Theoretical study of the solvatochromism of a donor-acceptor bithiophene

The solvation and the solvatochromic behavior of the 5-(methylthio)-5′-nitro-2,2′-bithiophene 1 in diethyl ether, dichloromethane, acetonitrile, methanol and formamide was theoretically investigated with an iterative molecular and quantum mechanics (QM/MM) approach. Calculated longest-wavelength solvatochromic absorption band of 1, obtained as averages of statistically uncorrelated configurations, including the solute and explicit solvent molecules of the first and second solvation layer, were in excellent agreement with the experimental results.

Degradation of polyvinyl alcohol under mechanothermal stretching

Mechanical and thermal properties of polyvinyl alcohol (PVA) are characterized and analyzed using in situ X-ray photoelectron spectroscopy (XPS) and quantum chemistry calculations. It is found that the carbon peaks—commonly used as the reference for spectroscopic analysis—shift under mechanical and thermal stretching. Results also indicate that, at different temperatures and among the various functional groups present in PVA, the carbon in the C–O group is the most stable. Computational calculations showed that Hartree–Fock/10-31G (d) reproduces the binding energy of core carbon electrons with an accuracy of 95 %, which is enough to characterize bonds, allowing the results of the spectroscopic analysis to be corroborated.

Exploration of various electronic properties along the reaction coordinate for hydration of Pt(II) and Ru(II) complexes; the CCSD, MPx, and DFT computational study

In the study behavior of molecular electrostatic potential, averaged local ionization energy, and reaction electronic flux along the reaction coordinate of hydration process of three representative Ru(II) and Pt(II) complexes were explored using both post-HF and DFT quantum chemical approximations. Previously determined reaction mechanisms were explored by more detailed insight into changes of electronic properties using ωB97XD functional and MP2 method with 6–311++G(2df,2pd) basis set and CCSD/6–31(+)G(d,p) approach. The dependences of all examined properties on reaction coordinate give more detailed understanding of the hydration process.

Natures of benzene-water and pyrrole-water interactions in the forms of σ and π types: theoretical studies from clusters to liquid mixture

A combined and sequential use of quantum mechanical (QM) calculations and classical molecular dynamics (MD) simulations was made to investigate the σ and π types of hydrogen bond (HB) in benzene-water and pyrrole-water as clusters and as their liquid mixture, respectively. This paper aims at analyzing similarities and differences of these HBs resulted from QM and MD on an equal footing. Based on the optimized geometry at ωb97xD/aug-cc-pVTZ level of theory, the nature and property of σ and π types of HBs are unveiled by means of atoms in molecules (AIM), natural bond orbital (NBO) and energy decomposition analysis (EDA). In light of the above findings, MD simulation with OPLS-AA and SPC model was applied to study the liquid mixture at different temperatures. The MD results further characterize the behavior and structural properties of σ and π types HBs, which are somewhat different but reasonable for the clusters by QM. Finally, we provide a reasonable explanation for the different solubility between benzene/water and pyrrole/water.

A molecular dynamics study on sI hydrogen hydrate

A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.

Investigation of the binding network of IGF-I on the cavity surface of IGFBP4

Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employed to study the interaction mechanism of IGFBP4 and IGF-I by molecular dynamics (MD) simulation. In IGF-I, residues Gly7 to Asp12 were found to be the hot spots and they mainly anchored on the N-domain of IGFBP4. The contact area, the shape and size of protein, the surroundings of the binding site, the hydrophobic and electrostatic interaction between the two proteins worked as a complex network to regulate the protein-protein interaction. It was also found that the unfolding of the helix was not inevitable in the mutant, and it could be regulated by careful selection of the substituted amino acid.

Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif

Protein farnesyltransferase (FTase) is an important target in many research fields, more markedly so in cancer investigation since several proteins known to be involved in human cancer development are thought to serve as substrates for FTase and to require farnesylation for proper biological activity. Several FTase inhibitors (FTIs) have advanced into clinical testing. Nevertheless, despite the progress in the field several functional and mechanistic doubts on the FTase catalytic activity have persisted. This work provides some crucial information on this important enzyme by describing the application of molecular dynamics simulations using specifically designed molecular mechanical parameters for a variety of 22 CaaX peptides known to work as natural substrates or inhibitors for this enzyme. The study involves a comparative analysis of several important molecular aspects, at the mechanistic level, of the behavior of substrates and inhibitors at the dynamic level, including the behavior of the enzyme and peptides, as well as their interaction, together with the effect of the solvent. Properties evaluated include the radial distribution function of the water molecules around the catalytically important zinc metal atom and cysteine sulfur of CaaX, the conformations of the substrate and inhibitor and the corresponding RMSF values, critical hydrogen bonds, and several catalytically relevant distances. These results are discussed in light of recent experimental and computational evidence that provides new insights into the activity of this enzyme.

