A theoretical model for the critical micelle concentration of bile salts

Critical micelle concentration (CMC) is a fundamental parameter in the evaluation of the biological activity of natural and synthetic bile salts. The CMC is logarithmically related to the free energy of solute micellization in aqueous solution. Hydrophobic and hydrogen bonding interaction energies were identified as the primary contributors to this free energy and the logarithm of the CMC was modeled as a linear function of relevant chemical group contributions to the solvent accessible molecular surface area of the solute. The structures (three-dimensional atomic coordinates) of 23 mono-, di-, and tri-hydroxyl bile acids were generated and optimized by energy minimization. The accessible surface area for each structure was computed and partitioned according to calculated charge distribution and polar group orientation. Experimental CMC values were fitted to these computed quantities by least squares multiple linear regression. Two regression equations, based on slightly different surface area partition schemes, were derived and compared. Their significance in explaining the aggregation process and in predicting the CMC of new bile salts is discussed.     

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature

New computer programs, SurfRace and FastSurf, perform fast calculations of the solvent accessible and molecular (solvent excluded) surface areas of macromolecules. Program SurfRace also calculates the areas of cavities inaccessible from the outside. We introduce the definition of average curvature of molecular surface and calculate average molecular surface curvatures for each atom in a structure. All surface area and curvature calculations are analytic and therefore yield exact values of these quantities. High calculation speed of this software is achieved primarily by avoiding computationally expensive mathematical procedures wherever possible and by efficient handling of surface data structures. The programs are written initially in the language C for PCs running Windows 2000/98/NT, but their code is portable to other platforms with only minor changes in input-output procedures. The algorithm is robust and does not ignore either multiplicity or degeneracy of atomic overlaps. Fast, memory-efficient and robust execution make this software attractive for applications both in computationally expensive energy minimization algorithms, such as docking or molecular dynamics simulations, and in stand-alone surface area and curvature calculations.     

Release and molecular transport of cationic and anionic fluorescent molecules in mesoporous silica spheres

We describe here a method for study of bulk release and local molecular transport within mesoporous silica spheres. We have analyzed the loading and release of charged fluorescent dyes from monodisperse mesoporous silica (MMS) spheres with an average pore size of 2.7 nm. Two different fluorescent dyes, one cationic and one anionic, have been loaded into the negatively charged porous material and both the bulk release and the local molecular transport within the MMS spheres have been quantified by confocal laser scanning microscopy. Analysis of the time-dependent release and the concentration profiles of the anionic dye within the spheres show that the spheres are homogeneous and that the release of this nonadsorbing dye follows a simple diffusion-driven process. The concentration of the cationic dye varies radially within the MMS spheres after loading; there is a significantly higher concentration of the dye close to the surface of the spheres (forming a "skin") compared to that at the core. The release of the cationic dye is controlled by diffusion after an initial period of rapid release. The transport of the cationic dye within the MMS spheres of the dye from the core to near the surface is significantly faster compared to the transport within the surface "skin". A significant fraction of the cationic dye remains permanently attached to the negatively charged walls of the MMS spheres, preferentially near the surface of the spheres. Relating bulk release to the local molecular transport within the porous materials provides an important step toward the design of new concepts in controlled drug delivery and chromatography.     

Gradient discontinuities in calculations involving molecular surface area

The free energy of solvation of a polypeptide or a protein can be expressed in terms of the accessible surface area of the molecule. Algorithms for energy minimization or for molecular dynamics, which involve the first derivatives of the energy, including the free energy of solvation, are commonly used in the conformational analysis of proteins. Discontinuities of the first derivatives, which occur in the accessible surface area and, hence, in the solvation energy, can cause serious numerical problems. In this paper, we describe all the situations in which the gradient of the molecular surface area becomes discontinuous.     

Molecular Simulation study of Alkyl Monolayers on Si(III) Surface

The preparation of monolayers on silicon surface is of growing interest for potential applications in biosensor or semiconductor technology. Different experimental technique can be used to investigate the alkyl modified Si(III) surfaces1-4, such as X-ray photoelectron spectroscopy (XPS), Fourier transform infrared absorption spectra(FTIR), scanning electron microscopy (SEM), Auger electron spectroscopy (AES), scanning tunneling microscope (STM), and so on. These experimental results…     

