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Synthetic organic chemists are beginning to exploit electrochemical methods in increasingly creative ways. This is leading to a surge in productivity that is only now starting to take advantage of the full-potential of electrochemistry for accessing new structures in novel, more efficient ways. In this perspective, we provide insight into the potential of electrochemistry as a synthetic tool gained through studies of both direct anodic oxidation reactions and more recent indirect methods, and highlight how the development of new electrochemical methods can expand the nature of synthetic problems our community can tackle.

The interactions between a wide variety of molecules having σ-holes or π-holes and several nitrogen bases have been analyzed computationally. The σ- and π-hole atoms span groups III–VII of the periodic table. The interaction energies range from quite weak, typical of non-covalent bonding, to unusually strong: from −4.6 to −22.0 kcal/mol for σ-hole bonding and from −4.0 to −42.4 kcal/mol for π-hole bonding. The markedly greater strengths of some bonds does not imply that any new factors or types of bonding are involved; they simply reflect higher degrees of the polarization that is part of any Coulombic interaction. To explain the stronger bonding, this polarization must be explicitly taken into account. We show that the interaction energies can be related quite well to (a) the maximum positive electrostatic potentials associated with the σ- or π-holes on their molecular surfaces, (b) the polarizabilities of the nitrogen bases, and especially (c) the polarizing electric fields of the σ- or π-hole molecules...

Evaluation of molecular surfaces plays the key role in a wide range of cutting-edge scientific fields and technologies, due to the well-characterized dependency between molecular surfaces and condensed phase thermodynamics. Numerous methods to evaluate molecular surfaces such as van-der-Waals and solvent accessible surface areas and various parameterizations for each one, have been proposed in the literature and typically yield quite diverse estimations of molecular surfaces. Despite this diversity, numerous successful applications have been reported for each one, which has become possible via ad-hoc modifications and parametrizations employed to accommodate inappropriately defined molecular surfaces. The main aim of the present study is to propose “thermodynamically effective” molecular surface which unlike the conventionally accepted molecular surfaces, can be defined only uniquely, can be measured experimentally for each molecule directly and straightforwardly, is defined based on a well-characterized theoretically described dependency between molecular surfaces and solution thermodynamics, and is highly accurate in evaluating various thermodynamics quantities in solution for a wide temperature range and different types of molecules, without requiring any ad-hoc modification.

COordinated Responsive Arrays of Surface-Linked polymer islands (CORALS) allow for the creation of molecular surfaces with novel and switchable properties. Critical components of CORALs are the uniformly distributed islands of densely grafted polymer chains (nanoislands) separated by regions of bare surface. The grafting footprint and separation distances of nanoislands are comparable to that of the constituent polymer chains themselves. Herein, we characterize the structural features of the nanoislands and semiflexible polymers within to better understand this critical constituent of CORALs. We observe different characteristics of grafted semiflexible polymers depending on the polymer island’s size and distance from the center of the island. Specifically, the characteristics of the chains at the island periphery are similar to isolated tethered polymer chains (full flexible chains), while chains in the center of the island experience the neighbor effect such as chains in the classic polymer brush. Chains close to the edge of the islands exhibit unique structural features between these two regimes. These results can be used in the rational design of CORALs with specific interfacial characteristics and predictable responses to external stimuli. It is hoped that this the discussion of the different morphologies of the polymers as a function of distance from the edge of the polymer will find applications in a wide variety of systems.

This paper presents the methods that have participated in the SHREC 2021 contest on retrieval and classification of protein surfaces on the basis of their geometry and physicochemical properties. The goal of the contest is to assess the capability of different computational approaches to identify different conformations of the same protein, or the presence of common sub-parts, starting from a set of molecular surfaces. We addressed two problems: defining the similarity solely based on the surface geometry or with the inclusion of physicochemical information, such as electrostatic potential, amino acid hydrophobicity, and the presence of hydrogen bond donors and acceptors. Retrieval and classification performances, with respect to the single protein or the existence of common sub-sequences, are analysed according to a number of information retrieval indicators.

Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their binding versatility, antibodies are currently the largest class of biotherapeutics, with five monoclonal antibodies ranked in the top 10 blockbuster drugs. Computational advances in protein modelling and design can have a tangible impact on antibody-based therapeutic development. Antibody-specific computational protocols currently benefit from an increasing volume of data provided by next generation sequencing and application to related drug modalities based on traditional antibodies, such as nanobodies. Here we present a structured overview of available databases, methods and emerging trends in computational antibody analysis and contextualize them towards the engineering of candidate antibody therapeutics.

The Solvent Similarity Index (SSI) is a quantitative parameter we introduce for the comparison of the solvation properties of any solvent or solvent mixture. The Surface Site Interaction Model for Liquids at Equilibrium (SSIMPLE) was used to calculate the free energy of solvation of a single Surface Site Interaction Point (SSIP) on a solute. The SSIP representation of molecular surfaces was used to calculate the free energy of solvation for all possible solute polarities, generating a unique solvation profile for any solvent or solvent mixture. Quantitative comparison of the solvation profiles of two solvents was used as the basis for calculating the solvation similarity index. Values of SSI were calculated for all pairwise comparisons of 261 pure solvents at 298 K, and the results were used to classify solvents into groups according to their solvation properties. Applications to understanding the solvation properties of binary solvent mixtures and for identification of alternative solvents are illustrated.

sensaas is a tool developed for aligning and comparing molecular shapes and sub‐shapes. Alignment is obtained by registration of 3D point‐based representations of the van der Waals surface. The method uses local properties of the shape to identify the correspondence relationships between two point clouds containing up to several thousand colored (labeled) points. Our rigid‐body superimposition method follows a two‐stage approach. An initial alignment is obtained by matching pose‐invariant local 3D descriptors, called FPFH, of the input point clouds. This stage provides a global superimposition of the molecular surfaces, without any knowledge of their initial pose in 3D space. This alignment is then refined by optimizing the matching of colored points. In our study, each point is colored according to its closest atom, which itself belongs to a user defined physico‐chemical class. Finally, sensaas provides an alignment and evaluates the molecular similarity by using Tversky coefficients. To assess the efficiency of this approach, we tested its ability to reproduce the superimposition of X‐ray structures of the benchmarking AstraZeneca (AZ) data set and, compared its results with those generated by the two shape‐alignment approaches shaep and shafts. We also illustrated submatching properties of our method with respect to few substructures and bioisosteric fragments. The code is available upon request from the authors (demo version at https://chemoinfo.ipmc.cnrs.fr/SENSAAS).

A protein and a ligand have a process of recognizing each other when they are remote before approaching for binding. In this process, there should be a local portion corresponding to a target of the recognition (a recognition spot) on the protein molecular surface. In this paper, we proposed a new biclustering algorithm BISERS for predicting recognition spots on protein molecular surfaces, in which a portion of the molecular surface of a query protein that frequently shows the similarity to other specific proteins binding to the similar ligand is extracted by biclustering. In BISERS, the similarity between rows as well as the similarity between columns is introduced into the evaluation function for updating the biclusters. In addition, the random sampling is applied to the process of exclusive selection of the column for reducing the computational cost effectively. Experimental results for 60 proteins show the effectiveness of our BISERS algorithm.

The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode-Elastic server for normal mode analysis, a virtual reality system for the eF-site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.

Predicting interactions between proteins and other biomolecules solely based on structure remains a challenge in biology. A high-level representation of protein structure, the molecular surface, displays patterns of chemical and geometric features that fingerprint a protein's modes of interactions with other biomolecules. We hypothesize that proteins participating in similar interactions may share common fingerprints, independent of their evolutionary history. Fingerprints may be difficult to grasp by visual analysis but could be learned from large-scale datasets. We present MaSIF (molecular surface interaction fingerprinting), a conceptual framework based on a geometric deep learning method to capture fingerprints that are important for specific biomolecular interactions. We showcase MaSIF with three prediction challenges: protein pocket-ligand prediction, protein-protein interaction site prediction and ultrafast scanning of protein surfaces for prediction of protein-protein complexes. We anticipate that our conceptual framework will lead to improvements in our understanding of protein function and design.

