A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients

In the calculation of thermodynamic properties and three-dimensional structures of macromolecules, such as proteins, it is important to have an efficient algorithm for computing the solvent-accessible surface area of macromolecules. Here, we propose a new analytical method for this purpose. In the proposed algorithm we consider the transformation that maps the spherical circles formed by intersection of the atomic surfaces in three-dimensional space onto the circles on a two-dimensional plane, and the problem of computing the solvent-accessible surface area is reduced to the problem of computing the corresponding curve integrals on the plane. This allows to consider only the integrals along the circular trajectories on the plane. The algorithm is suitable for parallelization. Testings on many proteins as well as the comparison to the other analogous algorithms have shown that our method is accurate and efficient.     

Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations

Continuing advances in computer hardware and software are permitting atomic-resolution molecular simulations for longer time scales and on larger systems. Despite these advances, routinely performing atomistic simulations with explicit water for even small proteins, which reach the folding time of such proteins, remains intractable for the foreseeable future. An implicit approximation of the solvent environment using a solvent accessible surface area (SASA) term in a molecular mechanics potential function allows exclusion of the explicit water molecules in protein simulations. This reduces the number of particles by approximately an order of magnitude. We present a fast and acceptably accurate approximate all-atom SASA method parameterized using a set of folded and heat-denatured conformations of globular proteins. The parameters are shown to be transferable to folded and heat-denatured conformations for another set of proteins. Calculation of the approximate SASA and the associated derivatives with respect to atomic positions for a 4644 atom protein requires only 1/11th the CPU time required for calculation of the nonbonded interactions for this system. On a per atom basis, this algorithm is three times faster than the fastest previously published approximate SASA method and achieves the same level of accuracy.     

Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues

Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, C^α and C^β atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of ‘hard’ degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available.     

Effects of surface structure on the molecular projection area. Adsorption of argon and nitrogen onto defective surfaces

This paper studies the effects of surface structure (defective surfaces) on the molecular projection area of argon and nitrogen at 77 K. The determination of the molecular projection area is based on choice of the surface area of the structure studied and the adsorption data obtained from the GCMC simulation. Two methods were used to determine the surface area: the flat surface area that are commonly used in the literature and the geometrical surface area. The molecular projection areas of argon and nitrogen at 77 K vary with pressure over the recommended range for BET plot (reduced pressures from 0.05 to 0.3) and also they varies with the percentage of defects on the surface. Additionally, it is seen that the geometrical surface area method gives molecular projection area of defective surfaces values that are in accordance with the experimental value reported in the literature.     

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.     

Synergistic tuning of electrochemical surface area and surface Co3+ by oxygen plasma enhances the capacities of Co3O4 lithium–oxygen battery cathodes

Modifying electrochemical surface area (ECSA) and surface chemistry are promising approaches to enhance the capacities of oxygen cathodes for lithium–oxygen (Li–O₂) batteries. Although various chemical approaches have been successfully used to tune the cathode surface, versatile physical techniques including plasma etching etc. could be more effortless and effective than arduous chemical treatments. Herein, for the first time, we propose a facile oxygen plasma treatment to simultaneously etch and modify the surface of Co₃O₄ nanosheet arrays (NAs) cathode for Li–O₂ batteries. The oxygen plasma not only etches Co₃O₄ nanosheets to enhance the ECSA but also lowers the oxygen vacancy concentration to enable a Co³⁺-rich surface. In addition, the NA architecture enables the full exposure of oxygen vacancies and surface Co³⁺ that function as the catalytically active sites. Thus, the synergistic effects of enhanced ECSA, modest oxygen vacancy and high surface Co³⁺ achieve a significantly enhanced reversible capacity of 3.45 mAh/cm² for Co₃O₄ NAs. This work not only develops a promising high-capacity cathode for Li–O₂ batteries, but also provides a facile physical method to simultaneously tune the nanostructure and surface chemistry of energy storage materials.     

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。     

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 simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: Application to peptides

A computational strategy to model flexible molecules tethered to a rigid inert surface is presented. The strategy is able to provide uncorrelated relaxed microstructures at the atomistic level. It combines an algorithm to generate molecules tethered to the surface without atomic overlaps, a method to insert solvent molecules and ions in the simulation box, and a powerful relaxation procedure. The reliability of the strategy has been investigated by simulating two different systems: (i) mixed monolayers consisting of binary mixtures of long‐chain alkyl thiols of different lengths adsorbed on a rigid inert surface and (ii) CREKA (Cys‐Arg‐Glu‐Lys‐Ala), a short linear pentapeptide that recognizes clotted plasma proteins and selectively homes to tumors, covalently tethered to a rigid inert surface in aqueous solution. In the first, we examined the segregation of the two species in the monolayers using different long‐chain:short‐chain ratios, whereas in the second, we explored the conformational space of CREKA and ions distribution considering densities of peptides per nm² ranging from 0.03 to 1.67. Results indicate a spontaneous segregation in alkyl thiol monolayers, which enhances when the concentration of longest chains increases. However, the whole conformational profile of CREKA depends on the number of molecules tethered to the surface pointing out the large influence of molecular density on the intermolecular interactions, even though the bioactive conformation was found as the most stable in all cases. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

