Electronic Structure Of Molecules Research Articles

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.

Electron Exchange and the Photophysics of Metal-Quinone Complexes. 1. Synthesis and Spectroscopy of Chromium-Quinone Dyads.

The synthesis, structural and spectroscopic characterization of monosemiquinone and monocatechol complexes of chromium(III) are described. Compounds of the general form [Cr(N(4))Q](n+), where N(4) represents a tetradentate or bis-bidentate nitrogenous ligand or ligands and Q represents a reduced form of an orthoquinone, have been prepared by two different routes from Cr(III) and Cr(II) starting materials. The complex [Cr(tren)(3,6-DTBSQ)](PF(6))(2), where tren is tris(2-aminoethyl)amine and 3,6-DTBSQ is 3,6-di-tert-butylorthosemiquinone, crystallizes in the monoclinic space group P2(1)/c with a = 11.9560(2) Å, b = 17.0715(4) Å, c = 17.1805(4) Å, beta = 90.167(1) degrees, V = 3506.6(1) Å(3), Z = 4, with R = 0.056 and R(w) = 0.070. Alternating C-C bond distances within the quinoidal ligand confirm its semiquinone character. Variable temperature magnetic susceptibility data collected on solid samples of both [Cr(tren)(3,6-DTBSQ)](PF(6))(2) and [Cr(tren)(3,6-DTBCat)](PF(6)) in the range 5-350 K exhibit temperature-independent values of 2.85 +/- 0.1 &mgr;(B) and 3.85 +/- 0.1 &mgr;(B), respectively. These data are consistent with a simple Cr(III)-catechol formulation (S = (3)/(2)) in the case of [Cr(tren)(3,6-DTBCat)](PF(6)) and strong antiferromagnetic coupling (|J| > 350 cm(-)(1)) between the Cr(III) and the semiquinone radical in [Cr(tren)(3,6-DTBSQ)](PF(6))(2). The absorption spectrum of the semiquinone complex exhibits a number of sharp, relatively intense transitions in fluid solution. Group theoretical arguments coupled with a qualitative ligand-field analysis including the effects of Heisenberg spin exchange suggest that several of the observed transitions are a consequence of exchange interactions in both the ground- and excited-state manifolds of the compound. The effect of electron exchange on excited-state dynamics has also been probed through static emission as well as time-resolved emission and absorption spectroscopies. It is suggested that the introduction of exchange coupling and subsequent change in the molecule's electronic structure may contribute to an increase of nearly 4 orders of magnitude in the rate of radiative decay (k(r)), and a factor of ca. 10(7) in the rate of nonradiative decay (k(nr)).

Manifestations of hyperfine interaction in plasticity

A mechanism is proposed of how the hyperfine interaction of the electron and nuclear spins in the paramagnetic obstacle‐dislocation system may influence the plastic properties of crystals in a magnetic field. It is shown that the hyperfine interaction leads to a threshold-type behavior of the magnetic-field dependence of various plasticity-related quantities. A strong influence of the hyperfine interaction on the behavior of the internal friction of dislocations in weak magnetic fields is predicted. @S0163-1829~97!01142-9# The theory of mechanical properties of crystals usually considers nuclei as point charges disregarding their internal structure. A similar approximation has been widely used in the theory of electronic structure of molecules. This approximation is justified as long as various characteristics of nuclei, such as mass, spin, size, and shape, do not appreciably influence static properties of molecules or crystals. However, it is known that the role of nuclear magnetic moments may appear to be of importance for chemical reaction rates in a magnetic field. 1,2 This leads to the phenomenon called the magnetic isotope effect in chemical reactions in which the hyperfine interaction of the electron and nuclear spins changes populations of various electronic states of radical pairs thereby changing their chemical reactivity. When addressing plasticity-related phenomena we have to consider the motion of dislocations and their pinning by point defects—obstacles. The dynamics of formation of the obstacle‐dislocation bonds in a magnetic field was recently discussed in Ref. 3 ~see also Refs. 4‐7 discussing various plasticity-related phenomena!. It is assumed that the dangling bond of a paramagnetic obstacle forms a radical pair with a dangling bond of the dislocation core. The magnetic field influences the transitions between different spin states of such pairs, which are characterized by different binding energies, and thus changes the depinning probability. This is a mechanism of how the plastic properties of crystals ~both metals and dielectrics! may be influenced by a magnetic field in a broad temperature range. In pure undeformed metals at low temperatures there is also a large contribution from the Kravchenko mechanism, 8 in which the magnetic field increases the electron component of the dislocation viscous drag. An analogy with chemical reaction theory suggests that a hyperfine interaction in the obstacle‐dislocation system also may play an important role in plasticity of crystals in a magnetic field. This may also lead to a magnetic isotope effect in plasticity. This paper discusses the part played by the hyperfine interaction in the dynamics of obstacle‐dislocation radical pairs in a magnetic field and presents results for several experimentally measurable quantities. The influence of hyperfine interactions on the plasticity will be considered within the framework of the model outlined in Ref. 3, which considers the dislocation motion at low stresses, not exceeding the Peierls stress, which occurs by means of depinning of dislocation kinks from paramagnetic obstacles. Unsaturated electron states in the kink and the obstacle form a radical pair whose binding energy depends strongly on the total spin of the pair. This energy is usually much higher in the singlet S state than in a triplet T state. The pair in a T state allows the kink to pass the obstacle freely and the dislocation depins. This model allows one to explain various effects related to a change of plasticity in a magnetic field. 3 Now we modify this model by introducing an interaction between the spins of electrons forming the radical pair and the spins of nuclei of the obstacle or/and dislocation core. The simple, but still rather general, situation is considered here when only one nucleus in the kink-obstacle radical pair has a nonzero spin I51/2. Then the spin Hamiltonian of the system can be written in the form

