Electronic Structure Of Molecules Research Articles

Some recent developments in quantum Monte Carlo for electronic structure: Methods and application to a bio system

A brief review of recent advances in quantum Monte Carlo for the electronic structure of molecules at the University of California, Berkeley, is given based on an invited talk presented at the WATOC meeting, Cape Town, South Africa, January 2005.

Quantum chemical study of nickel(II) complexes with cyclic diimine ligands on the base of bis[3,3′-iminopropyl]methylamine

A quantum chemical study of spatial and electronic structures of molecules in the frame complexes, bis[3,3′(RR′)-ketiminepropyl]methylamine nickel dichlorides, where R = H, CH3, and R′ = H, CH3, has been performed by DFT(B3LYP/LANL2DZ) method. The molecules of these complexes were found to be in a triplet state. Energy stability of the endo form of the complex molecules was shown. In the molecule of bis[3,3′-aldiminopropyl]methylamine nickel dichloride (R = R′ = H), a considerable strengthening of the bond Ni-N(amine) takes place when passing from the diamagnetic into paramagnetic state, and all bonds Ni-N become equivalent with respect to interatomic distance values. The topology analysis of the electron density for the complexes with R = R′ =H and R = R′ = CH3 was carried out. It is stated that all Ni-N bonds are covalent in the molecules of paramagnetic complexes.

Quantum chemical study of the hydrogen-bonded HXeOH–H 2O complex

A combined MP2 and DFT/B3LYP study of the HXeOH–H 2O complex is presented. These computational methods have been used to extract information on the structural, energetical and vibrational properties of the complex. Additionally, we have applied anharmonic vibrational calculations based on the MP2-computed intermolecular potential energy surface. Large perturbations both on the subunit structures and their fundamental vibrational modes are found upon complexation. Large changes of anharmonicity of the HXeOH subunit reflects the perturbation of the molecule's electronic structure. The computed BSSE-corrected interaction energies are −40.23 and −38.94 kJ mol −1 at the CCSD(T)//MP2 and CCSD(T)//B3LYP levels of theory, respectively. The estimated deformation energy contribution to the interaction energy is about 5%, which is very large compared with classical hydrogen-bonded complexes. The topological analysis of the Electron Localization Function (ELF) was applied to study further the hydrogen-bonded interaction between the two complex partners. The obtained interaction pattern suggests that the interaction between HXeOH and H 2O is a typical hydrogen bond interaction driven mainly by electrostatic interactions.

Relationship between the Structure and Photostability of Decahydroacridine Derivatives

The absorption and photoluminescence spectra of a number of derivatives of 3,3,6,6-tetramethyl-N-phenyl-decahydroacridine-1,8-dione with a regular change in the structure of molecules are investigated. Their electronic structure is calculated. The nature of some of the spectral bands is established. Significant differences in the efficiency of the processes of photochemical transformations of dyes exposed to UV irradiation have been revealed; these changes are attributable to the different donor-acceptor properties of the substituents introduced. A mechanism of phototransformations that agrees with both calculations of the electronic structure of molecules and the spectral-luminescent characteristics of the initial and irradiated compounds is suggested.

Elucidation of the Electronic Structure of Molecules with the Help of NMR Spin−Spin Coupling Constants: The FH Molecule

It is demonstrated how the one-bond NMR spin-spin coupling constant (SSCC) (1)J(FH) can be used as a source of information on the electronic structure of the FH molecule. For this purpose, the best possible agreement between measured and calculated SSCC is achieved by large basis set coupled perturbed density functional theory calculations. Then, the calculated value is dissected into its four Ramsey terms: Fermi contact, the paramagnetic spin-orbit term, the diamagnetic spin-orbit term, and the spin dipole term, which in turn are decomposed into orbital contributions and then described by their spin densities and orbital current densities. In this way, the SSCC gives detailed information about the electronegativity of F, the bond polarity, the bond polarizability, the volume and the polarizability of sigma and pi lone pair orbitals, the s- or p-character of the bond orbital, the nature of the LUMO, and the density distribution around F.

