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Supramolecular systems may be used to stabilize otherwise unstable isomers to find alternative synthetic pathways. It has been reported that cucurbit[8]uril can stabilize trans-I and trans-II Cu II cyclam, whereas trans-III is the only non-substituted trans Cu II cyclam diastereoisomer found outside of the host molecule experimentally. Quantum chemistry methods can provide valuable insight into the intermolecular interactions involved in these inclusion complexes. All five possible trans diastereoisomers of Cu II cyclam were studied within the host molecule to calculate the interaction energy and free energy of association for each complex. The relative free energies of the five free cyclams confirm that trans-I and trans-II are the most energetically accessible diastereoisomers from the initial trans-III starting point. Energy decomposition analysis was used to identify the attractive and repulsive interactions between cyclam and cucurbit[8]uril and showed that trans-II encounters repulsive forces almost three times greater than trans-I, which may explain the 7:3 ratio of trans-I to trans-II within cucurbit[8]uril that occurs experimentally. Optimized complex geometries with trans-III, IV, and V show that the cyclams protrude out of cucurbit[8]uril, whereas trans-I and trans-II become more encapsulated and elongate the host, suggesting that the position of the cyclam is extremely important when forming non-covalent interactions. Our results agree with the experimental findings and provide greater insight into why the most stable isolated cyclam diastereoisomer, trans-III, does not form a complex. [ABSTRACT FROM AUTHOR]

Accurate determination of intermolecular non-covalent-bonded or non-bonded interactions is the key to potentially useful molecular dynamics simulations of polymer systems. However, it is challenging to balance both the accuracy and computational cost in force field modelling. One of the main difficulties is properly representing the calculated energy data as a continuous force function. In this paper, we employ well-developed machine learning techniques to construct a general purpose intermolecular non-bonded interaction force field for organic polymers. The original ab initio dataset SOFG-31 was calculated by us and has been well documented, and here we use it as our training set. The CLIFF kernel type machine learning scheme is used for predicting the interaction energies of heterodimers selected from the SOFG-31 dataset. Our test results show that the overall errors are well below the chemical accuracy of about 1 kcal/mol, thus demonstrating the promising feasibility of machine learning techniques in force field modelling. [ABSTRACT FROM AUTHOR]

Abstract Two oxindole based π-conjugated polymers with same structures except the positions of selenium atoms in the main chains have been synthesized. The effects of heavy atom substitution on optical, electrochemical, and photovoltaic properties have been investigated. The polymer solar cell devices based on the new polymers as electron donors also have been studied. The oxindole based polymers showed intramolecular non-bonded interactions between divalent sulfur/selenium and carbonyl oxygen. The selenophene based polymers showed narrow optical band gaps. However, the introduction of selenophene led to the decline of optical absorption in both the monomer and the polymers compared with the thiophene based counterparts. The diminution of absorption in selenium containing polymers can have adverse effect on solar photon harvesting. Graphical abstract Image 1 Highlights • The effect of Se replacement on the optoelectronic properties of the polymers. • Introduction of Se atoms led to the decline of optical absorption in the polymers. • Intramolecular non-bonded interactions between divalent S/Se and carbonyl oxygen. [ABSTRACT FROM AUTHOR]

Four unusual in,in -cyclophanes have been synthesized—the macrobicyclic in,in -bisphosphine 11 , its Ag(I) complex 12 , the in -hydroxysilane- in -phosphine 16 , and an inseparable mixture of 16 with the in -fluorosilane- in -phosphine 17 —and the in,in geometries have been confirmed by X-ray crystallography. In complex 12 , the silver atom is encapsulated in a hydrophobic cavity, and it experiences strong spin-spin coupling to the phosphorus atoms. In the cyclophanes 16 and 17 an inwardly directed hydroxyl group or fluorine atom is pressed against the lone pair of the opposing, inwardly directed phosphine. [ABSTRACT FROM AUTHOR]

