Nonempirical Investigation of Equilibrium Geometry and Electronic Structure of Kynurenine and 3-Hydroxykynurenine Molecule

By Hartree-Fock-Roothaan method with complete geometry optimization in the basis 6-31G* ab initio calculations of equilibrium geometry and electronic structure were performed for kynurenine C₁₀H₁₂N₂O₃ and 3-hydroxykynurenine C₁₀H₁₂N₂O₃ molecules in the singlet ground state and the first triplet excited state. The molecules in the triplet state can react at the oxygen of the carbonyl group adjacent to the aromatic ring by quite different pathway compared to the molecules in the ground singlet state.     

Interpretation of resonance cars and shpolskii spectra with calculated molecular geometries,vibrational frequencies and relative intensities: Chrysene in it's lowest excited singlet and triplet state

Coherent anti-Stokes Raman scattering (CARS) spectra of excited molecules as well as Shpolskii spectra provide information about geometry changes between ground and excited states. Vibrational frequencies and relative intensities from recently obtained CARS spectra of the chrysene S₁ and T₁ state and earlier observed Shpolskii spectra are interpreted in terms of molecular geometry and force-field changes by means of quantum-chemical consistent force field (QCFF) and Franck-Condon factor calculations. The comparison of observed and calculated relative intensities indicates a coupling between the S₁ and S₂ state enhancing some of the vibrational radiative singlet transitions both in absorption and fluorescence spectra whereas within the phosphorescence spectra proportionality to calculated Franck-Condon factors is obeyed. The T₁ state is the more loosely bound state and its geometry change is different from that of the S₁ state. The resonance CARS transitions in the S₁ state are assigned to totally symmetric vibrations getting their intensity by a coupling scheme analogous to the A term of the resonance Raman effect: the relative intensity of a transition is shown to be proportional to the Franck-Condon factor to the higher excited state and to the squared vibrational frequency. Using this relation this state can be identified by means of its finger-print-like intensity pattern.     

Gleichgewichtsgeometrie und spektroskopische Eigenschaften des Biphenyls im S0-und S1-Zustand

Equilibrium geometry and spectroscopic properties of biphenyl in the S₀ and S₁ state Equilibrium geometries for the S₀ and S₁ state of biphenyl were determined by minimization of the total energy with respect to all cartesian coordinates. The molecule is twisted in the S₀ state (20°), but becomes planar in the S₁ state. Using these results, an interpretation of the fluorescence and absorption spectra can be given. In passing from the S₀ to the S₁ state equilibrium geometry a remarkable change of the state ordering occurs.     

Ab initio molecular orbital theory study of GaAs clusters: The geometry

We have studied the structure and geometry of neutral and charged atomic clusters consisting of Ga and As atoms via ab initio Hartree–Fock (HF) and second‐order Møller–Plesset methods. The Ga_mAs_n cluster with m≠n composition prefers a nontetrahedral geometry in the charge neutral (q=0) state. These clusters tend to be stable in tetrahedral geometry when appropriately charged. The Ga_mAs_n cluster with m=n composition (1:1 ratio of Ga to As atoms) tends to be stable in a tetrahedral geometry in the charge neutral (q=0) state. With increasing size of the cluster, the geometry of Ga_nAs_n cluster approaches the zinc‐belende‐type crystalline structure. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 563–573, 2000     

Influence of the protein and DFT method on the broken‐symmetry and spin states in nitrogenase

The enzyme nitrogenase contains a complicated MoFe₇CS₉ cofactor with 35 possible broken‐symmetry (BS) states. We have studied how the energies of these states depend on the geometry, the surrounding protein, the DFT functional and the basis set, studying the resting state, a one‐electron reduced state and a protonated state. We find that the effect of the basis set is small, up to 11 kJ/mol. Likewise, the effect of the surrounding protein is restricted, up to 10 and 7 kJ/mol for the electrostatic and van der Waals energy terms. Single‐point energies calculated on a single geometry give a good correlation (R² = 0.92‐0.98) to energies calculated after geometry optimization, but some BS states may be disfavored by up to 37 kJ/mol. A change from the pure TPSS functional to the hybrid B3LYP functional may change the relative energies by up to 58 kJ/mol and the correlation between the two results is only 0.57‐0.72. Both functionals agree that BS7 is the most stable BS state and that the ground spin state is the quartet for the resting state and the quintet for the reduced state. With the TPSS functional, the BS6 state is the second most stable state, always at least 21 kJ/mol less stable than the BS7 state. However, with the B3LYP functional, BS10 is the second most stable state and for the protonated state it comes close in energy. Based on these results, we suggest a procedure how to consider the 35 BS states in future investigations of the nitrogenase reaction mechanism.     

