Human thymidylate synthase (hTS) is a validated drug target for chemotherapy. A virtual screening experiment was used to prioritize a list of compounds from African Natural Products Databases docked against the orthosteric binding pocket of hTS. Consensus scores of binding affinities from ensemble-based virtual screening, hydrated docking and MM-PBSA calculations ranked compounds NEA4433 and NEA4434 as the best candidates owing to binding affinity scores in the picomolar order, their excellent ADMET profiles and the good stability of the protein-ligand complexes formed. The current study demonstrates the role of water in small molecule binding to hTS in mediating protein-ligand interactions. Similarly, the robust ensemble docking (relaxed scheme complex) ranked NEA4433 and NEA4434 as the best candidates. Furthermore, the best candidates prioritized were shown to strongly interact with the same residues that interacted with hTS substrate and cofactor.

This study corresponds to a molecular electron density theory (MEDT) investigation to shed light on the energetics, selectivities, and molecular mechanistic aspects of an experimental domino reaction. Theoretical evidences at the M06-2X/6-31G(d) level indicates that this domino reaction includes three different successive steps and is initialized by a stepwise HCl elimination from precursor chlorohydrazone NPCH to yield nitrile imine NI-2. A subsequent stepwise and highly regioselective [3 + 2] cycloaddition (32CA) reaction of NI-2 toward tetramethylguanidine TMG-3 affords corresponding formal [3 + 2] cycloadduct CA-1 as the sole product. Finally, a stepwise HNMe2 elimination experienced by CA-1 leads to amino triazole ATA as an aromatic five-membered target product. Computed rate constants reveal that the HCl elimination step should be considered as the bottleneck of this domino reaction. However, a topological analysis of electron localization function (ELF) of NI-2 demonstrates a zwitterionic type (zw-type) 32 C A reaction is expected between NI-2 and TMG-3. This 32CA reaction also displays an almost noticeable polar character arising from moderate electrophilicity and strong nucleophilicity of NI-2 and TMG-3, respectively. The regioselectivity of 32CA reaction can be explained via analysis of Parr functions values calculated at the reactive sites of reagents. The molecular mechanism of the 32CA reaction was explored through portraying bond forming/breaking patterns involved in this polar, stepwise, and zw-type reaction by means of the ELF analysis. Indeed, formation of both C-N single bonds along the first and second steps takes place through coupling of the corresponding pseudoradical centers.

The reaction mechanism of ethylene (ET) polymerization catalyzed by the phenoxy-imine (FI) ligands using DFT calculations was studied. Among five possible isomers, isomer A which has an octahedral geometry and a (cis-N/trans-O/cis-Cl) arrangement is the most stable pre-reaction Ti-FI dichloride complex. The isomer A can be activated by MAO to form the active catalyst and the active form was used for the study of the mechanism for Ti-FI. The second ethylene insertion was found to be the rate-determining step of the catalyzed ethylene polymerization. To examine the effect of group IVB transition metals (M = Ti, Zr, Hf) substitutions, calculated activation energies at the rate-determining step (EaRDS) were compared, where values of EaRDS of Zr < Hf < Ti agree with experiments. Moreover, we examined the effect of substitution on (O, X) ligands of the Ti-phenoxy-imine (Ti-1) based catalyst. The results revealed that EaRDS of (O, N) > (O, O) > (O, P) > O, S). Hence, the (O, S) ligand has the highest potential to improve the catalytic activity of the Ti-FI catalyst. We also found the activation energy to be related to the Ti-X distance. In addition, a novel Ni-based FI catalyst was investigated. The results indicated that the nickel (II) complex based on the phenoxy-imine (O, N) ligand in the square-planar geometry is more active than in the octahedral geometry. This work provides fundamental insights into the reaction mechanism of M - FI catalysts which can be used for the design and development of M - FI catalysts for ET polymerization.

In this study, four hole-transporting materials (JY-M1, JY-M2, JY-M3, and JY-M4) are designed by modifying benzothiadiazole-based core with diphenylamine-based carbazole via acceptors through thiophene linkers. The designed molecules exhibited deeper HOMO energy with smaller energy gaps than the reference JY molecule which enhance their hole mobility. The absorption spectra of the JY-M1, JY-M2, JY-M3, and JY-M4 molecules are located at 380 nm to 407 nm in the gaseous phase and 397 nm to 433 nm in the solvent phase, which is red-shifted and higher than the reference molecule, demonstrating that designed molecules possess improved light absorption properties and enhanced effective hole transfer. The dipole moments of the designed molecules (14.74 D to 26.12 D) indicate a greater ability for charge separation, solubility and will be beneficial to produce multilayer films. Moreover, the results of hole reorganization energy (0.38198 eV to 0.45304 eV) and charge transfer integral (0.14315 eV to 0.14665 eV) of designing molecules show improved hole mobility and lower recombination losses compared to the JY molecule. Overall, we suggested that the structural modifications in the designed molecules contributed to their enhanced efficiency in converting light energy into electrical energy and have the potential for utilization in solar devices, paving the way for future advancements in the field of photovoltaics.

