Electronic structure of the PYP chromophore in its native protein environment

We report on supermolecular ab initio calculations which clarify the role of the local amino acid environment in determining the unique electronic structure properties of the photoactive yellow protein (PYP) chromophore. The extensive ab initio calculations, at the level of the CC2 and EOM-CCSD methods, allow us to explicitly address how the interactions between the deprotonated p-coumaric thio-methyl ester (pCTM-) chromophore and the surrounding amino acids act together to create a specifically stabilized pCTM- species. Particularly noteworthy is the role of the Arg52 amino acid in stabilizing the chromophore against autoionization, and the role of the Tyr42 and Glu46 amino acids in determining the hydrogen-bonding properties that carry the dominant energetic effects.     

Electronic and geometric structure of isomers of nitric acid. DFT quantum chemical calculations

Based on the B3LYP/6-311++G(3df,3pd) density functional method, quantum chemical calculations of the electronic structure, geometry, and thermodynamic parameters of eight isomers of nitric acid (three known isomers in the form of peroxynitrous acid ONOOH and five new isomers in the form of oxo-conformation OON(H)O) are presented in the work. The molecular structure of each isomer is characterized by a local minimum on the potential energy hypersurface of the HNO₃ molecular system and corresponds to one of its stationary states. A theoretical study of the reactivity of nitric acid oxo-isomers characterized for the first time can provide adequate explanation for experiments on the autocatalytic use of nitric acid vapors in binding molecular nitrogen. The results obtained can be a direction for developing principally new methods to bind atmospheric nitrogen and activate methane, which are fundamental problems in chemical science and technology.     

Electronic structure of metastable isomers of Ru nitroso complexes

Geometrical structures of nitroso complexes trans- [Ru(NO)(NH₃)₄(Cl)]²⁺, trans-[Ru(NO)(NH₃)₄(H2O)]³⁺, [Ru(NO)(Cyclam)(Cl)]²⁺(Cyclam is 1,4,8,11-tetraazocyclodecane), and [Ru(NO)(Bipy)₂(Cl)]²⁺ (Bipy is 2,2-bipyridine) are optimized using the density functional method. The potential energy surface of all four complexes was found to contain local minima corresponding to a stable state with the ¹-coordination of NO through the N atom and to two metastable isomers with the ¹-O and ²-NO coordination. For [Ru(NO)Cl₅)]^2-, trans-[Ru(NO)(NH₃)₄(Cl)]²⁺, and trans-[Ru(NO)(NH₃)₄(H₂O)]³⁺, the lowest electronically excited triplet states are calculated, as well as the reduced complexes with one additional electron. It is shown that the electron excitation and reduction are accompanied by bending of the RuNO group with a substantial elongation of the Ru-O and N-O bonds, which makes this group unstable. These processes do not cause any significant changes in the metal or in the nitroso ligand oxidation states because of the electron density delocalization in the RuNO group.Translated from Koordinatsionnaya Khimiya, Vol. 31, No. 1, 2005, pp. 32–42.Original Russian Text Copyright © 2005 by Sizova, Lubimova.     

Solvation of p-coumaric acid in water

The photoactive yellow protein (PYP) is an important model protein for many (photoactive) signaling proteins. Key steps in the PYP photocycle are the isomerization and protonation of its chromophore, p-coumaric acid (pCA). In the ground state of the protein, this chromophore is in the trans configuration with its phenolic oxygen deprotonated. For this paper, we studied four different configurations of pCA solvated in water with ab initio molecular dynamics simulations as implemented in CP2K/Quickstep. We researched the influence of the protonation and isomerization state of pCA on its hydrogen-bonding properties and on the Mulliken charges of the atoms in the simulation. The chromophore isomerization state influenced the hydrogen-bonding less than its protonation state. In general, more charge yielded a higher hydrogen-bond coordination number. Where deprotonation increases both the coordination number and the residence time of the water molecules around the chromophore, protonation showed a somewhat lower coordination number on two of the three pCA oxygens but much higher residence times on all of them. This could be explained by the increased polarization of the OH groups of the molecule. The presence of the chromophore also influenced the charge and polarization of the water molecules around it. This effect was different in the four systems studied and mainly localized in the first solvation shell. We also performed a proton-transfer reaction from hydronium through various other water molecules to the chromophore. In this small charge-separated system, the protonation occurred within 6.5 ps. We identified the transition state for the final step in this protonation series.     

Electronic structure and stability of fullerene C82 isolated-pentagon-rule isomers

All nine isolated-pentagon-rule isomers of fullerene C(82) were investigated by the DFT method with the B3LYP functional at the 6-31G, 6-31G*, and 6-31+G* levels. The distribution of single, double, and delocalized π-bonds in the molecules of these isomers is shown for the first time. The obtained results are fully supported by DFT quantum-chemical calculations of electronic and geometrical structures of these isomers. The molecules of isomers 7 (C(3v)), 8 (C(3v)), and 9 (C(2v)) contain some radical substructures (such as the phenalenyl-radical substructure), which indicates that they are unstable and cannot be obtained as empty molecules. Thus, there is a possibility of obtaining them only as endohedral metallofullerenes or exohedral derivatives. Isomers 1 (C(2)), 2 (C(s)), 4 (C(s)), 5 (C(2)), and 6 (C(s)) with closed electronic shell are supposed to be stable, resembling isomer 3 (C(2)), which has just been extracted experimentally as an empty fullerene. We assume they can be produced as empty molecules.     

