High-order Harmonic Generation of Aligned Acetylene in Elliptically Polarized Strong Laser Fields?

We perform an experimental study on high-order harmonic generation (HHG) of aligned acetylene molecules induced by a 35-fs 800-nm strong laser field, by using a home-built HHG spectrometer. It is observed that the molecular HHG probability declines with increasing the laser ellipticity, which is in consistence with the deduction from the well-known tunneling-plus-rescattering scenario. By introducing a weak femtosecond laser pulse to nonadiabatically align the molecules, we investigated the molecular orbital effect on the HHG in both linearly and elliptically polarized driving laser fields. The results show that the harmonic intensity is maximum for the molecular axis aligned perpendicularly to the laser electric field. It indicates that both the highest occupied molecular orbitals (HOMO) and HOMO-1 contribute to the strong-field HHG of acetylene molecules. Our study should pave the way for understanding the interaction of molecules with ultrafast strong laser fields.     

A molecular dynamics study of nitric oxide in water: diffusion and structure

We present molecular dynamics simulations of the diffusion coefficients and structure of water-nitric oxide mixtures at ambient (298 K) and in vivo (310 K) conditions. A two-site rigid-body molecular model with partial charges and a Lennard-Jones potential on both sites is proposed for nitric oxide and used in conjunction with the extended simple point-charge model for liquid water in our simulations. The diffusion coefficients obtained from the simulations are in good agreement with experimental data. The results from intermolecular partial pair functions show that under these thermodynamic conditions, the existence of nitric oxide in liquid water has little impact on the structure of water and the tendency to form H bonds between water molecules. We also find that it is unlikely that H bonds form between the hydrogen atoms in water and either the nitrogen or the oxygen atom on the nitric oxide at the temperatures and densities examined in this study. This study suggests that in low concentrations nitric oxide molecules exist as free molecules in liquid water rather than forming complexes with water molecules.     

A study of hydration effects on the conformational aspects of gaba mediators

The conformation of numerous chemical compounds is strongly influenced by solvents. Knowledge of their structure in solution is necessary, especially for a discussion of the biological and pharmacological activity of the molecules. The neurotransmitters and their agonists and antagonists are known to be flexible molecules that interact with quite distinct receptors. The conformational properties of several GABA (γ-aminobutyric acid) mediators have been studied by the MNDO technique. The optimized geometries of the molecules have been used to study the solvent effects on their conformational properties considering the supermolecule approach for their first hydration shell. A conjectural pharmacophoric pattern for several GABA inhibitors has already been suggested from the molecular electrostatic potentials (MEP ) of several molecules using a localized bond orbital technique. In the present work, MEP calculations have been carried out considering a solvent effect on the MNDO optimized geometries to investigate any deviation from the earlier results.     

Identification of a Peripheral Substitution Symmetry Effect in Self‐Assembled Architectures

Two complementary classes of molecules based on a triphenylene core are synthesized. The two‐dimensional (2D) assemblies of these molecules deposited on a highly oriented pyrolytic graphite (HOPG) surface are identified with scanning tunneling microscopy (STM). Structures with large cavities are formed by symmetric molecules, while uniform and closely packed stripe‐assembled structures are obtained for asymmetric molecules. X‐ray diffraction (XRD) results support the observation of an ordered hexagonal columnar mesophase for symmetric molecules and a rectangular columnar mesophase for asymmetric molecules. The study demonstrates that the substitution symmetry has significant effects on the assembly characteristics of molecular architectures and also on the three‐dimensional (3D) macroscopic properties of the molecular materials.     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center of Rps.viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteria Rhodopseudomonas (Rps.) viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises the ELUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease the ELUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacterioc     

Computer simulation of interactions between liquid crystal molecules and polymer surfaces I. Alignment of nematic and smectic A phases

Results are presented from computer simulations of liquid crystal molecules in contact with polymeric surfaces. These form part of a study of the complex alignment interactions which operate in liquid crystal displays. The liquid crystal molecules considered are 4-n-pentyl-4'-cyanobiphenyl (5CB) and 4-n-octyl-4'-cyanobiphenyl (8CB); the polymeric surfaces simulated were crystalline polyethylene, polypropylene, poly(vinyl alcohol) and Nylon 6. Additional simulations were performed using graphite as a substrate. Polyethylene, poly(vinyl alcohol) and Nylon 6 were all found to induce orientation of the 5CB and 8CB molecules parallel to the polymer chain axes, as would be expected from experimental studies. On the other hand, polypropylene induces many different orientations with no clear preference for either. No evidence was found for the alignment of 8CB molecules on graphite substrates, in disagreement both with experimental findings and the results from previous simulations. The nature of the alignment interactions and possible reasons for the observed discrepancies are discussed.     