Physicochemical properties of the binary mixtures based on Caprylic acid: Quaternary ammonium salts (QAS) (7:3 mol ratio) are investigated using MD simulations. Considering the hydrophobic character of eutectic solvents based on long-chain fatty acids, the stability of the binary mixtures was investigated in the adjacent water. In order to investigate the effect of water on intermolecular interactions in binary mixtures, the structural properties of the binary mixtures in the pure state and adjacent to water were investigated at 310 K. Assessed structural properties include the combined distribution functions (CDFs), the radial distribution functions (RDFs), the angular distribution functions (ADFs), and the Hydrogen bonding network between HBA and HBD and Spatial distribution functions (SDF). We aimed to represent the structural stability of eutectic solvents based on Caprylic acid and Quaternary ammonium salts (QAS) as a function of the alkyl chain length of cations, the evidence was found for the interaction between the chloride anion leads to the transition of HBA to the water-rich phase. The alkyl chain length of cations of Quaternary ammonium salts shows the stability of eutectic solvents in the adjacent water.

The glucocorticoid receptor (GR) is a nuclear receptor that controls critical biological processes by regulating the transcription of specific genes. GR transcriptional activity is modulated by a series of ligands and coenzymes, where a ligand can act as an agonist or antagonist. GR agonists, such as the glucocorticoids dexamethasone (DEX) and prednisolone, are widely prescribed to patients with inflammatory and autoimmune diseases. DEX is also used to induce osteogenic differentiation in vitro. Recently, it has been highlighted that DEX induces changes in the osteogenic differentiation of human mesenchymal stromal cells by downregulating the transcription factor SRY-box transcription factor 9 (SOX9) and upregulating the peroxisome proliferator-activated receptor γ (PPARG). SOX9 is fundamental in the control of chondrogenesis, but also in osteogenesis by acting as a dominant-negative of RUNX2. Many processes remain to be clarified during cell fate determination, such as the interplay between the key transcription factors. The main objective pursued by this work is to shed light on the interaction between GR and SOX9 in the presence and absence of DEX at an atomic level of resolution using molecular dynamics simulations. The outcome of this research could help the understanding of possible molecular interactions between GR and SOX9 and their role in the determination of cell fate. The results highlight the key residues at the interface between GR and SOX9 involved in the complexation process and shed light on the mechanism through which DEX modulates GR-SOX9 binding and exerts its biological activity.

Density functional theory calculations at the M06-2X/aug-cc-pVTZ level of theory have been used to examine the Nitroso-Diels-Alder (N-D-A) cycloaddition reaction between the CH3N=O and cis-1,3-butadiene in the presence of PO2X (X=F, Cl, OH) as a catalyst. The effect of the above PO2X compounds on the activation energy of the N-D-A reaction, has been studied here. In the first stage, the energies of two different bonding interactions, via P⋯N versus P⋯O binding, between the PO2X and CH3N=O molecules were calculated. The results showed that the largest values of the interaction energy between the above molecules belong to the PO2F, when connects to the nitrogen atom of the CH3N=O. Also, calculations showed that all the above PO2X compounds, decrease the activation energies of N-D-A reaction studied here via both P⋯N and P⋯O interactions. However, the largest effect on activation energies of the reaction belongs to the PO2F catalyst when acts via P⋯N bonding. The activation strain model (ASM) was used to analyze the influence of the PO2X catalyst on the studied reaction. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis were performed to understand the nature of forming interactions at the TS structures. The results of this study showed that the PO2X (X=F, Cl, OH) compounds may be suggested as efficient catalysts for N-D-A reactions.

The comprehension of the factors affecting the adsorption of ethanol over metals and metal alloys is a crucial step for the rational development of new catalysts for hydrogen production through ethanol reforming. In this work, we analyze the effect of combining Pt and Sn on a metal cluster on the complexation energy and reactivity for OH dehydrogenation of ethanol. Metal clusters of Pt10, Sn10 and Pt5Sn5 had their putative minimum located with the help of the artificial bee colony algorithm. Whereas the isolated Pt cluster shows a high degree of polarization (ESP surface), the Sn cluster shows a quite uniform electron density surface. The PtSn cluster is strongly polarized, with Pt atoms withdrawing electron density of Sn atoms. Complexation occurs with the oxygen atom of ethanol directed towards the point of highest electron potential in the ESP surface. Pt presents the highest complexation energy, -20.90 kcal/mol, against only -7.83 kcal/mol (at the B97-3c level). For the PtSn cluster, the value is intermediate, namely -12.39 kcal/mol. The more malleable electron density of Pt and its electron affinity are responsible for its highest complexation energy. These characteristics are partially transferred to the PtSn cluster. QTAIM results show that, for the PtSn cluster, the O-H bond in ethanol is somewhat weaker than for pure Pt and Sn. As a consequence, the energy barrier for the O-H dehydrogenation has its lowest value for the PtSn cluster, which shows that the alloying of two metals can lead to quite quite unexpected results opening the perspective for a more rational fine tuning of catalysts properties.