A generalized expression for the ratio of the critical temperature to the critical pressure with the van der Waals surface area

Using an extensive database of experimental critical properties for heavy compounds, which have been compiled mostly from recent literature sources, it is shown that the ratio T_c: P_c (critical temperature over critical pressure) can be expressed in terms of the van der Waals surface area (Q_w), which is readily available for any compound from the group contributions of Bondi (given also in UNIFAC tables). The proposed correlation is based on the hole theory of Kurata and Isida for n-paraffin liquids, which is mathematically equivalent to Flory's theory of polymer solutions. The method is suitable for medium to high molecular weight compounds with unknown critical constants. For example, if only one of the two critical constants is available, then the proposed generalized equation offers a useful rapid procedure for the estimation of the other critical property for use in corresponding states, and other relevant applications where knowledge of the critical properties is required. Furthermore, the T_c: P_c method can be used in many cases for identifying the most suitable among the existing group contribution methods for estimating the critical properties of heavy and complex compounds for which experimental values are, very often, not available.     

A generalized direct-particle-deletion scheme for the calculation of chemical potential and solubilities of small- and medium-sized molecules in amorphous polymers

The development, validation, and first applications of a generalized version of an inverse Widom method are described. It permits the calculation of solubility coefficients for molecules as large as, e.g., benzene in all polymers for which reasonable forcefield parameters exist. Predicting the solubility is a key to the knowledge-based design of materials utilized to solve permeability related problems. For long time, particle insertion methods, such as the Widom method, were the only way to predict solubilities from molecular models, but they, in most cases, only worked well for rather small penetrants (e.g., H2, O2, N2). Therefore, a few years ago, a new particle deletion algorithm "DPD" was introduced by Boulougouris, Economou, and Theodorou to overcome this problem in principle. The related computer code was, however, only applicable to special, relatively simple model systems. As application examples for the generalized version described here, solubility calculations for nitrogen, oxygen, and benzene in poly(dimethyl siloxane) are presented.     

Segmentation and additive approach: A reliable technique to study noncovalent interactions of large molecules at the surface of single‐wall carbon nanotubes

This investigation explores a new protocol, named Segmentation and Additive approach (SAA), to study exohedral noncovalent functionalization of single‐walled carbon nanotubes with large molecules, such as polymers and biomolecules, by segmenting the entire system into smaller units to reduce computational cost. A key criterion of the segmentation process is the preservation of the molecular structure responsible for stabilization of the entire system in smaller segments. Noncovalent interaction of linoleic acid (LA, C₁₈H₃₂O₂), a fatty acid, at the surface of a (10,0) zigzag nanotube is considered for test purposes. Three smaller segmented models have been created from the full (10,0)‐LA system and interaction energies were calculated for these models and compared with the full system at different levels of theory, namely ωB97XD, LDA. The success of this SAA is confirmed as the sum of the interaction energies is in very good agreement with the total interaction energy. Besides reducing computational cost, another merit of SAA is an estimation of the contributions from different sections of the large system to the total interaction energy which can be studied in‐depth using a higher level of theory to estimate several properties of each segment. On the negative side, bulk properties, such as HOMO‐LUMO (highest occupied molecular orbital ‐ lowest occupied molecular orbital) gap, of the entire system cannot be estimated by adding results from segment models. © 2016 Wiley Periodicals, Inc.     

Synthesis of large surface area nano-sized BiVO4 by an EDTA-modified hydrothermal process and its enhanced visible photocatalytic activity

In this work, monoclinic scheelite-type BiVO₄ nanoparticle with large surface area has been successfully synthesized, using Bi(NO₃)₃ and NH₄VO₃ as raw materials, through a hydrothermal process in the presence of ethylene diamine tetraacetic acid (EDTA). It is demonstrated that the nanoparticle size of as-prepared BiVO₄ becomes small by decreasing hydrothermal temperature, shortening hydrothermal reaction time and increasing EDTA amount used. The resulting BiVO₄ nanoparticle with large surface area exhibits a good photocatalytic performance for degrading phenol solution as a model organic pollutant under visible illumination. The key of this method is the chelating role of EDTA group in the synthetic process that it can greatly control the concentration of Bi³⁺, leading to the growth inhibition of BiVO₄ crystallite. The work provides a route for the synthesis of Bi-containing nano-sized composite oxides with large surface area.     