Molecular visualization is often challenged with rendering of large molecular structures in real time. The key to LOD (level-of-detail), a classical technology, lies in designing a series of hierarchical abstractions of protein. In the paper, we improved the smoothness of transition for these abstractions by constructing a complete binary tree of a protein. In order to reduce the degree of expansion of the geometric model corresponding to the high level of abstraction, we introduced minimum ellipsoidal enveloping and some post-processing techniques. At the same time, a simple, ellipsoid drawing method based on graphics processing unit (GPU) is used that can guarantee that the drawing speed is not lower than the existing sphere-drawing method. Finally, we evaluated the rendering performance and effect on series of molecules with different scales. The post-processing techniques applied, diffuse shading and contours, further conceal the expansion problem and highlight the surface details.

In this short review, an electroorganic synthesis approach to the construction of addressable, complex molecular surfaces is described along with the parameters that guided the development of that synthetic approach. The result of the work is a synthetic toolbox that will allow microelectrode arrays to be used for the "real-time" monitoring of small molecule interactions with biological targets.

Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there have been many progresses in the development of methodology and instrumentation in the SFG-VS toolbox that have significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, some of the controversial issues that have been puzzling the community are discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.

Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K-0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. (c) 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

The molecular surface has been suggested to be a region of the molecule, where information of non-covalent intermolecular interactions is present. Many workers have pursued this idea by constructing models based on statistical parameters Φ extracted from the electrostatic potential on a particular molecular surface. We claim that a better approach is to define a family of equivalent molecular surfaces, each associated with a particular electron density e. The demand that any model must give the same predictions on all such molecular surfaces yields a mathematical requirement restricting the space of permissible parameters. We prove that linear single-variable models of the form property = α Φ + β will only yield invariant predictions if the parameter values of Φ computed on equivalent surfaces are linearly related. This claim is not restricted to the use of the electrostatic potential, but holds for any parameter extracted from the surface of molecules. By using a set of 44 molecules, we also demo...

Motivation: Hydration largely determines solubility, aggregation of proteins and influences interactions between proteins and drug molecules. Despite the importance of hydration, structural determination of hydration structure of protein surfaces is still challenging from both experimental and theoretical viewpoints. The precision of experimental measurements is often affected by fluctuations and mobility of water molecules resulting in uncertain assignment of water positions. Results: Our method can utilize mobility as an information source for the prediction of hydration structure. The necessary information can be produced by molecular dynamics simulations accounting for all atomic interactions including water–water contacts. The predictions were validated and tested by comparison to more than 1500 crystallographic water positions in 20 hydrated protein molecules including enzymes of biomedical importance such as cyclin-dependent kinase 2. The agreement with experimental water positions was larger than 80% on average. The predictions can be particularly useful in situations where no or limited experimental knowledge is available on hydration structures of molecular surfaces. Availability and implementation: The method is implemented in a standalone C program MobyWat released under the GNU General Public License, freely accessible with full documentation at http://www.mobywat.com. Contact: csabahete@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online.

The 2017 Faraday Discussion on Complex Molecular Surfaces and Interfaces brought together theoreticians and experimentalists from both physical and chemical backgrounds to discuss the relevant applied and fundamental research topics within the broader field of chemical surface analysis and characterization. Main discussion topics from the meeting included the importance of "disordered" two-dimensional (2D) molecular structures and the utility of kinetically trapped states. An emerging need for new experimental tools to address dynamics and kinetic pathways involved in self-assembled systems, as well as the future prospects and current limitations of in silico studies were also discussed. The following article provides a brief overview of the work presented and the challenges discussed during the meeting.

Ion scattering using ultralow energy projectiles is considered to be a unique method to probe the nature of molecular surfaces because of its capacity to probe the very top, atomically thin layers. Here, we examine one of the most studied molecular solids, water-ice, using this technique. When ice surface undergoes the amorphous to crystalline transition, an ultralow energy reactive projectile identifies the change through the reaction product formed. It is shown that ultralow energy (2, 3, 4, 5, 6, and 7 eV) CH2 + (or CD2 +) collision on amorphous D2O (or H 2O) ice makes CHD+, while crystalline ice does not. The projectile undergoes H/D exchange with the dangling -OD (-OH) bond present on amorphous ice surfaces. It is also shown that H/D exchange product disappears when amorphous ice is annealed to the crystalline phase. The H/D exchange reaction is shown to be sensitive only to the surface layers of ice as it disappears when the surface is covered with long chain alcohols like 1-pentanol as the ice surfaces become inaccessible for the incoming projectile. This article shows that ultralow energy reactive ion collision is a novel method to distinguish phase transitions in molecular solids. � 2013 American Chemical Society.

