New evaluation of reconstructed spatial distribution function from radial distribution functions

Although three dimensional (3D) solvation structure is much more informative than one dimensional structure, its evaluation is difficult experimentally and theoretically. In our previous Communication [Yokogawa et al., J. Chem. Phys. 123, 211102 (2005)], we proposed a new method to present reconstructed spatial distribution function (RC-SDF) from a set of radial distribution functions (RDFs). In this article, we successfully extended the method more accurately with new basis sets. This new method was applied to two liquid solvation structures, methanol and dimethyl sulfoxide, as examples. Their RC-SDFs evaluated here clearly show that the former solvation structure is well defined while the latter one is broad, which agrees well with the SDFs calculated directly from molecular dynamics simulations. These results indicate that the method can reproduce well these 3D solvation structures in reasonable computational cost.     

The molecular structure of some amorphous organogold compounds studied by the radial distribution function method

The method of radial distribution functions (RDF) of atoms obtained from powder X-ray diffraction patterns has been applied to the determination of the molecular structure of a number of polynuclear organogold derivatives in the form of amorphous powders. The distances between Au atoms producing the strongest peaks on RDF have been measured directly. The modes of addition of (AuPPh₃)⁺ cation to aurated phenylacetylene, acetonitrile and diaurated malonitrile and the presence of binuclear groupings (AuPPh₃)₂ with a direct AuAu bond, connected with cyclopentadienyl rings in tetragold derivatives of ferrocene, have been found.     

A new quantum method for electrostatic solvation energy of protein

A new method that incorporates the conductorlike polarizable continuum model (CPCM) with the recently developed molecular fractionation with conjugate caps (MFCC) approach is developed for ab initio calculation of electrostatic solvation energy of protein. The application of the MFCC method makes it practical to apply CPCM to calculate electrostatic solvation energy of protein or other macromolecules in solution. In this MFCC-CPCM method, calculation of protein solvation is divided into calculations of individual solvation energies of fragments (residues) embedded in a common cavity defined with respect to the entire protein. Besides computational efficiency, the current approach also provides additional information about contribution to protein solvation from specific fragments. Numerical studies are carried out to calculate solvation energies for a variety of peptides including alpha helices and beta sheets. Excellent agreement between the MFCC-CPCM result and those from the standard full system CPCM calculation is obtained. Finally, the MFCC-CPCM calculation is applied to several real proteins and the results are compared to classical molecular mechanics Poisson-Boltzmann (MM/PB) and quantum Divid-and-Conque Poisson-Boltzmann (D&C-PB) calculations. Large wave function distortion energy (solute polarization energy) is obtained from the quantum calculation which is missing in the classical calculation. The present study demonstrates that the MFCC-CPCM method is readily applicable to studying solvation of proteins.     

Investigation of the local structure of nanosized CdS crystals stabilized with glutathione by the radial distribution function method

For stabilized nanoparticles of cadmium sulfide, a highly resolved radial distribution function was derived from the dispersion curve of synchrotron radiation ( = 0.08824 Å). The nanoparticle core has dimensions of 15 Å–20 Å and consists of Cd and S atoms in a 1:1 ratio. In the inner part of the nanoparticle, these atoms have a random tetrahedral coordination similar to that in crystalline CdS. Half of all core S atoms belong to the ligands and are coordinated by the surface Cd atoms. In contrast to the inner S atoms, these S atoms each binds two or three Cd atoms, forming a CdSCd bond angle of 100°, which is smaller than the tetrahedral angle. The Cd-S bond lengths are similar for both types of sulfur and vary within 2.52 Å–2.53 Å. The spatial arrangement of the Cd and S atoms beyond the first coordination sphere is significantly different from that of bulk CdS, which may be caused by perturbations induced by the surface S atoms.Original Russian Text Copyright © 2004 by V. I. Korsunskii, R. Neder, K. Hradil, J. Neuefeind, K. Barglik-Chory, and G. MüllerTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 3, pp. 452–461, May–June 2004.     

A new formulation of the PCM solvation method: PCM-QINTn

A new formulation of the PCM electrostatic solution problem is proposed. Through a new derivation of the PCM-CLSn expression we propose an interpolation formula that improved the convergence: PCM-QINTn. All the available formulations are applied to the evaluation of the electrostatic component of the free energy of solvation for some molecular systems. In addition, PCM-QINT derivatives of G _el with respect to atomic coordinates are evaluated. The computational costs are compared with those of PCM-direct formulation. Received: 21 October 1996 / Accepted: 7 January 1997     

Electron microtomography: A new method for studying the spatial structure of catalysts

The spatial arrangement of active component (Pt) particles on the surface of a support (Sibunit globule) has been studied by bright-field electron tomography. A tomographic attachment for a standard specimen holder and tomographic grids have been designed. The tomographic procedure has been refined, and adequate tilt series alignment and tomographic reconstruction algorithms have been chosen. The 3D distribution of the active component in the catalyst grain has been studied: particles hidden in micropores have been directly observed, and the size of the pores connecting internal cavities with the exterior has been estimated.     

