Accurate modeling of nonbonded interactions between protein kinases and their small molecule inhibitors is essential for structure-based drug design. Quantum chemical methods such as density functional theory (DFT) hold significant promise for quanti...
Accurate determination of intermolecular non-covalent-bonded or non-bonded interactions is the key to potentially useful molecular dynamics simulations of polymer systems. However, it is challenging to balance both the accuracy and computational cost...
In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X). Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as t...
Introducing organic functional groups to adsorbent surfaces enhances vanadium adsorption, an effective strategy for vanadium enrichment. In a quest for a profounder comprehension of the above adsorption mechanism, this study synthesized five types of...
Using the DFT method, an analogue of R,R-t-Bu-BenzP* was tried as a potential ligand for Ni-catalyzed asymmetric hydrogenation. This ligand contains benzyl groups instead of the t-Bu groups in R,R-t-Bu-BenzP*. Computational results imply that the R,R...
In this paper, we report the synthesis and biological evaluation of picolylamide-based diselenides with the aim of developing a new series of diselenides with O···Se non-bonded interactions. The synthesis of diselenides was performed by a simple and...
DFT-D3 calculations based on structural X-ray diffraction data obtained for 3-oxo-camphorsulfonyl imine (1), camphorsulfonyl chloride (2) and seven camphor sulfonimines (O2SNC10H13NR, L1−L7), from which L2 (R=4-OHC6H4), L4 (R=4-ClC6H4) and L6 (...
The electrostatic potential near to the oxygen atom in each of the cyclic ethers 2,5-dihydrofuran, oxetane and oxirane has been calculated by using a distributed multipole analysis (DMA) of each molecule. The electrostatic potential energy V(φ) of a...
A melt of short semi-flexible polymers with hard-sphere-type non-bonded interaction undergoes a first-order crystallisation transition at lower density than a melt of hard-sphere monomers or a flexible hard-sphere chain. In contrast to the flexible h...
The anion, cation, and radical structural forms of B2N (−,0,+) were studied in the case of symmetry breaking (SB) inside a (5, 5) BN nanotube ring and were also compared in terms of non-covalent interaction between these two parts. The non-bond...
In QTAIM dual-functional analysis, Hb(rc) is plotted versus Hb(rc) − Vb(rc)/2 for the interactions, where Hb(rc) and Vb(rc) are the total electron energy densities and potential energy densities, respectively, at the bond critical points (BCPs)...
Since the first preparation of triptycene, great progress has been made with respect to its synthesis and the understanding of its properties. Interest in triptycene-based systems is intense; in recent years, advances in the synthetic methodology and...
Herein, we describe a simple and efficient route to access aniline-derived diselenides and evaluate their antioxidant/GPx-mimetic properties. The diselenides were obtained in good yields via ipso-substitution/reduction from the readily available 2-ni...
The intrinsic dynamic and static nature of the π···π interactions between the phenyl groups in proximity of helicenes 3–12 are elucidated with the quantum theory of atoms-in-molecules dual functional analysis (QTAIM-D...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continually undergoes mutation, leading to variants with altered pathogenicity and transmissibility. The Omicron variant (B.1.1.529), first identified in S...
Chiral bifunctional dual H-bond donor catalysts have become one of the pillars of organocatalysis. They include squaramide, thiosquaramide, thiourea, urea, and even selenourea-based catalysts combined with chiral amines, cinchona alkaloids, sulfides,...
In order to understand the structure-property relationship, SPR, an energy-partitioning quest for the origin of the barrier to the internal rotation of two iso-structuralmolecules, hydrogen peroxide, H2O2, and fluorine peroxide, F2O2 is performed. Th...
Protein kinases are key enzymes in many signal transduction pathways, and play a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. However, aberrant function of kinases has been associated with cancers an...
Generic polymer models capturing the chain connectivity and the non-bonded excluded-volume interactions between polymer segments can be classified into hard- and soft-core models depending on their non-bonded pair potential. Here we compared the corr...
In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I) and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus ch...
In this work, we propose a machine learning (ML)-based technique that can learn interatomic potential parameters for various particle–particle interactions employing quantum mechanics (QM) calculations. This ML model can be used as an alternati...
The role of specific interactions in the self-assembly process of low molecular weight gelators (LMWGs) was studied by altering the nonbonding interactions responsible for gel formation via structural modification of the gelator/nongelator. This was...
Atomistic modeling methods are successfully applied to understand interfacial interaction in nanoscale size and analyze adhesion mechanism in the organic–inorganic interface. In this paper, we review recent representative atomistic simulation works,...
In micro-injection molding, the interaction between the polymer and the mold insert has an important effect on demolding quality of nanostructure. An all-atom molecular dynamics simulation method was performed to study the effect of nanostructure sha...
Diaryl ureas (DU) are a cornerstone scaffold in organic and medicinal chemistry, celebrated for their unique structural attributes and broad range of biomedical applications. Their therapeutic reach has broadened beyond kinase inhibition in cancer th...