ChemInform Abstract: Molecular Geometry and Fluxionality in the AX6E System ClF- 6.

The analysis of the calculated charge distribution and corresponding Laplacian distributions of the ClF₆^- ion in both its equilibrium geometry (C3v) and its fluxional transition state geometry (C2v) confirms the suggestion that AX6E systems should distort from Oh symmetry because of the presence of a stereochemically active lone pair.     

Theoretical study of the π→π* excited states of linear polyenes: The energy gap between 11Bu+ and 21Ag− states and their character

Multireference perturbation theory with complete active space self-consistent field (CASSCF) reference functions is applied to the study of the valence π→π* excited states of 1,3-butadiene, 1,3,5-hexatriene, 1,3,5,7-octatetraene, and 1,3,5,7,9-decapentaene. Our focus was put on determining the nature of the two lowest-lying singlet excited states, 1¹B_u⁺ and 2¹A_g⁻, and their ordering. The 1¹B_u⁺ state is a singly excited state with an ionic nature originating from the HOMO→LUMO one-electron transition while the covalent 2¹A_g⁻ state is the doubly excited state which comes mainly from the (HOMO)²→(LUMO)² transition. The active-space and basis-set effects are taken into account to estimate the excitation energies of larger polyenes. For butadiene, the 1¹B_u⁺ state is calculated to be slightly lower by 0.1 eV than the doubly excited 2¹A_g⁻ state at the ground-state equilibrium geometry. For hexatriene, our calculations predict the two states to be virtually degenerate. Octatetraene is the first polyene for which we predict that the 2¹A_g⁻ state is the lowest excited singlet state at the ground-state geometry. The present theory also indicates that the 2¹A_g⁻ state lies clearly below the 1¹B_u⁺ state in decapentaene with the energy gap of 0.4 eV. The 0–0 transition and the emission energies are also calculated using the planar C_2h relaxed excited-state geometries. The covalent 2¹A_g⁻ state is much more sensitive to the geometry variation than is the ionic 1¹B_u⁺ state, which places the 2¹A_g⁻ state significantly below the 1¹B_u⁺ state at the relaxed geometry. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 157–175, 1998     

High resolution laser spectroscopy of the Na3 B — X system

The B-X system of Na₃ has been investigated at rotational resolution by using cw resonant two photon ionization spectroscopy. Model calculations of the spectra were performed with bond angles and distances as adjustable parameters. In this way, information on the geometry of the ground state and the B state of the sodium trimer was derived.     

Theoretical investigation of the isomers photolysis reaction for chlorine nitrate

For the reactant ClONO₂ the equilibrium geometry and energy have been calculated by using various density functional (DFT) theory methods. The harmonic vibrational frequencies were computed using the B3LYP method for the ground state of the reactant; the results were in good agreement with those of the experiment. It was shown that the DFT methods were superior to other ab initio methods in optimizing geometry and predicting vibrational frequencies. In the process of forming the products from the dissociation reactions of ClONO₂, the results indicated it undergoes the TS₂, but not the TS₁ transition state. According to the relative energies of various species, the potential energy surface reflected intuitively the mechanisms of these dissociation reactions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 44–50, 2003     

X-ray absorption fine structure study of amorphous metal oxide thin films prepared by photochemical metalorganic deposition

The oxidation state and local geometry of the metal centers in amorphous thin films of Fe₂O₃ (Fe³⁺ oxidation state), CoFe₂O₄ (Co²⁺/Fe³⁺ oxidation states), and Cr₂O₃ (Cr³⁺ oxidation state) are determined using K edge X-ray absorption near-edge structure (XANES) spectroscopy and extended X-ray absorption fine structure (EXAFS) spectroscopy. The metal oxide thin films were prepared by the solid-state photochemical decomposition of the relevant metal 2-ethylhexanoates, spin cast as thin films. No peaks are observed in the X-ray diffraction patterns, indicating the metal oxides are X-ray amorphous. The oxidation state of the metals is determined from the edge position of the K absorption edges, and in the case of iron-containing samples, an analysis of the pre-edge peaks. In all cases, the EXAFS analysis indicates the first coordination shell consists of oxygen atoms in an octahedral geometry, with a second shell consisting of metals. No higher shells are observed beyond 3.5 Å for all samples, indicating the metal oxides are truly amorphous, consistent with X-ray diffraction results.     