Energy of the O–NO 2 bond dissociation and the mechanism of the gas-phase monomolecular decomposition of aliphatic alcohol nitroesters

The equilibrium geometrical parameters, enthalpies of the formation of compounds and radicals, and the dissociation energies of the O–NO 2 bond for nitroesters of mono- and polyatomic aliphatic alcohols have been determined by the density functional B3LYP method. The basic tendencies in the changes of parameters of the geometrical and electronic structure of molecules, enthalpies of the formation and dissociation energies have been analyzed. Various mechanisms of the initial event of the gas-phase decomposition of nitroesters of mono- and polyatomic aliphatic alcohols have been studied.

Low temperature scanning tunneling microscopy of phthalocyanine multilayers on Au(1 1 1) surfaces

We have studied epitaxial trilayer films of cobalt–phthalocyanine (CoPc) on Au(1 1 1) 22× 3 surfaces using a scanning tunneling microscope at 78 K. Molecules in each layer were found to form square lattices and stacked along the [ 1 1 ̄ 0 ] axis of the Au(1 1 1) surface. While CoPc molecules in the first layer were observed at bias voltages of −2.5 to +2.5 V, there were certain ranges of bias voltage in which molecules in the upper layers were invisible. The electronic structures of molecules in upper layers are more localized than those of the first layer, which is affected by the substrate surface.

Nuclear dynamics and electronic structure of molecules by resonant Auger spectroscopy

Resonant Auger spectroscopy is used to study the molecular core-excited states with an inner-shell electron promoted to the lowest unoccupied molecular orbital. Dissociating Cl2p→σ ∗ excitations are investigated in the HCl and Cl 2 molecules, where the resonant Auger electron spectra exhibit both molecular and atomic features, depending on the time scale of the dissociation. The use of electron time-of-flight analyzers in combination with two-dimensional (in electron and photon energies) mapping technique allows to create a detailed picture of the interplay between dissociation and Auger decay. Also a Renner–Teller-split bound excited state, C1s→π ∗ is studied in the CO 2 molecule. Here, the Auger spectra recorded with high-resolution SES-200 hemispherical analyzer exhibit strong photon energy dependency across the resonance. From the analysis and semi-empirical modelling, properties of the core-excited state are derived.

Surface Second Harmonic Generation of Cationic Water-Soluble Porphyrins at the Polarized Water|1,2-Dichloroethane Interface

Reference LEPA-ARTICLE-2002-011doi:10.1021/la0256329View record in Web of Science Record created on 2005-11-07, modified on 2017-05-12

The first dirhodium tetracarboxylate molecule without axial ligation: new insight into the electronic structures of molecules with importance in catalysis and other reactions.

The first crystalline tetracarboxylato dirhodium paddlewheel complex with no axial ligation has been synthesized and structurally characterized. The compound, tetrakis(2,4,6-triisopropylbenzoato)dirhodium(II,II), Rh(2)(TiPB)(4), exhibits a Rh-Rh bond length of 2.3498(4) A. Interestingly, this is only ca. 0.02 A shorter than that in the corresponding bis-acetone adduct, 2.3700(4) A. The electronic spectrum exhibits two bands in the visible region; the low-energy band A has been previously attributed to a pi(Rh(2))-->sigma(Rh(2)) transition in various bis-adducts. The spectrum of Rh(2)(TiPB)(4)(acetone)(2) shows this band at 610 nm, while that of Rh(2)(TiPB)(4) is greatly displaced to 760 nm. This is very persuasive evidence that the assignment for this transition is correct.