The bottom-up preparation of mixed crystals, co-crystals and photoreactive materials starting from molecular building blocks across the borders of organic, organometallic and metal–organic chemistry is described., The conceptual relationship between crystal reactivity, stability and meta­stability, solubility and morphology on the one hand and shape, charge distribution, chirality and distribution of functional groups over the molecular surfaces on the other hand is discussed, via a number of examples coming from three decades of research in the field of crystal engineering at the University of Bologna. The bottom-up preparation of mixed crystals, co-crystals and photoreactive materials starting from molecular building blocks across the borders of organic, organometallic and metalorganic chemistry is recounted.

We review physicochemical factors and processes that describe how cellular life can emerge from prebiotic chemical matter; they are: (1) prebiotic Earth is a multicomponent and multiphase reservoir of chemical compounds, to which (2) Earth-Moon rotations deliver two kinds of regular cycling energies: diurnal electromagnetic radiation and seawater tides. (3) Emerging colloidal phases cyclically nucleate and agglomerate in seawater and consolidate as geochemical sediments in tidal zones, creating a matrix of microspaces. (4) Some microspaces persist and retain memory from past cycles, and others re-dissolve and re-disperse back into the Earth's chemical reservoir. (5) Proto-metabolites and proto-biopolymers coevolve with and within persisting microspaces, where (6) Macromolecular crowding and other non-covalent molecular forces govern the evolution of hydrophilic, hydrophobic, and charged molecular surfaces. (7) The matrices of microspaces evolve into proto-biofilms of progenotes with rudimentary but evolving replication, transcription, and translation, enclosed in unstable cell envelopes. (8) Stabilization of cell envelopes 'crystallizes' bacteria-like genetics and metabolism with low horizontal gene transfer-life 'as we know it.' These factors and processes constitute the 'working pieces' of the jigsaw puzzle of life's emergence. They extend the concept of progenotes as the first proto-cellular life, connected backward in time to the cycling chemistries of the Earth-Moon planetary system, and forward to the ancient cell cycle of first bacteria-like organisms. Supra-macromolecular models of 'compartments first' are preferred: they facilitate macromolecular crowding-a key abiotic/biotic transition toward living states. Evolutionary models of metabolism or genetics 'first' could not have evolved in unconfined and uncrowded environments because of the diffusional drift to disorder mandated by the second law of thermodynamics.

The standardization of HIV-1 strains for vaccine tests include the use of viral reference panels. We determined a series of pharmacological descriptors (molecular surfaces, volumes, electrostatic energies, solvation energies, number of atoms, number of hydrogen donors or acceptors and number of rigid bonds) for the gp120 CD4-binding sites structures in the unliganded state from a reference panel of 60 diverse strains of HIV-1. We identified the descriptors that varied significantly between the strains, the outliner strains for each descriptor set and the possible correlations between the descriptors. Our results improve the knowledge about gp120, its molecular and possible neutralization properties.

This paper provides an overview of recently developed two dimensional (2D) fragment-based QSAR methods as well as other multi-dimensional approaches. In particular, we present recent fragment-based QSAR methods such as fragment-similarity-based QSAR (FS-QSAR), fragment-based QSAR (FB-QSAR), Hologram QSAR (HQSAR), and top priority fragment QSAR in addition to 3D- and nD-QSAR methods such as comparative molecular field analysis (CoMFA), comparative molecular similarity analysis (CoMSIA), Topomer CoMFA, self-organizing molecular field analysis (SOMFA), comparative molecular moment analysis (COMMA), autocorrelation of molecular surfaces properties (AMSP), weighted holistic invariant molecular (WHIM) descriptor-based QSAR (WHIM), grid-independent descriptors (GRIND)-based QSAR, 4D-QSAR, 5D-QSAR and 6D-QSAR methods.

