Description of functional groups by means of domain-restricted reduced density matrices

This report constitutes an application of our previous theoretical works on partitionings of the first-order reduced density matrix according to the atomic domains defined in the theory of atoms in molecules. The numerical determinations obtained reveal that the domain-restricted reduced density matrices, which are the tools resulting from the former treatments, are suitable devices to describe chemical features of molecular fragments. We have focused attention on a study of functional groups in several series of organic compounds confirming the usefulness of these tools.     

Dynamics of Atomic and Molecular Hydrogen Elimination from Hydrocarbons at VUV Excitation

Elimination of atomic hydrogen (H) and molecular hydrogen (H₂) are important elementary chemical processes in photochemistry and combustion chemistry. Recently, unique and sensitive detection techniques for atomic and molecular hydrogen detection were developed in our laboratory. Using the advanced molecular beam methods, we have studied the photodissociation of a few typical hydrocarbons at 157 nm excitation, especially their atomic and molecular hydrogen elimination processes. In this report, we will briefly describe the results from photodissociation of propane, ethylene, propyne and methanol at 157 nm excitation. These molecules represent different classes of hydrocarbons such as alkane, alkene, alkyne and alcohol. Through careful studies on differently deuterated compounds, clear pictures of selective atomic and molecular hydrogen elimination processes can be constructed for all of the above compounds. These results will help us to understand the dissociation dynamics of the small hydrocarbon molecules.     

Atomic orbitals in molecules: general electronegativity and improvement of Mulliken population analysis

An approach of atomic orbitals in molecules (AOIM) has been developed to study the atomic properties in molecules, in which the molecular orbitals are expressed in terms of the optimized minimal atomic orbitals. The atomic electronegativities are calculated using Pauling's electronegativity of free atom and are employed to find the electronegativity equilibrium in molecules and to describe the amphoteric properties of the transition metals from the groups 4 to 10. AOIM can also improve the numerical stability and accuracy of the original Mulliken population analysis.     

Molecule‐specific determination of atomic polarizabilities with the polarizable atomic multipole model

Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near‐quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability. © 2012 Wiley Periodicals, Inc.     

A study of the partitioning of the first-order reduced density matrix according to the theory of atoms in molecules

This work describes a simple spatial decomposition of the first-order reduced density matrix corresponding to an N-electron system into first-order density matrices, each of them associated to an atomic domain defined in the theory of atoms in molecules. A study of the representability of the density matrices arisen from this decomposition is reported and analyzed. An appropriate treatment of the eigenvectors of the matrices defined over atomic domains or over unions of these domains allows one to describe satisfactorily molecular properties and chemical bondings within a determined molecule and among its fragments. Numerical determinations, performed in selected molecules, confirm the reliability of our proposal.     

Cumulative atomic multipole representation of the molecular charge distribution and its basis set dependence

A simple procedure to decompose the theoretical molecular charge distribution into cumulative atomic multipoles supplementing any population analysis scheme has been described and tested for a number of molecules in extended basis sets. This approach may be applied to describe local charge distributions in neutral as well as charged systems and also leads to a simplified point-charge model conserving the local anisotropy of the atomic charge distribution in molecules. Such an approach may be useful in estimating intermolecular interactions, representing the molecular environment in solvent effect or enzyme catalytic activity studies, evaluation of molecular electrostatic potentials or tracing the quality of basis set functions.     

Analytical method for the representation of atoms-in-molecules densities

We present analytic refinements and applications of the deformed atomic densities method [Fernández Rico, J.; López, R.; Ramírez, G. J Chem Phys 1999, 110, 4213-4220]. In this method the molecular electron density is partitioned into atomic contributions, using a minimal deformation criterion for every two-center distributions, and the atomic contributions are expanded in spherical harmonics times radial factors. Recurrence relations are introduced for the partition of the two-center distributions, and the final radial factors are expressed in terms of exponential functions multiplied by polynomials. Algorithms for the practical implementation are developed and tested, showing excellent performances. The usefulness of the present approach is illustrated by examining its ability to describe the deformation of atoms in different molecular environments and the relationship between these atomic densities and some chemical properties of molecules.     

Atomic orbital basis sets for molecular interactions

We describe a general approach to the parametrization of linear combinations of Gaussian atomic orbitals, useful for atomic and molecular interactions. We use a Gaussian transform method and Gauss-Legendre quadratures to express hydrogenic atomic orbitals, with varying effective charges, in terms of Gaussian-type orbitals. This procedure provides well-defined rules for calculating exponent factors and combination coefficients of the linear combinations of Gaussians in problems where nuclear distances may vary over large ranges during interactions. © 1994 by John Wiley & Sons, Inc.     

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.     

Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor

Six rigid-body parameters (Shift, Slide, Rise, Tilt, Roll, Twist) are commonly used to describe the relative displacement and orientation of successive base pairs in a nucleic acid structure. The present work adapts this approach to describe the relative displacement and orientation of any two planes in an arbitrary molecule-specifically, planes which contain important pharmacophore elements. Relevant code from the 3DNA software package (Nucleic Acids Res. 2003, 31, 5108-5121) was generalized to treat molecular fragments other than DNA bases as input for the calculation of the corresponding rigid-body (or "planes") parameters. These parameters were used to construct feature vectors for a fuzzy relational clustering study of over 700 conformations of a flexible analogue of the dopamine reuptake inhibitor, GBR 12909. Several cluster validity measures were used to determine the optimal number of clusters. Translational (Shift, Slide, Rise) rather than rotational (Tilt, Roll, Twist) features dominate clustering based on planes that are relatively far apart, whereas both types of features are important to clustering when the pair of planes are close by. This approach was able to classify the data set of molecular conformations into groups and to identify representative conformers for use as template conformers in future Comparative Molecular Field Analysis studies of GBR 12909 analogues. The advantage of using the planes parameters, rather than the combination of atomic coordinates and angles between molecular planes used in our previous fuzzy relational clustering of the same data set (J. Chem. Inf. Model. 2005, 45, 610-623), is that the present clustering results are independent of molecular superposition and the technique is able to identify clusters in the molecule considered as a whole. This approach is easily generalizable to any two planes in any molecule.     

Geometries of functional group interactions in enzyme-ligand complexes: Guides for receptor modelling

Summary An approach is described which makes use of X-ray structural data from enzyme-ligand complexes in order to obtain information for application in receptor modelling. The atomic surroundings of five different ligand functional groups were determined for all complex structures recorded in the Brookhaven Protein Data Bank. These atomic surroundings were then superimposed with respect to the atoms of the functional groups of the ligands in order to obtain clouds of neighbouring atoms. General principles were sought to describe the orientiation or favoured position of groups or atoms around those functional groups when bound to a macromolecule. Some simple conclusions and leads for further modelling were thus derived.     

Communication: Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors

A double-atom partitioning of the molecular one-electron density matrix is used to describe atoms and bonds. All calculations are performed in Hilbert space. The concept of atomic weight functions (familiar from Hirshfeld analysis of the electron density) is extended to atomic weight matrices. These are constructed to be orthogonal projection operators on atomic subspaces, which has significant advantages in the interpretation of the bond contributions. In close analogy to the iterative Hirshfeld procedure, self-consistency is built in at the level of atomic charges and occupancies. The method is applied to a test set of about 67 molecules, representing various types of chemical binding. A close correlation is observed between the atomic charges and the Hirshfeld-I atomic charges.     

石英玻璃分子动力学模拟中的原子电荷转移与系综选择

介绍了SiO2体系分子动力学模拟中的Si、O原子电荷转移问题;采用Morse势函数研究了原子电荷转移对石英玻璃模拟的影响,发现原子电荷转移在影响模型密度的同时,还直接影响着原子的最近邻距离.NPT和NVT系综下的模拟结果对比显示,系综对模型中原子最近邻情况影响不大,但在NVT系综下模拟结果表明实际玻璃中存在的较大的空隙结构,找到了以往模拟中密度结果偏高的原因,提出了一种较好的石英玻璃分子动力学建模的方法.该方法不但解决了在调整电荷时维持原子最近邻距离与保证模型密度之间的矛盾,而且可以很好地描述石英玻璃在远程结构上密度不均、存在较大空隙的无序结构.此外,原子自扩散系数的计算结果展示了空隙结构在石英玻璃扩散性质研究中的作用.     

Light absorption during alkali atom-noble gas atom interactions at thermal energies: a quantum dynamics treatment

The absorption of light during atomic collisions is treated by coupling electronic excitations, treated quantum mechanically, to the motion of the nuclei described within a short de Broglie wavelength approximation, using a density matrix approach. The time-dependent electric dipole of the system provides the intensity of light absorption in a treatment valid for transient phenomena, and the Fourier transform of time-dependent intensities gives absorption spectra that are very sensitive to details of the interaction potentials of excited diatomic states. We consider several sets of atomic expansion functions and atomic pseudopotentials, and introduce new parametrizations to provide light absorption spectra in good agreement with experimentally measured and ab initio calculated spectra. To this end, we describe the electronic excitation of the valence electron of excited alkali atoms in collisions with noble gas atoms with a procedure that combines l-dependent atomic pseudopotentials, including two- and three-body polarization terms, and a treatment of the dynamics based on the eikonal approximation of atomic motions and time-dependent molecular orbitals. We present results for the collision induced absorption spectra in the Li-He system at 720 K, which display both atomic and molecular transition intensities.     