New generation of the reference interaction site model self-consistent field method: introduction of spatial electron density distribution to the solvation theory

The authors propose the new generation of the reference interaction site model self-consistent field (RISM-SCF) method for the solvation effect on the electronic structure of a solute molecule, in which the procedure proposed by Gill et al. [J. Chem. Phys. 96, 7178 (1992)] is adopted. Main improvements are the introduction of spatial electron density distribution and the removal of the grid dependency that is inherent in the original RISM-SCF. The procedure also provides very stable determination of the effective charges even if a buried atom exists in the target molecule and eventually extends the applicability of the RISM-SCF. To demonstrate the superiority of our method, sample calculations for H2O, C2H5OH, and HLi in aqueous solution are presented.     

A new angle on heat capacity changes in hydrophobic solvation

The differential solubility of polar and apolar groups in water is important for the self-assembly of globular proteins, lipid membranes, nucleic acids, and other specific biological structures through hydrophobic and hydrophilic effects. The increase in water's heat capacity upon hydration of apolar compounds is one signature of the hydrophobic effect and differentiates it from the hydration of polar compounds, which cause a decrease in heat capacity. Water structuring around apolar and polar groups is an important factor in their differential solubility and heat capacity effects. Here, it is shown that joint radial/angular distribution functions of water obtained from simulations reveal quite different hydration structures around polar and apolar groups: polar and apolar groups have a deficit or excess, respectively, of "low angle hydrogen bonds". Low angle hydrogen bonds have a larger energy fluctuation than high angle bonds, and analysis of these differences provides a physical reason for the opposite changes in heat capacity and new insight into water structure around solutes and the hydrophobic effect.     

A RISM approach to the liquid structure and solvation properties of ionic liquids

We test for the first time the performance of the reference interaction site model (RISM) to predict the liquid structure and solvation of room-temperature ionic liquids (RTILs) represented with different degrees of accuracy. The model gives satisfactory results, proposing itself as a possible method to explore and to describe at a chemically realistic level the solvation shell in ionic liquids, which is believed to play a fundamental role in the static electronic and vibrational properties of these systems.     

From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins

An improved scheme to help in the prediction of protein structure is presented. This procedure generates improved starting conformations of a protein suitable for energy minimization. Trivariate gaussian distribution functions for the π, ψ, and χ¹ dihedral angles have been derived, using conformational data from high resolution protein structures selected from the Protein Data Bank (PDB). These trivariate probability functions generate initial values for the π, ψ, and χ¹ dihedral angles which reflect the experimental values found in the PDB. These starting structures speed the search of the conformational space by focusing the search mainly in the regions of native proteins. The efficiency of the new trivariate probability distributions is demonstrated by comparing the results for the α-class polypeptide fragment, the mutant Antennapedia (C39 → S) homeodomain (2HOA), with those from two reference probability functions. The first reference probability function is a uniform or flat probability function and the second is a bivariate probability function for π and ψ. The trivariate gaussian probability functions are shown to search the conformational space more efficiently than the other two probability functions. The trivariate gaussian probability functions are also tested on the binding domain of Streptococcal protein G (2GB1), an α/β class protein. Since presently available energy functions are not accurate enough to identify the most native-like energy-minimized structures, three selection criteria were used to identify a native-like structure with a 1.90-Å rmsd from the NMR structure as the best structure for the Antennapedia fragment. Each individual selection criterion (ECEPP/3 energy, ECEPP/3 energy-plus-free energy of hydration, or a knowledge-based mean field method) was unable to identify a native-like structure, but simultaneous application of more than one selection criterion resulted in a successful identification of a native-like structure for the Antennapedia fragment. In addition to these tests, structure predictions are made for the Antennapedia polypeptide, using a Pattern Recognition-based Importance-Sampling Minimization (PRISM) procedure to predict the backbone conformational state of the mutant Antennapedia homeodomain. The ten most probable backbone conformational state predictions were used with the trivariate and bivariate gaussian dihedral angle probability distributions to generate starting structures (i.e., dihedral angles) suitable for energy minimization. The final energy-minimized structures show that neither the trivariate nor the bivariate gaussian probability distributions are able to overcome the inaccuracies in the backbone conformational state predictions to produce a native-like structure. Until highly accurate predictions of the backbone conformational states become available, application of these dihedral angle probability distributions must be limited to problems, such as homology modeling, in which only a limited portion of the backbone (e.g., surface loops) must be explored. © 1996 John Wiley & Sons, Inc.     