Graphical abstract Electrostatic potential on an electron density iso-surface (0.0067 eÅ−3) of an APE substrate in the active site pocket of the SARS main protease Mpro. Geometry data from PDB entry 2A5I., To contribute to an understanding of biological recognition and interaction, an easy-to-use procedure was developed to generate and display molecular surfaces and selected electron density based surface properties. To overcome the present limitations to derive electron densities of macromolecules, the considered systems were reduced to appropriate substructures around the active centers. The combination of experimental X-ray structural information and aspherical atomic electron density data from theoretical calculations resulted in properties like the electrostatic potential and the Hirshfeld surface which allowed a study of electronic complementarity and the identification of sites and strengths of drug-receptor interactions. Applications were examined for three examples. The anilinoquinazoline gefitinib (Iressa®) belongs to a new class of anticancer drugs that inhibit the tyrosine kinase activity of the epidermal growth factor receptor (EGFR). In the second example, the interaction of epoxide inhibitors with the main protease of the SARS coronavirus was investigated. Furthermore, the progesterone receptor complex was examined. The quantitative analysis of hydrogen bonding in the chosen substructure systems follows a progression elaborated earlier on the basis of accurate small molecule crystal structures. This finding and results from modified substructures suggest that also the surface properties seem robust enough to provide stable information about the recognition of interacting biomolecular species although they are obtained from medium molecular weighted subfragments of macromolecular complexes, which consist of no more than ∼40 residues.

Noncovalent self-assembly of biopolymers is driven by molecular interactions between functional groups on complementary biopolymer surfaces, replacing interactions with water. Since individually these interactions are comparable in strength to interactions with water, they have been difficult to quantify. Solutes (osmolytes, denaturants) exert often large effects on these self-assembly interactions, determined in sign and magnitude by how well the solute competes with water to interact with the relevant biopolymer surfaces. Here, an osmometric method and a water-accessible surface area (ASA) analysis are developed to quantify and interpret the interactions of the remarkable osmolyte glycine betaine (GB) with molecular surfaces in water. We find that GB, lacking hydrogen bond donors, is unable to compete with water to interact with anionic and amide oxygens; this explains its effectiveness as an osmolyte in the Escherichia coli cytoplasm. GB competes effectively with water to interact with amide and cationic nitrogens (hydrogen bonding) and especially with aromatic hydrocarbon (cation-pi). The large stabilizing effect of GB on lac repressor-lac operator binding is predicted quantitatively from ASA information and shown to result largely from dehydration of anionic DNA phosphate oxygens in the protein-DNA interface. The incorporation of these results into theoretical and computational analyses will likely improve the ability to accurately model intra- and interprotein interactions. Additionally, these results pave the way for development of solutes as kinetic/mechanistic and thermodynamic probes of conformational changes and formation/disruption of molecular interfaces that occur in the steps of biomolecular self-assembly processes.

For well-structured, rigid proteins, the prediction of rotational tumbling time (tau(c)) using atomic coordinates is reasonably accurate, but is inaccurate for proteins with long unstructured sequences. Under physiological conditions, many proteins contain long disordered segments that play important regulatory roles in fundamental biological events including signal transduction and molecular recognition. Here we describe an ensemble approach to the boundary element method that accurately predicts tau(c) for such proteins by introducing two layers of molecular surfaces whose correlated velocities decay exponentially with distance. Reliable prediction of tau(c) will help to detect intra- and intermolecular interactions and conformational switches between more ordered and less ordered states of the disordered segments. The method has been extensively validated using 12 reference proteins with 14 to 103 disordered residues at the N- and/or C-terminus and has been successfully employed to explain a set of published results on a system that incorporates a conformational switch.

Enzyme linked immunosorbent assay (ELISA) was used for the analysis of tetracycline, chlortetracycline, oxytetracycline, and their transformed compounds in environmental water samples. The antibodies employed in ELISA showed high relative affinity for tetracycline, epitetracycline, chlortetracycline, and epichlortetracycline as compared to anhydrotetracycline, epianhydrotetracycline, and anhydrochlortetracycline. The specificity and crossreactivity of these antibodies are discussed in relation to the electrostatic potentials and average local ionization energies computed on the molecular surfaces of tetracycline antibiotics and their transformed compounds with an objective of identifying common features as well as differences that may be related to the experimentally observed variation in cross-reactivity values. The computations were performed at both the HF/STO-3G and HF/6-31+G* levels using the Gaussian 98 program. The results in this study are based upon molecular electrostatic potentials and local ionization energies computed on isodensity molecular surfaces. The surface electrostatic potentials are characterized in terms of a group of statistically defined quantities, which include the average deviation, the positive, negative, and total variances, positive and negative surface extrema, and a parameter indicating the degree of electrostatic balance.

