At high temperature, silicon oxycarbide (SiCO) exhibits excellent mechanical properties and thermal stability. The incorporation of boron in SiCO results in improved performance in creep temperatures. In this work, large-scale molecular dynamics calculations were applied to obtain amorphous SiCO structures containing boron. Phase separation of C–C, B–C and Si–O was achieved for three compositions, and silicon-centered mixed-bond tetrahedrons were reproduced successfully. As the boron content increases, the boron atoms tend to form B–C and B–Si bonds in the voids, which stretches the free carbon network in some instances, causing a increase in C–C distance. Young’s modulus remains stable at high temperature for the high-carbon case, which indicates that the free carbon network plays a critical role in the structural and thermal stability of SiBCO.
Graphical Abstract Three major typical structures in the cooling down process for silicon boron oxycarbide (Si5BC2O8). Bonds: red Si–O, blue Si–C, black C–C, green B–C, purple Si–B
In this work, through a docking analysis of compounds from the ZINC chemical library on human β-tubulin using high performance computer cluster, we report new polycyclic aromatic compounds that bind with high energy on the colchicine binding site of β-tubulin, suggesting three new key amino acids. However, molecular dynamic analysis showed low stability in the interaction between ligand and receptor. Results were confirmed experimentally in in vitro and in vivo models that suggest that molecular dynamics simulation is the best option to find new potential β-tubulin inhibitors.
In this work, we address the effects of molecular doping on the electronic properties of fluorinated and chlorinated silicon nanowires (SiNWs), in comparison with those corresponding to hydrogen-passivated SiNWs. Adsorption of n-type dopant molecules on hydrogenated and halogenated SiNWs and their chemisorption energies, formation energies, and electronic band gap are studied by using density functional theory calculations. The results show that there are considerable charge transfers and strong covalent interactions between the dopant molecules and the SiNWs. Moreover, the results show that the energy band gap of SiNWs changes due to chemical surface doping and it can be further tuned by surface passivation. We conclude that a molecular based ex-situ doping, where molecules are adsorbed on the surface of the SiNW, can be an alternative path to conventional doping.
A series of three star-shaped compounds containing both donor (carbazole) and acceptor (2,4,6-triphenyl-1,3,5-triazine) moieties linked through various linking bridges was studied theoretically at the linear response TD-DFT level of theory to describe their absorption and fluorescence spectra. The concept of a localized charge-transfer excited state has been applied successfully to explain the observed strong solvatochromic effect in the emission spectra of the studied molecules, which can be utilized for the fabrication of color tunable solution-processable OLEDs. The concept is in particularly applicable to donor–acceptor species with a C3 symmetry point group where the static dipole moment changes dramatically upon electronic excitation. An important peculiarity of the studied molecules is that they are characterized by non-zero values of the HOMO and LUMO orbitals in the same common part of molecular space that provides a large electric dipole transition moment for both light absorption and emission.
A new compound based on the D-π-A concept, where D = dimethylamino-phenyl and A = naphthoic acid, separated by an imine motif, was designed, synthesized and characterized. The spectral, energetics, and structural characteristics of the compound were studied thoroughly theoretically by density functional theory (DFT) in the gas and aqueous phases and experimentally (steady-state absorption) in aqueous media with various degrees of polarity and hydrogen bonding ability. This compound shows high sensitivity to the polarity, basicity and proton affinity of the environment. Based on DFT, TD-DFT and NBO analysis, the compound exists in the ground-state with both intermolecular and intramolecular hydrogen bond conformations in association with the –COOH, with latter isomer calculated to be more stable. Furthermore, structural changes via intermolecular solute–solvent interactions, dictate electronic modifications and spectral changes.
Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and \( {HO}_2/{O}_2^{-} \) radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of \( {HO}_2/{O}_2^{-} \) radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton.
The anti-hypertensive drugs amlodipine, atenolol and lisinopril, in ordinary and PEGylated forms, with different combined-ratios, were studied by molecular dynamics simulations using GROMACS software. Twenty simulation systems were designed to evaluate the interactions of drug mixtures with a dimyristoylphosphatidylcholine (DMPC) lipid bilayer membrane, in the presence of water molecules. In the course of simulations, various properties of the systems were investigated, including drug location, diffusion and mass distribution in the membrane; drug orientation; the lipid chain disorder as a result of drug penetration into the DMPC membrane; the number of hydrogen bonds; and drug surface area. According to the results obtained, combined drugs penetrate deeper into the DMPC lipid bilayer membrane, and the lipid chains remain ordered. Also, the combined PEGylated drugs, at a combination ratio of 1:1:1, enhance drug penetration into the DMPC membrane, reduce drug agglomeration, orient the drug in a proper angle for easy penetration into the membrane, and decrease undesirable lipotoxicity due to distorted membrane self-assembly and thickness.