Core Ionization Energies, Mean Dipole Moment Derivatives, and Simple Potential Models for B, N, O, F, P, Cl, and Br Atoms in Molecules

Simple potential models relating experimental 1s electron ionization energies for B, N (sp and sp3 hybrids), O, and F atoms; 1s and 2p ionization energies for P atoms; and 2s and 2p ionization energies for Cl atoms as a function of their atomic mean dipole moment derivatives determined from experimental gas phase infrared fundamental band intensities are reported. Potential models using theoretical Koopmans' energies and generalized atomic polar tensor (GAPT) charges are found to form even more precise models than those using experimental data. This is expected because the potential models depend only on the electronic structures of molecules before ionization takes place and do not take into account relaxation effects. If the experimental ionization energies are adjusted by their relaxation energies, models similar to those obtained using Koopmans' energies are determined. The models permit a simple understanding of substituent effects on core ionization energies in terms of atomic charges in molecules. Most of the potential model slopes investigated are shown to be approximately proportional to the inverse atomic radii of the atom being ionized. Core-valence electron repulsion values inferred from the potential models obtained from experimental data are somewhat smaller than those calculated using Slater orbitals of isolated atoms. The potential model intercepts for 1s and 2p electrons are shown to be proportional to the square of the nuclear charge, consistent with their interpretation as core electron ionization energies of neutral atoms. 1s He, Ne, and Ar and 2p Ar, Kr, and Xe core ionization energies obey the linear relationships obtained for the model intercepts. The results suggest that mean dipole moment derivatives obtained from infrared intensities can be interpreted as atomic charges.

A tool for the interactive 3D visualization of electronic structure in molecules and solids

This paper presents the Vienna ab initio simulation package (VASP) data viewer, a desktop 3D visualization application for the analysis of valence electronic structure information derived from first-principles quantum-mechanical density functional calculations. This tool allows a scientist to directly view and manipulate the calculated charge density or electron localization function (ELF) from an electronic structure calculation, providing insight into the nature of chemical bonding. Particular attention was given to the design and implementation of the user interface (UI) for the data viewer. It provides for expert and novice usage, and both natural direct manipulation and precise numerical control. The data viewer has proven useful to chemical scientists for understanding the results of electronic structure calculations.

Molecular geometry and electronic structure of molecules in free‐radical copolymerization of styrene and methyl methacrylate derived from density functional calculations

AbstractThe molecular geometry and electronic structure of styrene and methyl methacrylate as well as corresponding radicals formed by the addition of a methyl radical to the β‐carbon of the monomer were determined using the density functional theory at the B3LYP/6‐311+G** level. Results were in good agreement with the theoretical and experimental data available in the literature. Full optimized molecular geometry of methyl methacrylate showed the trans form of the molecule. Monomers transformed into corresponding radicals preserved the main structural parameters of substituents whereas bonds between substituents and adjacent radical carbon atoms shortened. It was found that the correlation of the theoretically calculated electronic parameters for monomers and the corresponding radicals with the Q and e parameters from the Alfrey–Price scheme strongly depends on the level of calculations. Application of the higher level of theory including the correlation effect changes the relationship discussed in the literature between energy (EY) of formation of a radical from the monomer, the experimental e parameter, and the Q parameter and monomer/average electronegativity, respectively. The total atomic spin density at the radical carbon atom correlated with the radical parameter P in the Alfrey–Price scheme was computed to be higher for the methoxycarbonyl‐1‐methyl‐ethyl radical when compared with the 1‐phenyl‐propyl radical. These values are in good agreement with the localization energies and the P values determined from the kinetic measurements for macroradicals ending with styrene and methyl methacrylate monomer units. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3761–3769, 2001

A semi-empirical electrostatic potential in the studies of molecular crystals

A model based on incorporation of the external electrostatic potential into a semi-empirical Hamiltonian has been applied to explore the effect of crystal packing on the electronic structure of molecules within crystals. Different schemes for representation of charge distribution within a molecule are compared. The results obtained using this model were compared to the results of calculations carried out with the COSMO method. The effect of electrostatic potential is subject to wide variations, depending on the packing motif, and it may exceed the effect of very polar solvents. For three pairs of polymorphs, the incorporation of electrostatic potential into the INDO/S scheme allowed the rationalization of their difference in color.