Recently, surface spectroscopies and simulations have begun to characterize the non-uniform distributions of salt ions near macroscopic and molecular surfaces. The thermodynamic consequences of these non-uniform distributions determine the often-large ion-specific effects of Hofmeister salts on a very wide range of processes in water. For uncharged surfaces, where these non-uniform ion distributions are confined to the first few layers of water at the surface, a two-state approximation to the distributions of water and ions, called the salt ion partitioning model (SPM) has both molecular and thermodynamic significance. Here, we summarize SPM results quantifying the local accumulation of H+, exclusion of HO−, and range of partitioning behavior of Hofmeister anions and cations near macroscopic and molecular interfaces. These results provide a database to interpret or predict Hofmeister salt effects on aqueous processes in terms of structural information regarding amount and composition of the surface exposed or buried in these processes.

We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).

In present study, quantum chemistry calculations of geometric parameters, harmonic vibrational wavenumbers and the 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts values of 4-(methoxymethyl)-1,6-dimethyl-2-oxo-1,2-dihydropyridine-3-carbonitrile [C 10 H 12 N 2 O 2 ] molecule in the ground state were calculated using HF/6-311++G(d,p) and DFT/B3LYP/6-311++G(d,p) methods. The results of the optimized molecular structure were presented and compared with the experimental values. The observed and the calculated values were found to be in good agreement. In addition, nonlinear optical (NLO) analysis, the molecular frontier orbital energies, thermodynamic parameters, molecular surfaces, Mulliken, APT and NBO charges were investigated using HF and DFT quantum chemical calculations.

The 1/1 diacetyl/water complex is of atmospheric relevance. Previous experimental and theoretical studies have focused on two isomeric forms, and geometry optimizations were carried out on them. Herein, we propose a six-step methodological approach based on topological properties to search for and characterize all of the isomeric forms of the 1/1 noncovalent diacetyl/water complex: (1) a molecular electrostatic potential (MESP) study to get an overview of the V min and V max regions on the molecular surfaces of the separate molecules (diacetyl and water); (2) a topological (QTAIM and ELF) study allowing thorough characterization of the electron densities (QTAIM) and irreducible ELF basins of the separate molecules; (3) full optimization of the predicted structures based on the interaction between complementary reaction sites; (4) energetic characterization based on a symmetry-adapted perturbation theory (SAPT) analysis; (5) topological characterization of the optimized complexes; (6) analysis of the complexes in terms of orbital overlaps (natural bond orbitals, NBO analysis). Using this approach, in addition to achieving the topological characterization of the two isomeric forms already reported, a third possible isomer was identified and characterized. Graphical Abstract Topological tools to study monohydrated complexes.

Protein surface motifs, which can be defined as commonly appearing patterns of shape and physical properties in protein molecular surfaces, can be considered "possible active sites". We have developed a system for mining surface motifs: SUMOMO which consists of two phases: surface motif extraction and surface motif filtering. In the extraction phase, a given set of protein molecular surface data is divided into small surfaces called unit surfaces. After extracting several common unit surfaces as candidate motifs, they are repetitively merged into surface motifs. However, a large amount of surface motifs is extracted in this phase, making it difficult to distinguish whether the extracted motifs are significant to be considered active sites. Since active sites from proteins with a particular function have similar shape and physical properties, proteins can be classified based on similarity among local surfaces. Thus, in the filtering phase, local surfaces extracted from proteins of the same group are considered significant motifs, and the rest are filtered out. The proposed method was applied to discover surface motifs from 15 proteins belonging to four function groups. Motifs corresponding to all 4 known functional sites were recognised.

In the post-genome sequencing era, “Structural Genomics” has become one of the most important research fields in life science. Here I introduce the outline of the study of structural genomics in RIKEN Genomic Sciences Center and also the connection between surface science and structural genomics. Structural genomics is an emerging research field, which examines the enormous amounts of information stored in the genomes of living organisms. We are trying to determine a variety of three-dimensional structures of protein mainly by NMR and also to analyze the structure-function relationship of the proteins systematically and comprehensively. In the process of protein function analysis, molecular interaction analysis is very important and we use various methods including in silico screening, mass spectrometry, surface plasmon resonance, NMR, and so on. All of these analytical methods are based on protein-ligand interaction on molecular surfaces.