醋酸离子液体[C2mim][OAc]水溶液的摩尔表面Gibbs自由能

在288.15-318.15 K温度范围内测定了不同浓度离子液体1-乙基-3-甲基咪唑醋酸盐([C₂mim][OAc])水溶液的表面张力和密度;在改进李以圭等人的溶液表面张力模型基础上,提出摩尔表面Gibbs自由能新概念,建立了摩尔表面Gibbs自由能随溶液浓度变化的线性经验方程,利用这个经验方程估算了[C₂mim][OAc]水溶液的摩尔表面Gibbs自由能,并进一步预测了该溶液的表面张力,其预测值与相应的表面张力实验值高度相关并非常相似。由此可见,摩尔表面Gibbs自由能与等张比容极其类似,可能成为预测离子液体及其溶液性质的一种新的半经验方法。在指定溶液浓度下,根据溶液的摩尔表面Gibbs自由能随温度呈线性变化的规律,得到了新的Eötvös方程,与传统的Eötvös方程相比,新Eötvös方程的每一个参数都有明确的物理意义:斜率的负值是摩尔表面熵,截距是摩尔表面焓,在指定浓度的溶液中摩尔表面焓几乎不随温度变化。     

Molecular dynamics simulation of surface morphology and thermodynamic properties of polyaniline nanostructured film

To develop predictive models in nanostructured films, there is an ongoing research to validate molecular dynamics (MD) simulation results with experimental data. The morphology and surface topography of polyaniline (PANI) nanostructured film coated on a TiO₂ nanocrystalline surface were investigated by scanning electron microscopy and atomic force microscopy, respectively. The atomistic model of the simulated PANI was generated using energy minimization with a condensed‐phase optimized molecular potential for atomistic studies force field function to reach a thermodynamic equilibrium state. Various parameters of PANI such as density, energy, cavity size, and free volume distributions are calculated. MD simulation has also been used to obtain specific volume (V) as a function of temperature (T). It is demonstrated that this V–T curve can be used to determinate glass transition temperature T_g, reliably. Although experimental data available for the PANI film are very limited, simulation results such as density and T_g are in good agreement with the experimental values reported in the literature. Comparison of the surface topography of PANI demonstrates a reasonable trend between atomic force microscopy image analysis and the MD simulation results at various temperatures. Copyright © 2014 John Wiley & Sons, Ltd.     

Molecular simulation of alkyl monolayers on the Si(111)surface

The structure of twelve-carbon monolayers on the H-terminated Si(111) surface is investigated by molecular simulation method. The best substitution percent on Si(111) surface obtained via molecular mechanics calculation is equal to 50%, and the (8×8) simulated cell can be used to depict the structure of alkyl monolayer on Si surface. After two-dimensional cell containing alkyl chains and four-layer Si(111) crystal at the substitution 50% is constructed, the densely packed and well-ordered monolayer on Si(111) surface can be shown through energy minimization in the suitable-size simulation cell. These simulation results are in good agreement with the experiments. These conclusions show that molecular simulation can provide otherwise inaccessible mesoscopic information at the molecular level, and can be considered as an adjunct to experiments.     

Molecular simulation of alkyl monolayers on the Si(lll) surface

The structure of twelve-carbon monolayers on the H-terminated Si(111) surface is investigated by molecular simulation method. The best substitution percent on Si(111) surface obtained via molecular mechanics calculation is equal to 50%, and the (8 ε 8) simulated cell can be used to depict the structure of alkyl monolayer on Si surface. After two-dimensional cell containing alkyl chains and four-layer Si(111) crystal at the substitution 50% is constructed, the densely packed and well-ordered monolayer on Si(111) surface can be shown through energy minimization in the suitable-size simulation cell. These simulation results are in good agreement with the experiments. These conclusions show that molecular simulation can provide otherwise inaccessible mesoscopic information at the molecular level, and can be considered as an adjunct to experiments.     

Molecular simulation of alkyl monolayers on the Si(111) surface YUAN

The preparation of monolayers on silicon surface is of growing interest for potential applica-tions in biosensor or semiconductor technology[1—5]. The alkyl modified Si(111) surfaces[6—10] can be obtained using the thermal, catalyzed, or photochemical reaction of hydrogen-terminated sili-con with alkenes, Grignard reagents, and so on. At the same time, the monolayer properties on Si(111) surface have been studied by a variety of experimental methods[8—10] such as X-ray photo-electron spect…     

Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins

The classical simplex method is extended into the Semiglobal Simplex (SGS) algorithm. Although SGS does not guarantee finding the global minimum, it affords a much more thorough exploration of the local minima than any traditional minimization method. The basic idea of SGS is to perform a local minimization in each step of the simplex algorithm, and thus, similarly to the Convex Global Underestimator (CGU) method, the search is carried out on a surface spanned by local minima. The SGS and CGU methods are compared by minimizing a set of test functions of increasing complexity, each with a known global minimum and many local minima. Although CGU delivers substantially better success rates in simple problems, the two methods become comparable as the complexity of the problems increases. Because SGS is generally faster than CGU, it is the method of choice for solving optimization problems in which function evaluation is computationally inexpensive and the search region is large. The extreme simplicity of the method is also a factor. The SGS method is applied here to the problem of finding the most preferred (i.e., minimum free energy) solvation sites on a streptavidin monomer. It is shown that the SGS method locates the same lowest free energy positions as an exhaustive multistart Simplex search of the protein surface, with less than one-tenth the number of minizations. The combination of the two methods, i.e.. multistart simplex and SGS, provides a reliable procedure for predicting all potential solvation sites of a protein.     

Bisquare robust polynomial fitting method for dimple distortion minimization in surface quality analysis

In this paper, the bisquare robust polynomial fitting (BSRPF) method for surface texture features assessment was proposed. Plateau-honed cylinder liner bronze surfaces with additionally burnished microcavities (defined as dimple, holes, and/or cavities) were taken into consideration. Analyzed details were measured with stylus (Talyscan 150) or white light interferometer (Talysurf CCI Lite) methods. It was assumed that application of commonly used (in surface contact and noncontact measurement technology) polynomial fitting procedures did not allow to extract required features; distortion of microreservoir dimples for oil consumption assessment was falsely estimated when valleys were near edge or on the edge located. Application of bisquare robust polynomial fitting method caused a minimization of microflattens of dimples irrespective of valley distribution; the biggest degree of polynomial fitting method applied, the minimal distortions of oil reservoirs were noticed. The valley size (depth and width) and valley-to-valley distance were also taken into account.     

Parametrization strategy for the MolFESD concept: quantitative surface representation of local hydrophobicity

We derive a new model for the established concept of the molecular free energy surface density (MolFESD) yielding a more rigorous representation of local surface contributions to the overall hydrophobicity of a molecule. The model parametrization makes efficient use of both local and global information about solvation thermodynamics, as formulated earlier for the problem of predicting free energies of hydration. The free energy of transfer is separated into an interaction contribution and a term related to the cavity formation. Interaction and cavity components are obtained from the statistical three-dimensional (3D) free energy density and a linear combination of surface and volume terms, respectively. An appropriate molecular interaction field generated by the program Grid is used as an approximate representation of the interaction part of the 3D free energy density. We further compress the 3D density by means of a linear combination of localized surface functions allowing for the derivation of local hydrophobic contributions in the form of a free energy surface density. For a set of 400 compounds our model yields significant correlation (R(2) = 0.95, sigma = 0.57) between experimental and calculated log P values. The final model is applied to establish a correlation between partial free energies of transfer for a series of sucrose derivatives and their relative sweetness, as studied earlier in the group of the authors. We find considerable improvement regarding the rms error of the regression thus validating the presented approach.     

Extended surface chirality for enantiospecific adsorption

A rapid development of nanotechnology opens up a way for the fabrication of solid surfaces containing unique adsorption properties. In this article, we present the concept of a chiral nanostructured surface as a potential environment for the separation of chiral molecules. In particular, we focus on the effect of size and shape of the adsorbing molecules on the effectiveness of their separation on a surface with a special distribution of active sites. The Monte Carlo simulation method was used to study enantiospecific adsorption of model chiral molecules that differ in molecular footprint and adsorption energy. It was demonstrated that manipulating the footprint offers many possibilities for tuning the preference of the surface for adsorption of a selected enantiomer. One interesting finding was that subtle differences in the interaction pattern of the molecule with the chiral surface can lead to a reversal of enantioselectivity. The results of this work highlight the role of extended surface chirality in enantiospecific adsorption of enantiomers. They also suggest that the proposed mechanism of chiral selection can be a realistic alternative to those inherent in conventional enantioselective adsorbents.     

Application of the level-set method to the implicit solvation of nonpolar molecules

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model [Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. 104, 527 (2006); J. Chem. Phys. 124, 084905 (2006)]. In the level-set method, a possible solute-solvent interface is represented by the zero level set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy functional that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerence C(60). The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system.     