A new model for simulating 3-d crystal growth and its application to the study of antifreeze proteins

A novel computational technique for modeling crystal formation has been developed that combines three-dimensional (3-D) molecular representation and detailed energetics calculations of molecular mechanics techniques with the less-sophisticated probabilistic approach used by statistical techniques to study systems containing millions of molecules undergoing billions of interactions. Because our model incorporates both the structure of and the interaction energies between participating molecules, it enables the 3-D shape and surface properties of these molecules to directly affect crystal formation. This increase in model complexity has been achieved while simultaneously increasing the number of molecules in simulations by several orders of magnitude over previous statistical models. We have applied this technique to study the inhibitory effects of antifreeze proteins (AFPs) on ice-crystal formation. Modeling involving both fish and insect AFPs has produced results consistent with experimental observations, including the replication of ice-etching patterns, ice-growth inhibition, and specific AFP-induced ice morphologies. Our work suggests that the degree of AFP activity results more from AFP ice-binding orientation than from AFP ice-binding strength. This technique could readily be adapted to study other crystal and crystal inhibitor systems, or to study other noncrystal systems that exhibit regularity in the structuring of their component molecules, such as those associated with the new nanotechnologies.     

Molecular topology analysis of the differences between drugs, clinical candidate compounds, and bioactive molecules

A new method to decompose molecules is proposed and used to analyze drugs, clinical candidate compounds and bioactive molecules. The method classifies a set of molecules into a few well-defined classes based on their molecular framework. It is then possible to use these classes to investigate differences between drugs, clinical candidates and bioactive molecules. The analysis shows that in comparison with clinical candidates and bioactive compounds, drugs have a higher fraction of compounds with only one ring system. This conclusion is still valid after correcting for lipophilicity (ClogP) and molecular size, as well as any potential protein target bias in the data sets. Furthermore the molecular bridge part of compounds in the drug set has on average fewer ring systems than molecules from the other sets. The ring system complexity (RSC) was also investigated and for most topological classes drugs have a lower RSC than the clinical candidates and bioactive molecules. Hence, this study highlights differences in topology between drugs, clinical candidate compounds and bioactive molecules.     

Computer simulation of interactions between liquid crystal molecules and polymer surfaces I. Alignment of nematic and smectic A phases

Results are presented from computer simulations of liquid crystal molecules in contact with polymeric surfaces. These form part of a study of the complex alignment interactions which operate in liquid crystal displays. The liquid crystal molecules considered are 4-n-pentyl-4'-cyanobiphenyl (5CB) and 4-n-octyl-4'-cyanobiphenyl (8CB); the polymeric surfaces simulated were crystalline polyethylene, polypropylene, poly(vinyl alcohol) and Nylon 6. Additional simulations were performed using graphite as a substrate. Polyethylene, poly(vinyl alcohol) and Nylon 6 were all found to induce orientation of the 5CB and 8CB molecules parallel to the polymer chain axes, as would be expected from experimental studies. On the other hand, polypropylene induces many different orientations with no clear preference for either. No evidence was found for the alignment of 8CB molecules on graphite substrates, in disagreement both with experimental findings and the results from previous simulations. The nature of the alignment interactions and possible reasons for the observed discrepancies are discussed.     

Polymer-centered theory in comparison with surfactant-centered theory: a lattice Monte Carlo study

Lattice Monte Carlo simulation is used to study micellization of both pure and surfactant-polymer mixture, with an emphasis on cluster size distribution. The amphiphile molecule is of the type H(4)T(4) where the H (head) monomers like the solvent molecules and the T (tail) monomers are solvophobic. To compare polymer- and surfactant-centered theories, copolymers with the structure of (H(4)T(4))(5) are used instead of homopolymers. Since above copolymer molecules have the structural unit like the structure of surfactant molecules, it is possible to study the competition between the binding of surfactant molecules to the copolymer and the micellization in a copolymer-free solution. Results show that, first, surfactant molecules bind to the copolymer molecules, and not until copolymers are saturated do micelles form. Furthermore, it is shown that for the model used in this paper, the polymer-centered theory is more appropriate than the surfactant-centered theory, and finally the cooperative nature of cluster formation on copolymers is also discussed.     

