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.

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.

Density functional investigation of CO adsorption on Ni-doped single-walled armchair (5,5) boron nitride nanotubes

The adsorption of CO onto Ni-doped boron nitride nanotubes (BNNTs) was investigated using density functional theory at the B3LYP/LanL2DZ level of theory. The structures of the Ni-doped BNNTs and their CO-adsorbed configurations were obtained. It was found that the strength of adsorption of CO onto Ni-doped perfect BNNTs is higher than that on defective BNNTs. The electronic properties of all of the adsorption configurations of CO on Ni-doped BNNTs are reported.

Effects of protein binding on a lipid bilayer containing local anesthetic articaine, and the potential of mean force calculation: a molecular dynamics simulation approach

Articaine, as a local anesthetic drug has been simulated in neutral and charged forms, and its interaction with the dimyristoylphosphatidylcholine (DMPC) lipid bilayer membrane is investigated by molecular dynamics simulation using GROMACS software. In order to obtain the optimum location of the drug molecules, as they penetrate into the membrane, umbrella sampling is applied and the free energy is calculated. The effect of protein binding to DMPC membrane on the process of drug diffusion through the membrane is considered. Five simulation systems are designed and by applying the potential of mean force, the molecular dynamics simulation on the system is performed. In light of the obtained results, the electrostatic potential, variation of lipid bilayer’s order parameter and the diffusion coefficient of drug are discussed.

Role of gold in a complex cascade reaction involving two electrocyclization steps

Quantum chemical computations (B3LYP/LACVP**) were applied to assess the impact of Au(I) complexation on activation barriers for sequential electrocyclization reactions (one a 1,2-dihydroazete ring-opening and another a pentadienyl cation ring-closure) proposed to occur during a complex reaction cascade that converts alkynes and imines to cyclopentenimines.

Cubitane: a rare diterpenoid skeleton

There are only 15 diterpenoids known sharing the rare cubitane skeleton (1,3-diisopropyl-6,10-dimethylcyclododecane, Fig. 1) named after the natural product (+)-cubitene ((+)-1) from the termite Cubitermes umbratus. Cubitane-type diterpenoids (“cubitanoids”) have since then been isolated from gorgonian corals and there are reports that cubitene also occurs in plants. The twelve-membered ring of the cubitanoids is an interesting feature for which we have developed a novel synthesis involving bicyclic precursors. In this review, we discuss the state-of-research regarding isolation, structure elucidation, biological activity, biosynthesis, and total synthesis of cubitane-type diterpenoids.

In pursuit of negative Fukui functions: examples where the highest occupied molecular orbital fails to dominate the chemical reactivity

In our quest to explore molecules with chemically significant regions where the Fukui function is negative, we explored reactions where the frontier orbital that indicates the sites for electrophilic attack is not the highest occupied molecular orbital. The highest occupied molecular orbital (HOMO) controls the location of the regions where the Fukui function is negative, supporting the postulate that negative values of the Fukui function are associated with orbital relaxation effects and nodal surfaces of the frontier orbitals. Significant negative values for the condensed Fukui function, however, were not observed.

Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials

Coarse-grained studies of CH₃SH, CH₃CHO and CHCl₃ liquids, based on anisotropic Gay-Berne (GB) and electric multipole potentials (EMP), demonstrate that the coarse-grained model is able to qualitatively reproduce the results obtained from the atomistic model (AMOEBA polarizable force field) and allows for significant saving in computation time. It should be pointed out that the accuracy of the coarse-grained model is very sensitive to how well the anisotropic GB particle is defined and how satisfactorily the EMP sites are chosen.

Structural characterization of the (MeSH)4 potential energy surface

A random walk on the PES for (MeSH)₄ clusters produced 50 structural isomers held together by hydrogen-bonding networks according to calculations performed at the B3LYP/6–311++G** and MP2/6–311++G** levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted.

Effect of novel synthetic evodiamine analogue on sexual behavior in male rats

Currently phosphodiestrase5 (PDE5) inhibitors are the first-line treatment for erectile dysfunction. Drugs such as sildenafil and tadalafil are available as PDE5 inhibitors which are potent and reversible but lack selectivity with side effects such as headache, facial flushing, dyspepsia, and visual disturbances. We herein report for the first time novel condensed thienopyrimidines as evodiamine analogue and their effect on sexual behavior in male rats hitherto unreported. Novel synthetic evodiamine significantly showed improvement in male rat copulatory behavior. The test compound MKAC9 could be of promising importance in the treatment of sexual disorders like desire disorder or erectile dysfunction.

