Congested molecules. Where is the steric repulsion? An analysis of the electron density by the method of interacting quantum atoms

The computed electron density of several congested saturated hydrocarbons and halogenated derivatives has been analyzed by the method of interacting quantum atoms (IQA). For all the molecules studied, the calculations show the existence of a bond path between the congested atoms and which, according to the Quantum Theory of Atoms in Molecules, indicates that there is a stabilizing interaction between these atoms. The bond path is found to exist up to interatomic distances well‐beyond the sum of the van der Waals radii. The IQA results indicate that steric hindrance is not a repulsive force between the congested atoms but that is the result of an increase in the intra‐atomic or self‐energy of the congested atoms. This increase in self‐energy is caused by the deformation of the atomic basin of the congested atoms. © 2013 Wiley Periodicals, Inc.     

Variational Monte Carlo calculations for some cations and anions of the first‐row atoms using explicitly correlated wave functions

The variational Monte Carlo method is applied to calculate ground‐state energies of some cations and anions of the first‐row atoms. Accurate values providing between 80 and 90% of the correlation energy are obtained. Explicitly correlated wave functions including up to 42 variational parameters are used. The nondynamic correlation due to the 2s ? 2p near degeneracy effect is included by using a multideterminant wave function. The variational free parameters have been fixed by minimizing the energy that has shown to be a more convenient functional than the variance of the local energy, which is the most commonly employed method in variational Monte Carlo calculations. The energies obtained improve previous works using similar wave functions. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/qua.10125     

Intermetallic Compounds and the Use of Atomic Radii in Their Description

Metallic radii, which are obtained from atomic distances in the pure elements, are generally used for the calculation of distances in intermetallic compounds. However, the procedure for using such radii depends on the individual structural type: (a) For high coordination numbers and only slightly differing distances between atoms of the same kind and different atoms, all distances in a structure are proportional to the sum of radii, weighted according to the compositon. Such a “Vegard” relationship for ordered compounds is obeyed by intermetallic compounds with topological close packings, but strictly only if the various kinds of distances are correlated via symmetry relationships. For compounds with low coordination numbers the simple sum of radii holds for atoms participating in the shortest bond (e.g. in ionic crystals).-(b) The number of neighbors determines the size of each atom. It can be shown that the bond strength-bond length concept, developed for valence compounds, and often dealt with in the literature over the last ten years, is also applicable for alloys. On this basis a formalism is developed which uniformly describes the size of the atoms as a function of the coordination number for both the limiting cases of multiple bonds in molecules and for close packed atomic arrangements in alloys.     

Theoretical study of atoms by the electronic kinetic energy density and stress tensor density

The electronic structure of atoms in the first, second, and third periods were analyzed using the electronic kinetic energy density and stress tensor density, which are local quantities motivated by quantum field theoretic consideration, specifically the rigged quantum electrodynamics. The zero surfaces of the electronic kinetic energy density, which are called as the electronic interfaces, of the atoms were computed. It was found that their sizes exhibited clear periodicity and were comparable to the conventional atomic and ionic radii. The electronic stress tensor density and its divergence, tension density, of the atoms, were also computed and how their electronic structures were characterized by them was discussed. © 2016 Wiley Periodicals, Inc.     

The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method

We present a model to calculate the free energies of solvation of small organic compounds as well as large biomolecules. This model is based on a generalized Born (GB) model and a self-consistent charge-density functional theory-based tight-binding (SCC-DFTB) method with the nonelectrostatic contributions to the free energy of solvation modeled in terms of solvent-accessible surface areas (SA). The parametrization of the SCC-DFTB/GBSA model has been based on 60 neutral and six ionic molecules composed of H, C, N, O, and S, and spanning a wide range of chemical groups. Effective atomic radii as parameters have been obtained through Monte Carlo Simulated Annealing optimization in the parameter space to minimize the differences between the calculated and experimental free energies of solvation. The standard error in the free energies of solvation calculated by the final model is 1.11 kcal mol(-1). We also calculated the free energies of solvation for these molecules using a conductor-like screening model (COSMO) in combination with different levels of theory (AM1, SCC-DFTB, and B3LYP/6-31G*) and compared the results with SCC-DFTB/GBSA. To assess the efficiency of our model for large biomolecules, we calculated the free energy of solvation for a HIV protease-inhibitor complex containing 3,204 atoms using the SCC-DFTB/GBSA and the SCC-DFTB/COSMO models, separately. The computed relative free energies of solvation are comparable, while the SCC-DFTB/GBSA model is three to four times more efficient, in terms of computational cost.     