Additive overlap populations of atomic orbitals

The additive overlap populations of atomic orbitals ξab= Re(Sab(PS)ba) and Ξab= ξab+ ξba, relating McWeeny’s and Mulliken’s additive populations of AO naM= Re(PS)aa with Davidson’s total electron populations na= (SPS)aa, are suggested for a quantum chemical description of the electronic structure of molecules and crystals. The theory is illustrated by an electron population analysis for HCN, N2, F2, and B2H6 molecules.

On the electronic structure of Li2 (X1) and its changes with internuclear distance

A compact, yet accurate, and strictly virial-compliant ab initio electronic wavefunction for ground-state Li2 is exploited for a study of the molecule's electronic structure and electron density. Symmetry-breaking problems that emerge at the single-configuration level are solved in a multiconfigurational spin-coupled approach that enables simultaneous optimization of angularly correlated “resonating” configurations. Particular emphasis is placed on the accurate determination of the electron density's bifurcation points and of the quadrupole moment as a function of internuclear distance R. Tentative connections are drawn between the R dependence of the electron density's topological structure and quadrupole moment and that of the electronic wavefunction. Computation of the latter constitutes the first application to systems other than isolated atoms of the optimized basis set generalized multiconfiguration spin-coupled method, which entails use of nonorthogonal orbitals and Slater-type basis functions with variationally optimized exponential parameters. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 378–397, 2000

Improvement of near-field fluorescence imaging of bulk materials by metal coating

By using a simple model based on a linear susceptibility approach and taking into account the dynamic nature of the molecule's electronic structure, the electric field diffracted by the near-field probe is evaluated in the presence or absence of a thin silver layer deposited on the surface of a bulk fluorescent material. This modeling points out that the far-field signal emitted by the molecules situated far from the tip is important in the absence of metal coating and can reduce the near-field detection sensitivity. It shows that surface metal coating enhances the near-field contribution and decreases the far-field one. Cathodoluminescence images obtained on a fluorite (CaF2:Eu) sample confirm the results predicted by modeling.

Electronic structure and biological activity of steroids

We present the analysis of the electronic structure for 31 steroids by using HeI UV photoelectron spectroscopy (UPS) and MO calculations. The electronic structure of molecules in the gas phase is related directly to steroid–receptor binding measurements. The results indicate that formally `inert' σ-skeleton plays a crucial role in diversifying the electronic structures of the title compounds (`ribbon-orbital effect'). This is an attempt to rationalize the biological activity of steroids (represented through steroid–receptor binding) by making direct correlation between spectroscopic and biological data.

The effect of metal coating in near-field fluorescence imaging

The effect of a thin metal coating in near-field fluorescence imaging is studied by using a model based on the plane wave decomposition, that takes into account the dynamic nature of the molecule's electronic structure, namely the modification of the fluorescence lifetime due to the near-field environment (the metal layer and the probe's presence). The electromagnetic wave crossing the metal layer generates a plasmon excitation, the effect of which is the more important when the molecules, considered as dipoles, are polarized perpendicularly to the surface and when they are in a saturated excitation state. The consequence of the plasmon excitation is a decrease in fluorescence lifetime and, for the case of molecules polarized perpendicularly to the surface, a decrease in lateral resolution. When the molecules are polarized parallel to the surface, plasmon excitation is weaker and its effect on the resolution seems to be beneficial. The interaction with the probe is also studied; its effect on imaging of molecules is weak in the presence of the metal coating.

Protonation of the ozone analogue S2O: structures, energies and vibrational spectra of HS2O+ isomers

Protonation is a simple reaction that can both reveal and induce changes in the electronic structure of molecules. The protonation of various S2O isomers: SSO, cyclic S2O, and SOS does not qualitatively change the underlying potential energy surface of these isomers. The protonated SSO isomers are lowest in energy, and cis-SSOH+ is the lowest of these. S-protonated and O-protonated cyclic S2O are next highest in energy, with the S-protonated isomer slightly lower in energy than the O-protonated isomer. For SOS we find, contrary to previous results, that the lowest energy isomer is a 3B2 rather than a 3A2 state. Protonated SOS, however, has a singlet ground state. Both geometry changes and vibrational frequency changes upon protonation illustrate the nature of the bonding in the various S2O isomers.