The effect of nonbonded interactions on the electronic structure of anions in XSCN crystals (X=NH 4, Na)

We recently proposed a conception of the influence of nonbonded intermolecular interactions on the electronic structure of molecules (ions). The latter may cause phase transitions to proceed without any change in crystal and molecular structure. The object of this investigation is to test this assumption. For this purpose, ab initio calculations of model complexes have been carried out by the authors. The object of these calculations is the simulation of structural changes with lowering temperature in the NH 4SCN and NaSCN crystals. It is shown that the appearance of phase transitions may be connected with a change in the electronic structure of anions in a NH 4SCN crystal caused by a change in the nonbonded interactions under the action of temperature. In the NaSCN crystal, the changes in the nonbonded interactions on lowering the temperature have almost no effect on the electronic structure of the anions in the absence of phase transitions. © 1997 Elsevier Science B.V.

Soft XMCD in Molecule Based Magnets

X-ray absorption spectroscopy at the L 2,3 edges of 3d transition metals has been used to study the electronic structure of molecule based magnets with Curie temperatures ranging from 66 K to 315 K. These magnets are bimetallic cyanides of the Prussian blue family, constructed by a three dimensional assembling of -NC-Cr III -CN-A II - units. Using Ligand Field Multiplet calculations, where hybridization is mainly taken into account through configuration interaction, we have been able to reproduce nicely the spectra and to determine the exact ground state of the transition metals. We have separated covalence and charge transfer effects occurring in the bond between the 3d ions and the cyano ligand. We have also recorded X-ray Magnetic Circular Dichroism (XMCD) at nickel L 2,3 edges in the ferromagnet Cs I [Ni II Cr III (CN) 6 ].2H 2 O (T c = 90 K). With Ligand Field Multiplet calculations the shape of the experimental XMCD signal can be reproduced. The application of the orbital and spin sum rules gives a too small magnetic moment on nickel. A complete calculation taking covalence into account showed that hybridization cannot be responsible for the experimental low nickel magnetic moment.

Recent progress in surface NMR-electrochemistry

NMR spectroscopy is one of the newer spectroscopic techniques for investigating the static, dynamic and electronic structures of molecules adsorbed onto metal catalyst surfaces. We review recent progress in the application of solid-state NMR methods to the investigation of molecules adsorbed onto metal surfaces in an electrochemical environment: in the presence of electrolyte, and at an electrified interface under external potentiostatic control. While at a very early stage of development, the NMR-electrochemistry approach has considerable potential for investigating otherwise inaccessible aspects of electrode and adsorbate structure, and should enable a comparison of results obtained from different spectroscopies, in particular from IR spectroscopy. We present a brief review of the development of the subject, followed by details of the instrumentation necessary for NMR-electrochemistry studies. We show how spin–spin relaxation can give information on surface structure and surface diffusion, how spin–lattice relaxation can give information on the presence of conduction electron spillover onto the adsorbate, and how the NMR of surface species responds to an externally applied electric field. The 13 C-NMR of CO on Pt in an electrochemical environment is compared with the 13 C-NMR of CO on Pt catalysts in vacuum, which are well characterized. In the case of CN on Pt, we show large spectral shifts of the resonance as the electrode potential is varied, providing an independent measurement of the effects of the electrified interface on the chemisorption bond. Spectral sensitivity is also now adequate to observe nuclei which produce even weaker signals than 13 C, such as 15 N. The NMR-electrochemistry method thus opens up a broad new array of possibilities for probing static structures (from T 2 ), surface diffusion (from the temperature dependence of T 2 ) as well as electronic properties of the chemisorption bond (from T l , and from electrode potential effects) at electrochemical interfaces, and for studying reactive intermediates and poisons on high-surface-area catalysts, such as those utilized in hydrogen and organic fuel cells.