Cooperativity and Anticooperativity in Ion-Water Interactions: Implications for the Aqueous Solvation of Ions

Non-additive effects in hydrogen bonds (HB) take place as a consequence of electronic charge transfers. Therefore, it is natural to expect cooperativity and anticooperativity in ion-water interactions. Nevertheless, investigations on this matter are scarce. This paper addresses the interactions of (i) the cations Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ together with (ii) the anions F⁻, Cl⁻, Br⁻, NO₃⁻ and SO₄²⁻ with water clusters (H₂O)_n, n=1–8, and the effects of these ions on the HBs within the complete molecular adducts. We used quantum chemical topology tools, specifically the quantum theory of atoms in molecules and the interacting quantum atoms energy partition to investigate non-additive effects among the interactions studied herein. Our results show a decrease on the interaction energy between ions and the first neighbouring water molecules with an increment of the coordination number. We also found strong cooperative effects in the interplay between HBs and ion-dipole interactions within the studied systems. Such cooperativity affects considerably the interactions among ions with their first and second solvation shells in aqueous environments. Overall, we believe this article provides valuable information about how ion-dipole contacts interact with each other and how they relate to other interactions, such as HBs, in the framework of non-additive effects in aqueous media.     

New Born radii deriving method for Generalized Born model

Here we report a method to calculate Born radii, an important parameter used in a Generalized Born model. Traditional methods to derive Born radii are mostly based on a complicated formula, while our method is easier and more direct. Atoms are classified according to their atom type, and the Born radii of each type are obtained by fitting to experimental solvation free energy. The SMARTS language is used for the exact definition of atoms types, and Ullmann's subgraph isomorphism algorithm is used to deduce the environment. A generic algorithm is used for the parameter fitting because of its efficiency in searching a huge phase space, and its results are then optimized by using the conjugate gradient method. The final parameter set is fitting from a training set containing 357 molecules and is tested using a test set of 44 small organic molecules, and the average error is 0.58 kcal/mol for 36 neutral molecules and is 1.67 kcal/mol for 8 ions. The model is further tested under organic molecules, biopolymers, and a protein-inhibitor complex and yields reliable results in all these cases. This method can be used to accelerate molecular docking calculations.     

Molecular polarizability of organic compounds and their complexes: LIX. Molar volumes, intrinsic atomic solvation radii, and spatial structures of certain conformationally flexible compounds in solutions

The molar volumes and structures in individual liquids and solutions of a series of conformationally flexible compounds, such as alkanes and diaryl-substituted systems with sp ³-hybridized bridging atoms, were analyzed in terms of intrinsic solvation radii of atoms constituting the molecule. Intrinsic solvation atomic radii were determined for various molecules to show that they are larger than the van der Waals radii of the same atoms. An approach to parametrization of the intrinsic solvation radii of atoms constituting a molecule, using appropriate model compounds, was proposed. From the resulting values of intrinsic atomic solvation radii, the possible conformations of a series of diphenylmethanes, diphenylsilanes, diphenyl sulfides, diphenyl sulfoxides, and diphenyl sulfones in solutions were assessed.     

Design of a high-sensitivity negative ion source time-of-flight mass analyzer assembly created by cylindrical electrodes with a common axis

The new design incorporates the negative ion source and the mass analyzer, both constructed from cylindrical electrodes. The ion source is formed by three gridded cylindrical electrodes: a pulsed grid, the intermediate grid and the final accelerating grid. During a first time lapse, the electrons penetrate through the pulsed grid into the retarding field between this grid and the intermediate grid. The electrons are turning at some depth inside this intergrid space, where the attachment to neutral molecules most probably occurs. Next, the pulsed grid becoming strongly negative and ions are extracted towards the final acceleration grid. The ions from the cylindrical surface where they were created concentrate on the common axis of the electrodes (lateral focusing). The source lateral and time focus are coincident. A cylindrical electrostatic mirror is fitted to the source. The design, with a single stage, ensures also lateral focusing of the ions diverging from the common axis of the electrodes. The mirror electric and geometric parameters were selected to ensure both lateral and time focusing on the final detector with subsequent high luminosity. The basic parameters of the specific negative ion source time-of-flight mass analyzer design proposed here, are ion source final acceleration, intermediate, pulsed cylindrical grid radii 10, 20 and 30 mm, respectively, electrostatic mirror earthed grid and ion turning points surface radii 0.6 and 0.8 m, respectively. Ion packet smearing by the ion energy spread (resulting from the initial electron energy spread as electrons are turning at different depths inside the ionization region, from the moment when ions were created, being accelerated towards the pulsed grid during ionization) and by the turnaround time inside the cylindrical field was accounted for. Maintaining very high sensitivity, a resolution of the order of 100 is expected.     

