A theoretical study of electronic excited states of photosynthetic reaction center in Rhodopseudomonas viridis

As well known,photosynthesis is the most impor-tant biochemical process on the earth.With a few mi-nor exceptions,photosynthesis is the only mechanism by which an external source of energy is harnessed by the living world.As a crucial composition of photo…     

Rhodium-catalyzed cyclopropanations of allylsilanes and allylstannanes: the role of the silyl/stannyl group in trans–cis stereoselection

The stereochemistry of cyclopropanation reactions between allylsilanes and allylstannanes 6 with four representative diazoalkanes in the presence of rhodium acetate has been studied. Cyclopropanations with ethyl diazoacetate show a preference for the formation of the trans cyclopropane esters 7, whereas the corresponding reactions with (trimethylsilyl)diazomethane favor the cis stereoisomers. In both cases, overall stereoselection is low, ranging from 1.3:1 to 2.4:1. The product ratios show a small dependence on the nature of the silyl or stannyl groups, with silyl substituents giving better stereoselection than stannyl, and larger ligands on the metal center leading to lower selectivity. On the other hand, rhodium-catalyzed cyclopropanations using methyl 2-diazo-4-phenyl-3-butenoate or 1-aryldiazoacetates occur with excellent stereocontrol. The stereochemical patterns found in these reactions are in accord with an open transition state model wherein the rhodium carbenoid approaches the allylmetal π-bond from an antiperiplanar orientation with respect to the allylic carbonML₃ bond. While the metal center may help stabilize developing β-cationic charge in the transition states, hyperconjugation effects appear to play a minor role, if any, in directing the stereochemical course of cyclopropanation.     

Trans-cis photoisomerization of azobenzene by n→π* excitation:A semiclassical dynamics study

A realistic dynamics simulation study is reported for the trans-cis photoisomerization of azobenzene triggered by the n→π*excitation and the results show that the formation of cis isomer follows the rotational motion around the N=N bond.The simulation find that the CNN bond angle bending vibrations also play a significant role in the vibronic coupling between the HOMO and LUMO,which essentially leads a nonadiabatic transition of the molecule to the electronic ground state.     

A theoretical study of the copper–cysteine bond in blue copper proteins

 The accuracy of theoretical calculations on models of the blue copper proteins is investigated using density functional theory (DFT) Becke's three-parameter hybrid method with the Lee–Yang–Parr correlation functional (B3LYP) and medium-sized basis sets. Increasing the basis set to triple-zeta quality with f-type functions on all heavy atoms and enlarging the model [up to Cu(imidazole-CH₃)₂(SC₂H₅) (CH₃SC₂H₅)^0/+] has only a limited influence on geometries and relative energies. Comparative calculations with more accurate wave-function–based methods (second-order M?ller–Plesset perturbation theory, complete-active-space second-order perturbation theory, coupled-cluster method, including single and double replacement amplitudes and in addition triple replacement perturbatively) and a variety of basis sets on smaller models indicate that the DFT/B3LYP approach gives reliable results with only a small basis set dependence, whereas the former methods strongly depend on the size of the basis sets. The effect of performing the geometry optimizations in a continuum solvent is quite small, except for the flexible Cu-S_Met bond. The results of this study confirm the earlier results that neither the oxidized nor the reduced copper site in the blue proteins is strained to any significant degree (in energy terms) by the protein surrounding. Received: 7 July 2000 / Accepted: 17 November 2000 / Published online: 21 March 2001     

Trans-cis photoisomerization of azobenzene by n →π^＊ excitation： A semiclassical dynamics study

A realistic dynamics simulation study is reported for the trans-cis photoisomerization of azobenzene triggered by the n →π^＊ excitation and the results show that the formation ofcis isomer follows the rotational motion around the N=N bond. The simulation find that the CNN bond angle bending vibrations also play a significant role in the vibronic coupling between the HOMO and LUMO, which essentially leads a nonadiabatic transition of the molecule to the electronic ground state.     

Electronic spectra and trans—cis photoisomerism of carbocyanines. A theoretical (CS INDO CI) and experimental study