N‐Methyl‐N‐[(Z)‐2‐phenyl­propenyl]­thio­benz­amide

The crystal structure of the title thio­benz­amide, C₁₇H₁₇NS, was determined to investigate the relationship between the photoreactivity in solid state and the structure. The geometry was confirmed to be the Z isomer.     

The structure of minimal magnetite cluster

Geometry and electronic structure of magnetite minimal cluster (Fe₃O₄)₁ have been simulated by density functional theory and semiempirical PM6 method. Data on the cluster geometry obtained by different methods have been consistent; however, the ground state electronic structures as determined by different methods have not been identical. The existence of two states of similar stability, low-spin and high-spin ones, has been predicted. The correlation of the simulated geometry, vibration spectra, and magnetic properties of the cluster with experimentally determined properties of magnetite, nanomagnetite, and magnetite thin films has been discussed.     

Packing forces in dichloridobis(3,5‐diphenyl‐1H‐pyrazole‐κN2)cobalt(II) dichloromethane hemisolvate

The title compound, [CoCl₂(C₁₅H₁₂N₂)₂]·0.5CH₂Cl₂, was crystallized from a binary mixture of dichloromethane and hexane and a dimeric supramolecular structure was isolated. The Co^II centre exhibits a distorted tetrahedral geometry, with two independent pyrazole‐based ligands occupying two coordination sites and two chloride ligands occupying the third and fourth coordination sites. The supramolecular structure is supported by complementary hydrogen bonding between the pyrazole NH group and the chloride ligand of an adjacent molecule. This hydrogen‐bonding motif yields a ten‐membered hydrogen‐bonded ring. Density functional theory (DFT) simulations at the PBE/6‐311G level of theory were used to probe the solid‐state structure. These simulations suggest that the chelate undergoes a degree of conformational distortion from the lowest‐energy geometry to allow for optimal hydrogen bonding in the solid state.     

Geometries and energies of the excited states of pyridazine studied by sac and sac CI calculations

The geometries and energies of the ground and excited states of pyridazine are calculated by an ab initio calculation which includes electron correlation. It is found that electron correlation plays an essential role in determining the geometries of the excited states. The optimized geometry of the T₁ state as well as that of the ground state are planar. On the other hand, the force constant along the twisted mode of the NN bond in the T₁ state is much smaller than that in the ground state. It is suggested that this distorted potential produces a large Franck-Condon factor between the T₁ and S₀ states, which leads to a very large radiationless decay rate constant of the T₁ state. The location of the S₂ origin is discussed on the basis of the present results.     

Ab initio calculation of the potential surfaces and the electronic transition moments for the valence and Rydberg doublet electronic states of BH2

The bending and symmetric stretching potential curves for the low-lying doublet electronic states of the BH₂ radical are calculated by means of the configuration interaction method. Special attention is paid to consideration of the interaction between valence and Rydberg-type species. The dissociation of BH₂ in its various electronic states into H + B + H is studied. The results of calculations predict a complicated structure of both, the absorption and emission spectra caused by a number of avoided crossings between the excited states of the same symmetry in the geometry region close to the equilibrium geometry of the ground state.     

A Redox‐Confused Bismuth(I/III) Triamide with a T‐Shaped Planar Ground State

Reaction of a tethered triamine ligand with Bi(NMe₂)₃ gives a Bi triamide, for which a Bi^I electronic structure is shown to be most appropriate. The T‐shaped geometry at bismuth provides the first structural model for edge inversion in bismuthines and the only example of a planar geometry for pnictogen triamides. Analogous phosphorus compounds exhibit a distorted pyramidal geometry because of different Bi?N and P?N bond polarities. Although considerable Bi^I character is indicated for the title Bi triamide, it exhibits reactivity similar to Bi^III electrophiles, and expresses either a vacant or a filled p orbital at Bi, as evidenced by coordination of either pyridine N‐oxide or W(CO)₅. The product of the former shows evidence of coordination‐induced oxidation state change at bismuth.     

Abnormal g tensor and multiconfigurational ground state of

The shift of g_lj = 2.0094 in

(geometry D_3d, state ^2A_2u) from 2.0023 is too large to be rationalized with theories of the g tensor based on a single-configurational ground state. This abnormality can be explained with a multi-configurational ground state representing spin polarization.