Characterization of Electronic Structure in Molecules by One-Center Expansion Techniques. No Three-Center Four-Electron Bond in PF5

The one-center expansion technique is applied to analyze the electronic structure of molecules in terms of angular momentum eigenfunctions (s, p, d, ...) of the participating atoms. That is, by scanning through a continuous set of spherical neighborhoods of a given atom, the surrounding molecular electronic structure is characterized by functions of radius from an otherwise unbiased atomic point of view. These functions include (a) radial densities/populations of angular momentum eigenfunctions, (b) their responses, e.g., to structural changes, and (c) the extent to which the one-particle density matrix can locally be described in terms of a preset number of “natural” orbitals (study of hypervalence). Covalence and delocalization, which by definition are not attributable to a single atom, are characterized by the degree of electron sharing between angular momentum eigenstates referring to different atomic neighborhoods. A concept of hybrid orbitals in chemical bonding with no other ingredients than principles of quantum mechanics and (spherical) atomic neighborhoods is outlined. The proposed approach is applicable to any approximation of electronic structure that allows the construction of a one-particle density operator in terms of an arbitrary one-particle basis set. Elementary applications to H2, ethane, F2, and benzene and a thorough analysis of the electronic structure of PF5 are presented. The main results with respect to D3h-symmetric PF5 are the following: (a) a model of (spectroscopic) sp3d hybrid orbitals at phosphorus is inappropriate; (b) a Rundle model with three two-center two-electron bonds and one three-center four-electron bond does not apply; (c) strong 3s participation at P in covalent bonding with all five fluorine atoms creates different delocalization patterns instead; (d) a description of the valence region of phosphorus by only four orbitals is unsatisfactory (octet rule violation), and is best improved by an additional orbital of local d character; (e) the corresponding d population is only weakly bound to phosphorus, and should not be considered as chemically bonding.

Electronic structure of molecules by the numerical generalized-valence-bond wave functions

mThe generalized valence bond method is extended for use in electronic structure calculations of two-atomic molecules made up of the heavy atoms. By applying a purely numerical Hartree-Fock (HF) or Dirac-Hartree-Fock (DHF) basis set, we were able to efficiently produce the potential curves for a large range of the interatomic distances. The configuration interaction and nonorthogonal basis sets are used to obtain an accurate solution for the realistic molecular systems. Adaptation for parallelism allows the simulation to be partitioned and carried out on the coupled multiprocessor network (SP-2) at the NIST. Calculations have been performed for Na, and In, quasi-molecules in excited states. 0 1995 John Wiley & Sons, Inc.

Statistical electron correlation ? coefficients and ? holes in molecules

Electron correlation in the H2, LiH and BH molecules has been analyzed in terms of the statistical correlation coefficients introduced by Kutzelnigg, Del Re, and Berthier. Angular, radial (in-out), longitudinal (left-right) and transverse correlation coefficients have been evaluated from both self-consistent-field (SCF) and configuration interaction (CI) wave functions. It has been found that these coefficients reflect fairly well the correlation behavior in the molecular system. The lack of spherical symmetry in molecular densities adds new features to these correlation coefficients and this information can be useful for the study of electronic structure in molecules. The correlation hole function, Fermi and Coulomb holes in these systems have also been calculated and discussed.

Multicavity reaction field method for the solvent effect description in flexible molecular systems

A multicavity reaction field method is proposed for the quantum-chemical calculation of medium dielectric effects on the electronic structure of molecules in solution. This method is based on the gauge-independent partitioning of the molecule total reaction field in the polarizable medium into the partial reaction fields which belong to the rotationally or inversionally flexible groups in the molecule. The results of the calculations of the solvation free energies in aqueous solution of molecules containing such groups are presented and compared with the results obtained using the single spherical cavity self-consistent reaction field (SCRF) method

(e, 2 e)-Spectroscopy and the Electronic Structure of Molecules. A Short Review with Selected Examples

Abstract The simple plane wave target Hartree-Fock impulse approximation for the (e, 2e) reaction is developed. One result of the approximation is the separation of the expression for the (e, 2e) cross-section into a kinematic factor and a structure factor that contains all of the information about the target. When the target is a molecule, the structure factor can be further separated into atomic terms and a geometric term. This is illustrated for a simple one-electron homonuclear diatomic molecule. Three examples of the application of (e, 2e) spectroscopy to systems of chemical interest are given. They are borazine (inorganic benzene), the methyl siloxanes and the inorganic complex trimethylamine boron trifluoride.