In this study, a detailed computational spectroscopic investigation of sabizabulin, a small molecule known as a tubulin inhibitor with potential antineoplastic, antiviral, and anti-inflammatory activities, has been presented. Our work utilizes Density Functional Theory (DFT) calculations to explore molecular optimization, thermodynamic characteristics, and the analysis of normal modes with vibrational assignments. We calculate essential properties such as standard zero-point vibrational energy, entropy, dipole moment, etc., based on data extracted from the optimized molecular structure. Additionally, we examine Mulliken charges and the Molecular Electrostatic Potential (MEP) plot to comprehend the electronic distribution and chemical activity of sabizabulin. Our findings provide valuable insights into the spectroscopic properties of sabizabulin, highlighting its potential therapeutic applications. Our work aims to explore future research directions that could expand the understanding of sabizabulin's actions and enhance its applicability in medical treatments.

Structures and UV-vis absorption spectra of the host-guest interaction of the methoxy cinnamic acid (MCA) derivatives and cyclodextrins (CDs) were performed by using the density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. All geometries of MCA derivatives (4-MCA, 245-MCA, 246-MCA), three types of CD (αCD, βCD, γCD), and five host-guest inclusion complexes between MCA and CD consisting of 4-MCA/αCD (1), 4-MCA/βCD (2), 245-MCA/βCD (3), 246-MCA/βCD (4), and 246-MCA/γCD (5) were fully optimized by using the M06-2X/6-31G (d,p) levels of theory. Two orientations (A and B) of the MCA guest molecule were considered. Upon examining the optimized geometry, five complexes of the methoxy cinnamic acid molecules are located inside the cavity of CD. Orientation B was more stable than orientation A because of the stronger intermolecular hydrogen bonds between the hydroxyl group of CD and the carboxylic group of MCA. The results indicated that the intermolecular hydrogen bond is mainly the driving force of formation between methoxy cinnamic acid and cyclodextrins. To reveal the host-guest interaction that is relevant to UV-filter compounds, the UV-vis absorption spectra were performed using TD-DFT calculations. The obtained results confirmed that orientation B is the most stable orientation and can absorb in both UVB and UVA regions which is similar to the parent MCA. Therefore, this knowledge will bring to understand the host-guest interaction between methoxy cinnamic acid and cyclodextrin complexes. The theoretical results are expected to provide valuable information for improving the stability of further UV-filter compounds.

In this paper we have studied the density functional theory of four drugs ibuprofen, alendronate, Sulfasalazine and paracetamol with quartz, propylamine, trimethylamine functionalized quartz and carboxyl modified carbon nanotube. The attractive and repulsive interaction energies between drugs and quartz is obtained at various pH values. The attractive and repulsive energies are well correlated with experimental drug loading and releasing behavior by mesoporous silica nanoparticles. Further, a theoretical model is developed that accounts the electrostatic interaction between silica and drug and the model can predict the drug loading and releasing behavior by silica nanoparticles at various pH values. Sulfasalazine can be taken orally and loaded with trimethyl ammonium functionalized mesoporous silica nanoparticles, which keeps the drug in tact with the carrier in the acidic environment of the stomach and releases it into the neutral or basic medium of the small intestine. Alendronate may be loaded and released from propylamine functionalized mesoporous silica nanoparticles in the ranges of 1-5 and > 8, respectively. Ibuprofen is absorbed in an acidic environment and released in basic conditions for carboxyl modified carbon nanotube. The loading and releasing pH ranges for paracetamol in trimethylammonium functionalized mesoporous silica nanoparticles are 4-8 and >8, respectively. We also convert the pH-dependent variant of the diffusion-controlled Higuchi equation. We have changed the original Higuchi equation to produce the pH-dependent variation by incorporating the Nernst-Planck equation into Flick's first law. The updated equation could be used to forecast when medication particles with varying release times will emerge from a nanoparticles matrix.

