Journal of Molecular Modeling

Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation. AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman’s combined atoms. The binding free energies were calculated using the Amber 10 package. The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.

The dynamics of a rotary nano ion pump, inspired by the F 0 part of the F0F1-ATP synthase biomolecular motor, were investigated. This nanopump is composed of a rotor, which is constructed of two carbon nanotubes with benzene rings, and a stator, which is made of six graphene sheets. The molecular dynamics (MD) method was used to simulate the dynamics of the ion nanopump. When the rotor of the nanopump rotates mechanically, an ion gradient will be generated between the two sides of the nanopump. It is shown that the ion gradient generated by the nanopump is dependant on parameters such as the rotary frequency of the rotor, temperature and the amounts and locations of the positive and negative charges of the stator part of the nanopump. Also, an electrical potential difference is generated between the two sides of the pump as a result of its operation.

The energetically favoured conformations of β-N-acetyl-Muramic acid, its C6-O-acetylated form, the methylamide and the methyl-glycoside have been investigated using the semiempirical PM3 and AM1 methods. All these compounds are either components or fragmentary structures of the murein network. The atomic coordinates of the starting set of the β-N-acetyl-Muramic acid molecule have been obtained by a PM3 minimization of one saccharide molecule cut out from the murein single strand model proposed by Barnickel at al. [1]. The sidegroups of the derivatives have been introduced by a molecular editor. These conformations served as starting points in conformational space for a grid search by scanning all sidechain torsional angles for non-hydrogen atoms with exception of the N-acetyl group which was held in cisoid position (i.e. N2-H bond is parallel to C1-H and C3-H bond) and only minimized. The PM3 method with an additional amide correction potential and the AM1 method were used. The torsional angle distributions of the lactyl sidechain (free acid and methylamide), the C6-O-acetylated sidechain and the C1-methoxy sidechain have been investigated, showing distinct energetically favoured torsional angle regions. The results are compared to earlier studies on β-N-acetyl-Muramic acid by J.S. Yadav et al. [2,3] who were using the MNDO and PCILO methods and by P.N.S. Yadav et al. [4] who were using the empirical MM2 force-field.

An in-depth understanding of the diffusion process in liquid metals is a key to design and engineering new high-performance materials. In this study, using molecular dynamics simulations supplemented with the embedded atom potential, we investigate/compare the self-diffusion process in liquid Aluminium. To understand the self-diffusion process, we analyse the radial distribution functions, velocity distributions, mean square displacements, and self-diffusion coefficients at various temperatures well above the melting temperature of Aluminium in the temperature range of 1000 K to 1800 K. As a key result, in both the $$\alpha$$ and $$\beta$$ phases, the self-diffusion coefficients show a non-linear variation with rise in temperatures in the range of 1000 K to 1200 K. From 1300 K to 1800 K, the self-diffusion coefficients increase more or less monotonically with rise in temperature. We found that a higher temperature in the range of 1300 K to 1800 K leads to a greater self-diffusion coefficient, suggesting the more violent movement of the atoms around their equilibrium positions. The results presented in this work can help to understand the differences in the self-diffusion process in the technologically relevant Al phases.

The phosphatidylinositol 3-kinase α (PI3Kα) was genetically validated as a promising therapeutic target for developing novel anticancer drugs. In order to explore the structure-activity correlation of benzothiazole series as inhibitors of PI3Kα, comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) were performed on 61 promising molecules to build 3D-QSAR models based on both the ligand- and receptor-based methods. The best CoMFA and CoMSIA models had a cross-validated coefficient rcv 2 of 0.618 and 0.621, predicted correlation coefficient rpred 2 of 0.812 and 0.83, respectively, proving their high correlative and predictive abilities on both the training and test sets. In addition, docking analysis and molecular dynamics simulation (MD) were also applied to elucidate the probable binding modes of these inhibitors at the ATP binding pocket. Based on the contour maps and MD results, some key structural factors responsible for the activity of this series of compounds were revealed as follows: (1) Ring-A has a strong preference for bulky hydrophobic or aromatic groups; (2) Electron-withdrawing groups at the para position of ring-B and hydrophilic substituents in ring-B region may benefit the potency; (3) A polar substituent like -NHSO2- between ring-A and ring-B can enhance the activity of the drug by providing hydrogen bonding interaction with the protein target. The satisfactory results obtained from this work strongly suggest that the developed 3D-QSAR models and the obtained PI3Kα inhibitor binding structures are reasonable for the prediction of the activity of new inhibitors and be helpful in future PI3Kα inhibitor design.