Two carbocyanine dyes, DOC(3,3′-diethyloxacarbocyanine) and DTC (3,3′-diethylthiacarbocyanine), were studied in detail by a combined experimental and theoretical treatment previously adjusted on simple streptocyanines. The BPPC (bisphenylaminopentamethine cyanine) dye was also studied to better correlate the properties of DOC and DTC with those of their parent streptocyanine BMPC (bisdimethylaminopentamethine cyanine). In the experimental part of the work, carried out on methanol solutions of BPPC⁺, Cl⁻, DOC⁺, I⁻ and DTC⁺, I⁻, we determined the separate spectra of the stable forms and the photoisomers produced by irradiation into the visible absorption region. The theoretical part, based on CS INDO S + D + T - CI calculations, was especially devised to provide as thorough an interpretation as possible of the electronic spectra (both S₀S_n and S₀T_n) of BPPC, DOC and DTC in terms of molecular subunits and to try to identify each observed species as a specific geometrical isomer (all-trans or mono-cis). In all cases the properties of the stable forms were consistent with the molecules assuming the all-trans structure. The lowest singlet excited state (S₁), responsible for the colour band, retained nearly pure cyanine character (¹B in Platt's notation), while the states falling in the second (medium UV) absorption region had prevailing aromatic (¹H) or charge transfer (¹G) character. This provided an explanation for the absence of a definite “cis peak” effect in these compounds. BPPC was found to give rise to the same photoisomer as BMPC (3–4 cis) and an additional photoisomer clearly identified as the 1–2 cis form. On the other hand, in DOC and DTC, where the spectral changes caused by the irradiation were far weaker, the single observed photoisomer could be better assigned as 2–8 cis, i.e. corresponding to the 2–3 cis form of BMPC.     

FT Raman spectroscopic study of the diimide hydrogenation of cis-polybutadiene: Some evidence of cis—trans isomerization

The diimide hydrogenation of cis-polybutadiene is studied. p-Toluenesulfonylhydrazide is used to fully and partially hydrogenate cis-polybutadiene. The microstructure and hydrogenation of the samples obtained are subsequently studied by FT Raman spectroscopy. Cis—trans isomerization is found to take place during the reaction. A mechanism of isomerization and hydrogenation is also proposed.     

Quantum mechanical study of energetics and mechanisms of cis–trans isomerization of some four-membered heterocycles

Ab initio quantum mechanical calculations using density functional (B3LYP) method and 6-311G** basis set have been performed on two cis and trans conformers of 2,4-diphenyl thietane dioxide (DPTD), 2,4-diphenyl thietane (DPT), 2,4-diphenyl azetidine (DPA) and 2,4-diphenyl oxetane (DPO). The calculated stability energy for cis–trans isomerization in gas phase and in different solvents such as benzene, DMSO, water and methanol indicated that the cis conformer is more stable than trans in all above-mentioned compounds about 11–2 kcal mol^?1. In the next step, a transition states for cis–trans inter-conversion for all four-membered heterocycles (DPTD, DPT, DPA and DPO) were proposed in methanol as solvent. Thermodynamic functions such as standard enthalpies of isomerization (?Hº_iso), standard entropy of isomerization (?Sº_iso) and standard Gibbs free energy of isomerization (?Gº_iso) for all studied compounds were also evaluated. The calculation showed that the conversion of trans to cis isomer is exothermic and spontaneous. In all calculations, solvent effects were considered using a polarized continuum model.     

Tuning the electronic structures and optical properties of fluorene-based donor–acceptor copolymers by changing the acceptors: a theoretical study

Five fluorene-based conjugated copolymers were studied to explore the effect of acceptor on the electronic and optical properties. Their ground-state, excited-state electronic structures and the tunable optical properties were theoretically investigated using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. The acceptors including quinoxaline (Q), 2,1,3-benzothiadiazole (BT), thieno[3,4-b]pyrazine (TP), 2,1,3-benzooxadiazole (BO), and pyridopyrazine (PP) can significantly influence the copolymers’ electronic structures, molecular orbitals, geometric conformations, and optical properties. Calculations were made on systems containing one, two, three, and four oligomers in the neutral, cationic, and anionic structures, which can be extrapolated to infinite chain length polymers. The result indicated that the sequence of the band gap was on the reverse trend of emission wavelength. The strong electron-withdrawing strength of TP unit and coplanar backbone in poly[2,7-(9,9′-dihexylfluorene)-alt-2,3-dimethyl-5,7-dithien-2-yl-thieno[3,4-b] pyrazine] resulted in the enhanced degree of intramolecular charge transfer (ICT) and lowest band gap. The contribution of acceptors to IP was also found to follow the sequence of TP < Q < PP < BT < BO. The absorption and emission spectra exhibited red-shift with increasing the conjugation lengths. The present study suggested that the electronic and optical properties of donor–acceptor conjugated copolymers were affected by the acceptor structure.     