Exploiting the versatility of pyridyl ligands for the preparation of diorganotin (IV) adducts: spectral,crystallographic and Hirshfeld surface analysis studies

Diorganotin (IV) complexes SnR₂X₂ (R = Me, Ph; X = Cl, NCS) form a series of versatile complexes when react with bidentate substituted pyridyl ligands. The reaction of dimethyltin dichloride with 5,5′‐dimethyl‐2,2′‐bipyridine (5,5′‐Me₂bpy) resulted in the formation of [SnMe₂Cl₂(5,5′‐Me₂bpy)] ( 1 ). Moreover, the reaction of SnMe₂(NSC)₂ with 4,4′‐di‐tert‐butyl‐2,2′‐bipyridine (bu₂bpy), 1,10‐phenanthroline (phen) and 4,7‐diphenyl‐1,10‐phenanthroline (bphen) affords the hexa‐coordinated complexes [SnMe₂(NCS)₂(bu₂bpy)] ( 2 ), [SnMe₂(NCS)₂(phen)] ( 3 ) and [SnMe₂(NCS)₂(bphen)] ( 4 ), respectively. The resulting complexes have been characterized using elemental analysis, IR, multinuclear NMR (¹H, ¹³C, ¹¹⁹Sn) and DEPT‐135^° NMR spectroscopy. On the other hand, the reaction of diphenyltin dichloride with 2,2′‐biquinoline (biq) and 4,7‐phenantroline (4,7‐phen) led to the formation of polymeric complexes of [SnPh₂Cl₂(4,7‐phen)]_n ( 5 ) and [SnPh₂Cl₂(biq)]_n ( 6 ). The NMR spectra, however, reveal the ligand lability in solution and suggest a coordination number of 5 . The X‐ray crystal structures of complexes [SnMe₂Cl₂(5,5′‐Me₂bpy)] ( 1 ), [SnMe₂(NCS)₂(bu₂bpy)] ( 2 ) and [SnMe₂(NCS)₂(bphen)] ( 4 ) have been determined which reveal that the geometry around the tin atom is distorted octahedral with trans‐[SnMe₂] configuration. Interestingly, the crystal structure of (H₂biq)₂[SnPh₂Cl₄]?2CHCl₃ ( 7 ) was characterized by X‐ray crystallography from a chloroform solution of [SnPh₂Cl₂(biq)]_n ( 6 ) indicating the formation of doubly protonated [H₂biq]⁺ and [Ph₂SnCl₄]^2? which are stabilized by a network of hydrogen bonds with a feature of trans‐[SnPh₂]. The 3D Hirshfeld surface analysis and 2D fingerprint maps were used for quantitative mapping out of the intermolecular interactions for 1 , 2 , 4 and 7 which show the presence of π‐π and hydrogen bonding interactions which are associated between donor and acceptor atoms (N, S, Cl) in the solid state.     

Hypercrosslinking: new approach to porous polymer monolithic capillary columns with large surface area for the highly efficient separation of small molecules

Monolithic polymers with an unprecedented surface area of over 600 m(2)/g have been prepared from a poly(styrene-co-vinylbenzyl chloride-co-divinylbenzene) precursor monolith that was swollen in 1,2-dichloroethane and hypercrosslinked via Friedel-Crafts reaction catalyzed by ferric chloride. Both the composition of the reaction mixture used for the preparation of the precursor monolith and the conditions of the hypercrosslinking reaction have been varied using mathematical design of experiments and the optimized system validated. Hypercrosslinked monolithic capillary columns contain an array of small pores that make the column ideally suited for the high efficiency isocratic separations of small molecules such as uracil and alkylbenzenes with column efficiencies reproducibly exceeding 80,000 plates/m for retained compounds. The separation process could be accelerated while also improving peak shape through the use of higher temperatures and a ternary mobile phase consisting of acetonitrile, tetrahydrofuran, and water. As a result, seven compounds were well separated in less than 2 min. These columns also facilitate separations of peptide mixtures such as a tryptic digest of cytochrome c using a gradient elution mode which affords a sequence coverage of 93%. A 65 cm long hypercrosslinked capillary column used in size exclusion mode with tetrahydrofuran as the mobile phase afforded almost baseline separation of toluene and five polystyrene standards.     

2H NMR spectroscopy of liquid crystals: structure and orientational order of a chiral smectogen in its A,C* and J* phases

²H NMR spectroscopy is employed to investigate the orientational order, molecular structure and phase transitions of the chiral smectic liquid crystal 1-methylheptyl 4'-(4-n-decyloxybenzoyloxy)biphenyl-4-carboxylate (10B1M7), showing smectic A, C* and J phases, as well as several sub-smectic C* phases. Two optically pure, differently deuteriated isotopomers have been purposely synthesized and studied.