Catalytic effects as the origin of some interferences in flame spectrometry

A new explanation for a range of hitherto quite unexplained interference phenomena is put forward and subjected to experimental verification. It is suggested that the interfering metal may be acting through a catalysis of the recombination of excess free radical concentrations in the flame, thereby leading to the possibility of significant disturbance of the proportion of analyte metal bound up in compound form. It is suggested, for example, that the metals Mg, Ca, Sr, Ba, Sn, Cr, U, and Mn may, in described circumstances, interfere with certain of the (either) atomic or molecular emissions from each other or with certain of the (either) atomic or molecular emissions from Li, K, Rb, Cs, Al, Ga, In and Cu.     

Comparative density functional theory study of the structures and properties of metallophthalocyanines of group IV B

Density functional theory (DFT) calculations were carried out to comparatively describe the molecular structures, molecular orbital energy gaps, atomic charges, infrared (IR) and Raman spectra of lead phthalocyaninate (PbPc), tin phthalocyaninate (SnPc), germanium phthalocyaninate (GePc), tin (IV) dichlorophthalocyaninate (PcSnCl₂), and germanium (IV) dichlorophthalocyaninate (PcGeCl₂). The calculated structural data and the simulated IR spectrum of PbPc correspond well with the experimental result. The important effects of axial ligands and ionic radius of metal center to the molecular structures, molecular orbital and atomic charges are described, and the metal-sensitive peaks in the IR and Raman spectra are identified by comparative study of the five complexes with different central metals and axial ligands.     

Role of counterion condensation in the self-assembly of SDS surfactants at the water-graphite interface

The aggregate structure of sodium dodecyl sulfate (SDS) adsorbed at the graphite-water interface has been studied with the aid of molecular dynamics (MD) simulations. As expected, our results show that adsorbed SDS yields hemi-cylindrical micelles. The hemi-cylindrical aggregates in our simulations closely resemble all structural and morphological details provided by previous solution atomic force microscopy (AFM) experiments. More interestingly, our data indicate that SDS head groups do not provide a complete shield to the hydrophobic tails. Instead, we found regions in which the hydrophobic tails are exposed to the aqueous solution. By conducting a parametric study for SDS-like nonionic surfactants we show that electrostatic interactions between SDS head groups and counterions are responsible for the unexpected result. Our interpretation is corroborated by density profiles, analysis of the coordination states, and mean square displacement data for both the adsorbed SDS surfactants and the counterions in solution. Counterion condensation appears to be a physical phenomenon that could be exploited to direct the assembly of advanced nanostructured materials.     

Are atoms sic to molecular electronic wavefunctions? II. Analysis of fors orbitals

Electronic wavefunctions that describe molecules in the full optimized reaction space (FORS) are multiconfigurational wavefunctions which are invariant under non-singular linear transformations of the occupied molecular orbitals. They offer therefore a considerably wider scope for orbital interpretations than the single-configuration Hartree-Fock approximation. For example they can be analyzed in terms of natural MOs and in terms of localized MOs. The latter turn out to be remarkably atomic in character and a new localization procedure can be formulated which yields atom-adapted molecular orbitals. These have the character of minimal-basis-set AOs that are optimally adapted to the molecular environment and furnish an unambigious atomic population analysis. On the other hand, chemically adapted molecular orbitals can be defined by an appropriate compromise between natural orbitals and localized orbitals. The freedom to use, as configuration-generating molecular orbitals, atom-adapted FORS MOs as well as chemically adapted FORS MOs makes FORS wavefunctions particularly suitable for chemical interpretations. The ensuing analysis establishes the minimal basis set (in molecule-adapted form) as a theoretically sound concept for the understanding of accurate molecular wavefunctions. An illustrative example is discussed.     

Novel atomic-level-based AI topological descriptors: application to QSPR/QSAR modeling

Novel atomic level AI topological indexes based on the adjacency matrix and distance matrix of a graph is used to code the structural environment of each atomic type in a molecule. These AI indexes, along with Xu index, are successfully extended to compounds with heteroatoms in terms of novel vertex degree v(m), which is derived from the valence connectivity delta(v) of Kier-Hall to resolve the differentiation of heteroatoms in molecular graphs. The multiple linear regression (MLR) is used to develop the structure-property/activity models based on the modified Xu and AI indices. The efficiency of these indices is verified by high quality QSPR/QSAR models obtained for several representative physical properties and biological activities of several data sets of alcohols with a wide range of non-hydrogen atoms. The results indicate that the physical properties studied are dominated by molecular size, but other atomic types or groups have small influences dependent on the studied properties. Among all atomic types, -OH groups seem to be most important due to hydrogen-bonding interactions. On the contrary, -OH groups play a dominant role in biological activities studied, although molecular size is also an important factor. These results indicate that both Xu and AI indices are useful model parameters for QSPR/QSAR analysis of complex compounds.