Valence-space-only calculations on molecules: polarization effects

A previously proposed approach [1] to the calculation of the electronic structure of molecules is reconsidered in connection with the study of systems containing atoms with diffuse, polarizable cores. Previous inconsistencies are overcome and a possible solution to the problem of core and valence polarization inside the core volumes is proposed. A test application is performed obtaining improved results for both the energy and the electron density in the whole physical space without substantially increasing the computational effort with respect to the previous formulation of the approach.

Analysis in terms of valence‐bond structures of environmental effects on the electronic structure of molecules

AbstractEnvironmental effects on the electronic structure of molecules caused by external perturbations are studied by means of an expansion of molecular orbital wave functions into valence‐bond (VB) wave functions. Applications are carried out to the π system of butadiene, hydroxyethylene, acrolein, and carbonyl oxide and also to the full electronic system of water. The external perturbations considered are uniform electric fields, nonuniform electric fields, and reaction fields created by solvents. A different behavior is found between nonpolar and polar species in the presence of solvents. Some consequences on the behavior of molecules under the influence of the different electric fields are discussed.

Valence bonds in the Main Group elements. 2. The sulfur oxides

A new bonding description is presented for SO{sub 2}, S{sub 2}O, S{sub 3}, SO{sub 3}, H{sub 2}SO{sub 4}, and SO{sub 4}{sup 2{minus}}, based on a single valence bond (VB) structure in each case. The results are derived from generalized valence bond (GVB) calculations, which provide accurate predictions of the experimental geometries, and contrast with the usual valence bond models for these species, which require more than one VB structure (i.e., resonance). The molecules SO{sub 2}, S{sub 2}O, and S{sub 3} possess sulfur lone pairs that are angularly correlated. This angular separation of the two electrons within a long pair occurs when charge is removed from the sulfur atom by electronegative atoms. Such a separation of lone pair electrons allows for the formation of additional bonds beyond that permitted by the Octet Rule. The role of d functions in the electronic structure of molecules containing second-row atoms is also considered. All calculations were performed within the GVB-PP method, i.e. incorporating the strong orthogonality and perfect pairing (SOPP) approximations.

Some comments on the present situation of quantum chemistry in view of the discussions at the Dubrovnik workshop on the electronic structure of molecules

Abstract

Metabolic activation of carcinogens and toxic chemicals.

1. The spatial parameters and electronic structures of 100 exogenous and endogenous chemicals have been determined by computer graphics, from which their oxidative metabolism by the cytochrome P-448 (activation) or the other families of cytochromes P-450 (generally detoxication) have been predicted. 2. The spatial parameters of these chemicals primarily determine the family of cytochrome P-450 by which the chemicals are metabolized and the electronic structures primarily determine their ease of oxidative metabolism. 3. The role of oxidative metabolism of xenobiotics by the cytochromes P-448, and their binding to the cytosolic Ah receptor, are considered in relationship to the mechanisms of chemical toxicity, mutagenicity, carcinogenicity, and co-carcinogenicity. 4. The mechanisms of chemical toxicity and carcinogenesis are considered in respect of activation through cytochrome P-448-mediated, conformationally-hindered oxygenation to reactive intermediates which, unlike most cytochrome P-450-oxygenated metabolites, are not acceptable substrates for conjugation and detoxication and therefore react with essential intracellular macromolecules. 5. The computer graphic method of determining the molecular conformations and electronic structures of molecules is a rapid, scientifically-based procedure for evaluation of the potential toxicity, mutagenicity and carcinogenicity of chemicals.

Intramolecular interactions and nature of the lowest electronically excited states in compounds modeling the structural unit of lignin. I. Molecular form

Quantum-chemical calculations of the electronic structure of molecules of model compounds of lignin in the ground and electronically excited states have been made by the CNDO/S method. The paper gives results on the energies and strengths of the oscillators of the electronic transitions and on the type of excited singlet and triplet states, shows the main configurations of the HOMOs and LUMOs participating in the transitions and their energies and statistical weights, and gives the distribution of charges and their redistribution on the passage of the molecules from the ground into the excited states. Donor-acceptor interactions in the molecules under investigation are discussed on the basis of the results obtained.

On the Hartree-Fock approximation to the electronic structure of molecule in the intense radiation field and the strong vibronic coupling

The Hartree-Fock approximation has been generalized to incorporate the nonadiabatic effect of molecular vibration previously by Tachibana et al. Here, we will derive the Hartree-Fock equation which reflects also the nonlinear effect of the infrared radiation field as well by using the Bloch-Nordsieck transformation which was discussed first by Nguyen-Dang and Bandrauk in the field of molecular physics. The Hartree-Fock equation reflects the non-adiabatic coupling between an electron and a molecular vibration and between the electron and a infrared radiation fields. The infrared radiation field also affects the dynamics of nuclear motion.