Electronic structure of anionic σ complexes of m-dinitrobenzene and its derivatives

It has been established as a result of calculations of the electronic structure of products of the addition of nucleophilic agents (H^– and CH ₃ ^– ) to m-dinitrobenzene and its derivatives by the CNDO/S method that the negative charge of these anions is delocalized over the system of the cyclohexadiene ring (50%) and the nitro groups (15–20% each), of which the nitro group in the para position (to the sp³-hybridized carbon atom) is more negatively charged. A certain fraction of the charge of the anion is distributed according to an induction mechanism to the hydrogen atoms and the geminal substituents. The data on the bond orders and the distribution of charges attest to the quinoidal structure of the carbon ring in the a complexes. The results of the calculations make it possible to predict the direction of the reactions of the anionic complexes with electrophilic and nucleophilic reagents. The calculated values of the total energies of the complexes correctly reflect their relative stability.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 25, No. 1, pp. 27–33, January–February, 1989.     

Features of the alkynyl ruthenium chromophore with modified anionic subsystem UV absorption

Theoretical simulation of UV-vis absorption for a new series of alkynyl ruthenium chromophores spectra and investigations the influence of anionic substituence on a spectral shift of UV absorption was presented. The MM(+) molecular force field method was used for total energy minimization and for building of the molecular optimized geometry [S.J. Weiner, P.A. Kollman, D.A. Case, U.C. Ghio, G. Alagona, J.S. Profeta, P. Weiner, J. Am. Chem. Soc. 106 (1984) 765; S.J. Weiner, P.A. Kollman, D.T. Nguyen, D.A. Case, J. Comput. Chem. 7 (1986) 230]. All quantum chemical calculations were performed by semi-empirical ZINDO/1 method within a framework of the restricted Hartree-Fock approach and convergence limit up to 10(-6)eV after 500 iterations was achieved. Good agreement between the theoretically calculated and experimentally measured spectra was observed. The largest spectral shift in position of absorption peaks was observed for compound containing the anionic (Cl), substituent. The theoretically calculated absorption maximum is blue shifted with respect to the experimental spectra for all compounds what is connected with the changes of the charge transfer determining the corresponding state dipole moments. Analysis of the theoretical spectra shows a substantial sensitivity to the backside groups.     

Electronic structure and absorption spectra of the anionic σ complexes of nitrobenzenes and nitrostyrenes

Institute of High-Molecular Compounds, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 32, No. 4, pp. 36–45, July–August, 1991.     

Electronic structure and geometry of the active centres in anionic polymerization of vinyl monomers

The charge distributions in the ions (CH₃CHR) and in the molecules CH₃CHRLi (RNO₂, CN, COOCH₃, C₆H₅, CHCH₂, H, NH₂ or OCH₃), modelling the active centres of the two extreme types in anionic polymerization, were calculated by the CNDO/2 method. The geometry of these compounds was partly optimized. Both the geometry and the charge distribution in anions were found to exhibit no strong dependence on R. This suggests that in free ion polymerization, the equality r₁r₂ = 1 holds. The active centres of the polarized bond type are fairly varied. Two reasons for their reactivity may exist: the polarity of their CLi bond and their geometry facilitating the insertion of a monomer. The electronic structure of the neutral molecules considered correlates with the low degree of association of the living chains.     

Electronic structure of light-induced lophyl radical derived from a novel hexaarylbiimidazole with pi-conjugated chromophore

A novel photochromic hexaarylbiimidazole with a bithienyl group as an extended pi-conjugation unit was synthesized and the light-induced lophyl radical was found to be stabilized due to the delocalization of an unpaired electron, and to strongly absorb near-infrared light.     

Resolving the ultrafast dynamics of the anionic green fluorescent protein chromophore in water

The chromophore of the green fluorescent protein (GFP) is critical for probing environmental influences on fluorescent protein behavior. Using the aqueous system as a bridge between the unconfined vacuum system and a constricting protein scaffold, we investigate the steric and electronic effects of the environment on the photodynamical behavior of the chromophore. Specifically, we apply ab initio multiple spawning to simulate five picoseconds of nonadiabatic dynamics after photoexcitation, resolving the excited-state pathways responsible for internal conversion in the aqueous chromophore. We identify an ultrafast pathway that proceeds through a short-lived (sub-picosecond) imidazolinone-twisted (I-twisted) species and a slower (several picoseconds) channel that proceeds through a long-lived phenolate-twisted (P-twisted) intermediate. The molecule navigates the non-equilibrium energy landscape via an aborted hula-twist-like motion toward the one-bond-flip dominated conical intersection seams, as opposed to following the pure one-bond-flip paths proposed by the excited-state equilibrium picture. We interpret our simulations in the context of time-resolved fluorescence experiments, which use short- and long-time components to describe the fluorescence decay of the aqueous GFP chromophore. Our results suggest that the longer time component is caused by an energetically uphill approach to the P-twisted intersection seam rather than an excited-state barrier to reach the twisted intramolecular charge-transfer species. Irrespective of the location of the nonadiabatic population events, the twisted intersection seams are inefficient at facilitating isomerization in aqueous solution. The disordered and homogeneous nature of the aqueous solvent environment facilitates non-selective stabilization with respect to I- and P-twisted species, offering an important foundation for understanding the consequences of selective stabilization in heterogeneous and rigid protein environments.

