Steered molecular dynamics simulations of protein-ligand interactions

Molecular recognition and specific protein-ligandinteractions are central to many biochemical processes,such as enzyme catalysis, assembly of organelles, en-ergy transduction, signaling, diverse control functions,and replication, expression and storage of the geneticmaterial[1]. Moreover, protein-ligand interactions pro-vide the mechanism of many drug therapies and un-derstanding of such interactions is thus significant forrational drug design[1,2]. For the experimental studiesof protein-ligan…     

Stability of mechanical properties of molecular layer–deposited alucone

We report on the effect of aging on the mechanical properties of molecular layer–deposited (MLD) thin films. We studied the mechanical failure of the films during uniaxial tensile testing and observed a sixfold difference in the crack-onset strain (COS) and related flexibility within the first two days after the samples were exposed to ambient air. The MLD films made using trimethylaluminum and ethylene glycol are notorious for exhibiting structural changes after the fabrication; we show that these changes are detrimental for mechanical robustness of the films. This information aids to plan the handling or the protection of these films to achieve better performance with these materials. The interfacial shear strains and COSs of the shortly air-exposed 300-nm-thick films were observed to be roughly 0.3% and 1.8%, respectively. These values are the highest reported so far for hybrid organic–inorganic MLD thin films and would extrapolate to about 14% COS for 5-nm-thick film, indicating potential applications as interfacial adhesion layer for films on polymer substrates and as a protective coating in battery applications.     

Effects of molecular structure parameters on ring-opening reaction of benzoxazines

A colorless monoclinic crystal of dichloro-benzoxazine was obtained and examined by single crystal X-ray diffraction analysis. At the same time, molecular modeling analysis of nine benzoxazine compounds with different substituting groups was performed. Both single crystal X-ray diffraction analysis and molecular modeling analysis provide a detailed picture of molecular structure on molecular level and show good consistence with each other. On the basis of structural analysis, the effects of molecular structure parameters on ring-opening polymerization of ben-zoxazines have been explored.     

The chemist’s concept of molecular structure

The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The Born–Oppenheimer separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the Born–Oppenheimer approximation introduces new paradigms, bringing fresh insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models.

A molecular theory of stress–strain relationship of spherulitic materials

A primitive molecular theory for stress–strain relationship of spherulitic polymers is presented based on a consideration of changes in conformational free energy in the tie chains and floating chains located between crystalline lamellae within an ideal spherulite which is assumed to undergo an affine deformation. Numerical stress–strain curves are calculated as a function of temperature, crystallinity, and tie chain fraction.     

Ab initio molecular dynamics — Applications to the molecular and solid state physics of phosphorus

Summary We review combined molecular dynamics (MD) and density functional (DF) simulations and their applicability in chemistry and physics. This method (also termedab initio MD, first principles MD or Car-Parrinello method) exhibits characteristic strengths and weaknesses, and we demonstrate both in a set of typical example applications from molecular physics (phosphorus clusters) and solid state physics/chemistry (liquid phosphorus). Dynamical, finite temperature, simulations deriving interatomic forces from state-of-the-art density functional calculations represent a substantial advance over both (i) traditional pointwise total energy and electronic band structure calculations and (ii) classical MD simulations with empirical or semi-empirical forces, and have already yielded qualitatively new insights in several fields.     

A molecular simulation study of the distribution of cation in zeolites

NVT Monte Carlo simulations are first used to describe the distribution of Na cations in Faujasite for several Si/Al ratios. These calculations were performed by combining two different sets of potential parameters combined with both T-atoms and explicit Si,Al models. Grand Canonical Monte Carlo simulations are then employed to investigate the influence of water adsorption on the distribution of cations in the case of a Faujasite sample with 56 cations (NaY56). These simulations data are compared to available experimental data and the influence of the choice of the forcefield for describing the cation/zeolite interaction on these results is discussed.     

The molecular structure and conformation of 1,1′-dimethyl-bicyclopropyl

The molecular structure and conformation of 1,1′-dimethyl-bicyclopropyl have been studied by the gas electron diffraction method, extended by normal coordinate and molecular mechenics calculations. The experimental data are in accordance with all molecules having the gauche conformation, with a dihedral angle of 58°.     