Cytotoxic effect and molecular docking of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide—a novel topoisomerase II inhibitor

The preliminary cytotoxic effect of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide hydrochloride (1)—a potent topoisomerase II inhibitor—was measured using a MTT assay. It was found that the compound decreased the number of viable cells in both estrogen receptor-positive MCF-7 and estrogen receptor-negative MDA-MB-231breast cancer cells, with IC₅₀ values of 146?±?2 and 132?±?2 μM, respectively. To clarify the molecular basis of the inhibitory action of 1, molecular docking studies were carried out. The results suggest that 1 targets the ATP binding pocket.

Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies

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.

Molecular dynamics study of hell’s gate globin I (HGbI) from a methanotrophic extremophile: oxygen migration through a large cavity

Hell’s gate globin I (HGbI), a heme-containing protein from the extremophile Methylacidiphilum infernorum, has fast oxygen-binding/slow release characteristics due to its distal residues Gln and Tyr. The combination of Gln/Tyr distal iron coordination, adaptation to extreme environmental conditions, and lack of a D helix suggests that ligand migration in HGbI differs from other previously studied globins. Locally enhanced molecular dynamics trajectories of oxygen migration indicate a large internal cavity. This may increase the tendency of oxygen to exit from portals other than the most direct exit from the space near the heme. Oxygen may reside transiently in shallow surface depressions around the exits. Such surface trapping may enhance both oxygen uptake by increasing contact time between molecules, and decrease release by increasing the probability of oxygen reentry from the vicinity of the portal.

Stability and electronic properties of 3D covalent organic frameworks

Covalent organic frameworks (COFs) are a class of covalently linked crystalline nanoporous materials, versatile for nanoelectronic and storage applications. 3D COFs, in particular, have very large pores and low mass densities. Extensive theoretical studies of their energetic and mechanical stability, as well as their electronic properties, have been carried out for all known 3D COFs. COFs are energetically stable and their bulk modulus ranges from 3 to 20 GPa. Electronically, all COFs are semiconductors with band gaps corresponding to the HOMO–LUMO gaps of the building units.

Predicting the preferred conformations of luteolin-4′-O-β-D-glucoside in gas phase: a comparison of two computational approaches

A tree-step computational approach has been applied to determine the lowest-energy conformers of luteolin-4′-O-β-D-glucoside (L4′G). Fifty-seven starting structures of the L4′G have been built, and then by performing with density functional theory (DFT) optimizations and second-order Møller-Plesset (MP2) calculations, the preferred conformations of L4′G are predicted. In order to test the accuracy of the computational approach, a hybrid Monte-Carlo multiple minimum (MCMM)/quantum mechanical (QM) approach is applied to determine the favorable conformers of L4′G. The alternative classification is employed to put similar conformations into the same catalogue according to the dihedral angles among the luteolin rings, glycosidic dihedral angles, and the orientations of hydroxyl and hydroxymethyl groups. The low-energy conformations are located after the optimizations at the HF/6-31G(d) and B3LYP/6-311+G(d) levels. Compared with the hybrid MCMM/QM approach, the tree-step computational approach not only remains accurate but also saves a lot of computing resources.

Theoretical evaluation of flotation performance of carboxyl hydroxamic acids with different number of polar groups on the surfaces of diaspore (010) and kaolinite (001)

The adsorption behaviors of three carboxyl hydroxamic acids on diaspore (010) and kaolinite (001) have been studied by density functional theory (DFT) and molecular dynamics (MD) method. The results indicated that carboxyl hydroxamic acids could adsorb on diaspore surface by ionic bonds and hydrogen bonds, and adsorb on kaolinite surface by hydrogen bonds. The models of carboxyl hydroxamic acids adsorbed on diaspore and kaolinite surfaces are proposed.