The electronic structure of thorium monoxide: Ligand field assignment of states in the range 0–5 eV

Configuration interaction ligand field theory (CI LFT) calculations of the electronic energy levels of ThO were performed by treating the molecular electronic states as Th ^{2 +} free-ion levels perturbed by the ligand field of O²⁻. Twenty nine experimentally characterized ThO v = 0 energy levels, together with the energy difference between the v = 0 levels of the Y and W states were fitted using a CI LFT model that included Th ^{2 +} 7s ² , 6d7s, 6d², 7s7p, 6d7p, 5f7s, and 7p² configurations. Predictions from these calculations were used to provide tentative assignments for 171 out of 250 ThO band heads listed by Gatterer et al. [“Molecular Spectra of Metallic Oxides”, Specola Vaticana (1957)]. Term energies for 30 electronic states have been determined based on these assignments. Subsequently, the CI LFT model was refined by fitting to a set of 59 electronic term energies. The inclusion of CI effects together with integer valence, atomic-in-molecule, ionic bonding ideas reveals atomic energy level patterns that are multiply replicated in the molecular energy level patterns of six Th ^{2 +} O²⁻ atomic ion configurations (6d7s, 6d², 7s7p, 6d7p, 5f7s, and 7p²) revealing the underlying atomic ion structure that gives rise to the complex and seemingly erratic unassigned bands reported in the Vatican Atlas. © 2018 Wiley Periodicals, Inc.     

Electronic spectra and trans—cis isomerism of streptopolymethine cyanines. A CS INDO CI study

The understanding of the role played by cyanine dyes in various fields of application calls for a thorough knowledge of the excited state properties of their parent chromophores, i.e. cationic streptopolymethyne cyanines. For this aim we performed a detailed CS INDO CI investigation on the electronic spectra of tri-, penta- and heptamethine cyanines, both unsubstituted (TC, PC, HC) and terminally substituted by methyl groups (BMTC, BMPC, BMHC). The study comprised S₀S_n, and S₀T_n transitions of the trans and all mono-cis isomers. CI expansions involved solely π orbitals of the polymethine chains and pseudo-π orbitals of the substituents and included all singly-excited and the most important doubly- and triply-excited configurations. The spectroscopic effects of methyl substitution are fairly well described and are shown to be especially important in the upper excited states. The identification of the photochemically formed stereoisomers is attempted in terms of mono-cis isomers. For BMPC, in particular, we report the absorption spectrum of the phototropic form and show that the photoisomer is identifiable as the 3–4 cis form.     

Variationally determined electronic states for the theoretical analysis of intramolecular interaction: I. Resonance energy and rotational barrier of the C–N bond in formamide and its analogs

We present a new method that produces a variationally determined zeroth-order wave function for the analysis of intramolecular interactions between the fragments of a molecule. In our method, called the space-restricted wave function (SRW) method, this wave function is defined with nonorthogonal orbitals, which are obtained using the appropriately restricted variational spaces. The wave function thus obtained represents the electronic state with the target interactions deactivated, and it is constructed without unnecessarily breaking bonds, in contrast to some of the existing methods. Furthermore, we can perform energy decomposition analysis of intramolecular interactions using the zeroth-order functions that the SRW method yields. The validity of the SRW method is demonstrated in the analysis of the resonance energy and the rotational barrier of the C–N bond in formamide and its analogs. This method gives energy components that are different from those given by existing methods. With these components, we elucidate the origin of the rotational barrier from another point of view. Our SRW method gives meaningful results for the investigation of electron behavior and the nature of the molecular system.     

A theoretical study of beta-sheet models: is the formation of hydrogen-bond networks cooperative?

The cooperativity in terms of enthalpy contribution for beta-sheet formation of polyglycine models in a vacuum has been studied theoretically by using a repeating unit approach. No cooperativity is found in the parallel direction for both the parallel and antiparallel beta-sheets. Cooperativity in the perpendicular direction is dependent upon the residue number (m) in each beta-strand. While there is large cooperativity in the acetamide hydrogen-bond chain (m = 0), the cooperativity is not large in beta-sheet networks (m > 0). SCIPCM solvent model calculations also significantly reduce the cooperativity in hydrogen-bond chains. It is concluded that cooperativity is mainly due to long-range electrostatic interactions and not due to the resonance effect.     

Vibronic coupling in the A2Π and B2Σ+ electronic states of the NCS radical

The spin-rovibronic energy levels of the A(2)Π and B(2)Σ(+) electronic states of thiocyanate radical have been calculated variationally, using high-level ab initio coupled diabatic potential energy surfaces. Computations up to J = 7∕2 have been performed, obtaining all levels with K ≤ 3 (Σ(1/2),Π(1/2,3/2),Δ(3/2,5/2),Φ(5/2,7/2)), for energies up to 2000 cm(-1) above the A(000)(2)Π(3∕2) level. The available experimental data have been critically reviewed in the light of the theoretical findings.     

A Mild Procedure for the Stereospecific Transformation of trans Cinnamic Acid Derivatives to cis β-Bromostyrenes

A new mild procedure has been developed for the synthesis of cis β-bromostyrene analogs with complete Z/E selectivity and good to excellent yields (58.4 - 90.9%). The process involves carboxyl-halo-elimination of cinnamic acid dibromides by using triethylamine in N,N-dimethylformamide at room temperature. A one-pot procedure has also been described for the direct transformation of cinnamic acids to β-bromostyrenes.