Benzothiazole derivatives were synthesized and their antidiabetic potential evaluated using α-glucosidase, α-amylase, non-enzymatic glycosylation of hemoglobin and advanced glycation end product inhibition assays. Compound 3l showed low IC values of 0.31, 0.98, 0.59 and 0.19 mM in α-amylase, α-glucosidase, non-enzymatic glycosylation of hemoglobin and AGE inhibition assays, respectively, and outperformed the standard acarbose. Enzyme kinetic studies revealed that it has a K of 0.39 and 1.5 mM for α-amylase and α-glucosidase, respectively. The non-bonded interactions of 3l with α-amylase (3OLD) and α-glucosidase (2ZE0) showed that it binds in the active site pocket and is surrounded by residues Asp197, Glu233, Asp300 in 3OLD and Asp199, Glu256, Asp326 in 2ZE0. [ABSTRACT FROM AUTHOR]

The NMR spin–spin scalar coupling constants ( J HH 's) of closely contacting, but non-bonded hydrogen atoms in a series of highly strained molecules (including a new in , in -cyclophane made specifically for this study) have been examined both experimentally and computationally. The experimental J HH 's are invariably quite small (0.1–0.6 Hz), but common DFT methods with modest basis sets nearly always overestimate these values, by factors of 10–30, and even with quite large basis sets (up to cc-pVQZ) the J HH 's of two of the molecules are overestimated by a factor of 10 or more. Possible reasons for these discrepancies are discussed. [ABSTRACT FROM AUTHOR]

Abstract: A series of cyclophanes composed of two triarylelement caps linked by two-atom bridges has been synthesized. The bridgehead functional groups include phosphines in combination with amines, hydrosilanes, methylsilanes, and ethoxysilanes. Computational studies accurately predicted that when the bridgehead substituents are small (lone pairs or protons), an in , in bridgehead stereochemistry is strongly favored, but larger bridgehead substituents favor the formations of in , out stereoisomers. The X-ray structures, spectra, and reactivity of these compounds are discussed, as well as the resolution of one of the cyclophanes into pure enantiomers. [Copyright &y& Elsevier]

A long standing problem in normal mode analysis is identifying the right internal coordinates given only the cartesian coordinates, the masses of the atoms and the cartesian force constants without using any other additional chemical information. A possible solution is suggested here as drawing the normal modes obtained from the mass weighted cartesian force constant matrix and identifying the correct bonds and angles from the normal mode pictures. If chosen properly, the internal coordinates will have minimum mixing in the normal mode representation. This can in principle lead to an automation algorithm. A complete basis of internal coordinates is defined as the minimum number of valence internal coordinates that describe all the normal modes as completely as possible. It was shown in the literature that the relaxed force constants could be used as a measure of bond order in all atom-atom distance coordinates. Some of the bonded and non-bonded atom pairs can have similar values of the relaxed force constants and hence to use the relaxed force constant as a measure of bond order we need to separate the bonded pairs from the non-bonded ones. This needs extra chemical information of which pairs are bonded. The new definition of complete basis of non-redundant valence internal coordinates helps to identify the bonded pairs effectively without extra information. The hydrogen bonded water clusters (HO), n = 2-6, methane dimer and methane-water complex are used as examples to verify that the relaxed force constants of bonded pairs are indeed a measure of bond order. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

SUMMARY This paper analyses the buckling behaviour of single-walled and double-walled carbon nanotubes. The total potential of the atomic structure consists of the bonded energy and the non-bonded energy, both resulting from interatomic potentials, as well as the energy of external contributions. In particular, the influence of the in-layer and inter-layer non-bonded interactions is investigated. These non-bonded interactions are important to avoid the nanotubes from self-intersection or penetration and govern the morphology of the buckled tubes. The simulation model is based on a molecular statics approach embedded in the finite element framework. The search for equilibrium configurations of the structure leads to a non-linear system of equations, which is linearised and solved iteratively. Therefore, the model relies on the fully non-linear description of the interatomic potential and the atomic kinematics. Stability points of the loaded carbon nanotubes are detected by an accompanying eigenvalue analysis in combination with a bisection algorithm. By means of branch switching, the continuation of the non-linear load-deformation path in the postbuckling regime is enabled. With this framework, the buckling characteristics of carbon nanotubes in consequence of different loading conditions is studied. Results of numerical simulations are given for carbon nanotubes under torsion, axial compression and bending. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Abstract: Two series of heterocyclic tin compounds of general formula [(S{C6H3(CH2)nS}2O)SnR1R2] with different central ring sizes were prepared. The ten-membered series includes the compounds with n =1 and R1 =R2 =Ph (5); R1 =Cl, R2 =Ph (6); R1 =Cl, R2 = n-Bu (7); R1 =R2 =Cl (8); the eight-membered series includes the compounds with n =0 and R1 =R2 =Ph (10); R1 =Cl, R2 = n-Bu (11) and R1 =R2 =Cl (12). The compounds 5, 7, 8, 10, and 11 were investigated by single-crystal X-ray diffraction. The chloro compounds 7, 8, and 11 displayed a bipyramidal geometry at the tin atom with different degrees of distortion ranging from 57% to 62%. The diphenyl compounds 5 and 10 displayed a tetrahedral geometry at Sn. The conformation of the central ring in the ten-membered series is similar and is described as boat; the other series displayed two different conformations described as boat–chair and boat–boat. The possible conformers in the gas state of compounds 5, 7, 8, 10, 11, and 12 were investigated by MMFF, LSDA, BLYP, B3LYP, and M06 functionals using the DGDZVP and TZVP basis sets. The structural data of the total optimization agreed with the experimental results. The topological analysis indicated that bond critical points are present along the O⋯Sn direction in the compounds 7, 8, 11, and 12. [Copyright &y& Elsevier]