Synthesis and antitumor activities of structure-related small molecular compounds of gambogic acid

Through simplifying the complicated skeleton of the natural product gambogic acid, two series derivatives of chromone and xanthone were synthesized and examined for their antitumor activities against several cancer cells in vitro by MTT method. The results showed that appropriate introduction of prenyl group to the small molecular compounds could elevate their antitumor activities. The structure-activities relationship of synthesized compounds certified that the bridgecore in gambogic acid was very important for keeping its antitumor activities.     

Radical chain mechanism of the oxidation of α-terpinene by molecular oxygen

The oxidation of -terpinene by molecular oxygen is shown to occur by a radical chain mechanism involving hydroperoxy radicals. The principal molecular reaction products are H₂O₂ and 1-methyl-4-isopropylbenzene. The rate constants for chain propagation and chain breaking measured at 35–70°C are (liter/mol·s) lgk₃ = 7.10– (6700±400)/4.57T and lgk₅ = 9.80– (2700±300)/4.57T respectively.Translated from Teoreticheskaya Éksperimental'naya Khimiya, Vol. 30, No. 3, pp. 143–146, May–June, 1994The authors thank the Ukraine National Committee for the Basic Research Fund for financing this work.     

Consideration of dipole–quadrupole interactions in molecular based equations of state

The thermodynamic behaviour of a number of real substances is determined by dipolar as well as quadrupolar interactions of the molecules. In equations of state (EOS) like, e.g. BACKONE separate contributions to the Helmholtz energy for the dipolar and the quadrupolar interactions are considered but no cross contributions. Here, the concept of effective dipole and quadrupole contributions is suggested in which the effective dipole strength μ_e is influenced by the quadrupole cross interaction. Similarily, the effective quadrupole strength Q_e takes into account the dipole cross interaction. In order to arrive at these effective dipolar and quadrupolar strengths, molecular simulations are performed. From the simulation results correlation equations are derived which are used in combination with BACKONE for the calculation of vapour–liquid equilibria (VLE) of real mixtures. By using these effective moments, the only required binary mixing rule parameter k_ij tends to small values of about 0.01 and becomes temperature-independent. Moreover, the VLE pressures are predicted now considerably better than without consideration of the cross contributions.     

Effect of intermolecular O-H ⋯ O hydrogen bonding on the molecular structure of phenol: An ab initio molecular orbital study

The effect of intermolecular O-H O hydrogen bonding on the molecular structure of phenol has been studied by SCF ab initio MO calculations at the HF/6-31G * level. The systems investigated are eight phenol-water complexes and the dimer and trimer of phenol. Optimized geometries show that hydrogen bond formation causes a consistent pattern of changes in the structure of the molecule. When phenol acts as a proton donor, the expected increase ofr (O-H) is accompanied by a slight decrease ofr(C-O) and of the internal ring angles at theipso andpara positions, and by an increase ofr(C _ipso © _ortho ). These changes suggest that the relative contribution of polar canonical forms to the electronic structure of the molecule increases upon hydrogen bond formation, since this enhances the strength of the interaction. The opposite changes occur when phenol acts as a proton acceptor, except forr(O-H), which is the same as in the free molecule. If phenol acts as a proton donorand as a proton acceptor, the two hydrogen bonds become stronger due to a synergic effect. In this case, however, the structural deformation of the molecule is less pronounced than in the previous cases, due to the opposite effect of the two hydrogen bonds. The available experimental evidence on gas-crystal structural differences for phenol is critically reviewed, also in the light of the present results on gas-phase complexes.     

