Covalent bond orders and atomic anisotropies from iterated stockholder atoms

Iterated stockholder atoms are produced by dividing molecular electron densities into sums of overlapping, near-spherical atomic densities. It is shown that there exists a good correlation between the overlap of the densities of two atoms and the order of the covalent bond between the atoms (as given by simple valence rules). Furthermore, iterated stockholder atoms minimise a functional of the charge density, and this functional can be expressed as a sum of atomic contributions, which are related to the deviation of the atomic densities from spherical symmetry. Since iterated stockholder atoms can be obtained uniquely from the electron density, this work gives an orbital-free method for predicting bond orders and atomic anisotropies from experimental or theoretical charge density data.     

A possible construction of a complex chemical reaction network

A procedure is suggested for the construction of chemical reaction networks. We define the kinetic communication as a transfer of atoms or atomic groups between two species and determine all the kinetic communications occurring in the possible mechanism of a complex chemical process. The set of kinetic communications is the basis of the communication matrices resulting in the complete network of the overall reaction.Limiting the consideration for certain types of kinetic communications we obtain the reaction subnetworks and selecting arbitrarily species among those participating in the possible mechanism we introduced the concept of the partial subnetworks which correspond to subsets of the complete network.By the simple analysis of the subnetworks it is easy to obtain the sequence network indicating the pathways via which the selected species are formed in the course of the overall process, by the transfer of chosen atoms or atomic groups.     

Subshell fitting of relativistic atomic core electron densities for use in QTAIM analyses of ECP-based wave functions

Scalar-relativistic, all-electron density functional theory (DFT) calculations were done for free, neutral atoms of all elements of the periodic table using the universal Gaussian basis set. Each core, closed-subshell contribution to a total atomic electron density distribution was separately fitted to a spherical electron density function: a linear combination of s-type Gaussian functions. The resulting core subshell electron densities are useful for systematically and compactly approximating total core electron densities of atoms in molecules, for any atomic core defined in terms of closed subshells. When used to augment the electron density from a wave function based on a calculation using effective core potentials (ECPs) in the Hamiltonian, the atomic core electron densities are sufficient to restore the otherwise-absent electron density maxima at the nuclear positions and eliminate spurious critical points in the neighborhood of the atom, thus enabling quantum theory of atoms in molecules (QTAIM) analyses to be done in the neighborhoods of atoms for which ECPs were used. Comparison of results from QTAIM analyses with all-electron, relativistic and nonrelativistic molecular wave functions validates the use of the atomic core electron densities for augmenting electron densities from ECP-based wave functions. For an atom in a molecule for which a small-core or medium-core ECPs is used, simply representing the core using a simplistic, tightly localized electron density function is actually sufficient to obtain a correct electron density topology and perform QTAIM analyses to obtain at least semiquantitatively meaningful results, but this is often not true when a large-core ECP is used. Comparison of QTAIM results from augmenting ECP-based molecular wave functions with the realistic atomic core electron densities presented here versus augmenting with the limiting case of tight core densities may be useful for diagnosing the reliability of large-core ECP models in particular cases. For molecules containing atoms of any elements of the periodic table, the production of extended wave function files that include the appropriate atomic core densities for ECP-based calculations, and the use of these wave functions for QTAIM analyses, has been automated.     

Controlling crystallization and its absence: proteins, colloids and patchy models

The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and technological importance. Much can be learnt from the exquisite control that biological systems exert over the behaviour of proteins, where protein crystallization and aggregation are generally suppressed, but where in particular instances complex crystalline assemblies can be formed that have a functional purpose. We also explore the insights that can be obtained from computational modelling, focussing on the subtle interplay between the interparticle interactions, the preferred local order and the resulting crystallization kinetics. In particular, we highlight the role played by "frustration", where there is an incompatibility between the preferred local order and the global crystalline order, using examples from atomic glass formers and model anisotropic particles.     