Hypercholesterolemia is a significant risk factor for atherosclerotic cardiovascular disease (ASCVD). Successful management of cholesterol metabolism disorders can prevent these ASCVD effectively. Asialoglycoprotein receptor 1 (ASGR1) is the main subtype of sialoglycoprotein receptor, which is specifically expressed in the liver and mediates the endocytosis of blood asialoglycoprotein to lysosome degradation. Recently, ASGR1 has been reported as a new therapeutic target for the treatment of hypercholesterolemia. In this study, the main aim was to identify natural ASGR1 inhibitors from plant food chemicals library through pharmacophore and docking based virtual screening. Total 14 phytochemicals of potential ASGR1 inhibitors were identified, which presented docking affinity higher than control compound through docking based virtual screening. The docking pose showed the top three hits interacted residues were located at active pocket of ASGR1 with hydrogen bonds, hydrophobic interactions and electrostatic interactions. The top three hits (ZINC85664954, ZINC169372863, and ZINC195764535) were then subjected to 200 ns molecular dynamics simulation to evaluate the stability of docked complexes. These results showed that selected phytochemicals bound to ASGR1 with higher stability than control compound. Binding free energy of each docked complex was calculated by the Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) method. The binding free energy of ZINC85664954, ZINC169372863, ZINC195764535, and control-ASGR1 docked complexes were -18.359, -13.303, -14.389, and -6.229 kcal/mol, respectively. This indicated that selected hits bound to ASGR1 with higher affinity than control compound. Network pharmacology analysis shows that these phytochemicals have obvious multiple-effects and can regulate various biochemical pathways related to hypercholesterolemia. Besides, selected phytochemicals have suitable pharmacokinetics properties, suggesting that these compounds may be potential drug candidates. This study may be contributed to rational design of novel ASGR1 inhibitors for treatment of hypercholesterolemia.

Minimizing the energy loss and improving the open circuit voltage of organic solar cells is still a primary concern for scientists working in this field. With the aim to enhance the photovoltaic performance of organic solar cells by minimizing energy loss and improving open circuit voltage, seven new acceptor molecules (LC1-LC7) are presented in this work. These molecules are designed by modifying the terminal acceptors of pre-existed "LC81" molecule based on an indacinodithiophene (IDT) fused core. The end-group modification approach is very fruitful in ameliorating the efficacy and optoelectric behavior of OSCs. The newly developed molecules presented remarkable improvements in performance-related parameters and optoelectronic properties. Among all designed molecules, LC7 exhibited the highest absorption maxima (λmax = 869 nm) with the lowest band-gap (1.79 eV), lowest excitation energy (Ex = 1.42 eV), lowest binding energy, and highest excited state lifetime (0.41 ns). The newly designed molecules LC2, LC3, and LC4 exhibited remarkably improved Voc that was 1.84 eV, 1.82 eV, and 1.79 eV accordingly, compared to the LC81 molecule with Voc of 1.74 eV LC2 molecule showed significant improvement in fill factor compared to the previously presented LC81 molecule. LC2, LC6, and LC7 showed a remarkable reduction in energy loss by showing Eloss values of 0.26 eV, 0.18 eV, and 0.25 eV than LC81 molecule (0.37 eV). These findings validate the supremacy of these developed molecules (especially LC2) as potential components of future OSCs.

Traditionally, nanocones as a drug delivery material allow controlled drug delivery close to the target area while reducing the toxicity and generic accumulation associated with traditional intravenous injection methods. In the current study, density functional theory (DFT) is employed to investigate the therapeutic potential of carbon nanocone oxide (ONC) as a carrier with zidovudine drug for the treatment of human immunodeficiency virus (HIV). The electronic ground state and excited state were studied to evaluate the drug carrier potential of ONC and Zidovudine-ONC complex. The Frontier Molecular Orbitals (FMOs) and Molecular Electrostatic Potential (MEPs) revealed that the ONC carrier acts as a donor and zidovudine as an acceptor. The FMOs confirmed the interaction between drug and carrier stabilization energy by calculating chemical hardness, material softness, electronegativity, Ionization energy and electron affinity. The natural bond analysis (NBO), non-covalent interaction (NCI) and electron localization function (ELF) revealed the charge transfer between zidovudine and ONC. The density of state (DOS) and Charge Deposition analysis (CDA) provided the charge transfer. To study the excited state of zidovudine, transition density matrix (TDM), UV(Ultra-visible), IR (infrared), Raman, and NMR (Nuclear Magnetic Resonance) spectra of ONC and zidovudine-ONC complex have been plotted. The spectra showed a significant red shift in the zidovudine-ONC complex. Photoinduced electron studies (PET) showed fluorescence quenching because of the interaction between the drug and the carrier and provided a graphical explanation of the distinct excited state. All the results show that the ONC carrier has therapeutic potential as a zidovudine carrier for the treatment of Human Immunodeficiency Virus (HIV).

The complete sets of homodesmotic reactions (HDR) for 107 acyclic alkyl free radicals С4-С9 of normal and branched structure were constructed using the graph-theoretic representation and analysis of a tested compound. The absolute enthalpies of the studied compounds and HDR reference structures were calculated using the M062X/cc-pVTZ level of theory. Based on these data, the thermal effects of HDRs were calculated and then applied to determine the standard enthalpies of formation of the studied radicals using the known enthalpies of formation of reference structures. The dissociation energies of BDE C-H and C-CH3 bonds were also calculated. The effect of radical structure on the BDE value is discussed, and a new effect of stabilization of the radical center in the skewed conformation of free radical is established; this effect has not been previously described in the scientific literature.