Abstract: The synthesis of a series of l-fuco-configured selenosugars, isosters of the potent glycosidase inhibitor isofucofagomine has been accomplished by a double nucleophilic displacement of a dimesylated derivative with selenide anion generated in situ. Se-Alkylation and oxidation of the corresponding selenane afforded a selenonium and a selenoxide, respectively. The biological activities of such compounds have been evaluated, finding a dual activity caused by the presence of the selenium atom: the selenane exerted a good glutathione peroxidase mimicry by efficiently scavenging H2O2 in the presence of thiols, whereas the stable selenoxide derivative was found to be the first example of a selenosugar acting as a good α-l-fucosidase inhibitor. [Copyright &y& Elsevier]

For 12 acetylacetonates of the composition M(acac) ( n = 2, 3, or 4) and M(acac)(CH) (M is a metal) the total area ( S) of the faces of Voronoi-Dirichlet polyhedra (VDP) corresponding to all intermolecular contacts of one molecule in the crystal structure and the total volume of pyramids ( V), whose bases are formed of such faces and the vertices are occupied by the nuclei of atoms participating in intermolecular contacts, are determined. The key features of non-bonded interactions are considered. The existence of a linear dependence of the sublimation enthalpy of acetylacetonates on the S or V parameters of their molecular VDP is revealed. It is shown that the sublimation enthalpy of Ga(acac) requires the refinement and theoretically should be 124 kJ/mol. [ABSTRACT FROM AUTHOR]

Abstract: The title complex was synthesized under self-assembly conditions using Cu(acetate)2·H2O, 2-amp (=2-aminomethylpyridine) and KSCN, and was characterized by IR, elemental analysis and single crystal structural analysis, and its spectral and RT magnetic properties were investigated. The asymmetric unit consists of a square planar Cu(II) center, with two ligand N atoms and two anionic Ns forming the square plane. In the unit cell, the monomeric complex assembles into 2-D layers through very weak non-bonded interactions between anionic S and Cu2+. Further, the structure was satisfactorily modeled by calculations based on Density Functional Theory (DFT), and the UV–Vis and IR spectra are analyzed in depth with the help of Time Dependent DFT (TDDFT). The results indicate that the absorption maxima are at relatively high energy and are mainly assigned to π→π∗ transitions (in pyridine), with a fair contribution of metal to ligand charge transfer (MLCT) and ligand to ligand charge transfer (LLCT) transitions. All the low lying transitions are categorized as mixed MLCT/LLCT. A very weak but broad band in the higher wavelength region has been detected and identified as a d–d transition band. Also, it has been found that when the ligand ratio is modified, the formation of Cu(2-amp)2(SCN)2 takes place under the same self-assembly conditions, whose structure only has been recently reported. Structural, spectral and theoretical comparisons are presented for both complexes. [Copyright &y& Elsevier]