ESCA investigations on pyrolytic carbon films for fiber coatings

Photoelectron spectroscopy on pyrolytic carbon films revealed a main part of carbon atoms in graphitic planes and a smaller part of functional groups with oxygen bonded to carbon atoms. Oxygen totalled a share of 10 at% and more of the carbon coating. The films with a turbostratic structure consist of nearly parallel oriented atomic layers of hexagonal rings with dimensions in the nanometer scale, which is well known from HREM investigations. The oxygen atoms are proposed to saturate the numerous dangling bonds around these individual atomic planes. The oxygen atoms form double bonds or bridges between carbon atoms. Received: 15 July 1998 / Revised: 28 January 1998 / Accepted: 2 February 1998     

Measuring electron sharing between atoms in first-principle simulations

Calculations of large scale electronic structure within periodic boundary conditions, mostly based on solid state physics, allow the modeling of atomic forces and molecular dynamics for atomic assemblies of 100–1000 atoms, thus providing complementary information in material and macromolecular sciences. Nevertheless, these methods lack connections with the chemistry of simple molecules as isolated entities. In order to contribute to establish a conceptual connection between solid state physics and chemistry, the calculation of the extent of electron sharing between atoms, also known as delocalization index, is performed on simple molecules and on complexes with transition metal atoms, using density functional calculations where the Kohn–Sham molecular orbitals are represented in terms of plane waves and in periodic boundary conditions. These applications show that the useful measure of electron sharing between atomic pairs can be recovered from density functional calculations using the same set-up applied to large atomic assemblies in condensed phases, with no projections of molecular orbitals onto atomic orbitals.     

基于电负性均衡理论快速计算多肽分子中原子电荷的新方法

Atomic charges play a crucial role in the understanding and modeling of the chemical behavior of proteins. Fast assessment of atomic charge distributions in larger molecules can be performed by implementing the electronegativity equalization method (EEM). To further improve the accuracy of the EEM approach, a novel and efficient method based on Bader's concept of high degree fragment transferability of atomic charges has been proposed for the parameterization of atoms-in-molecules (AIM) charges of polypeptides or proteins. The EEM parameterization method considers both the factors of connectivity and hybridized states, and the effect of the local chemical environment in fragments or groups. The types of atoms were defined on the basis of the local chemical environments of the fragments or functional groups of these atoms. The fragment transferability feature of QTAIM indicates that the atomic properties for the contributing atoms can be reproduced if the chemical environment is comparable. The constituent fragments or functional groups of macromolecules such as polypeptides and proteins can be utilized as building blocks for the additive generation of their electronic densities. The main peptide group (NH―HαCα―C＝O) of the polypeptide in the backbone was used as a building block to model the EEM parameters for reproducing the atomic charges in the polypeptides. A training set of 20 terminally blocked amino acids (Ac-X-NHMe, X = any neutral residue), which recreated the immediate local environment of the main chain fragments or functional groups of the polypeptides, were chosen for the calibration of AIM charges using the differential evolution (DE) algorithm. The effects of the optimized methods on the results were discussed and it was found that the DE algorithm showed a better performance for the objective function. The quality of the AIM charges obtained from the EEM method presented in this study was evaluated by comparison with those obtained from B3LYP/6-31G+(d, p) calculations for the two test tetrapeptides not contained in the training set. It was found that a remarkable improvement was achieved using the EEM model developed in this study as compared to the previous studies. The introduction of Bader's high fragment charge transfer model into the EEM provided a new scheme for its calibration and parameterization for larger systems such as polypeptides or polynucleotides, which possess highly repetitive segments. Among all types of atomic charges, only the AIM charges showed a significant meaning in experiments and could be obtained by X-ray diffraction experiments. Rapidly reproducing the accurate AIM charge for large systems seems to be more meaningful, especially for the prediction of protein-protein, protein-DNA, and drug-receptor recognition and interactions.     

