Triangulation algorithms for the representation of molecular surface properties

Summary A triangulation algorithm for a dotted surface (i.e. a surface defined by point coordinates in three dimensions) is given. The individual triangles are generated on the basis of a hierarchy of strategies according to increasing surface complexity. While for small molecules an elementary algorithm is sufficient to triangulate the surface, large molecules-like proteins-generally need all steps of the hierarchy. Although this program has been developed with the aim of triangulating molecular surfaces, it can in principle be applied to any surface defined by 3D point coordinates.     

Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations

Different integrator time steps in NVT and NVE simulations of protein and nucleic acid systems are tested with the GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple SWitching) methods. The simulation stability and energy conservation is investigated in relation to the agreement with the Poisson theory. It is found that very close agreement between generalized Born methods and the Poisson theory based on the commonly used sharp molecular surface definition results in energy drift and simulation artifacts in molecular dynamics simulation protocols with standard 2-fs time steps. New parameters are proposed for the GBMV method, which maintains very good agreement with the Poisson theory while providing energy conservation and stable simulations at time steps of 1 to 1.5 fs.     

Pattern recognition strategies for molecular surfaces. II. Surface complementarity

Fuzzy logic based algorithms for the quantitative treatment of complementarity of molecular surfaces are presented. Therein, the overlapping surface patches defined in article I1 of this series are used. The identification of complementary surface patches can be considered as a first step for the solution of molecular docking problems. Standard technologies can then be used for further optimization of the resulting complex structures. The algorithms are applied to 33 biomolecular complexes. After the optimization with a downhill simplex method, for all these complexes one structure was found, which is in very good agreement with the experimental results.     

Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory

A new method for the characterization of molecules based on the model approach of molecular surfaces is presented. We use the topographical properties of the surface as well as the electrostatic potential, the local lipophilicity/hydrophilicity, and the hydrogen bond density on the surface for characterization. The definition and the calculation method for these properties are reviewed shortly. The surface is segmented into overlapping patches with similar molecular properties. These patches can be used to represent the characteristic local features of the molecule in a way that is beyond the atomistic resolution but can nevertheless be applied for the analysis of partial similarities of different molecules as well as for the identification of molecular complementarity in a very general sense. The patch representation can be used for different applications, which will be demonstrated in subsequent articles.     

Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network

An algorithm for the identification of possible binding sites of biomolecules, which are represented as regions of the molecular surface, is introduced. The algorithm is based on the segmentation of the molecular surface into overlapping patches as described in the first article of this series.1 The properties of these patches (calculated on the basis of physical and chemical properties) are used for the analysis of the molecular surfaces of 7821 proteins and protein complexes. Special attention is drawn to known protein binding sites. A binding site identification algorithm is realized on the basis of the calculated data using a neural network strategy. The neural network is able to classify surface patches as protein-protein, protein-DNA, protein-ligand, or nonbinding sites. To show the capability of the algorithm, results of the surface analysis and the predictions are presented and discussed with representative examples.     

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.     

Obtaining surface tension from contact angle data by the individual representation approach

Young equation is the fundamental equation of wetting theory in which the connection among the surface tensions, \(\gamma _{{\varphi \psi }} \) and the contact angle, θ _L, are given. The surface tension of solid surfaces, however, cannot be obtained directly from the Young equation. In this paper, the application of the individual representation theory is demonstrated for the determination of surface tensions of solids (or any phase pair) using experimentally obtained contact angle data. According to this approach, the state of the interfacial layers depends upon, by definition, the properties of the bulk phases in every heterogeneous system, and thus, it complements the traditional capillary theory.     

The preparation of ribose-free ‘artificial dinucleotides’: A new approach to molecular recognition?

The synthesis of the cytosine-guanine linked dimer1, and its symmetric guanine-guanine analogue2 are described. Compound1 is the first homogeneous ribose-free system to be prepared and characterized in which molecular recognition by complementary guanine-cytosine base-pairing might be possible. It is thus prototypical of a new and potentially large class of artificial oligonucleotides.     

对-特辛基酚表面印迹聚合物的制备及吸附性能评价

以对-特辛基酚为模板、甲基丙烯酸为功能单体制备了对-特辛基酚表面印迹聚合物.采用扫描电子显微镜、紫外光谱以及红外光谱对印迹聚合物进行表征,通过平衡吸附实验对聚合物的吸附性能进行评价.结果表明:该分子印迹聚合物对对-特辛基酚具有较大的吸附容量和良好的选择性,其最大吸附量Qmax约为86.12mg/g.     

Investigation of the molecular surface area and volume: Defined and calculated by the molecular face theory

Based on the molecular face (MF) theory, the molecular face surface area (MFSA) and molecular face volume (MFV) are defined. For a variety of organic molecules and several inorganic molecules, the MFSA and MFV have been studied and calculated in terms of an algorithm of our own via the Matlab package. The MFV shows a very good linear relationship with the experimentally measured critical molar volume. It is also found that the MFSA and MFV have significant linear correlations with those of the commonly used hard‐sphere model and the electron density isosurface. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

A Symmetry adapted tessellation of the GEPOL surface: applications to molecular properties in solution

A procedure to partition the GEPOL molecular surface into tesserae that respects the molecular symmetry constraints is presented. Using this method it is possible to build a solvent reaction field for the Polarizable Continuum Model with the same symmetry of the nuclear potential. Several applications are reported and discussed to evaluate the performance of this new procedure. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1262–1272, 2001     

A surface site interaction point methodology for macromolecules and huge molecular databases

Determining the position and magnitude of Surface Site Interaction Points (SSIP) is a useful technique for understanding intermolecular interactions. SSIPs have been used for the prediction of solvation properties and for virtual co‐crystal screening. To determine the SSIPs for a molecule, the Molecular Electrostatic Potential Surface (MEPS) is first calculated using ab initio methods such as Density Functional Theory. This leads to a high cost in terms of computation time and is not compatible with the analysis of huge molecular databases. Herein, we present a method for the fast estimation of SSIPs, which is based on the MEPS calculated from MMFF94 atomic partial charges. The results show that this method can be used to calculate SSIPs for large molecular databases with a much higher speed than the original ab initio methodology. © 2017 Wiley Periodicals, Inc.     