气液界面磷脂单分子膜的表面增强拉曼光谱

采用纳米银胶作为成膜亚相, 原位获得了十八胺单分子膜、十八胺/卵磷脂复合膜的表面增强拉曼信号.研究表明,增强主要来源于亚相中的银粒子与成膜分子之间较强的作用.通过在磷脂膜内添加十八胺分子辅助增强而获取了卵磷脂的分子振动信息.     

The effect of the diversity of molecules in sets and similarity of sets on the quality of prediction in QSAR studies

We report here: (a) formulas/procedures for calculating the similarity of molecules, considering their chemical structure, size, shape and hydrophilicity (b) a procedure for clusterization of the sets of molecules, according to similarity (c) formulas/procedures for calculating the diversity of molecules in clusterized sets as well as similarity of clusterized sets, based on Shannon Entropy formalism The paper analyses the influence of the diversity of molecules and similarity of calibration/prediction sets on the quality of prediction for prediction set molecules. The calculated influence of certain molecular feature (chemical structure, size, shape and hydrophilicity) on toxicity depends on the structure of the database, specifically the number of molecules and diversity of molecules having analyzed molecular feature. A QSAR analysis of 49 phenol derivatives revealed the effect of the diversity of molecules in sets and of the similarity of sets on the quality of prediction for prediction set molecules: (a) a direct correlation with the similarity of sets, regardless of analyzed molecular feature (b) an inverse correlation with the diversity of molecules in the calibration set, from the point of view of chemical structure, size and shape (c) a direct correlation with the diversity of molecules in calibration set, from the point of view of hydrophilicity (d) a direct correlation with the diversity of molecules in prediction set, regardless of analyzed feature.     

New application of proton nuclear spin relaxation unraveling the intermolecular structural features of low-molecular-weight organogel fibers

Proton nuclear spin relaxation has been for the first time extensively used for a structural and dynamical study of low-molecular-weight organogels. The gelator in the present study is a modified phenylalanine amino acid bearing a naphthalimide moiety. From T(1) (spin-lattice relaxation time in the laboratory frame) and T(1ρ) (spin-lattice relaxation time in the rotating frame) measurements, it is shown that the visible gelator NMR spectrum below the liquid-gel transition temperature corresponds to a so-called isotropic compartment, where gelator molecules behave as in a liquid phase but exchange rapidly with the molecules constituting the gel structure. This feature allows one to derive, from accessible parameters, information about the gel itself. Nuclear Overhauser effect spectroscopy (NOESY) experiments have been exploited in view of determining not only cross-relaxation rates but also specific longitudinal rates. The whole set of relaxation parameters (at 25 °C) leads to a correlation time of 5 ns for gelator molecules within the gel structure and 150 ps for gelator molecules in the isotropic phase. This confirms, on one hand, the flexibility of the organogel fibers and, on the other hand, the likely presence of clusters in the isotropic phase. Concerning cross-relaxation rates, a thorough theoretical investigation in multispin systems of direct and relayed correlations in a NOESY spectrum allows one to make conclusions about contacts (around 2-3 ?) not only between naphtalimide moieties of different gelator molecules but also between the phenyl ring and the naphtalimide moiety again of different gelator molecules. As a result, not only is the head-to-tail structure of amino acid columns confirmed but also the entangling of nearby columns by the naphthalimide moieties is demonstrated.     

Study of the adsorptive behavior of water-soluble dye molecules (rhodamine 6G) at the air-water interface using confocal fluorescence microscope

A confocal fluorescence microscope was applied to directly study the characteristic behaviors of adsorbed molecules at the air-water interface for a water-soluble chromophore, rhodamine 6G (R6G), in its extremely low-concentration region (below 10(-10) M). Significant photon bursts were observed only from the surface, and their width, height, and frequency were found to depend on the bulk concentration, suggesting the inhomogeneous distribution of R6G molecules at the air-water interface. This property of the adsorbed molecules is different from that of the bulk one. The influence of the ionic strength on photon bursts from the interface was investigated. It was found that the addition of NaCl to the R6G solution caused a decrease of the fluorescence signal. A change in the size of the aggregate and in the fluorescence quantum yield of the adsorbed molecules was suggested to be responsible for this experimental result.     