Abstract: Design and synthesis of organoselenium compounds with high thiol peroxidase (TPx) and low thiol oxidase (TOx) activities have been a difficult task and remains a synthetic-activity relationship dilemma. In this regard we are reporting for the first time a detail experimental data (both in vitro and in vivo) about the anti-oxidant and toxicological profile of an Imine (–Ning organoselenium compound (Compound A). The TPx activity of Compound A was significantly higher than diphenyl diselenide (DPDS). Both Compound A and DPDS protected sodium nitropruside (SNP) induced thiobarbituric acid reactive species (TBARS) production in rats tissue homogenate with significantly higher activity observed for Compound A than DPDS (p <0.05). The Compound A also exhibited strong antioxidant activity in the DPPH and ABTS radical scavenging assays. This study reveals that an imine group close to selenium atom drastically enhances the catalytic activities in the aromatic thiol (PhSH) assay systems. The oxidation of biologically significant thiols reflects the toxicity of the compounds. However, the present data showed that treatment with Compound A at 0, 10, 25 or 50mg/kg was not associated with mortality or body weight loss. Similarly it did not inhibit α-ALA-D and Na+1/K+1 ATPase (sulfhydryl group containing enzymes) activities after acute oral treatment; rather it enhanced non-protein thiols (NPSH) concentration. The Compound A did not cause any oxidative stress as measured by TBARS production in rat''s tissue preparation. Our data also indicate that exposure to Compound A did not affect plasma transaminase activities or levels of urea and creatinine in rats. Ascorbic acid is always considered a marker of oxidative stress and the reduction of its content may indicate an increase in oxidative stress. Treatment with Compound A did not alter Ascorbic acid levels in rats. The conducted in vitro and in vivo tests show the versatile therapeutic potential of this compound in the area of free radical induced damages, will undoubtedly enhance our understanding of the mechanism of model compounds and may ultimately yield insights that result in improved GPx mimics. [Copyright &y& Elsevier]

Abstract: Ronald J. Gillespie’s valence shell electron pair repulsion (VSEPR) model has been very successful in research and education within rather well-defined domains of inorganic compounds for predicting molecular shapes and variations in structural features. Considerations of non-bonded interactions have extended its applicability in the realm of smaller central atoms and larger ligands. The structure of xenon hexafluoride played a pivotal role in convincing the doubters of the validity and utility of the model in the early days of its history. Curiously, whereas most of the molecular structures of noble-gas compounds have been excellent examples of the VSEPR model, xenon hexafluoride represents a more involved case. Its structure is still not known in full, but currently it is not known at a much higher level of sophistication than before. [ABSTRACT FROM AUTHOR]

[Display omitted] • The collaboration of non-bonded interactions changes pulling force and facilitate ascorbic acid transporting inside CPNTs. • Hydrogen atoms of ascorbic acid have more contributions than its oxygen atoms in interaction with water molecules and CPNTs. • The configurational entropy of ascorbic acid changes in the transport pathway when the molecule moves throughout CPNTs. • The range of the binding energy changes of ascorbic acid with the peptide rings of each of CPNTs is different. Cyclic peptide nanotubes (CPNTs) are potential candidates for drug delivery, separation and recovery technologies, as well as self-assembling nanomaterials. In this study, we investigated the L-ascorbic acid transport behaviour through two CPNTs using computational studies, including quantum calculations, molecular docking and steered molecular dynamics (SMD) simulations. Two cyclic peptide nanotubes 8 × [L-Gln-(D-Leu-L-Trp) 4-D-Leu-] (QLWL) and 8 × [(D-Ala-L-Ala) 5] (AA), embedded in a fully hydrated membrane composed of DPPC/POPC/POPS/cholesterol, were considered. Our findings from SMD simulations revealed that ascorbic acid moves differently in AA nanotube compared to QLWL nanotube. The analysis of the number of hydrogen bonds shows that the hydrogen atoms of ascorbic acid hydroxyl groups form more hydrogen bonds compared to oxygen atoms with water molecules and the CPNTs. This result was supported using the calculations of radial distribution functions of various atoms of the ascorbic acid near the oxygen atom of water molecules and carbonyl groups of the CPNTs during the transport pathway in the lumen of each CPNTs. Entropy calculations show that the configurational entropy of ascorbic acid in the transport pathway is not monotonous, and it changes due to variable behaviour when the molecule moves throughout CPNTs. The interactions that the nanotubes form with their environment play an important role in the binding energy of ascorbic acid with each of the peptide ring that the binding energy value is significant for each of the peptide rings with ascorbic acid. These informations can be useful to future applications and studies in the field of nanoscience and nanotechnology, such as drug delivery and nanosensors. [ABSTRACT FROM AUTHOR]