Transport property of polyaniline and its molecular weight dependence

Ｔｈｅｅｌｅｃｔｒｉｃａｌｃｏｎｄｕｃｔｉｖｉｔｙ(σ)ｏｆｐｏｌｙａｎｉｌｉｎｅ(ＰＡｎ)ｄｏｐｅｄｗｉｔｈｉｎｏｒｇａｎｉｃｐｒｏｔｏｎｉｃａｃｉｄｓｉｓａｂｏｕｔ10Ｓ/ｃｍａｎｄσ(Ｔ)∝ｅｘｐ[-(Ｔ0/Ｔ)1/2].Ｉｔｍｅａｎｓｔｈａｔσｉｎｃｒｅａｓｅｓｗｉｔｈｉｎｃｒｅａｓｉｎｇｔｅｍｐｅｒａｔｕｒｅａｎｄｔｈｅｔｒａｎｓｐｏｒｔｐｒｏｐｅｒｔｙｉｓｉｎａｃｃｏｒｄａｎｃｅｗｉｔｈｔｈｅｖａｒｉａｂｌｅｒａｎｇｅｈｏｐｐｉｎｇ(ＶＲＨ)ｍｏｄｅｌ[1].Ａｆｔｅｒｓｔｒｅｔｃｈｉｎｇ,ｔｈｅＨＣｌｄｏｐ…     

Conductivity studies of the molecular encapsulation of sodium perfluoroctanoate byβ-cyclodextrin derivatives

The molecular encapsulation of sodium perfluoroctanoate (SPFO) by hydroxypropyl--cyclodextrin (HP--CD) or 2,6-di-O-methyl--cyclodextrin (DM--CD) has been analyzed by measuring the conductivity in solution of the ternary systems formed by CD + SPFO + H₂O. The studies were carried out at 25 °C using a fully computerized electrical conductivity technique. The measurements were made as a function of CD concentration at various non-micellar concentrations of SPFO, and as a function of CD and SPFO concentrations with [CD]/[SPFO] constant at stoichiometric ratio. The inclusion complexes, HP--CD-SPFO and DM--CD-SPFO, were characterized through the stoichiometry, which has been found to be 1 : 1 in both cases, and the binding constants, which have been evaluated from the conductivity data with a model proposed by us considering the variation of the ionic molar conductivities with the concentration and the association of the surfactant counterion to the inclusion complex. The resultingK values indicate that the interaction between the CD cavity and the monomeric SPFO is strong and similar in both cases.     

Calculations of heat of solvation by a simple electrostatic approach to molecular interactions

An extremely simple formula to estimate the heat of formation of complexes between anion and a polar molecule or between highly polar systems is presented.The formula is entirelyelectrostatic and the expression used is verified by means of perturbation theory.This formula is test-ed for several ion-molecule and molecule-molecule pairs.It is also applied to estimate the heat ofhydration of simple salts.     

A molecular dynamics study of the thermal response of crystalline cellulose Iβ

Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose Iβ. The latest version of the GLYCAM force field series (GLYCAM06) was used for the simulations. The unit cell parameters, density, torsion angles and hydrogen-bonding network of the crystalline polymer were carefully analyzed. The simulated data were validated against the experimental results obtained by X-ray diffraction for the crystal structure of cellulose Iβ at room and high temperatures, as well as against the temperature-dependent IR measurements describing the variation of hydrogen bonding patterns. Distinct low and high temperature structures were identified, with a phase transition temperature of 475–500 K. In the high-temperature structure, all the origin chains rotated around the helix axis by about 30° and the conformation of all hydroxymethyl groups changed from tg to either gt on origin chains or gg on center chains. The hydrogen-bonding network was reorganized along with the phase transition. Compared to the previously employed GROMOS 45a4 force field, GLYCAM06 yields data in much better agreement with experimental observations, which reflects that a cautious parameterization of the nonbonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.     

NMR studies of conformations and molecular recognition of pyridinio-appended and nicotinamide-appended β-cyclodextrin

Abstract

The conformations of pyridinio-appended β-cyclodextrin (CDP⁺) and nicotinamide-appended β-cyclodextrin (CDNA⁺) were studied by NMR spectroscopy. The orientations of the pyridine residue of CDP⁺ and the nicotinamide residue of CDNA⁺ were determined by using a combination of NMR spectroscopic techniques. NMR spectra indicate that the shapes of the cavities of CDP⁺ and CDNA⁺ were changed after forming complexes. This change depended on the shape of the guest. CDNA⁺ could separate the ¹H resonances at the Cβ position of racemic tryptophan into two sets of resonances for each enantiomer.