Selective chain reaction of acetone leading to the successive growth of mutually perpendicular molecular lines on the si(100)-(2 x 1)-H surface

The successive growth of mutually perpendicular molecular lines from one dangling-bond (DB) site on the Si(100)-(2 x 1)-H surface has been realized through a substrate-mediated chain reaction at 300 K. Among various molecules, acetone molecules undergo the most facile chain reaction with a DB site, which proceeds selectively on the Si(100)-(2 x 1)-H surface, resulting in only single molecular lines in the parallel-row (parallel to the dimer row) direction. The smaller size and higher reactivity of acetone molecules enable us to successively grow a parallel-row acetone line from the end of a cross-row (perpendicular to the dimer row) allylmercaptan line simply by changing the feed of gas molecules into the reaction chamber. Since the length of a molecular line is controlled by the number of gas molecules impinged, it is possible to turn a chain reaction from the cross-row direction to the parallel-row direction at any desired point on the surface. The reaction path of the adsorbing molecules is discussed. The present study provides a new means of fabricating mutually perpendicular molecular lines through a chain reaction initiating at a preselected DB site on the Si(100)-(2 x 1) surface.     

Physisorption of molecular oxygen on C60 thin films

The interaction of oxygen molecules with a fullerene surface has been studied using high resolution electron energy loss spectroscopy and temperature programmed desorption. Vibrational excitation of the adsorbed oxygen is observed at 190 meV, an energy value comparable with that for molecular oxygen in the gas phase. We take this to indicate physisorption of molecular oxygen on the C(60) surface. Thermal desorption results also show that the bonding of oxygen molecules to the C(60) overlayer is comparable to that on a graphite surface. A detailed study of the energy dependence of the vibrational excitation reveals an inelastic electron resonance scattering process. The angular dependence of the resonant vibrational excitation exhibits features distinctively different from those for molecular oxygen physisorbed on the related graphite surface, at a comparable coverage. One possible reason is that the corrugated surface potential, due to the curvature of the C(60) molecules, promotes the preferential ordering of the physisorbed oxygen molecules perpendicular to the surface plane of the C(60) overlayer.     

Experimental study on polarized surface enhanced resonance Raman scattering of rhodamine 6G adsorbed on porous Al2O3 substrates

The polarization properties of surface enhanced resonance Raman scattering (SE(R)RS) of rhodamine 6G molecules, adsorbed to a hexagonally ordered gold nanostructure, are studied with the purpose to discriminate between adsorption sites with different plasmonic properties. The nanostructure is based on a self-organizing hexagonally ordered porous Al(2)O(3) substrate sputter-coated with gold. Each hexagonal subunit has D(6h) symmetry, where the symmetry center may act as an isotropic site, whereas the six narrow gaps between the individual Au hemispheres may act as hot-spots. The variation of the depolarization ratio (DPR), measured in resonance for the eight most prominent vibrational modes of the xanthene moiety, is analyzed by rotating the sample. According to theory, the DPR of the SE(R)RS signal obtained from molecules physisorbed in the isotropic sites deviates from the DPR originating from molecules physisorbed in the hot-spots in two ways: 1. The DPR associated with the isotropic sites depends differently on the rotation angle than the DPR associated with the hot-spots. 2. The DPR of the SE(R)RS signal obtained from molecules physisorbed in the isotropic sites depends on the nature of the Raman modes, whereas it for molecules physisorbed in the hot-spots is independent of the nature of the Raman modes. By applying the latter in the analysis of the polarized SE(R)RS data, we conclude that the dominating SE(R)RS signal comes from molecules adsorbed in the hot-spots. However, since the DPR's obtained for Raman modes of different symmetry are slightly different, the SE(R)RS signal must contain an additional contribution. Our analysis shows that the small mode-dependent SE(R)RS signal most likely comes from molecules adsorbed in the isotropic sites. The general result that can be derived from the present study is that by measuring the polarization properties in SE(R)RS and SERS it is possible to discriminate between adsorption sites with different plasmonic properties present in a highly symmetric nanostructure, even when the magnitude of the different contributions are highly different. The consequence of the insufficient spatial resolution with respect to a detailed mapping of the substrate often encountered in unpolarized SE(R)RS and in two-photon luminescence microscopy may thereby be circumvented.     