Abstract: Treatment of Ph2PbCl2 with O(C6H4SH)2 (1a), S(C6H4SH)2 (2a) and S(C6H3SH)2O (3a) afforded the stable organolead compounds [{O(C6H4S)2}PbPh2] (1b), [{S(C6H4S)2}PbPh2] (2b) and [{S(C6H3S)2O}PbPh2] (3b). X-ray structure determinations of dithiolate-diphenyl lead compounds 1b–3b revealed that the trichalcogenated ligands are tridentate in 1b and 2b, and bidentate in 3b. The lead atom acts as an acceptor atom exhibiting weak intramolecular transannular interactions with the donor D atom, with tetrahedral distortions of 48% for 1b, 51% for 2b and 45% for 3b. The local geometry at the lead atom is described as monocapped tetrahedral. The crystal packing of title compounds is stabilized by several non-bonded interactions. [Copyright &y& Elsevier]

Ab initio and density-functional theory (DFT) modeling have proven to be important tools in the determination of the properties and reactivity of selenium with respect to biological activity. In this review, we address recent applications of quantum chemistry in three areas of interest to selenium chemistry: theoretical 77Se chemical shifts, analysis of Se...N,O interactions important to redox chemistry and mechanistic determinations for selenoenzymes and small selenium molecules. High-performance computing and DFT have allowed for large-scale calculations of both the enzyme active site and solution-phase reactivity. The latter development is important for understanding the complex mechanisms of small molecule GPx mimics. Application of solvent-assisted proton exchange to the redox scavenging mechanism of PhSeH by our research group is highlighted. [ABSTRACT FROM AUTHOR]

A survey of crystal structures of organic molecules shows that there is strong evidence of stacking of aromatic rings and aliphatic rings and this packing motif may provide a fundamental stabilising interaction in crystal structure formation. Here this is probed by mainly focussing on interaction of six-membered aromatic groups with six-membered heterocyclic molecules, especially sugars. [Copyright &y& Elsevier]

A knowledge-based method for calculating the similarity of functional groups is described and validated. The method is based on experimental information derived from small molecule crystal structures. These data are used in the form of scatterplots that show the likelihood of a non-bonded interaction being formed between functional group A (the `central group') and functional group B (the `contact group' or `probe'). The scatterplots are converted into three-dimensional maps that show the propensity of the probe at different positions around the central group. Here we describe how to calculate the similarity of a pair of central groups based on these maps. The similarity method is validated using bioisosteric functional group pairs identified in the Bioster database and Relibase. The Bioster database is a critical compilation of thousands of bioisosteric molecule pairs, including drugs, enzyme inhibitors and agrochemicals. Relibase is an object-oriented database containing structural data about protein-ligand interactions. The distributions of the similarities of the bioisosteric functional group pairs are compared with similarities for all the possible pairs in IsoStar, and are found to be significantly different. Enrichment factors are also calculated showing the similarity method is statistically significantly better than random in predicting bioisosteric functional group pairs. [ABSTRACT FROM AUTHOR]

We compare experimental melting curves of short heterogeneous DNA oligomers with theoretical curves derived from statistical mechanics. Partition functions are computed with the one-dimensional Peyrard-Bishop (PB) Hamiltonian, already used in the study of the melting of long DNA chains. Working with short chains we take into account, in the computations, not only the breaking of the interstrand hydrogen bonds, but also the complete dissociation of the double helix into separate single strands. Since this dissociation equilibrium is of general relevance, independent of the particular microscopic model, we give some details of its treatment. We discuss how the non bonded three-dimensional interactions, not explicitly considered in the one-dimensional PB model, are taken into account through the treatment of the dissociation equilibrium. We also evaluate the relevance of the dissociation as a function of the chain length. [ABSTRACT FROM AUTHOR]

This paper describes a (6-8) variant of the Lennard-Jones (6-12) potential,for computing the energy of non-bonded interactions in molecular mechanicscalculations, which combines the overall precision of the Buckingham (6-exp)potential with the computational efficiency of the standard Lennard-Jones(6-12) potential. There is also a note on the radius of convergence of thefull matrix Newton–Raphson optimization procedure. [ABSTRACT FROM AUTHOR]