Modelling of substitutional defects in the structure of Ti-bearing hibonite

A local atomic structure around titanium positions in Ti-bearing hibonite (CaAl₁₂O₁₉) has been studied. The structural models of substitution of different substitution defects Ti–Al in hibonite by titanium atoms have been considered. Optimization of structural models of hibonite has been done by means of density functional theory calculations using pseudopotential approximation as implemented in VASP 5.3 code. Gibbs free energies analysis has shown that models of substitution of M2 and M4 aluminum positions by titanium atoms are the most probable. For the most probable structural models of Ti-bearing hibonite theoretical X-ray absorption near-edge structure (XANES) spectra near the titanium K edge have been calculated. Significant differences in theoretical XANES spectra calculated for different structural models with non-optimized and optimized atomic structure have been demonstrated. Changes in the intensity of pre-edge structure of TiK XANES spectra for different substitution models of aluminum by titanium have been observed which relate to different titanium coordination in structural models. Energy shift of spectral features towards lower energy for optimized models implies increase of interatomic distances in local surroundings of Ti absorbing atoms.     

Designed Precursor for the Controlled Synthesis of Highly Active Atomic and Sub‐nanometric Platinum Catalysts on Mesoporous Silica

The development of new methods to synthesize nanometric metal catalysts has always been an important and prerequisite step in advanced catalysis. Herein, we design a stable nitrogen ligated Pt complex for the straightforward synthesis by carbonization of uniformly sized atomic and sub‐nanometric Pt catalysts supported on mesoporous silica. During the carbonization of the Pt precursor into active Pt species, the nitrogen‐containing ligand directed the decomposition in a controlled fashion to maintain uniform sizes of the Pt species. The nitrogen ligand had a key role to stabilize the single Pt atoms on a weak anchoring support like silica. The Pt catalysts exhibited remarkable activities in the hydrogenation of common organic functional groups with turnover frequencies higher than in previous studies. By a simple post‐synthetic treatment, we could selectively remove the Pt nanoparticles to obtain a mixture of single atoms and nanoclusters, extending the applicability of the present method.     

Investigation of formation mechanism of Pt(111) nanoparticle layers grown on Ru(0001) core

A layer growth mechanism of Pt-Ru bimetallic nanoparticles has been proposed with supporting experiments and calculations by density functional theory (DFT). Elongated Pt atoms on Ru nanoparticles were synthesized via a two-step route, and their structural details were obtained by high-resolution transmission electron microscopy. Because of the intrinsic mismatch of lattice spacing between the two elements, such an unusual growth was analyzed with the DFT simulations to explore the mystery of the growth mechanism. Pt atoms would rearrange the packing order and adjust the Pt-Pt atomic distance, and so do the Ru nanoparticles in order to achieve the optimal energy status of the bimetallic system. The resultant Pt(111) layers could stack on top of the Ru(0001) core more tightly by fitting the pockets left between the Ru atoms. The findings give insight into the formation mechanism of the nanosized Pt-Ru bimetallic catalyst and pave the way for designing bimetallic catalysts with tailored properties at the atomic level.     

Atomic volumes and polarizabilities in density-functional theory

Becke and Johnson introduced an ad hoc definition of atomic volume [J. Chem. Phys. 124, 014204 (2006)] in order to obtain atom-in-molecule polarizabilities from free-atom polarizabilities in their nonempirical exchange-hole dipole moment model of dispersion interactions. Here we explore the dependence of Becke-Johnson atomic volumes on basis sets and density-functional approximations and provide reference data for all atoms H-Lr. A persuasive theoretical foundation for the Becke-Johnson definition is also provided.     

Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations

This work explores a new charge-dependent energy model consisting of van der Waals and polarization interactions between the quantum mechanical (QM) and molecular mechanical (MM) regions in a combined QMMM calculation. van der Waals interactions are commonly treated using empirical Lennard-Jones potentials, whose parameters are often chosen based on the QM atom type (e.g., based on hybridization or specific covalent bonding environment). This strategy for determination of QMMM nonbonding interactions becomes tedious to parametrize and lacks robust transferability. Problems occur in the study of chemical reactions where the "atom type" is a complex function of the reaction coordinate. This is particularly problematic for reactions, where atoms or localized functional groups undergo changes in charge state and hybridization. In the present work we propose a new model for nonelectrostatic nonbonded interactions in QMMM calculations that overcomes many of these problems. The model is based on a scaled overlap model for repulsive exchange and attractive dispersion interactions that is a function of atomic charge. The model is chemically significant since it properly correlates atomic size, softness, polarizability, and dispersion terms with minimal one-body parameters that are functions of the atomic charge. Tests of the model are examined for rare-gas interactions with neutral and charged atoms in order to demonstrate improved transferability. The present work provides a new framework for modeling QMMM interactions with improved accuracy and transferability.     

