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  • Atomic, Molecular and Optical Physics  (6)
  • Wiley-Blackwell  (6)
  • Oxford University Press
  • 1
    Electronic Resource
    Electronic Resource
    The influence of geometrical fluctuations on electron tunneling barriers in proteins (1988)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 34 (1988), S. 23-32 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have recently developed a new classification of the amino acid side chains based on doublet acceptor energy levels (DALs). These energy levels, taken as the eigenvalue of the highest occupied molecular orbital in the radical anion, provide insight into the shape of the tunneling barrier in protein electron transfer. We have used this classification to characterize several transfer pathways in myoglobin. We present here a study of the effect of changes in geometry on the doublet acceptor levels. We find that, in general, this influence is rather small for reasonable changes in bond lengths and angles (e.g., those resulting from thermal fluctuations in the protein structure). However, we have found that for serine, threonine and water, changes in geometry that might take place as a result of fluctuations in hydrogen bond geometries lead to rather large changes in DAL. We investigate these correlations in some detail. The relation between protein fluctuations and changes in the shape of the electron tunneling barrier is discussed. Additionally, based on the energetics of changes in the OH bond distance, we discuss aspects of the relation between electron transfer and proton transfer.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560340705
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  • 2
    Electronic Resource
    Electronic Resource
    Proton release pathway in bacteriorhodopsin: Molecular dynamics and electrostatic calculations (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 33-56 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We use molecular dynamics, electrostatic, and quantumchemical calculations to discuss chromophore and protein structural changes as well as proton transfer pathways in the first half of the bacteriorhodopsin photocycle. A model for the molecular mechanism is presented, which accounts for the complex pH dependence of the proton release and uptake pattern found for the M intermediates. The results suggest that transient transfer of the Schiff base proton to a nearby tightly bound water molecule is the primary step, which is accompanyied by dissipation of free energy to the protein. From there, the energetically most favorable proton transfer is to aspartate D85. Arginine R82 is involved in the protein reorientation switch, which catalyzes the pKa reduction of glutamate E204. This residue is, therefore, identified as extracellular proton release group whose acid base equilibrium regulates the pH-dependent splitting of the photocycle. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520705
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  • 3
    Electronic Resource
    Electronic Resource
    Proton transfer to ubiquinone QB in the photosynthetic reaction center of Rps. Viridis: The role of electrostatic interactions (1993)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 48 (1993), S. 89-106 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Electrostatic calculations of the pKa of ionizable groups in the reaction center of Rhodopseudomonas (Rps.) viridis were carried out to investigate three possible mechanisms for proton transfer to the singly reduced acceptor ubiquinone QB. The program DelPhi, which solves the Poisson-Boltzmann equation given the distribution of charges and dielectric boundaries, was used to determine the electrostatic potential. The shift in pKa of the titratable residues in the QB binding pocket in response to the one-electron reduction and following protonation of QB was obtained from calculated interactions with the reaction field, background protein dipoles, charged cofactors, and other ionizable residues. A limited number of bound waters was also included in the computations as titrating sites. Their titration behavior was shown to be strongly coupled to neighboring ionizable sites. The results show that strong electrostatic interaction between the radical anion QB-· and a neighboring serine residue (SER L 223) as well as the protein environment stabilize a system in which the incoming proton is localized on serine and only shared in a hydrogen-bonding relationship with QB-·. These results hint to the possibility that actual proton transfer to QB-· only occurs after a second negative charge has been added to the system through transfer of a second electron either to the menaquinone QA, with formation of the QB-· QA-· system, or to QB-·, leading to the doubly reduced QB2-. This preposition is consistent with spectroscopical and electron nuclear double resonance (ENDOR) experimental results for bacterial reaction centers (RCs) failing to find evidence for the existence of the protonated semiquinone QBH·. © 1993 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560480712
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  • 4
    Electronic Resource
    Electronic Resource
    Reversible photochemistry in the α-subunit of phycoerythrocyanin: Characterization of chromophore and protein by electrostatic calculations (1993)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 48 (1993), S. 199-212 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We used a macroscopic dielectric model to study the effects of solvation and interaction between titratable and permanent partial charges on the protein conformational energy and the acid-base equilibria in the cyanobacterial photoreceptor phycoerythrocyanin, whose photoreversible photochromic response is attributed to a Z/E isomerization of the covalently bound tetrapyrrole chromophore. The calculations revealed the stabilization of the charged protonation state of the chromophore by a small set of strong local interactions. Although the protein is globular and water-soluble, the complex counterion structure has a striking similarity to the arrangement found for the photochemical active transmembrane protein bacteriorhodopsin. This could be attributed to the fact that the protonation site in the α-subunit of phycoerythrocyanin is buried in the interior of the protein. Due to the strong shielding from solvent, the interaction pattern is conserved upon a ground-state isomerization of the chromophore. The partial solvent exposure of the isomerization site resulted in a drastic influence of the chromophore configuration on the aqueous solvation energy of the protein. Implications for the sensitivity of the photochemistry to environmental factors and molecular binding are discussed. © 1993 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560480721
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  • 5
    Electronic Resource
    Electronic Resource
    Magneto-optical properties of a spinless particle moving in a harmonic potential (1977)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 11 (1977), S. 525-542 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Exact solutions to the quantum mechanical problem of an anisotropic oscillator in a one-dimensional magnetic field are obtained. These solutions (eigenenergies and wave functions) are then applied to the problem of calculating the magneto-optical properties of a charged spinless particle constrained to move in a harmonic potential field. General expressions for the dipole strengths and rotational strengths associated with radiation induced transitions between the eigenstates of this model system are developed, and these quantities are further related to observables of magneto-optical absorption spectroscopy and Faraday effect studies.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560110402
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  • 6
    Electronic Resource
    Electronic Resource
    Evaluation of integrals appearing in the hylleraas CI method by expanding 1/rij in terms of a complete basis set (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 39-48 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new approach for solving multielectronic integrals in quantum chemistry is presented. The Coulomb potential r12-1 is expanded in a complete function set within a finite spherical domain of radius R. This expansion yields a series where the \documentclass{article}\pagestyle{empty}\begin{document}$ \vec r_1 {\rm and\, }\vec r_2 $\end{document} variables are symmetrically separated. The generalization to other potentials is briefly discussed. The Yukawa potential exp(-ζr12)/r12, and the functions exp(-ζr122) and exp(-ζr12) are considered as particular cases. As an example of the potentialities of this approach, a certain type of four-electron integrals that appear in the Hylleraas CI method are evaluated. Results thus obtained are discussed in terms of the approximations made and compared with values obtained using other procedures available in the literature. © 1994 John Wiley & Sons, Inc.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520808
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