Interactive molecular dynamics simulation in virtual reality (iMD-VR) is emerging as a promising technique in molecular science. Here, we demonstrate its use in a range of fifteen applications in materials science and heterogeneous catalysis. In this work, the iMD-VR package Narupa is used with the MD package, DL_POLY [1]. We show how iMD-VR can be used to: (i) investigate the mechanism of lithium fast ion conduction by directing the formation of defects showing that vacancy transport is favoured over interstitialcy mechanisms, and (ii) guide a molecule through a zeolite pore to explore diffusion within zeolites, examining in detail the motion of methyl n-hexanoate in H-ZSM-5 zeolite and identifying bottlenecks restricting diffusion. iMD-VR allows users to manipulate these systems intuitively, to drive changes in them and observe the resulting changes in structure and dynamics. We make these simulations available, as a resource for both teaching and research. All simulation files, with videos, can be found online (https://doi.org/10.5281/zenodo.8252314) and are provided as open-source material.

Optical and electronic characteristics of the graphene nanosheets (GNS) could be altered by some structural defects such as double-vacancy and Stone-Wales ones. The physisorption manner of [MPI][BF4], [MPT1][BF4], [MPT2][BF4], and [MPTT][BF4] ionic liquids on intact and defective GNS surfaces were investigated using M06-2X/cc-pVDZ computational method. Capability for adsorption on the DV and SW graphene surfaces by TILs is increased by about 1.0-4.3 and 0.4-2.0 kcal/mol respectively. The electrostatic potential of the GNS-DV surface is more negative than the GNS-SW one which enables it to interact with cation parts of the adsorbed TILs so extensively. The highest adsorption energy belongs to the [MPI][BF4]/GNS-DV system. Adsorption of the TILs on the GNS surfaces leads to a decrease in the energy of the LUMO molecular orbital as well as their energy gap of them. Results revealed that the electrical conductivity, as well as absorption spectra of the GNS surfaces, are affected by TILs adsorption and defect nature.

In this project, the possibility of drug delivery application of three anti-Multiple sclerosis (MS) agents (containing diroximel fumarate (DXF), dimethyl fumarate (DMF), and mono methyl fumarate (MMF)) by using some heteroatom decorated graphitic carbonitride (g-C3N4) (as nano-sized carriers) have been systematically investigated. The results of the study have indicated that As-g-C3N4 QD is not a suitable candidate for drug delivery (at least in the cases of DMF, and DXF drugs); while, it would be an accurate semiconductor sensor for selective detection of each mentioned agents. Also, the use of the P-doped as well as pristine g-C3N4 QD could lead to weak electronic signals with relatively same values (in electronvolts). It means that P-g-C3N4, and g-C3N4 QDs are not good sensors for detection of each of the three considered drugs. However, those two sorbents would be suitable carriers for delivering of all three mentioned pharmaceuticals.

This manuscript presents the all-atom molecular dynamics simulations to investigate intermolecular structure and solvation thermodynamics of Na+ ion in two different ammonium-based protic ionic liquids (1) Butyl Ammonium hydrogen bisulfate [BA+][HSO4-], (2) Tri-butyl ammonium hydrogen bisulfate [TBA+][HSO4-]. The ionic liquid [BA+][HSO4-] show a more coordinated behavior when compared to [TBA+][HSO4-], which is observed over the temperature range from 278 K to 348 K. Hydrogens of the cations show a hydrogen bonding interaction with oxygens of anions. The cationic [TBA+] molecules show more solvation behavior with anions when compared to the [BA+]. The Na+ ion show a strong coordination structure with [HSO4-] in [TBA+][HSO4-] when compared to the [BA+][HSO4-]. We further calculate the detailed solvation free energy (ΔG) calculations using thermodynamic integration. We found that the ΔG of Na+ is more favorable in [TBA+][HSO4-] when compared to [BA+][HSO4-] in the temperature range varying from 278 K to 348 K. With the temperature rise, we observe the more favorable solvation of Na+ in both ionic liquids. On the other hand, the solvation of Cl- becomes less favorable. Overall, this manuscript provides detailed molecular level structural and thermodynamic origins of Na+ in protic ionic liquids useful for designing and developing sustainable electrolytes for Na+ battery applications.

We present an assessment of different approaches to predict peptide structures using modeling tools. Several small molecule, protein, and peptide-focused methodologies were used for the fast prediction of conformers for peptides shorter than 30 amino acids. We assessed the effect of including restraints based on annotated or predicted secondary structure motifs. A number of peptides in bound conformations and in solution were collected to compare the tools. In addition, we studied the impact of changing single amino acids to non-natural residues using molecular dynamics simulations. Deep learning methods such as AlphaFold2, or the combination of physics-based approaches with secondary structure information, produce the most accurate results for natural sequences. In the case of peptides with non-natural modifications, modeling the peptide containing natural amino acids first and then modifying and simulating the peptide using benchmarked force fields is a recommended pipeline. The results can guide the modeling of oligopeptides for drug discovery projects.