Simulations on the aqueous green fluorescent protein (GFP) chromophore (in the equilibrium and non-equilibrium regimes) reveal that observed biexponential fluorescence originates from two competing torsional deactivation pathways.     

Electronic spectra of the 2-oxypurine isomers

The Pariser-Parr-Pople type calculations were carried out for tautomeric isomers of 2-oxypurine. The calculated transition energies for the keto form (III) of this compound are in a good agreement with the observed absorption spectrum.     

Electronic structure of the photoactive yellow protein chromophore: Ab initio study of the low-lying excited singlet states

The excited electronic states of the p-coumaric acid thio-ester chromophore of the Photoactive Yellow Protein (PYP) are characterized in view of identifying the key factors determining the chromophore's isomerisation. These factors include the anionic nature of the chromophore, the presence of sulfur (rather than oxygen or nitrogen) in the ester moiety, and the presence of a hydrogen-bonding environment stabilizing the phenolate moiety. Two twisted stationary S₁ structures are identified, corresponding to a twist around the double bond conjugated with the aromatic ring, and the single bond adjacent to the ring, respectively. The latter structure is accessed directly by relaxation from the Franck–Condon (FC) geometry. These structures are shown to entail a substantial polarization effect (increasing charge separation when moving towards the twisted geometry). Further, an inversion of charge character is observed for the double-bond twisted minimum, which can be accounted for by the vicinity of an S₁–S₀ conical intersection. The S₁–S₀ gap at the minimum geometries depends in a sensitive fashion on the -carbonyl heteroatom. Based upon these observations for the intrinsic properties of the chromophore, we further address the effect of the Arg52 residue, which acts as a counter-ion in the native protein environment.     

On the molecular structure of the phytochrome chromophore: X-ray analysis of two 2,3-dihydrobilatriene-abc derivatives

The molecular and crystal structures of the two 2,3-dihydrobilatrienes-abc1 and2, representing model compounds for the phytochrome chromophore, were determined by X-ray crystallography at 97 K. Crystals of the racemate1 contain disordered regions. Both molecules are found to be ofall-(Z) configuration, assuming a helical conformation. The acidic hydrogen atoms are localized at the nitrogen atoms of rings A, C and D. A summary of the geometries of unsaturated five-membered rings as observed in four accurate low-temperature crystal structures of bilatrienes-abc is given.Herrn Prof.Josef Schurz zum 60. Geburtstag gewidmet.     

Electronic structure and spectroscopic properties of the two structural isomers of donor-acceptor substituted sesquifulvalene in the gas and solution phases-a case study of sudden polarization

The ground state equilibrium structure and electric properties of two structural isomers of donor-acceptor substituted sesquifulvalene have been calculated at ab initio HF and MP2 levels for different conformations. The electronic properties of low lying excited singlets are calculated by using CI calculations including single excitations only. Isomer I in which the inter-ring charge transfer (CT) is reinforced in the presence of substituents shows sudden polarization in the ground and two lower lying excited states, while isomer II in which the longitudinal CT interaction is attenuated does not exhibit sudden polarization. The phenomenon of sudden polarization has been rationalized in terms of the easy polarization, smaller rotational barrier, and enhanced inter-ring CT on going from the planar to the orthogonal geometry. The appreciably large static second-order polarizability of I stems from its sudden polarized ground state. The solvent (using the conductor-like polarizable continuum model (CPCM)) plays a significant role on the modulation of ground and excited state electronic properties which, in general, predicts blue-shifts for I. However, for molecule II, the two lower energy transitions show a red-shift while the others show a weaker blue-shift at any conformation.     

Electronic structures of the seven C80 isomers

The Su-Schrieffer-Heeger (SSH) model has been extended and solved numerically to study the electronic structures of seven C₈₀ fullerene isomers. Then we analyze the electronic properties of the seven isomers and discuss the difference among their electronic structure. It is found that phonons considered in the SSH model induce different results from recent theoretical studies. We compare our results with those obtained with other methods and discuss the difference.     

Excited-state structure determination of the green fluorescent protein chromophore

Ultrafast polarization-sensitive infrared (IR) spectroscopy of the C=O stretching mode of the chromophore of the green fluorescent protein reveals a near complete twisting around the ethylenic bridge between the phenolate and imidazolidinone groups upon electronic excitation, hinting at a decisive role of this motion in the efficient internal conversion process.