Ecdysone receptor (EcR) is a significant target in the identification of new environmentally friendly pesticides. There are two types of ecdysone agonists: steroidal ecdysone agonists and dibenzoylhydrazines (DBHs). In this study, various modeling methods (homology modeling, molecular docking, MD simulation, binding free energy calculation, and per-residue binding free energy decomposition) were utilized to study the different binding mechanisms of two types of ecdysone agonists. Our theoretical results indicated that the relative binding potencies of DBHs can be ranked sufficiently accurately using the MOE docking method. However, MM/PBSA calculations more accurately predicted the binding affinities between steroidal ecdysone agonists and EcR-LBD. To identify the key residues involved in ecdysone agonist binding, the binding free energy (ΔGBind) was decomposed into the energy contributions of individual residues. The results revealed that nine residues—Ile339, Thr343, Met380, Met381, Tyr403, Tyr408, Asp419, Gln503, and Asn504—determined the binding affinities of the DBHs. Glu309, Met342, Arg383, Arg387, and Leu396 were important influences on the binding affinities of the steroidal ecdysone agonists.
Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure PT more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results.
Recently, a series of xanthone analogues has been identified as α-glucosidase inhibitors. To provide deeper insight into the three-dimensional (3D) structural requirements for the activities of these molecules, CoMFA and CoMSIA approaches were employed on 54 xanthones to construct 3D-QSAR models. Their bioactive conformations were first investigated by docking studies and optimized by subsequent molecular dynamics (MD) simulations using the homology modeled structure of the target protein. Based on the docking/MD-determined conformers, 3D-QSAR studies generated several significant models in terms of 47 molecules as the training set. The best model (CoMSIA-SHA) yielded q2 of 0.713, r2 of 0.967 and F of 140.250. The robustness of the model was further externally confirmed by a test set of the remaining molecules (q2 = 0.793, r2 = 0.902, and k = 0.905). Contour maps provided much information for future design and optimization of new compounds with high inhibitory activities towards α-glucosidase.
The activation mechanism of dopamine receptors is unknown. The amino acids S5.42, S5.43, and S5.46 located in helix 5 appear to be crucial, but their specific roles in receptor activation have not been studied. We modeled the D1 dopamine receptor using the crystal structures of the D3 dopamine and β2 adrenergic receptors. Molecular dynamics simulations show that the interaction of dopamine with the D1 receptor leads to the formation of a hydrogen-bond network with its catechol group and helices 3, 5, and 6, including water molecules. The para hydroxyl group of dopamine binds directly to S5.42 and N6.55, the latter also interacting with S5.43. Unexpectedly, S5.46 does not interact directly with the catechol; instead, it interacts through a water molecule with S5.42 and directly with T3.37. The formation of this hydrogen-bond network, part of which was previously observed in docking studies with dopamine agonists, triggers the opening of the E6.30–R3.60 ionic lock associated with the activation of GPCRs. These changes do not occur in the unbonded (apo) receptor or when it is in a complex with the antagonist 3-methoxy-5,6,7,8,9,14-hexahydrodibenz[d,g]azecine. Our results provide valuable insight into the T3.37–S5.46–water–S5.43–ligand interaction, which may be crucial to the activation of the D1 dopamine receptor and should be considered during the design of novel agonists.
Herein we report a study of the switchable [3]rotaxane reported by Huang et al. (Appl Phys Lett 85(22):5391–5393, 1) that can be mounted to a surface to form a nanomechanical, linear, molecular motor. We demonstrate the application of semiempirical electronic structure theory to predict the average and instantaneous force generated by redox-induced ring shuttling. Detailed analysis of the geometric and electronic structure of the system reveals technical considerations essential to success of the approach. The force is found to be in the 100–200 pN range, consistent with published experimental estimates.