Probing cavity versus surface preference of fluorescent template molecules in molecularly imprinted polystyrene microspheres

Functional polystyrene (PS) crosslinked microbeads were developed by dispersion polymerization as fluorescent molecularly imprinted polymers (MIPs) having cavities with specific recognition sites. The functional azobenzene molecule modified with pyridine was self‐assembled with Pyrenebutyric acid (template molecules), and introduced during the second stage of dispersion polymerization of polystyrene. The template molecule was removed from MIP by Soxhlet using acetonitrile as solvent. Non imprinted polymer (NIP) having no template was also synthesized for comparative study. Fluorescence spectroscopy could be used as a tool to derive insight into the location of the template molecules on the MIP or NIP. The template molecules were adsorbed on the surface of the NIPs during binding studies, which was evidenced from the pyrene excimeric emission observed at 440 nm. The template binding efficiency of the NIPs were much lower compared to MIPs. Pyrene emission from MIP upon rebinding showed typical monomeric emission in the 375–395 nm range, confirming its location in isolated cavities. In rebinding studies of the template molecules, the MIPs selectively took up the template for which the cavity was designed, which demonstrated their selectivity towards template molecules. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 1558–1565     

Growth mechanism of a gas clathrate hydrate from a dilute aqueous gas solution: a molecular dynamics simulation of a three-phase system

A molecular dynamics simulation of a three-phase system including a gas clathrate, liquid water, and a gas was carried out at 298 K and high pressure in order to investigate the growth mechanism of the clathrate from a dilute aqueous gas solution. The simulation indicated that the clathrate grew on interfaces between the clathrate and the liquid water, after transfer of the gas molecules from the gas phase to the interfaces. The results suggest a two-step process for growth: first, gas molecules are arranged at cage sites, and second, H(2)O molecules are ordered near the gas molecules. The results also suggest that only the H(2)O molecules, which are surrounded or sandwiched by the gas molecules, form the stable polygons that constitute the cages of the clathrate. In addition, the growth of the clathrate from a concentrated aqueous gas solution was also simulated, and the results suggested a growth mechanism in which many H(2)O and gas molecules correctively form the structure of the clathrate. The clathrate grown from the concentrated solution contained some empty cages, whereas the formation of empty cages was not observed during the growth from the dilute solution. The results obtained by both simulations are compared with the results of an experimental study, and the growth mechanism of the clathrate in a real system is discussed.     

A pharmacoinformatic approach on Cannabinoid receptor 2 (CB2) and different small molecules: Homology modelling,molecular docking,MD simulations,drug designing and ADME analysis

CB2 receptor belongs to the family of G-protein coupled receptors (GPCRs), which extensively controls a range of pointer transduction. CB2 plays an essential role in the immune system. It also associates in the pathology of different ailment conditions. In this scenario, the synthetic drugs are inducing side effects to the human beings after the drug use. Therefore, this study is seeking novel alternate drug molecules with least side effects than conventional drugs. The alternative drug molecules were chosen from the natural sources. These molecules were selected from cyanobacteria with the help of earlier research findings. The target and ligand molecules were obtained from recognized databases. The bioactive molecules are selected from various cyanobacterial species, which are selected by their biological and pharmacological properties, after, which we incorporated to the crucial findings such as homology modelling, molecular docking, MD simulations along with absorption, distribution, metabolism, and excretion (ADME) analysis. Initially, the homology modelling was performed to frame the target from unknown sequences of CB2, which revealed 44% of similarities and 66% of identities with the A2A receptor. Subsequently, the CB2 protein molecule has docked with already known and prepared bioactive molecules, agonists and antagonist complex. In the present study, the agonists (5) and antagonist (1) were also taken for comparing the results with natural molecules. At the end of the docking analysis, the cyanobacterial molecules and an antagonist TNC-201 are revealed better docking scores with well binding contacts than the agonists. Especially, the usneoidone shows better results than other cyanobacterial molecules, and it is very close docking scores with that of TCN-201. Therefore, the usneoidone has incorporated to MD simulation with Cannabinoid receptors 2 (CB2). In MD simulations, the complex (CB2 and usneoidone) reveals better stability in 30 ns. Based on the computational outcome, we concluded that usneoidone is an effectual and appropriate drug candidate for activating CB2 receptors and it will be serving as a better component for the complications of CB2. Moreover, these computational approaches can be motivated to discover novel drug candidates in the pharmacological and healthcare sectors.