In this work, ionogels fabricated by incorporating room temperature ionic liquids (ILs) in meso- and macroporous syndiotactic polystyrene (sPS) gels, are studied by using differential scanning calorimetry (DSC), polarized optical microscopy (POM), rheology, and nuclear magnetic resonance (NMR) spectroscopy. sPS gel network is prepared via thermo-reversible gelation in tetrahydrofuran and the pores are subsequently filled with the ionic liquid, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (PYR14TFSI). Using DSC and POM it is found that PYR14TFSI molecules in sPS gels show higher melting temperatures than that for the neat PYR14TFSI. 1H static NMR signals provide overall mobility of ILs in the sPS gels. Surprisingly, the ionogel prepared with 0.04 g/mL sPS solution apparently shows the broadest 1H NMR signals among the gels prepared with 0.04, 0.08, and 0.12 g/mL sPS concentration. This is attributed to a quasi-bulk state of ILs. Moreover, two-dimensional 1H NOESY spectra indicate that PYR14TFSI molecules in sPS show strong non-bonded through-space correlation peaks and their intensities increase proportionally with polymer concentration in the gel, while such correlation peaks are not observed for the neat PYR14TFSI molecules. The observed concentration dependence of constrained PYR14TFSI dynamics is interpreted in terms of the confined PYR14TFSI at the surface or closer to the surface of sPS scaffold. From these experimental results, it is suggested that PYR14TFSI melting-temperature are more related to quasi-bulk component than the constrained PYR14TFSI in the sPS gels. Image 1 • Ionic liquid (IL) molecules show constrained mobility in the pores of sPS gels. • The fraction of IL experiencing constrained mobility increases with polymer fraction. • Constrained mobility influences IL melting. [ABSTRACT FROM AUTHOR]

The understanding of polymer solution thermodynamics and characterization of pressure effects on fundamental polymer physics of macromolecular systems is significant in the manufacturing of polyolefins. Consequently, numerous experimental and theoretical efforts have been made towards understanding phase behavior of polymer solutions at elevated pressures. Despite this progress, only limited efforts are directed towards understanding the underlying phenomena behind the influence of high pressure upon the thermophysical properties of ternary polymer solutions at a molecular level. The present paper, therefore, reports on the influence of supercritical ethylene on the density of PE + hydrocarbon solvent system by exploring ternary mixtures of PE + hexane + ethylene for ethylene concentrations up to 10 wt% at varied temperatures and in a pressure range from 100 to 1000 bar via fully-atomistic molecular dynamics (MD) simulations. Additionally, the modified Sanchez-Lacombe equation of state (EOS) model is iteratively solved to capture the pressure, concentration, and temperature dependence of ternary PE solution density. It is shown that the small amounts of ethylene dissolved in the liquid mixtures of PE + hexane significantly decreases the polymer solution density. The presence of unreacted monomer in the solution polymerization process utilized in PE manufacturing was found to substantially lower the PE solution density particularly at the lower end of the investigated pressure range. This noteworthy reduction in mixture density as a consequence impacts design and operation of the liquid-liquid phase separator in manufacturing of PE via solution polymerization. Another key point to bear in mind is that the mixture density exhibits fairly less sensitivity to ethylene amount as external pressure raises. Nevertheless, pressure, solvent composition, and temperature dependence of density display less sensitivity as pressure increases. In relation to the characterization of the impact of addition of ethylene an atomistic-level insight is provided, which proves to be of great value in revealing intermolecular interactions in the binary subsystems of polymer/solvent/monomer. The MD computations are shown to be in excellent agreement with the theoretical EOS model, confirming the validity of the proposed methodology. Furthermore, the adopted OPLS-AA has been found a reliable atomistic force field, which provides detailed molecular information on the thermophysical properties of polyolefin in hydrocarbon solutions. Ultimately, it is demonstrated that the MD simulations complement parametric EOS predictions and costly experimental approaches. Image 1 • The ternary PE solution density raises with increase in pressure stemming from remarkable variations in non-bonded interactive forces. • The MD-simulated data were found to be in quantitative accordance with the EOS model. • The adopted OPLS atomistic force field is a highly reliable to gain in-depth insights into polyolefin in hydrocarbon solvents. • Molecular modeling supplies an abundant amount of knowledge on variations in intra- and intermolecular interactions versus pressure. [ABSTRACT FROM AUTHOR]