Amorphous solid dispersions (ASDs) have emerged as widespread formulations for drug delivery of poorly soluble active pharmaceutical ingredients (APIs). Predicting the API solubility with various carriers in the API–carrier mixture and the prin...
An amorphous polyethylene/silica (PE/S) interface exists in many materials. However, the research of the interfacial properties at microscale is lacking. Shear failure and adhesion properties of an amorphous PE/S interface are studied by molecular dy...
GTP-binding proteins are essential molecular switches that regulate a wide range of cellular processes. Their function relies on the specific recognition and binding of guanine within their binding pockets. This study aims to elucidate the molecular...
The X-ray structure of the title compound, formed at low conversion in the reaction of thiosalicylic acid with thionyl chloride, has been determined. The acid chloride groups are oriented to permit an attractive non-bonding O…S interaction. Me...
We investigate single and opposing silica plates, either bare of grafted, in contact with vacuum or melt phases, using self-consistent field theory. Solid–polymer and solid–solid nonbonded interactions are described by means of a Hamaker potential, i...
Injection molding is one of the main techniques for manufacturing microfluidic chips. As an important stage, the demolding process in injection molding will directly affect the quality of the functional unit of microfluidic chips (polymer microchanne...
PDE9 inhibitors have been studied to validate their potential to treat diabetes, neurodegenerative disorders, cardiovascular diseases, and erectile dysfunction. In this report, we have selected highly potent previously reported selective PDE9 inhibit...
In previous work by the authors, a new methodology was developed for Brownian dynamics/kinetic Monte Carlo (BD/kMC) simulations of polymer melts. In this study, this methodology is extended for dynamical simulations of crosslinked polymer networks in...
Herein, we report the single-crystal X-ray diffraction analysis of supramolecular host–guest systems based on triflate-functionalized pillar[5]arenes and 1,4-dibromobutane or n-hexane. The guest molecule was stabilized inside the pillar[5]arene...
Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been dev...
The effect of the temperature and salt solution on the structural characteristics of the protein 1BBL was investigated by molecular dynamics simulations. The paper presents simulation results regarding the non-bonded energy and the structural stabili...
For the first time, the thermal conductivities of vulcanized polybutadiene and polyisoprene have been investigated according to their degree of crosslinking. The C-C and C-S-S-C crosslink bridges, which can be obtained via vulcanization processes usi...
A systematic simulation study was performed to investigate the interlayer interactions in a 1:1 layered phyllosilicate clay, kaolinite. Atomistic simulations with classical realistic force fields (INTERFACE and ClayFF) were used to examine the influe...
The longevity of asphalt pavements is a key focus of road engineering, which closely relates to the self-healing ability of bitumen. Our work aims to establish a CGMD model and matched force field for bitumen and break through the limitations of the...
Concerns have been raised about the high number of mutations in the spike protein of the new emergence of the highly transmissible Omicron variant (B.1.1529 lineage) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This variant’...
The SARS-CoV-2 main protease (Mpro), essential for viral replication, remains a prime target for antiviral drug design against COVID-19 and related coronaviruses. In this study, we present a systematic investigation into the molecular determinants of...
Manganese monoxide (MnO), a versatile manganese oxide, is highly regarded for its potential to address heavy metal and radioactive contamination effectively. In this study, we investigated the adsorption mechanism of strontium nitrate solution on MnO...
With the ever-increasing interest in low-dimensional materials, it is urgent to understand the effect of strain on these kinds of structures. In this study, taking the CF2Si monolayer as an example, a computational study was carried out to investigat...
The self-assembly process of β-D-glucose oligomers on the surface of cellulose Iβ microfibril involves crystallization, and this process is analyzed herein, in terms of the length and flexibility of the oligomer chain, by means of molecular...
Density functional theory calculations were performed to elucidate the mechanistic details and origins of the selectivity of the nickel-catalyzed hydroboration of vinylarenes using B2pin2/MeOH. The catalytic cycles involved four sequential elementary...
The development of anticancer drugs is costly and time intensive. Computational approaches optimize the process by studying molecules such as naphthoquinones. This research explores the quantitative structure–activity relationship (QSPR) and mo...
Recently, the accumulation of Amyloid Beta (Aβ) in the brain has been linked to the development of Alzheimer’s disease (AD) through the formation of aggregated plaques and neurofibrillary tangles (NFTs). Although carbon nanoparticles were...
The importance of chirality in drug development is unquestionable, with chiral liquid chromatography (LC) being the most adequate technique for its analysis. Among the various types of chiral stationary phases (CSPs) for LC, brush-type CSPs provide t...
This paper presents a theoretical formalism for describing systems of semiflexible polymers, which can have density variations due to finite compressibility and exhibit an isotropic-nematic transition. The molecular architecture of the semiflexible p...
Nitryl cyanide, O2NCN, as a new high-energy molecule, has not yet been successfully synthesized. It has prompted us to conduct a theoretical study of its possible space structures and properties. The RESP charges and the most stable spatial structure...
of 3