Ar solvation shells in K(+)-HFBz: from cluster rearrangement to solvation dynamics

The effect of some leading intermolecular interaction components on specific features of weakly bound clusters involving an aromatic molecule, a closed shell ion, and Ar atoms is analyzed by performing molecular dynamics simulations on potential energy surfaces properly formulated in a consistent way. In particular, our investigation focuses on the three-dimensional Ar distributions around the K(+)-hexafluorobenzene (K(+)-HFBz) dimer, in K(+)-HFBz-Ar(n) aggregates (n ≤ 15), and on the gradual evolution from cluster rearrangement to solvation dynamics when ensembles of 50, 100, 200, and 500 Ar atoms are taken into account. Results indicate that the Ar atoms compete to be placed in such a way to favor an attractive interaction with both K(+) and HFBz, occupying positions above and below the aromatic plane but close to the cation. When these positions are already occupied, the Ar atoms tend to be placed behind the cation, at larger distances from the center of mass of HFBz. Accordingly, three different groups of Ar atoms are observed when increasing n, with two of them surrounding K(+), thus, disrupting the K(+)-HFBz equilibrium geometry and favoring the dissociation of the solvated cation when the temperature increases. The selective role of the leading intermolecular interaction components directly depending on the ion size repulsion is discussed in detail by analyzing similarities and differences on the behavior of the Ar-solvated K(+)-HFBz and Cl(-)-Bz aggregates.     

Theory and calculations of second-order anharmonic corrections to the radial distribution function of polyatomic molecules

A theory of the thermal averages of normal coordinates was suggested for polyatomic molecules. Second-order approximation equations were obtained on the basis of iterations of the Bloch integral equation. These equations can be used to calculate anharmonic corrections to the radial distribution function and the parameters that determine the intensity of fast electron scattering by molecules in gas-phase electron diffraction.     

Metallosupramolecular squares: from structure to function

Metallosupramolecular squares have been successfully evolved over the past years as versatile substitutes of the conventional organic macrocycles owing to the development of reliable synthetic protocols and abundant structural variability (metals and ligands). In this review we have presented the fundamental aspects of metallosupramolecular squares such as the strategies for their construction (self-assembly vs. kinetically controlled macrocyclization) and characterization. The major emphasis of this tutorial review lies on the function of metallosupramolecular squares. Thus, the introduction of functionality into these systems has been discussed in detail by highlighting the recent progress toward application in various fields, including molecular recognition, enantioselective sensing, photoluminescence, redox activity and electrochemical sensing, and homogeneous catalysis.     

Difference spatial distribution function analysis of aqueous solutions. IV. Hydration structure changes of ethylene glycol solutions throughout conformational change process from gGg' to tGg' conformers

Monte Carlo (MC) simulations were carried out for an infinitely dilute aqueous solution of two stable conformers (gGg' and tGg') and of three conformations between gGg' and tGg' conformers of ethylene glycol (EG) at 298K. Based on the spatial distribution function (SDF) goo(x,y,z), obtained from the MC simulation in the above conformations in liquid water, the high distribution of hydration water molecules could be divided into hydrogen acceptor (HA), hydrogen donor (HD), MIX (overlapped distribution of HA and HD), and hydrophobic hydration (HH) regions. The spatial orientations of hydrogen-bonded water molecules were found to be of a linear type with a triple-layer structure in the HA region and HA part (in the MIX region), and double-layer structures in the HD region and HD part (in the MIX region). In addition, it was apparent that the spatial orientations of these water molecules were of the linear type throughout the conformational change process from gGg' to tGg' conformers in liquid water. From the difference SDF (DSDF), deltagoo(x,y, z), between the SDFs of two conformations, we concluded that the distribution of hydration water molecules in the HA and HD parts of the MIX region are governed by the competition of internal hydrogen bonds between the hydrogen atom and two lone-pair electrons on the oxygen atom of an EG molecule.     

A new method to evaluate force constants from experimental spectral data

An iterative procedure is proposed to facilitate the determination of molecular vi-brational force constants from the experimental fundamental frequencies. Proper restrictions are introduced to the force constants based on physical considerations for getting reasonable results. The experimental data of Coriolis coupling coefficients and isotopic frequency shifts are utilized to reduce the uncertainty of the calculated force constants when they are available. A series of various kinds of molecules have been calculated by this method and the results are satisfactory.