Electronic structures of bisnoradamantenyl and bisnoradamantanyl dications and related species

The highly pyramidalized molecule bisnoradamantene is extremely reactive toward nucleophiles and dienes. In this work, we studied the electronic structure of bisnoaradamantene, as well as those of its cation and dication, which are previously unreported carbonium ions. According to QTAIM and MO analysis, there is a 3c-2e bonding system in the bisnoradamantenyl cation and a 4c-2e bonding system in the bisnoradamantenyl dication. A topological study indicated that, on going from bisnoradamantene to its dication, π-bond interaction with the bridgehead carbon atom increases. Additional study of the bisnoradamantanyl dication also indicated that it has two multicenter bonding systems. Comparison of the D3BIA and NICS aromaticity indices of these molecules and other derivatives indicates that these indices are well correlated, and analysis of these indices shows that the cationic and dicationic bisnoradamantenyl species are homoaromatic.

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.

Charge sensitivity approach to mutual polarization of reactants: molecular mechanics perspective

Charge sensitivity analysis (CSA) in force-field atoms resolution was applied to describe the mutual polarization of reactants as well as charge-transfer (CT) effects. An inclusion complex of β-cyclodextrin with salicylic acid was used as a model system. Three CSA models were taken into account and verified on a Born–Oppenheimer molecular dynamics (BOMD) trajectory. The models differed in terms of the equilibrium conditions imposed on the system. It was demonstrated that mutual polarization is an important source of stabilization, in contrast to the results obtained from static charge calculations. The energy lowering induced by CT was small and comparable to the CT stabilization that occurs in hydrogen-bonded systems. All models correctly described the main topological features of the BOMD energy surface. CSA in force-field atoms resolution qualitatively reproduced the charge reorganization accompanying hydrogen-bond formation. It was shown that CSA parameters are very sensitive to the bond formation process, which suggests that they could be applied in reactive force fields as detectors of newly formed chemical bonds.

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.

Nucleus-independent chemical shift criterion for aromaticity in π-extended tetraoxa[8]circulenes

Recently synthesized π-extended symmetrical tetraoxa[8]circulenes that exhibit electroluminescent properties were calculated at the density functional theory (DFT) level using the quantum theory of atoms in molecules (QTAIM) approach to electron density distribution analysis. Nucleus-independent chemical shift (NICS) indices were used to characterize the aromaticity of the studied molecules. The tetraoxa[8]circulene molecules were found to consist of two antiaromatic perimeters (according to the Hückel “4n” antiaromaticity rule) that include 8 and 24 π-electrons. Conversely, NICS calculations demonstrated the existence of a common π-extended system (distributed like a flat ribbon) in the studied tetraoxa[8]circulene molecules. Thus, these symmetrical tetraoxa[8]circulene molecules provide examples of diatropic systems characterized by the presence of induced diatropic ring currents.

Monte carlo study of the percolation in two-dimensional polymer systems

The structure of a two-dimensional film formed by adsorbed polymer chains was studied by means of Monte Carlo simulations. The polymer chains were represented by linear sequences of lattice beads and positions of these beads were restricted to vertices of a two-dimensional square lattice. Two different Monte Carlo methods were employed to determine the properties of the model system. The first was the random sequential adsorption (RSA) and the second one was based on Monte Carlo simulations with a Verdier-Stockmayer sampling algorithm. The methodology concerning the determination of the percolation thresholds for an infinite chain system was discussed. The influence of the chain length on both thresholds was presented and discussed. It was shown that the RSA method gave considerably lower thresholds for longer chains. This behavior can be explained by a different pool of chain conformations used in the calculations in both methods under consideration.

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.

Structural elucidation of supramolecular alpha-cyclodextrin dimer/aliphatic monofunctional molecules complexes

The structural elucidation of 2α-cyclodextrin/1-octanethiol, 2α-cyclodextrin/1-octylamine and 2α-cyclodextrin/1-nonanoic acid inclusion complexes by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling has been achieved. The detailed spatial configurations are proposed for the three inclusion complexes based on 2D NMR method. ROESY experiments confirm the inclusion of guest molecules inside the α-cyclodextrin (α-CD) cavity. On the other hand, the host-guest ratio observed was 2:1 for three complexes. The detailed spatial configuration proposed based on 2D NMR methods were further interpreted using molecular modeling studies. The theoretical calculations are in good agreement with the experimental data.

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.

Zinc-, cadmium-, and mercury-containing one-dimensional tetraphenylporphyrin arrays: a DFT study

This work describes theoretical and experimental studies on glycerol esterification to obtain acetins focusing on the obtained isomers. The reaction of glycerol with acetic acid was carried out on Amberlyst 36 wet. Density functional theory calculations on the level of M06-2X functional and 6-311+G(d,p) basis set are carried out and the most stable structures of the reactants and products are located by considering a large number of conformers. The thermodynamics is discussed in terms of the calculated reaction Gibbs free energy. The AIM theory was used to characterize reactants and products. The glycerol esterification with acetic acid is found to be thermodynamically favored, with exothermal property. These agree well with experiments and allow us to explain the relative selectivity of products.