Confinement of a liquid crystal to small droplets and its effect on nuclear magnetic relaxation

Abstract

The spatial dependence of the orientation of the molecular director and of the nematic order parameter is obtained by minimization of the Landau–de Gennes free energy of the nematic liquid crystal confined in a spherical droplet. Special attention is given to the vicinity of the nematic–isotropic transition. The influence of the resulting nematic structure, large liquid crystal–polymer interface and restricted molecular diffusion on the nuclear magnetic relaxation is analysed. The translationally-induced molecular reorientation and the liquid crystal–polymer cross relaxation are discussed in particular. The possibility of an indirect study of the molecular anchoring on the polymer surface is demonstrated.     

Study of Surface Cell Madelung Constant and Surface Free Energy of Nanosized Crystal Grain

1 INTRODUCTION 2. 1 Madelung constant of crystal Surface energy of crystal grain has crucial influ- The Madelung constant, which is used to calculate ence on the electrical and mechanical performances lattice energy and so on[1], is of central importance in of material, especially for material making up of na- the theory of ionic crystal and property of crystal nosized crystal grains because all outstanding per- structure. There is no special difficulty in calculating formances of the mat…     

大孔-介孔Ag/PDA/MMS复合材料的制备及其催化性能

用双模板法制备了介孔纳米薄膜构筑的毫米级尺寸的大孔-介孔SiO₂(MMS)，通过多巴胺(DA)在其孔道表面氧化自聚合成聚多巴胺(PDA)，得到 PDA 修饰的 MMS(PDA/MMS)，再经 PDA 原位还原 Ag⁺制得大孔-介孔 Ag/PDA/MMS 复合材料。应用扫描电镜、透射电镜、N₂吸附-脱附、X射线光电子能谱、X射线衍射、UV-Vis、FT-IR和热重技术对所制得的材料进行表征。结果表明，MMS兼具纳米介孔材料和宏观尺寸大孔材料的优点。Ag/PDA/MMS在催化还原对硝基苯酚(4-NP)反应中展现出高催化活性，转化频率(TOF)达2.97 min^-1。这归因于其独特的结构：相互连通的大孔孔道大大降低了传质阻力，短孔道的介孔显著增加了活性位点的可达性，大的比表面积为反应物提供了大量的活性位点。而且，毫米级尺寸的Ag/PDA/MMS可以很容易从反应体系中分离出来，在5次循环后仍能将4-NP完全转化为对氨基苯酚(4-AP)。另外，Ag/PDA/MMS对亚甲基蓝(MB)的还原也有良好的催化效果。     

A rapid method for molecular shape comparison of medium-sized molecules. Conformational calculations on sandalwood odor,IV

Summary A fast method of a surface comparison of two or more molecules to be matched is presented. The Van der Waals surfaces of molecules are described by points calculated as the intersection of grid lines with the molecular surface. The mean surface of various molecules with the same biological activity can be constructed. It is used for further comparisons with similar molecules lacking this activity. Deviations of any molecular surface from the mean surface can be mapped onto the surface. The method was tested on a distinct group of sandalwood odor molecules and it was shown that such matching and comparison procedures are useful in the investigation of odor structure-activity relationships proposed as CAFD (computer aided fragrance design).Dedicated to Prof. Dr. W. Fleischhacker, on occasion of his 60th anniversary     

Localization and quantification of hydrophobicity: The molecular free energy density (MolFESD) concept and its application to sweetness recognition

A method for the localization, the quantification, and the analysis of hydrophobicity of a molecule or a molecular fragment is presented. It is shown that the free energy of solvation for a molecule or the transfer free energy from one solvent to another can be represented by a surface integral of a scalar quantity, the molecular free energy surface density (MolFESD), over the solvent accessible surface of that molecule. This MolFESD concept is based on a model approach where the solvent molecules are considered to be small in comparison to the solute molecule, and the solvent can be represented by a continuous medium with a given dielectric constant. The transfer energy surface density for a 1-octanol/water system is empirically determined employing a set of atomic increment contributions and distance dependent membership functions measuring the contribution of the increments to the surface value of the MolFESD. The MolFESD concept can be well used for the quantification of the purely hydrophobic contribution to the binding constants of molecule-receptor complexes. This is demonstrated with the sweeteners sucrose and sucralose and various halogen derivatives. Therein the relative sweetness, which is assumed to be proportional to the binding constant, nicely correlates to the surface integral over the positive, hydrophobic part of the MolFESD, indicating that the sweetness receptor can be characterized by a highly flexible hydrophobic pocket instead of a localized binding site.