We describe a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema. Our approach avoids the need for explicit mathematical representation of the surface and can be implemented easily in existing graphical software, as it is based on the very popular representation of a surface as collection of polygons. We discuss applications involving the volumes, surface areas and molecular surface electrostatic potentials, and local ionization energies of a group of 11 molecules.

Tetrachlorodibenzodioxin (TCDD) is one of the most famous dioxin families that is hazardous to humans and the environment. Designing cheap and novel catalysts for its detecting and removing is an essential need for the environment. In this work, DFT + VdW is used to investigate the potentiality of proposed catalysts in adsorbing and dissociating TCDD. P-type and N-type charge carrier effects on the adsorption process are modeled by doping of B/Al and N/P atoms in the graphene. Al-doped graphene, with − 1.27 eV adsorption energy, has the highest possibility to adsorb TCDD. P-type dopants have higher interactions with TCDD in comparing with N-type dopants. Introducing positive and negative charges on the studied complexes shows that in all complexes, the driving force of complexation is π-π stacking except for the Al-doped graphene. Dissociative adsorption studies show that unlike literature data, chlorine atoms on the surface of studied catalysts are not dissociated from TCDD, and instead, C–O bonds in TCDD are dissociated symmetrically and asymmetrically. Data show that Al-doped graphene is the best catalyst for symmetrical dissociation, and pure graphene is the best one for asymmetrical dissociation of TCDD.

This work theoretically demonstrates a catalyst of copper monatomic wire supported on graphene nanoribbons (Cu-GNR) with a high efficiency for nitric oxide electroreduction reaction (NORR). This not only decreases the usage rate of noble metals but also possesses superior limiting potential comparable to pure Cu (− 0.69 and − 0.61 V, vs. reversible hydrogen electrode (RHE)). The key is that Cu-GNR will have more efficient catalytic activity for NORR when fully covered by NO, since these weaken the adsorption ability of the reduction steps at the beginning. In sum, our findings may offer a platform for clarifying the effects of the concentration of reactants on catalytic process. Spin-polarized DFT with ultrasoft pseudopotentials as implemented in the CASTEP code was used in this work. The exchange correlation effects were described by generalized gradient approximation (GGA) with Perdew-Burke-Ernzerhof (PBE) functional. The dispersion correction within Grimme scheme (DFT-D2) was employed to accurately describe the van der Waals (vdW) interactions. The Hirshfeld population analysis was adopted to evaluate the charge transfer.

This paper presents a study on a system comprised of a low-dimensional structure (Ga1-xAlxAs and GaAs quantum well wire), an intense laser field and an applied magnetic field in axial direction, resulting in a modified structure by interaction with the laser field. A variation of the concentration of aluminum is considered. So, the characteristics of the semiconductor such as the effective mass and width of the forbidden band vary due to the aluminum concentration. The electronic Landé factor control by changing of both intensity and frequency of a laser field on cylindrical quantum well wire was also reported. We use the laser dressed approximation for the treated “quantum wire + laser” system as quantum wire in the absence of radiation but with parameter (electronic barrier height and electronic effective mass) renormalized by laser effects. We consider a magnetic field applied in the parallel direction of symmetric axis of the quantum well wire. We take into account non-parabolicity and anisotropy effects on the conduction band by Ogg-McCombe Hamiltonian.