In the present work, we describe and discuss two interactive visual­ ization techniques recently added to the Udock software. First, we propose to display a spherical projection of the protein's molecular surface properties. The resulting 2D map allows to get in one glance a global view of the protein. Second, we propose to let the user choose a specific level of detail when visualizing the protein's 3D surface. We describe a simple smoothing algorithm that achieves this goal in real time. These techniques are designed to enhance the usability of molecular visualization and interactive simulation software.

We discuss three molecular/crystalline properties that we believe to be among the factors that influence the impact/shock sensitivities of energetic materials (i.e., their vulnerabilities to unintended detonation due to impact or shock). These properties are (a) the anomalously strong positive electrostatic potentials in the central regions of their molecular surfaces, (b) the free space per molecule in their crystal lattices, and (c) their maximum heats of detonation per unit volume. Overall, sensitivity tends to become greater as these properties increase; however these are general trends, not correlations. Nitramines are exceptions in that their sensitivities show little or no variation with free space in the lattice and heat of detonation per unit volume. We outline some of the events involved in detonation initiation and show how the three properties are related to different ones of these events.

M. De Zotti, B. Di Napoli, C. Mazzuca, A. Palleschi, G. M. L. Messina, G. Marletta, and F. Formaggio Department of Chemistry, University of Padova, Padova, I-35131, Italy; Department of Sciences and Chemical Technologies, University of Rome “Tor Vergata”, Rome, I-00133, Italy; Laboratory for Molecular Surfaces and Nanotechnology, Department of Chemical Sciences, University of Catania, Catania, I-95125, Italy

Rigid-body docking processes generate many protein complexes (decoys) for searching near-native decoys (NN-decoys) in post-docking processes with analyzing various pairs of surfaces on two input proteins, using properties of electrostatics and desolvations between two molecules or proteins. Many powerful docking computer softwares were developed and were used for resolving various categories of problems, for example, analysis of protein interaction networks or drug design. Rigid-body docking process is popular and useful in such works. However, there are some unfortunate cases, which could not obtain NN-decoys. Then, we developed Re-docking scheme using interaction fingerprints (IFPs). Re-docking scheme is the process of iterating rigid-body docking for generating more NN-decoys. After initial-docking, we classify decoys into several interaction surfaces. Thereafter, other docking processes are performed with more fine searching limited in every interaction surfaces classified. We could obtain NN-decoys even if no NN-decoys in initial-docking process [Uchikoga et. al. (2013) PLOS ONE 8:e69365]. Then, we approach a problem of prediction of protein-protein interactions by using IFPs, which gives us properties of physico-chemical interactions because IFPs are composed of interacting amino acid pairs [Uchikoga & Hirokawa (2010) BMC Bioinform. 11:236]. By using IFPs, we can obtain these properties easily and trace interaction surfaces in docking processes. In this work, docking search spaces become to be seen by using amino acid properties involved in molecular surfaces of many decoys, generating by Re-docking scheme. Then, we would like to discuss about understanding interaction mechanisms.

Sum-frequency generation vibrational spectroscopy (SFG-VS) can provide detailed information and understanding of the molecular composition, interactions, and orientational and conformational structure of surfaces and interfaces through quantitative measurement and analysis. In this review, we present the current status of and discuss important recent developments in the measurement of intrinsic SFG spectral lineshapes and formulations for polarization measurements and orientational analysis of SFG-VS spectra. The focus of this review is to present a coherent description of SFG-VS and discuss the main concepts and issues that can help advance this technique as a quantitative analytical research tool for revealing the chemistry and physics of complex molecular surfaces and interfaces.

Fuzzy logic-based algorithms for the quantitative treatment of complementarity of molecular surfaces are presented. The identification of complementary surface patches can be considered as a first step for the solution of molecular docking problems. Based on these initial guesses, docking structures can be further optimized by standard technologies. In this work a simple downhill simplex method for the optimization is used. The algorithms are applied to various biomolecular complexes. For all these complexes, at least one structure was found to be in very good agreement with the experimental data.