Shannon information entropy of fractional occupation probability as an electron correlation measure in atoms and molecules

A new method to determine electron correlation energy is presented for atoms and molecules. This method is based on Shannon information entropy that is obtained by fractional occupation probabilities of natural atomic orbitals. It is indicated that the Shannon entropy increases as the number of electrons increases and thus can be considered as a possible measure for the electron correlation in atomic and molecular systems. For neutral atoms and singly charged positive ions we proposed an expression for correlation energy with explicit dependence on the Shannon entropy and atomic number. The obtained correlation energies have been used to compute the first ionization potentials of the ground state of the main group elements from hydrogen through krypton. The calculated ionization potentials are in reasonably good agreement with their corresponding experimental values.We also developed the additivity scheme to find a connection between Shannon entropy and molecular correlation energy. The estimated molecular correlation energies show an excellent agreement with those obtained by elaborate G3 method with R² = 0.990.     

Statistical models in the polarization radiation theory

The survey is devoted to general results for polarization free–free and free–bound radiative transitions in collisions of charged particles with heavy atoms and ions following from statistical atomic models. The atomic plasma model results for dynamic atomic polarizabilities are presented. Polarization Bremsstrahlung in collisions of fast and moderate energy electrons with Thomas–Fermi atoms is analyzed in details. A new polarization electron-heavy ions recombination channel is considered and compared with known radiative recombination channel. It is shown that recombination channels can be compared or even dominates over standards static radiation channels. Polarization radiation of fast multicharged ions in condensed media is also under consideration.     

Thermodynamic Parameters of the Formation of 3<Emphasis Type="Italic">d</Emphasis> Transition Metal Complexes as Model Systems for Description of Substrate-Receptor Interaction

The thermodynamic characteristics of the doubly charged ions of 3d metals with ligands containing oxygen, nitrogen, and fluorine donor atoms are analyzed. The complexing reactions are separated into three main groups on the basis of the changes in the enthalpy and entropy components of the Gibbs free energy. It was shown that the assignation of a reaction to a particular group is determined by the nature of the donor atoms in the ligands. The correlations between the enthalpy and entropy components of the Gibbs free energy and the atomic number of the 3d elements are studied.__________Translated from Teoreticheskaya i Eksperimental’naya Khimiya, Vol. 41, No. 2, pp. 88–93, March–April, 2005.     

HRTEM-EELS cross-sectional structural analyses of glassy carbon substrate irradiated by platinum ions using a coaxial arc plasma gun

A glassy carbon (GC) substrate was irradiated by Pt ions using a coaxial arc plasma gun in vacuum. The structure of the substrate was studied in the atomic scale using high-resolution transmission electron microscopy (HRTEM) and electron energy loss spectroscopy (EELS) with a thin foil specimen prepared by cross-sectioning using focused ion beam milling. HRTEM combined with the EELS measurements of the cross-sectioned sample indicated a disordering of the GC substrate surface and the detection of phenol-type species, carbon atoms in aliphatic chain molecules, and carboxyl groups, which are considered to have been formed by chemical reaction between the carbon atoms of the GC substrate surface and hydrogen or oxygen atoms. Penetrated Pt atoms were observed inside the GC substrate, and the surface position of the GC substrate was located from the depth profiles of the EELS spectra. STEM-EELS analyses of a pristine GC substrate without Pt ion irradiation were also conducted for reference.     

Incident angle and energy dependences of low‐energy Ar+ ion sputtering of GaAs/AlAs multilayered system

Dependences of the depth resolution in Auger electron spectroscopy sputter‐depth profiling of a GaAs/AlAs superlattice reference material on the incident angle and energy of primary Ar⁺ ions were investigated. The results revealed that the depth resolution is improved for the lower primary energy as a square root of the primary energy of ions at both the incident angles of 50° and 70° , except for 100 eV at 50° , where the significant deterioration of the depth resolution is induced by the preferential sputtering of As in AlAs, and the difference in the etching rate between GaAs and AlAs. The deterioration of the depth resolution, i.e. the difference in the etching rate and the preferential sputtering, observed for 100 eV at 50° was suppressed by changing the incident angle of ions from 50° to 70° , resulting in the high‐depth resolution of ～1.3 nm. The present results revealed that the glancing incidence of primary ions is effective to not only reducing the atomic mixing but also suppressing the difference in the etching rates between GaAs and AlAs and the preferential sputtering in the GaAs/AlAs multilayered system. The results also suggest that careful attention is required for the optimization of conditions of sputter‐depth profiling using GaAs/AlAs superlattice materials under low‐energy ion irradiation. Copyright © 2009 John Wiley & Sons, Ltd.     