The current study involves the investigation of reducing properties of disulfide bonded heteraphanes. The calculated adiabatic electron affinity (AEA) values of heteraphanes are found comparable to that of cystine molecule and are capable of undergoing reversible redox reactions. In aqueous phase, these show high propensity to get reduced. The reaction energies calculated using isodesmic equations reflect the strain associated with the studied thiacyclophane models. Increase in the number of disulfide bonds results in less strain and more stabilization. Through-space transannular interactions in the selected heteraphanes have a decisive influence on the structure stabilization associated with the systems. The results reported in the current study are expected to play a vital role while designing redox driven drug carriers by incorporating these systems in biomolecules.

The aim of the following research is to assess the applicability of calculated quantum properties of molecular fragments as molecular descriptors in machine learning classification task. The research is based on bio-concentration and QM9-extended databases. A number of compounds with results from quantum-chemical calculations conducted with Psi4 quantum chemistry package was also added to the quantum properties database. Classification results are compared with a baseline of random guesses and predictions obtained with the traditional RDKit generated molecular descriptors. Chosen classification metrics show that results obtained with fragments quantum descriptors fall between results from baseline and those provided by molecular descriptors widely applied in cheminformatics. According to the results, the implementation of principal component analysis, causes a drop in categorization metrics.

Protein tyrosine phosphatase 1B (PTP1B) has proven to be an attractive target for the treatment of cancer, diabetes and other diseases. Although many PTP1B inhibitors with various scaffolds have been developed, there is still a lack of PTP1B inhibitor with high specificity and acceptable pharmacological properties. Therefore, it is urgent to develop more methods to explore complex action mode of PTP1B and ligands for designing ideal PTP1B modulators. In this work, we developed a potential molecular dynamics (MD) analytic mode to analyze the mechanism of active compounds 6a and 6e against PTP1B from different perspectives, including the stable ability, interactions and binding site of ligand and protein, the binding energy, relative movement between residues and changes in protein internal interactions. The simulated results demonstrated that compound 6a bound more stably to the active pocket of PTP1B than 6e due to its smaller molecular volume (326 Å3), matched electronegativity, and enhanced the positive correlation motion of residues, especially for WPD loop and P loop. Lastly, compound 6a as a competitive inhibitor for PTP1B was verified by enzyme kinetic assay. This work successfully studied the mechanism of compound 6a against PTP1B from various aspects, enriched the analysis of interaction mode between PTP1B and inhibitors. In summary, we hope that this work could provide more theoretical information for designing and developing more novel and ideal PTP1B inhibitors in the future.

The thermal stability of a protein is an important concern for its practical application in food processing industries. In this study, we have carried out classical molecular dynamics simulations to systematically investigate the effect of NADES (natural deep eutectic solvent) on the stabilization of the protein β-Lactoglobulin (BLG) at different temperatures. This study sheds light on the very aspects of NADES composed of betaine and sorbitol on the stability of the protein. NADES provides better stability to the protein up to a temperature of 400 K than in water. It is observed that the protein starts to unfold above temperature 400 K in spite of the presence of NADES which is quiet evident from the root mean square deviation (RMSD) and radius of gyration (Rg) plots. The decreasing average solvent accessible surface area (SASA) values and increasing intra-protein hydrogen bonds indicate better stability of the protein in NADES medium than in water at temperatures 300 K and 400 K. At high temperatures viz. 450 K and 500 K the number and distribution of solvent species (betaine and sorbitol) around the protein surface show an increment that are evident from the calculations of solvation shell, radial and spatial distribution functions. Increased number of betaine molecules that interact with the protein through electrostatic interaction may lead to destabilization of the protein at these temperatures. This study suggests that NADES could be used as an ideal medium for thermal stability of the protein BLG up to a temperature of 400 K. Beyond this temperature, NADES used for this study fails to exert stabilization effect on the protein.

To intensify the photovoltaic properties of organic solar cells, density functional theory (DFT) based computational techniques were implemented on six non-fullerene A-D-A type small molecules (N1-N6) modified from reference molecule (R) which consists of phenazine fused with 1,4- Dimethyl-4H-3,7-dithia-4-aza- cyclopenta [α] pentalene on both sides with one of its phenyl rings acting as the central donor unit, further attached with 2-(5,6-Difluoro-2-methylene-3-oxo-indan-1-ylidene)-malononitrile acceptor groups at terminal sites. All proposed compounds have a phenazine base modified with a variety of substituents at the terminals. Transition density matrix, density of states, frontier molecular orbitals, intramolecular charge transfer abilities and optoelectronic properties of these compounds were investigated using B3LYP/6-31G (d, p) and B3LYP/6-31G++ (d,p) level of theory. All six designed compounds exhibited a bathochromic sift in their λmax as compared to the R molecule. All designed molecules also have reduced band gap and smaller excitation energy than R. Among all, N6 exhibited highest λmax and lowest bandgap as compared to reference molecule indicating its promising photovoltaic properties. Decreased hole and electron reorganization energy in several of the suggested compounds is indicative of greater charge mobility in them. PTB7-Th donor was employed to calculate open circuit voltage of all investigated molecules. N1-N5 molecules had improved optoelectronic properties, significant probable power conversion efficiency as evident from their absorption aspects, high values of Voc, and fill factor, compared to R molecule. Designed A-D-A type NF based molecules make OSCs ideal for use in wearable devices, building-integrated photovoltaics and smart fabrics.