Overexpression or deregulation of c-Met enzyme has been reported to be associated with the formation and development of various types of human cancers, so an intense scientific work was devoted to design more potent inhibitors. We ran 17 molecular dynamics simulations of potent type I c-Met inhibitors to investigate the critical and stable interactions regarding the inherent flexibility of protein and ligand via dynamics ensembles. Protein-ligand interactions of hydrogen bond, pi-pi stacked and hydrophobic have been investigated throughout the equilibrium time to suggest critical pharmacophores. Also, the fluctuations of amino acid residues were monitored by root mean square fluctuation (RMSF) measure. MM-PBSA approach was also used to estimate the binding free energy of different complexes. The pi-pi stacked interaction of c-Met inhibitors with Tyr1230 or both Tyr1230 and Tyr1159 was shown critical for a good inhibitory activity and was defined as the most important interaction type in terms of binding energy. Almost in all codes, ligands showed van der Waals interactions with hydrophobic residues of ATP site. In addition, hydrogen bond interaction with Met1160 was found necessary for a ligand being a potent inhibitor of c-Met. RMSF analysis showed that Met1160 and Pro1158 which make the key hydrogen bond interactions and Tyr1230 that contributes in pi-pi stacked interactions with the ligands were quite fixed during ligand binding. Image 1 • Critical stable interactions of c-Met-inhibitor were resolved via dynamic ensembles. • Critical residues of Met1160 and Tyr1230 in c-Met complexes were quite fixed motion. • Pi-stacked interaction of inhibitor with Tyr1230 or Tyr1159 in c-Met is critical. • van der Waals interactions of ligands with hydrophobic residues is highly occurring. • Hydrogen bond between c-Met inhibitor and Met1160 is necessary. [ABSTRACT FROM AUTHOR]

Cyclic peptide nanotubes (CPNTs) are open-ended, hollow, and tubular structures that are made of several cyclic peptide rings. These structures can act as a transmembrane channel and transport ions or small molecules. In this work, we studied the stability of a cyclic peptide nanotube 8 × [(Trp-D-Leu)4-Gln-D-Leu] into a fully hydrated membrane composed of DPPC/POPC/POPS/cholesterol and also the transport mechanism of β-D-glucose through this nanotube was investigated. Our findings revealed that the CPNT was stable in the lipid bilayer during the simulation time and non-bonded interactions, especially hydrogen bonding have an important role to form a stable CPNT in the membrane. The glucose jumps from a Cα-region into the mid-Cα region and spends more time in this region because of its more desirable interactions with water molecules and the CPNT. In the transport pathway, non-bonded interactions between glucose, water molecules and the CPNT facilitate the transport of the glucose through the CPNT. The collaboration of hydrogen bonds, electrostatic and van der Waals interactions change the pulling force and lead to transport glucose through the CPNT. Potential of mean force (PMF) calculations revealed that the glucose has a minimum value of binding free energy and maximum configurational entropy in MPR regions. These findings can be used to design more CPNTs with different goals such as drug delivery.Communicated by Ramaswamy H. Sarma.

The structure and dynamics of hydrogen-bonded structures are of significant importance in understanding many binary mixtures. Since self-diffusion is very sensitive to changes in the molecular weight and shape of the diffusing species, hydrogen-bonded associated structures in dimethylsulfoxide-methanol (DMSO-MeOH) and DMSO-ethanol (DMSO-EtOH) mixtures are investigated using nuclear magnetic resonance (NMR) diffusion experiments and molecular dynamics (MD) simulations over the entire composition range at 298 K. The self-diffusion coefficients of DMSO-MeOH and DMSO-EtOH mixtures decrease by up to 15% and 10%, respectively, with DMSO concentration, indicating weaker association as compared to DMSO-water mixtures. The calculated heat of mixing and radial distribution functions reveal that the intermolecular structures of DMSO-MeOH and DMSO-EtOH mixtures do not change on mixing. DMSO-alcohol hydrogen-bonded dimers are the dominant species in mixtures. Direct comparison of the simulated and experimental data afford greater insights into the structural properties of binary mixtures., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)