DiTe2: Calculating the diffusion tensor for flexible molecules

We report on an extended hydrodynamic modeling of the friction tensorial properties of flexible molecules including all types of natural, Z-Matrix like, internal coordinates. We implement the new methodology by extending and updating the software DiTe [Barone et al. J. Comput. Chem. 30, 2 (2009)]. DiTe (DIffusion TEnsor) implements a hydrodynamic modeling of the generalized translational, rotational, and configurational friction and diffusion tensors of flexible molecules in which flexibility is described in terms of dihedral angles. The new tool, DiTe2, has been renewed to include also stretching and bending types of internal mobility. Furthermore, DiTe2 is able to calculate the friction and diffusion tensors along collective (or reaction) coordinates defined as linear combinations of the internal natural ones. A number of tests are reported to show the new features of DiTe2. As leitmotiv for the tests, the calmodulin protein is taken into consideration, described both at all-atom and coarse-grained levels. © 2018 Wiley Periodicals, Inc.     

Molecular modeling study on surface,thermal, mechanical and gas diffusion properties of chitosan

The motivation of this work is to provide reliable and accurate modeling studies of the physical (surface, thermal, mechanical and gas diffusion) properties of chitosan (CS) polymer. Our computational efforts have been devoted to make a comparison of the structural bulk properties of CS with similar type of polymers such as chitin and cellulose through cohesive energy density, solubility parameter, hydrogen bonding, and free volume distribution calculations. Atomistic modeling on CS polymer using molecular mechanics (MM) and molecular dynamics (MD) simulations has been carried out in three dimensionally periodic and effective two dimensionally periodic condensed phases. From the equilibrated structures, surface energies were computed. The equilibrium structure of the films shows an interior region of mass density close to the value in the bulk state. Various components of energetic interactions have been examined in detail to acquire a better insight into the interactions between bulk structure and the film surface. MD simulation (NPT ensemble) has also been used to obtain polymer specific volume as a function of temperature. It is demonstrated that these V–T curves can be used to locate the volumetric glass transition temperature (T_g) reliably. The mechanical properties of CS have been obtained using the strain deformation method. Diffusion coefficients of O₂, N₂, and CO₂ gas molecules at 300 K in CS have been estimated. The calculated properties of CS are comparable with the experimental values reported in the literature. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 1260–1270, 2007     

Effect of additives on the photovoltaic properties of organic solar cells based on triphenylamine-containing amorphous molecules

Photovoltaic performance of the organic solar cells(OSCs)based on 2-((5′-(4-((4-((E)-2-(5′-(2,2-dicyanovinyl)-3′,4-dihexyl-2,2′-bithiophen-5-yl)vinyl)phenyl)(phenyl)amino)styryl)-4,4′-dihexyl-2,2′-bithiophen-5-yl)methylene)malononitrile(L(TPAbTV-DCN))as donor and PC70BM as acceptor was optimized using 0.25 vol%high boiling point solvent additive of1-chloronaphthalene(CN),1,6-hexanedithiol(HDT),or 1,8-diodooctane(DIO).The optimized OSC based on L(TPA-bTVDCN)–PC70BM(1:2,w/w)with 0.25 vol%CN exhibits an enhanced power conversion efficiency(PCE)of 2.61%,with Voc of0.87 V,Jsc of 6.95 mA/cm2,and FF of 43.2%,under the illumination of 100 mW/cm2 AM 1.5 G simulated solar light,whereas the PCE of the OSC based on the same active layer without additive is only 1.79%.The effect of the additive on absorption spectra and the atomic force microscopy images of L(TPA-bTV-DCN)–PC70BM blend films were further investigated.The improved efficiency of the device could be ascribed to the enhanced absorption and optimized domain size in the L(TPA-bTV-DCN)–PC70BM blend film.     

Biphenyl: A stress tensor and vector‐based perspective explored within the quantum theory of atoms in molecules

We use quantum theory of atoms in molecules (QTAIM) and the stress tensor topological approaches to explain the effects of the torsion φ of the C‐C bond linking the two phenyl rings of the biphenyl molecule on a bond‐by‐bond basis using both a scalar and vector‐based analysis. Using the total local energy density H( r _b), we show the favorable conditions for the formation of the controversial H–H bonding interactions for a planar biphenyl geometry. This bond‐by‐bond QTAIM analysis is found to be agreement with an earlier alternative QTAIM atom‐by‐atom approach that indicated that the H–H bonding interaction provided a locally stabilizing effect that is overwhelmed by the destabilizing role of the C‐C bond. This leads to a global destabilization of the planar biphenyl conformation compared with the twisted global minimum. In addition, the H( r _b) analysis showed that only the central torsional C‐C bond indicated a minimum for a torsion φ value coinciding with that of the conventional global energy minimum. The H–H bonding interactions are found to be topologically unstable for any torsion of the central C‐C bond away from the planar biphenyl geometry. Conversely, we demonstrate that for 0.0° < φ < 39.95° there is a resultant increase in the topological stability of the C nuclei comprising the central torsional C‐C bond. Evidence is found of the effect of the H–H bonding interactions on the torsion φ of the central C‐C bond of the biphenyl molecule in the form of the QTAIM response β of the total electronic charge density ρ( r _b). Using a vector‐based treatment of QTAIM we confirm the presence of the sharing of chemical character between adjacent bonds. In addition, we present a QTAIM interpretation of hyperconjugation and conjugation effects, the former was quantified as larger in agreement with molecular orbital (MO) theory. The stress tensor and the QTAIM H atomic basin path set areas are independently found to be new tools relevant for the incommensurate gas to solid phase transition occurring in biphenyl for a value of the torsion reaction coordinate φ ≈ 5°. © 2015 Wiley Periodicals, Inc.     