Single crystal architecture and absorption spectra of octathio[8]circulene and sym-tetraselenatetrathio[8]circulene: QTAIM and TD-DFT approach

The single crystal architecture of the high-symmetry octathio[8]circulene and sym-tetraselenatetrathio[8]circulene is studied at the density functional theory (DFT) level with the quantum theory of atoms in molecules (QTAIMs) approach to the electron density distribution analysis. The presence of stabilizing intermolecular C---C, C---S and C---Se contacts in the longitudinal and transversal projections of the single crystals is postulated on the grounds of the previous high-resolution X-ray data for octathio[8]circulene; it is supported by the present QTAIM calculations and also predicted in some new details for both circulenes. We suggest that the appearance of the observed red color for the monocrystalline octathio[8]circulene is caused by strong intermolecular interactions between the molecules in the single crystal. However, the intermolecular interactions for the sym-tetraselenatetrathio[8]circulene crystal fragment are weaker and molecular layers are more friable in comparison to octathio[8]circulene crystal structure. These lead to the absence of visible absorption for the sym-tetraselenatetrathio[8]circulene crystal.

Entropy versus aromaticity in the conformational dynamics of aromatic rings

Comparison of the results of Car-Parrinello molecular dynamics simulations of isolated benzene, pyrimidine and 1,2,4-triazine molecules reveals that the unusually low population of planar geometry of the benzene ring is caused by entropy effects despite its high aromaticity. The decrease in symmetry of the molecule results in smaller changes in entropy and Gibbs free energy due to out-of-plane deformations of the ring, leading to an increase in the population of planar geometry of the ring. This leads to differences in the topology of potential energy and Gibbs free energy surfaces.

Insight on the interaction of polychlorobiphenyl with nucleic acid–base

The interaction between one polychlorobiphenyl (3,3′,4,4′,-tetrachlorobiphenyl, coded PCB77) and the four DNA nucleic acid–base is studied by means of quantum mechanics calculations in stacked conformations. It is shown that even if the intermolecular dispersion energy is the largest component of the total interaction energy, some other contributions play a non negligible role. In particular the electrostatic dipole-dipole interaction and the charge transfer from the nucleobase to the PCB are responsible for the relative orientation of the monomers in the complexes. In addition, the charge transfer tends to flatten the PCB, which could therefore intercalate more easily between DNA base pairs. From these seminal results, we predict that PCB could intercalate completely between two base pairs, preferably between Guanine:Cytosine pairs.

Conformation-dependent conductance through a molecular break junction

Ab initio molecular dynamics simulations have been performed of a gold—1,4-benzenedithiol (BDT)—gold nanojunction under mechanical stress. For three different pulling rates between 10 and 40 m s^-1, it is found that the nanowire always ruptures between the second and third Au atom from the thiol sulfur. Larger rupture forces and longer extensions are required at higher pulling rates and vice versa. The electrical conductance was calculated along a pulling trajectory using the DFT-NEGF method to study the effect of thermal and stress-induced structural changes on the electrical transport properties. While the mechanically induced stretching of the junction is seen to lower the time-averaged conductance, thermal conformational changes are capable of altering the conductance by one order of magnitude. No single geometric quantity could be identified as the main contributor to the conductance fluctuations. Small modulations, however, can be explained in terms of C=C double bond vibrations in the BDT molecule. The dependence of the conductance on different geometric variables has further been investigated systematically by performing constrained geometry optimizations along a number of angle and dihedral coordinates. The largest changes in the conductance are observed when the Au-S-C angle and the Au-S-C-C dihedral are simultaneously constrained.

MD simulation of self-diffusion and structure in some n-alkanes over a wide temperature range at high pressures

Self-diffusion and structural properties of n-alkanes have been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 600 K at pressures up to 300 MPa. The simulated results of lower n-alkanes are in good agreement with the existing experimental data, and support the reliability of results of the simulations of self-diffusion coefficients obtained at the extreme conditions. We predict the self-diffusion coefficients for methane, ethane, propane and n-butane at the similar reduced temperatures and pressures to draw a comparison between them. Then the correlation between self-diffusion and structural properties are further investigated by calculating the coordination numbers. Moreover, we define four distances and their corresponding relative deviations to characterize the flexibility of long-chain n-alkanes. The simulated results show that the self-diffusion of n-alkane molecules is mainly affected by the close packing, and the flexibility has a strong impact on the self-diffusion of longer n-alkane molecules.