In the present article, the DFT based computational manufacturing for hydrogen fuel cell has been performed because hydrogen storage applications as one of the utmost explored research fields of the modern era. The discovery of novel and potential hydride perovskites materials has developed the current attention for hydrogen fuel cell and related applications. The double hydride perovskite Cs2CaTlH6, Cs2SrTlH6, Cs2BaTlH6 materials are promising for the computational manufacturing of hydrogen fuel cell because calculated tolerance factors for the considered materials are listed as Cs2CaTlH6 (0.90) > Cs2SrTlH6 (0.86) > Cs2BaTlH6 (0.84) illustrating the structure stability and compatibility along with metallic electronic behavior favorable for hydrogen storage devices. The mechanical parameters for the considered materials are also calculated to encounter the Born reliability, stability and compatibility criterion. The Pugh's ratio, poison coefficient and Cauchy pressure calculations confirmed the brittle character favorable for hydrogen fuel cell. Furthermore, gravimetric ratios recommended that the considered materials are suitable and favorable for hydrogen fuel cell as hydrogen fuel can sustain for longer time and contribute extraordinary assistances in transportation handling applications and multiplicity of power. In addition, the considered materials are thermodynamic and vibrational symmetry as no soft (imaginary) mode of phonon in dispersion curve is observed. In short, the considered materials Cs2CaTlH6, Cs2SrTlH6, Cs2BaTlH6 are novel, significant and potential candidates for the hydrogen fuel cell and motivate the experimental researcher to synthesize these materials for experimental manufacturing of hydrogen fuel cell to meet the energy demand of the present day.

The density functional theory (DFT) was applied for the first time to study the doping and co-doping of Ga and Zn metals on graphitic carbon nitride (g-C3N4). The doping of these metal impurities into g-C3N4 leads to a significant decrease in the bandgap energy. Moreover, the co-doping leads to even lower bandgap energy than either individual Zn or Ga-doped g-C3N4. The theoretical electronic and optical properties including the density of state (DOS), energy levels of the frontier orbital, excited state lifetime, and molecular electrostatic potential of the doped and co-doped g-C3N4 support their application in UV-visible light-based technologies. The quantum mechanical parameters (energy band gap, binding energy, exciton energy, softness, hardness) and dipole moment exhibit higher values (ranging from 1.36 to 4.94 D) compared to the bare g-C3N4 (0.29 D), indicating better solubility in the water solvent. The time-dependent DFT (TD-DFT) calculations showed absorption maxima in between the UV-Vis region (309-878 nm). Additionally, charge transfer characteristics, transition density matrix (TDM), excited state lifetime and light harvesting efficiency (LHE) were investigated. Overall, these theoretical studies suggest that doped and co-doped g-C3N4 are excellent candidates for electronic semiconductor devices, light-emitting diodes (LEDs), solar cells, and photodetectors.

Abl is a nonreceptor tyrosine kinase involved in a variety of disease pathways such as rheumatic immune. Full-length Abl protein consists of a catalytic tyrosine kinase (TK) domain as well as two regulatory Src homology domains 2 and 3 (SH2 and SH3, respectively); the latter recognizes and binds to those natural proline-rich peptide segments containing a PxxP motif on the protein surface of its interacting partners. However, natural peptides cannot bind effectively to the modular domain in high affinity and strong selectivity due to their small size and broad specificity. Here, a synthetic proline-rich peptide p41 was used as template; its structural diversity was extended by combinationally replacing the Pro0 and Pro+3 residues with a number of N-substituted amino acids. Consequently, peptide affinity change upon the replacement was derived to create a systematic N-substituting perturbation profile, from which we identified several N-substitution combinations at the Pro0 and Pro+3 residues of p41 PxxP motif that may moderately or significantly improve the peptide binding potency to Abl; they represent potent peptoid binders of Abl SH3 domain, with affinity improved considerably relative to p41. More significantly, the designed potent peptoids were also found to exhibit a good SH3-selectivity for their cognate Abl over other noncognate nonreceptor tyrosine kinases, with S = 9.7-fold.