Prediction of densities for solid energetic molecules with molecular surface electrostatic potentials

The densities of high energetic molecules in the solid state were calculated with a simplified scheme based on molecular surface electrostatic potentials (MSEP). The MSEP scheme for density estimation, originally developed by Politzer et al., was further modified to calculate electrostatic potential on a simpler van der Waals surface. Forty-one energetic molecules containing at least one nitro group were selected from among a variety of molecular types and density values, and were used to test the suitability of the MSEP scheme for predicting the densities of solid energetic molecules. For comparison purposes, we utilized the group additivity method (GAM) incorporating the parameter sets developed by Stine (Stine-81) and by Ammon (Ammon-98 and -00). The absolute average error in densities from our MSEP scheme was 0.039 g/cc. The results based on our MSEP scheme were slightly better than the GAM results. In addition, the errors in densities generated by the MSEP scheme were almost the same for various molecule types, while those predicted by GAM were somewhat dependent upon the molecule types.     

Nanoparticles: scaffolds for molecular recognition

Monolayer and mixed-monolayer protected clusters (MPCs and MMPCs) have great potential to combine molecular functionality with the intrinsic properties of nanometer-sized scaffolds. This synergy can be used to create complex functional devices, including redox-active, electronic, or magnetic storage devices, solution-based sensors, and highly efficient catalysts. This review outlines some of the recent developments in nanoscale receptors based on synthetic and nonbiological recognition elements. In these nanoparticle systems, molecular recognition is achieved by covalent attachment of receptors on the nanoparticles coupled with noncovalent interactions to target substrates. Synthetic host-guest systems, hydrogen bonding, change in redox states, pi-pi stacking, rotaxane formation, and ion recognition are the main topics covered in this review.     

Simultaneous formation behaviour of surface structures and molecular alignment by patterned photopolymerisation

ABSTRACT

Highly functional soft materials with fine control of molecular alignment are of great interest for the applications in various fields. However, the current method of molecular alignment still has some challenges. Recently, we have developed a new alignment process based on a concept of scanning wave photopolymerisation (SWaP). When a sample is irradiated with spatially selected light, a polymerisation occurs only in an irradiated region, leading to a molecular motion between the irradiated and unirradiated regions. Such molecular motion generates the alignment of liquid crystal molecules. Moreover, a surface relief structure is formed in the polymer film by the molecular motion. In this study, we simultaneously formed the surface structure and molecular alignment by the patterned photopolymerisation. We compared the degree of molecular alignment with the shape of the created surface structure, and revealed that the degree of molecular alignment was maximized at the boundary of irradiated and unirradiated regions. This method enables one to form both molecular alignment patterning and surface structuring in a single step.     

分子极化效应与烷烃、醇的空腔表面积

烷烃以及醇在水中形成的空腔表面积CSA可由下式计算:CSA=122.984+8.65736SBL-103.862ΔMPEI。其中SBL是分子中所有化学键长度的总和, ΔMPEI是含有相同碳原子数目的(烷烃或者醇)支链异构体分子极化效应指数MPEI支与直链异构体分子极化效应指数MPEI直的差值。     

Non-covalent surface modification of metal-macrocycle framework with mono-substituted benzenes

Recently, we have reported a metal-macrocycle framework (MMF) with five enantiomerically paired molecular binding pockets that exhibit site-selective guest arrangement on the nano-channel surface in soaking experiments using a variety of guest molecules. The guest inclusion is based largely on molecular exchange between solvent molecules such as CH₃CN and guest molecules on the surface. Herein, we report that the molecular arrangement on the nano-channel surface varies with size, shape and/or chemical properties of functional groups of guests, mono-substituted benzene derivatives, such as benzonitrile, acetophenone and nitrobenzene. In their inclusion complexes, polar nitrile, acetyl and nitro groups serve as molecular anchors to a macrocyclic cavity through hydrogen bonding. Notably, benzonitrile and benzenesulphonic acid bind only to one pair of enantiomeric binding pockets. Such a highly site-selective binding would enable further multi-component surface modifications in the MMF.     

青霉噻唑酸表面分子印迹聚合物的制备及其吸附性能的考察

针对青霉素药物及乳制品中致敏杂质青霉噻唑酸(PEOA)的特异性分离分析,采用表面印迹聚合法,以青霉噻唑酸为模板分子,制备青霉噻唑酸分子印迹聚合物(PEOA-MIPs)。通过静态吸附、吸附动力学及选择性实验考察其吸附性能,结果显示PEOA-MIPs对青霉噻唑酸有特异的识别能力和快速的传质速率,饱和吸附量为122.78 mg/g,静态吸附和吸附速率分别符合Langmuir模型和准二级动力学方程,表明MIPs的吸附是以化学吸附为主的单分子层吸附。利用扫描电镜(SEM)、红外光谱(FT-IR)和热重分析(TGA)对聚合物进行表征,结果显示聚合物成功接枝在硅胶表面,并具有良好的热稳定性。PEOA-MIPs对PEOA具有特异的识别能力,可用作萃取介质,为建立快速分离分析致敏杂质青霉噻唑酸的方法提供基础。     

Derivatives of molecular surface area and volume: simple and exact analytical formulas

The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library.