Diffusion of small molecules in glassy polymers

Small molecules in glassy polymers are considered to occupy sites with a distribution of free energies of dissolution. Then their diffusivity depends on concentration and temperature in the same way as it has been derived for hydrogen atoms in metallic glasses. For hydrogen it was shown that the tracer diffusion coefficient is proportional to the activity coefficient of the solute atoms. The latter can be evaluated from measured data of sorption of the small molecules in the polymer. Knowing this quantity, the thermodynamic factor can be calculated and the concentration dependence of the mutual diffusion coefficient is obtained in excellent agreement with published experimental results. New experimental results are presented for the diffusion coefficient of CO₂ in Kapton and four polycarbonates (BPA-PC, BPZ-PC, TMBPA-PC, and TMC-PC) in the low CO₂ pressure range of a few mbar up to 1 bar. The results are in agreement with the model developed for hydrogen. The reference diffusion coefficient, which is a fitting parameter of the model that is independent of the distribution of free energies is smallest for the polycarbonate BPZ-PC having a high γ-relaxation temperature. This correlation between the diffusion coefficient and the dynamics of the polymer can be found for other substituted polycarbonates as well. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35 : 2397–2408, 1997     

Stress tensor eigenvector following with next-generation quantum theory of atoms in molecules

The eigenvectors of the electronic stress tensor have been identified as useful for the prediction of chemical reactivity because they determine the most preferred directions to move the bonds. A new 3–D vector based interpretation of the chemical bond that we refer to as the bond-path framework set B provides a version of the quantum theory of atoms in molecules (QTAIM) beyond the minimum definition for bonding that is particularly suitable for understanding changes in molecular electronic structure that occur during reactions. We demonstrate that the most preferred direction for bond motion using the stress tensor corresponds to the most compressible direction and not to the least compressible direction as previously reported. We show the necessity for a directional approach constructed using the eigenvectors along the entire bond-length and demonstrate the insufficiency of scalar measures for capturing the nature of the stress tensor within the QTAIM partitioning.     

PGSE-NMR studies of solvent diffusion in poly(N-isopropylacrylamide) colloidal microgels

The solvent self-diffusion coefficient has been studied in thermoshrinking poly(N-isopropyl acrylamide) microgel dispersions by the pulsed-gradient spin-echo PGSE-NMR technique, as a function of temperature and mass fraction. After suitable corrections for the temperature, the H₂O/D₂O ratio and the relative volume fractions, all the self-diffusion data obtained over a temperature range of approximately 40 °C and mass fraction (2–12 % wt/wt) could be superimposed with the volume fraction as the universal factor. The observed reduction in the solvent self-diffusion coefficient with volume fraction was greater than that predicted by simple obstruction theory. After correction for-, and the subsequent removal of the obstruction effect, the diffusion of the solvent through the core of the particle is elucidated. As found for other polymer-solvent systems, there were no specific binding effects. The diffusion of the solvent in these dispersions over such temperature and mass fraction ranges could be rationalised assuming a constant solvent self-diffusion coefficient in the core of the particles.     

Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants

The Atomic Solvation Parameter (ASP) model is one of the simplest models of solvation, in which the solvation free energy of a molecule is proportional to the solvent accessible surface area (SAS) of its atoms. However, until now this model had not been incorporated into the Self-Consistent Mean Field Theory (SCMFT) method for modelling sidechain conformations in proteins. The reason for this is that SAS is a many-body quantity and, thus, it is not obvious how to define it within the Mean Field (MF) framework, where multiple copies of each sidechain exist simultaneously. Here, we present a method for incorporating an SAS-based potential, such as the ASP model, into SCMFT. The theory on which the method is based is exact within the MF framework, that is, it does not depend on a pairwise or any other approximation of SAS. Therefore, SAS can be calculated to arbitrary accuracy. The method is computationally very efficient: only 7.6% slower on average than the method without solvation. We applied the method to the prediction of sidechain conformation, using as a test set high-quality solution structures of 11 proteins. Solvation was found to substantially improve the prediction accuracy of well-defined surface sidechains. We also investigated whether the methodology can be applied to prediction of folding free energies of protein mutants, using a set of barnase mutants. For apolar mutants, the modest correlation observed between calculated and observed folding free energies without solvation improved substantially when solvation was included, allowing the prediction of trends in the folding free energies of this type of mutants. For polar mutants, correlation was not significant even with solvation. Several other factors also responsible for the correlation were identified and analysed. From this analysis, future directions for applying and improving the present methodology are discussed.     

