNA viruses, making it an ideal target in the field of drug design. A virtual screening strategy to search for potential drugs was proposed, using molecular docking to explore a library of approved drugs available in the DrugBank database in order to identify possible NSP15 inhibitors to treat Covid19 disease. We found from the docking analysis that the antiviral drugs: Paritaprevir and Elbasvir, currently both approved for hepatitis C treatment which showed some of the lowest free binding energy values were considered as repositioning drugs to combat SARS‐CoV‐2. Furthermore, molecular dynamics simulations of the Apo and Holo‐Nsp15 systems were performed in order to get insights about the stability of these protein‐ligand complexes.

Shen, Shaojie; Jing, Xinyue; Zhang, Xueying; Li, Xiaoyan; Zeng, Yanli

doi: 10.1002/jcc.26513pmid: 33729600

The noncovalent interactions involving heteronuclear ethylene analogues H2CEH2 (E = Si, Ge and Sn) have been studied by the Møller–Plesset perturbation theory to investigate the competition and cooperativity between the hydrogen/halogen bond and π‐hole bond. H2CEH2 has a dual role of being a Lewis base and acid with the region of π‐electron accumulation above the carbon atom and the region of π‐electron depletion (π‐hole) above the E atom to participate in the NCX···CE (X = H and Cl) hydrogen/halogen bond and CE···NCY (Y = H, Cl, Li and Na) π‐hole bond, respectively. When HCN/ClCN interacts with H2CEH2 by two sites, the strength of hydrogen bond/halogen bond is stronger than that of π‐hole bond. The π‐hole bond becomes obviously stronger when the metal substituent of YCN (Y = Li and Na) interacting with H2CEH2, showing the character of partial covalent, its strength is much greater than that of hydrogen/halogen bond. In the ternary complexes, both hydrogen/halogen bond and π‐hole bond are simultaneously strengthened compared to those in the binary complexes, especially in the systems containing alkali metal.

Haghshenas, Hamed; Kaviani, Bita; Firouzeh, Monireh; Tavakol, Hossein

doi: 10.1002/jcc.26514pmid: 33719136

In continuation of the previous reports on a combination of 3D‐quantitative structure–activity relationships (QSAR) with computational molecular dynamics (MD) studies, a new variation of 3D‐QSAR/MD method has been employed for drug‐design as an alternative or supplementary for the typical experimental methods. The presented method is more cost‐effective and less time‐consuming than the previous methods and avoids several restrictions of experimental methods, such as validity estimation, and predictability. For this purpose, seven inhibitors for bromodomain (BRD)‐containing protein, as an important protein in the development of different types of cancer and responsible for oncogenic rearrangements, have been selected to study of their interactions by docking and MD simulations using molecular mechanics/generalized born surface area (MM/GBSA) method. To build the proposed model, a common variant of 3D‐QSAR methods, comparative molecular field analysis has been employed using a dataset of 100 MD‐extracted ligand conformations and their corresponding MM/GBSA BRD4‐binding energies. The results showed excellent predictability of the generated model for both the training set and test groups. Finally, two new inhibitors were selected among total 4000 designed derivatives (generated through evolutionary techniques) using the proposed 3D‐QSAR‐MD model. The potentials of these inhibitors were assessed by MD simulations, which showed the higher inhibitory of these compounds than the previous inhibitors. Therefore, this method showed high potentials for acceleration of the procedure of drug design and a basis for joining researchers in computational biology and pharmaceutical sciences.

Walter, Vivien; Ruscher, Céline; Benzerara, Olivier; Thalmann, Fabrice

doi: 10.1002/jcc.26508pmid: 33675541

Machine Learning‐assisted Lipid Phase Analysis (MLLPA) is a new Python 3 module developed to analyze phase domains in a lipid membrane based on lipid molecular states. Reading standard simulation coordinate and trajectory files, the software first analyze the phase composition of the lipid membrane by using machine learning tools to label each individual molecules with respect to their state, and then decompose the simulation box using Voronoi tessellations to analyze the local environment of all the molecules of interest. MLLPA is versatile as it can read from multiple format (e.g., GROMACS, LAMMPS) and from either all‐atom (e.g., CHARMM36) or coarse‐grain models (e.g., Martini). It can also analyze multiple geometries of membranes (e.g., bilayers, vesicles). Finally, the software allows for training with more than two phases, allowing for multiple phase coexistence analysis.

Andreadi, Nikolai; Mitrofanov, Artem; Eliseev, Artem; Matveev, Petr; Kalmykov, Stepan; Petrov, Vladimir

doi: 10.1002/jcc.26509pmid: 33665857

The assessment of the radiolytic stability of media is an important task in the fields of nuclear power engineering and radiochemistry. Such studies must be carried out in special laboratory conditions with the use of sources of ionizing radiation, which may increase personal doses of the staff. In addition, difficulties arise in studying the products of irradiated media. While it is impossible to abandon experiments to obtain reliable results in this area, computational methods of quantum chemistry can reduce the number of experiments and help understand the mechanisms of the reactions that occur during radiolysis. Here we would like to present a software shell of the Qb@ll program performing time‐dependent density functional theory simulations of the radiolysis process.