Antiviral drugs are important for the coronavirus disease 2019 (COVID-19) response, as vaccines and antibodies may have reduced efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Antiviral drugs that have been made available for use, albeit with questionable efficacy, include remdesivir (Veklury®), nirmatrelvir-ritonavir (Paxlovid™), and molnupiravir (Lagevrio®). To expand the options available for COVID-19 and prepare for future pandemics, there is a need to investigate new uses for existing drugs and design novel compounds. To support these efforts, we have created a comprehensive library of 750 molecules that have been sourced from in vitro, in vivo, and in silico studies. It is publicly available at our dedicated website (https://epimedlab.org/crl/). The EpiMed Coronabank Chemical Collection consists of compounds that have been divided into 10 main classes based on antiviral properties, as well as the potential to be used for the management, prevention, or treatment of COVID-19 related complications. A detailed description of each compound is provided, along with the molecular formula, canonical SMILES, and U.S. Food and Drug Administration approval status. The chemical structures have been obtained and are available for download. Moreover, the pharmacokinetic properties of the ligands have been characterised. To demonstrate an application of the EpiMed Coronabank Chemical Collection, molecular docking was used to evaluate the binding characteristics of ligands against SARS-CoV-2 nonstructural and accessory proteins. Overall, our database can be used to aid the drug repositioning process, and for gaining further insight into the molecular mechanisms of action of potential compounds of interest.

In this study, the thermodynamic stability, embedding voltage, volume change rate, electronic structure properties, mechanical properties and lithium-ion diffusion characteristics of the Mn, N co-doped LiFePO4 material are investigated using a first-principles approach based on density generalization theory. The results show that the doped system has a low formation energy and the material meets the thermodynamic stability criteria. During the de-lithium process, the volume change rate of the doped material decreases and the cycling performance is improved, but the battery energy density decreases slightly. It is also found that the doping of N led to the transformation of the material from a p-type semiconductor to an N-type semiconductor, while the doping of Mn and N lead to the creation of impurity bands, narrowing of the band gap and an increase in conductivity. At the same time, Mn, N co-doping greatly improve the ductility of the material, suppress the generation of microcracks, and reduce the possibility of shear deformation. In addition, it is noteworthy that the lithium-ion diffusion energy barrier of the doped system is reduced, which predicts an increase in the diffusion rate of lithium ions in the doped system.

Four well-suited porous materials for the selective adsorption of the most prominent CFC, which is CCl2F2, from the air are carbon nanotubes CNT (9,9) and CNT (11,11), NaY zeolite, and the Metal Organic Framework MIL-125(Fe). The adsorption has been investigated through molecular simulations. Simulation results and theoretical considerations show that reasons for the extraordinarily high selectivity in all four cases were found to be the differences in the enthalpy of adsorption for the various adsorbed gases rather than steric reasons. The four adsorbate-adsorbent systems have been examined at different temperatures, pressures, and concentration ratios in the mixture. Among them, the carbon nanotube CNT (11,11) exhibited the highest selectivity, reaching up to 104.

The structural behaviour of the RAPRKKG heptapeptide after individual or multiple mutations was inspected through molecular dynamics simulation. The nature of the mutations provided information on the flexibility of the heptapeptide and on how water molecules establish hydrogen bonds with it. The structural behaviour of the wild-type and the mutated structures were measured through the analysis of protein‒protein and protein‒solvent hydrogen bonds. The conformational behaviours of the different structures were analysed through free energy landscape analysis. The flexibility characteristics of the mutants seem to depend on the reorganization of water molecules and their static or dynamic behaviour around amino acid side chains.

In this study, inspired by the overall structure and operation of the aquaporin channel, graphene-based nanochannels are proposed to be used as potential membranes for the water purification process. To this end, an hourglass-shaped channel has been designed using the three-layer porous graphene sheets and the effects of some main channel's elements, such as the channel bending angle and attached functional groups to it, on the filtration performance have been examined by using molecular dynamics simulations. We find that a suitable bending channel shape can improve the channel efficiency, i.e. both the water permeability and the ion rejection rate of the suitable bent channels were more than for the straight channels. In addition, regarding the different functionalized channels, the half-functionalized channels were more efficient than the completed functionalized ones. Furthermore, by monitoring the dynamics of water molecules as they pass through the narrowest part of the channels, it was found that water molecule rotation assists water transport.

N-Nitrosodimethylamine (NDMA, ONN(CH3)2) is a highly potent carcinogenic investigated by health authorities in some countries. In this manuscript, density functional theory (DFT) is applied to study the NDMA molecular and dissociative adsorption on a Ni8 nanocluster. Molecular adsorption is two times stronger than the NDMA adsorption on the Ni{111} surface. NDMA dissociative adsorption is found more stable than molecular adsorption by ≈1 eV. To dissociate the NDMA molecule into O and NN(CH3)2 fragments, an activation energy is calculated in 0.954 and 0.810 eV from the two most stable molecular configurations. However, to dissociate the NDMA molecule into ON and N(CH3)2 fragments, a smaller activation energy of 0.654 eV is calculated. With the inclusion of the London dispersion forces (optB88-vdW functional), NDMA molecular interactions are a bit stronger. However, the activation energies are slightly smaller. Meta-GGA functional SCAN has also, been applied. The inclusion of the implicit solvation model displays a NDMA weaker interaction with the Ni8 nanocluster. Dissociative adsorption is more stable than molecular adsorption, but the energy difference is a bit smaller, ≈0.850 eV. Present results show that the Ni8 nanoclusters are promising catalysts to NDMA elimination from water.