Adsorption and diffusion on a stepped surface: atomic hydrogen on Pt(211)

We present density functional theory calculations for atomic hydrogen interacting with a stepped surface, the Pt(211) surface. The calculations have been performed at the generalized gradient approximation level, using a slab representation of the surface. This is the state-of-the-art method for calculating the interaction of atoms or molecules with metal surfaces, nevertheless only few studies have used it to study atoms or molecules interacting with stepped surfaces, and none, to the best of our knowledge, have considered hydrogen interacting with stepped platinum surfaces. Our goal has been to initiate a systematic study of this topic. We have calculated the full three-dimensional potential energy surface (PES) for the H/Pt(211) system together with the vibrational band structure and vibrational eigenfunctions of H. A deep global minimum of the PES is found for bridge-bonded hydrogen on the step edge, in agreement with experimental results for the similar H/Pt(533) system. All the local vibrational excitations at the global minimum have been identified, and this will serve as a helpful guide to the interpretation of future experiments on this (or similar) system(s). Furthermore, from the calculated PES and vibrational band structure, we identify a number of consequences for the interpretation or modelling of diffusion experiments studying the coverage and directional dependence of atomic hydrogen diffusion on stepped platinum surfaces.     

On the degeneracy of atomic states within exact-exchange (spin-) density functional theory

The problem of degenerate ground states of open-shell atoms is investigated in spin-restricted and spin-unrestricted density functional theories using the exact-exchange energy functional. For the spin-unrestricted case, spurious energy splittings of the order of 2-3 kcal/mol are found for atoms of the second and third periods which are larger than the splittings obtained from recently proposed approximate exchange functionals depending explicitly on the current density. In remarkable contrast, for spin-restricted calculations the degeneracy of different atomic ground states is recovered to within less than 0.6 kcal/mol.     

The role of the medium in electrochemical functionalization and dispersion of carbon nanotubes

An electrochemical method for dispersion of single-walled carbon nanotubes (SWNTs) is described. The technique is based on grafting of oxygen-containing functional groups to the nanotube surface during electrolysis in aqueous and nonaqueous potassium bromide solutions. A dependence of the degree of functionalization of nanotubes on the solvent was revealed experimentally. Nanotubes treated in DMSO have about 14 carbon atoms per oxygen atom from functional groups (cf. nearly four C atoms per oxygen atom in the nanotubes treated in aqueous solutions). The corresponding maximum specific capacities of the electrodes are nearly 10 and 60 F g⁻¹. The samples treated in solutions of KBr in DMSO have about 300 carbon atoms per bromine atom on the nanotube surface (cf. only 30 carbon atoms in the samples treated in aqueous solution). A mechanism of electrochemical modification of SWNTs is proposed. Its key step is production of atomic oxygen that oxidizes the nanotube surface with the formation of functional groups.     

Analysis of the atomic structure of colloidal quantum dots of the CdSe family: X-ray spectral diagnostics and computer modelling

Colloidal quantum dots of the CdSe family have been studied by X-ray absorption near edge structure (XANES) spectroscopy and computer modelling. CdK edge XANES spectra in colloidal quantum dots based on varisized CdSe nanoparticles have been recorded. Atomic structure of CdSe particles and also CdSe particles doped by transition metal atoms Mn and Co has been modelled based on the density functional theory. The embedding of the doping atoms is shown to result in considerable changes in the local atomic structure of CdSe particles. XANES spectra have been calculated above the CdK edge in CdSe particles, above the MnK edge in CdSe:Mn particles, above the CoK edge in CdSe:Co particles. The sensitivity of XANES spectroscopy to small changes in structural parameters of the nanoparticles of CdSe family has been demonstrated that furnishes an opportunity to apply it for the verification of atomic structure parameters around positions of cadmium and doping atoms of transition metals in quantum dots based on CdSe.     