Development of new energetic salts is the key factor in replacing low performance compounds in conventional formulations of high explosives as well as propellants. Ten salts based on the nitroformate anion and various nitrogen-rich cations were designed and their geometric optimizations carried out using the density functional method. With reasonable oxygen balance (from ?36 % to 0 %), heats of formation (47–624 kJ mol?1) and high densities (1.81–1.89 g cm?3), the detonation velocity (D) and pressure (P) values of salts were calculated as 8.62–9.36 km s?1 and 33.10–40.01 GPa, respectively. Lastly, the nitroformate salts studied in this work are of prospective interest as high performance explosives.
Density functional theory (B3LYP, B3LYP-D2 and wB97XD functionals) was used in finite models of zigzag carbon nanotubes (CNT), (n,0)×k with n?=?6–9 and k?=?2–4, to systematically investigate the effects of size on their structural and electronic properties. We found that the ratio between the length (Lt) and the diameter (dt) of the pristine CNT has to be larger than 2, i.e., Lt/dt?>?2, in order to provide the observed experimental trends of C=C bond distances, as well as to maintain the atomic charges nearly constant and zero around the center of the tube. Therefore, the concepts of useful length and volume were developed and tested for the encapsulation process of HCN and C2H2 into CNTs. The energies involved in these processes, as well as the changes in molecular structure and electronic properties of the dopants and the CNTs are discussed and rationalized by the amount of charge transferred between dopant and CNT.
The geometrical structures, electrical properties, and nonlinear optical (NLO) properties of AlNNT–Li and BNNT–Li nanotube systems were investigated by means of the density functional theory (DFT) method. Frontier molecular orbitals and density of states analyses show that adsorption of the Li atom can significantly narrow the wide HOMO–LUMO gaps of pure AlNNT and BNNT. The results reveal that AlNNT–Li and BNNT–Li systems containing diffuse excess electrons can be regarded as inorganic electrides. The formation of diffuse excess electrons leads to a decrease in transition energies, thereby increasing the first hyperpolarizabilities (β0) of AlNNT–Li and BNNT–Li. This work may contribute to the development of potential high-performance NLO materials.
Graphical abstract The structural characteristics and nonlinear optical properties of the AlNNT–Li and BNNT–Li systems were studied by means of density functional theory. Introduction of Li atoms greatly enhances the static first hyperpolarizabilities of AlNNT–Li and BNNT–Li
Catalytic fields illustrate topology of the optimal charge distribution of a molecular environment reducing the activation energy for any process involving barrier crossing, like chemical reaction, bond rotation etc. Until now, this technique has been successfully applied to predict catalytic effects resulting from intermolecular interactions with individual water molecules constituting the first hydration shell, aminoacid mutations in enzymes or Si→Al substitutions in zeolites. In this contribution, hydrogen to fluorine (H→F) substitution effects for two model reactions have been examined indicating qualitative applicability of the catalytic field concept in the case of systems involving intramolecular interactions.
The present paper reports the analysis of surface decoration on the structural, electronic, and optical properties of (n,0) ZnO nanotubes, performed by means of a density function theory based ab-initio approach. Fe functionalization induced buckling in ZnO nanotubes affects its electronic and optical properties. Increase in Fe functionalization leads to better stability of ZnO nanotube and shows enhanced metallic character. The possibility of its use in optoelectronics has been analyzed in terms of dielectric constant, absorption coefficient, and refractive index. In another observation, the high sensitivity of the HCN molecule for the Fe-incorporated ZnO nanotube suggests it as a potential gas sensor.
The static properties of two-dimensional athermal polymer solutions were studied by performing Monte Carlo lattice simulations using the cooperative motion algorithm (CMA) and taking into account the presence of explicit solvent molecules. The simulations were performed for a wide range of polymer chain lengths N (16–1024) and concentrations φ (0.0156–1). The results obtained for short chains (N?<?256) were in good agreement with those given by previous simulations. For the longest chains (512 or 1024 beads), some unexpected behavior was observed in the dilute and semidilute regimes. A pronounced change in the concentration dependence of chain size and shape was observed below a certain critical concentration (0.6 for the longest chains under consideration, consisting of 1024 beads). Longer chains became more extended below this concentration. The behavior of the single-chain structure factor confirmed these changes in the fractal dimension of the chain as a function of the concentration. The observed phenomena are related to the excluded volume of solvent molecules, which causes the chain statistics to be modified in the vicinity of other chains; this effect is important in strictly 2D systems.