Derivation of atomistic models for lattices consisting of weakly overlapping structural elements

A theoretical approach based on the arrow diagram technique within the group function theory is applied to an infinite crystal consisting of weakly overlapping structural elements (SE: ions, atoms, and molecules). A perturbation method is used to derive the lattice energy in terms of two‐body, three‐body, etc. types of interactions accompanied by electronic polarization of SEs for the system which is slightly away from some reference configuration. It is demonstrated how an atomistic model for the particular material can be derived from the general theory. A general approach to obtain a parametrization scheme is suggested which is based on a representation of transition and ground‐state reduced density matrices (RDM) of various orders via a finite set of basis functions. Using group theory and necessary conditions for N‐representability of the RDMs, the representation containing the least possible number of the fitting parameters is worked out. The method is illustrated on a special case of spherical SEs (e.g., atoms/ions in atomic/ionic solids) and it is discussed whether existing models are in accord with the ideas developed. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 306–330, 2000     

Atomic charges,dipole moments,and Fukui functions using the Hirshfeld partitioning of the electron density

In the Hirshfeld partitioning of the electron density, the molecular electron density is decomposed in atomic contributions, proportional to the weight of the isolated atom density in the promolecule density, constructed by superimposing the isolated atom electron densities placed on the positions the atoms have in the molecule. A maximal conservation of the information of the isolated atoms in the atoms-in-molecules is thereby secured. Atomic charges, atomic dipole moments, and Fukui functions resulting from the Hirshfeld partitioning of the electron density are computed for a large series of molecules. In a representative set of organic and hypervalent molecules, they are compared with other commonly used population analysis methods. The expected bond polarities are recovered, but the charges are much smaller compared to other methods. Condensed Fukui functions for a large number of molecules, undergoing an electrophilic or a nucleophilic attack, are computed and compared with the HOMO and LUMO densities, integrated over the Hirshfeld atoms in molecules.     

Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules

The aqueous solvation free energies of ionized molecules were computed using a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1, MNDO, and PM3 semiempirical molecular orbital methods for the solute molecule and the TIP3P molecular mechanics model for liquid water. The present work is an extension of our model for neutral solutes where we assumed that the total free energy is the sum of components derived from the electrostatic/polarization terms in the Hamiltonian plus an empirical “nonpolar” term. The electrostatic/polarization contributions to the solvation free energies were computed using molecular dynamics (MD) simulation and thermodynamic integration techniques, while the nonpolar contributions were taken from the literature. The contribution to the electrostatic/polarization component of the free energy due to nonbonded interactions outside the cutoff radii used in the MD simulations was approximated by a Born solvation term. The experimental free energies were reproduced satisfactorily using variational parameters from the vdW terms as in the original model, in addition to a parameter from the one-electron integral terms. The new one-electron parameter was required to account for the short-range effects of overlapping atomic charge densities. The radial distribution functions obtained from the MD simulations showed the expected H-bonded structures between the ionized solute molecule and solvent molecules. We also obtained satisfactory results by neglecting both the empirical nonpolar term and the electronic polarization of the solute, i.e., by implementing a nonpolarization model. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1028–1038, 1999     

Cavitation free energy for organic molecules having various sizes and shapes

Cavitation free energy DeltaG(cav), corresponding to the formation of an excluded volume cavity in water, is calculated for a large set of organic molecules employing the thermodynamic integration procedure, which is realized as the original two-step algorithm for growing the interaction potential between the hard cavity wall and the water molecules. A large variety of solute systems is considered. Their characteristic radii change in the range 3-7 A; spherical cavities with radii 3-6 A are also studied. The interaction between water molecules is described by the four-site nonpolarizable TIP4P model. The diversity of the trial molecular set is provided by using a specially formulated nonspherical criterion classifying the cavity shapes according to their deviation from a sphere. Molecular objects were partly taken from the data base NCI Diversity with the aid of this criterion. The so-computed free energies are approximated by the linear volume dependence DeltaG(cav)V = XiV, where V is the cavity volume. This relation works fairly well until the cavity size becomes very large (the effective radius larger than 7 A). The volume dependence valid for solutes of arbitrary shapes can be included in a calculation of the nonpolar free energy component as required in the implicit water model.