Electrophilicity kernel and its hierarchy through softness in conceptual density functional theory

In the context of long‐range density functional theory of softness kernel, the concepts of local and kernel electrophilicity are developed to obtain the local to global hierarchical criteria such as bilocal symmetry, asymptotic behavior, and integral local to global relationships. Further development into potential‐density dependence is also provided while considering the local plus nonlocal specification of softness kernel and the associated atomic scales for the derived kernel; local and global electrophilicity are provided whose reliability is judged through the periodical features along the periodic table especially for the alkali metal atoms and the halogen atoms. © 2013 Wiley Periodicals, Inc.     

Charge-dependent cavity radii for an accurate dielectric continuum model of solvation with emphasis on ions: aqueous solutes with oxo, hydroxo, amino, methyl, chloro, bromo, and fluoro functionalities

Dielectric continuum solvation models are widely used because they are a computationally efficacious way to simulate equilibrium properties of solutes. With advances that allow for molecular-shaped cavities, they have reached a high level of accuracy, in particular for neutral solutes. However, benchmark tests show that existing schemes for defining cavities are unable to consistently predict accurately the effects of solvation on ions, especially anions. This work involves the further development of a protocol put forth earlier for defining the cavities of aqueous solutes, with resulting advances that are most striking for anions. Molecular cavities are defined as interlocked spheres around atoms or groups of atoms in the solute, but the sphere radii are determined by simple empirically based expressions involving the effective atomic charges of the solute atoms (derived from molecular electrostatic potential) and base radii. Both of these terms are optimized for the different types of atoms or functional groups in a training set of neutral and charged solutes. Parameters in these expressions for radii were fitted by minimizing residuals between calculated and measured standard free energies of solvation (DeltaG(s)*), weighted by the uncertainty in the measured value. The calculations were performed using density functional theory with the B3LYP functional and the 6-311+G** basis set and the COnductor-like Screening MOdel (COSMO). The optimized radii definitions reproduce DeltaG(s)* of neutral solutes and singly charged ions in the training set to within experimental uncertainty and, more importantly, accurately predict DeltaG(s)* of compounds outside the training set, in particular anions (J. Phys. Chem. A 2003, 107, 5778). Inherent to this approach, the cavity definitions reflect the strength of specific solute-water interactions. We surmise that this feature underlies the success of the model, referred to as the CD-COSMO model for Charge-Dependent (also Camaioni-Dupuis) COSMO model. These findings offer encouragement that we can keep extending this scheme to other functional groups and obtain better accuracy in using continuum solvation models to predict equilibrium properties of aqueous ionic solutes. The approach is illustrated for a number of test cases, including the determination of acidities of an amine base, a study of the tautomerization equilibrium of a zwitterionic molecule (glycine), and calculating solvation energies of transition states toward a full characterization of reaction pathways in aqueous phase, here in S(N)2 exchange reactions. The calculated reaction barriers in aqueous solution are in excellent agreement with experimental values.     

Increasing physical constraints and improving performances in a parameter-free GGA functional

In this Letter we present an evolution of the TCA functional [V. Tognetti, P. Cortona, C. Adamo, J. Chem. Phys. 128 (2008) 034101] that gives a vanishing correlation energy for hydrogenoid atoms. This feature of the exact functional is incorporated in the TCA approximation at the generalized-gradient level, without kinetic energy density or higher order density derivatives dependence. A significant improvement of atomic and atomization energies, activation barriers and ionization potentials is found when the new correlation is coupled with modified PBE exchange functionals, while structural parameters are close in accuracy to those provided by the original PBE functional.