Three-dimensional visualization of the first hyperpolarizability tensor

With polarization dependent second harmonic generation (SHG) microscopy becoming a more popular method for investigating the structure of biological materials, there is a need to develop tools with which to understand and interpret the observed SHG properties. Quantum mechanical calculations of the hyperpolarizability tensor have become a popular method for understanding the SHG properties of biomolecules. Visualization of the full hyperpolarizability tensor, termed the unit sphere representation, has been developed to provide insight and intuition on the relationship between SHG properties and molecules. A single vector representation is also presented, which approximates the SHG properties of molecules for certain cases, where the anisotropy is negligible.     

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.     

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     

Closed capillary method for the diffusion of biological macromolecules

The closed capillary method for the determination of self-diffusion coefficients of trace species in liquids has been further developed for use with biological macromolecules. In this development, a new correction to permit its use with -emitting radioisotopes has been introduced. The improved method has been applied to the case of a human blood lipoprotein.     

How does the ambiguity of the electronic stress tensor influence its ability to serve as bonding indicator

The electronic stress tensor is not uniquely defined. Possible bonding indicators originating from the quantum stress tensor may inherit this ambiguity. Based on a general formula of the stress tensor this ambiguity can be described by an external parameter λ for indicators derived from the scaled trace of the stress tensor (whereby the scaling function is proportional to the Thomas–Fermi kinetic energy density). The influence of λ is analyzed and the consequences for the representation of chemical bonding are discussed in detail. It is found that the scaled trace of the stress tensor may serve as suitable bonding indicator over a wide range of λ values, excluding the value range between ?0.15 and ?0.48. Focusing on the eigenvalues of the stress tensor, it is found that the sign of the eigenvalues heavily depends on the chosen representation of the stress tensor. Therefore, chemical bonding analyses which are based on the interpretation of the eigenvalue sign (e.g., the spindle structure) are strongly dependent on the chosen form of the stress tensor. © 2014 Wiley Periodicals, Inc.     

Molecular mechanics and dynamics of biomolecules using a solvent continuum model

An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830-1842, 2001     

Electronic stress tensor analysis of molecules in gas phase of CVD process for gesbte alloy

We analyze the electronic structure of molecules which may exist in gas phase of chemical vapor deposition process for GeSbTe alloy using the electronic stress tensor, with special focus on the chemical bonds between Ge, Sb, and Te atoms. We find that, from the viewpoint of the electronic stress tensor, they have intermediate properties between alkali metals and hydrocarbon molecules. We also study the correlation between the bond order which is defined based on the electronic stress tensor, and energy‐related quantities. We find that the correlation with the bond dissociation energy is not so strong while one with the force constant is very strong. We interpret these results in terms of the energy density on the “Lagrange surface,” which is considered to define the boundary surface of atoms in a molecule in the framework of the electronic stress tensor analysis. © 2015 Wiley Periodicals, Inc.     

Joint neighbors approximation of macromolecular solvent accessible surface area

A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 A2, while for unfolded protein conformations it varies from 1.65 to 1.87 A2. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today.     

Differential permeation — Part I: A method for the study of solvent diffusion through membranes

We describe the differential permeation method for the study of the diffusion of solvents from a liquid (or liquid mixture) through flat or tubular membranes. This method consists of measuring the transient permeation rates through the membrane when one of its faces is suddenly put into contact with the liquid medium. The change in the transient rate with time is analyzed by numerical best fitting methods to determine the Fickian diffusion coefficient. A simplified equation is proposed for the fitting of the response of a tubular membrane. Deviations from the Fickian transport mechanism with concentration-independent diffusion coefficient can be evidenced and eventually analyzed by using other mechanistic models.     

Dual-mode free volume model for diffusion of gas molecules in glassy polymers

The development of a new model for the diffusion of gas molecules in glassy polymers is presented which utilizes concepts from free volume theory and relies on a dual-mode interpretation of sorptive dilation in glassy polymers. Three assumptions are made in the development of the model. First, the free volume available for molecular transport processes is taken as constant below the glass transition temperature. Second, two populations of gas molecules are assumed to exist—one which contributes to the maintenance of an iso-free volume state upon sorptive dilation and one which does not contribute owing to sorption into regions of unrelaxed volume. Third, the former population is assumed to be mobile while the latter is not. The resulting model predicts, at constant temperature, a diffusion coefficient that is independent of solute volume fraction. This is in contrast to the widely used dual-mode sorption model with partial immobilization for gas transport in glassy polymers which leads to a diffusion coefficient that is dependent on solute mole fraction through the molar gas concentration. The new model is used to interpret gas transport data from permeation experiments for carbon dioxide, methane, and ethylene in three polycarbonates. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 1737–1746, 1997