Notes

Stewart, Ethan; Mare, P. B. D. de la; Pritchard, Jane; Buckingham, A. D.; Holland, H. G.; Fèvre, R. J. W. Le; Davidson, G. F.; Lynch, B. M.; Pausacker, K. H.; Barduhn, Allen J.; Kobe, Kenneth A.; Whalley, W. B.

doi:10.1039/jr9540001643

Cited by 7 publications

(11 citation statements)

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“…Partial charges and van der Waals radii for the amino acids were taken from the CHARMm21 parameter set [36]. The partial charges for the free base and the protonated Schiff base retinal chromophore were calculated with the program package MOPAC 6.0 using the AM1 Hamiltonian [37].…”

Section: Electrostatic Calculationsmentioning

confidence: 99%

Proton release pathway in bacteriorhodopsin: Molecular dynamics and electrostatic calculations

Scharnagl

Hettenkofer

Fischer

1994

Int. J. Quantum Chem.

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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 accornpanyied 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 pK, 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.

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Section: Electrostatic Calculationsmentioning

confidence: 99%

Proton release pathway in bacteriorhodopsin: Molecular dynamics and electrostatic calculations

Scharnagl

Hettenkofer

Fischer

1994

Int. J. Quantum Chem.

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“…Furthermore, semiempirical methods have been shown in the past to present severe difficulties in finding the transition states of the reactions to be modeled. Fortunately, recent advances in the development of parameters have yielded a new set of parameters that are included in the new MNDO-PM3 method (Modified Neglected Diatomic Overlap, Parametric Method 3) [12,13]. This new method allows hypervalent systems to be treated with accuracies comparable to nonhypervalent compounds.…”

Section: °mentioning

confidence: 99%

Molecular modeling of the Wittig olefination reaction: Part 2: A molecular orbital approach at the MNDO‐PM3 level

Marí¹,

Lahti²,

McEwen³

1991

Heteroatom Chemistry

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“…Much effort has gone into studying the ZDO approximation, both in terms of constructing symmetrically orthogonalized basis sets in which ab initio calculations could be performed with ZDO satisfied to a good degree of approximation [22,23] and in theoretical elucidation of terms in the energy expression according to orders in a parameter of the magnitude of a typical two-center overlap intergral [24]. Some authors have carried through ab initio calculations using an ordinary atomic orbital basis and arbitrarily adopting ZDO but naturally have met with disappointing results [25].…”

Section: An Exact Zdo Lcao Methodsmentioning

confidence: 99%

Discontinuous approximate molecular electronic wave‐functions

Stuebing

Weare

Parr

1977

Int J of Quantum Chemistry

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AbstractsFollowing Kohn (reference 4), Schlosser and Marcus (reference 3), and Weare and Parr (reference 2), an energy functional is defined for a molecular problem which is stationary in the neighborhood of the exact solution and permits the use of trial functions that are discontinuous. The functional differs from the functional of the standard Rayleigh-Ritz method in thereplacement of the usual kinetic energy operators T ( p ) with operators T ( p ) = T ( p ) + I ( p ) , where I(p) generates contributions from surfaces of nonsmooth behavior. If one uses the VT . VV way of writing the usual kinetic energy contributions, one must add surface integrals of the product of the average of VT and the change of T across surfaces of discontinuity. Various calculations are carried out for the hydrogen molecule-ion and the hydrogen molecule. It is shown that a6 initio calculations on molecules can be carried out quite generally with a basis of atomic orbitals exactly obeying the zero-differential overlap (ZDO) condition, and a firm basis is thereby provided for theories of molecular electronic structure invoking the ZOO approximation. It is demonstrated that a valence bond theory employing orbitals exactly obeying ZDO can provide an adequate account of chemical bonding, and several suggestions are made regarding molecular orbital methods. Si la forme V q . VV est utiliste, il faut aussi tenir compte de certaines integrales de surface.Divers calculs ont Ctt faits pour l'ion de la molicule d'hydrogkne et la molecule d'hydrogkne. II est demontrt que des calculs de type ab initio peuvent $tre effectuts d'une faGon gtnirale avec un jeu de base d'orbitales atomiques, qui satisfont exactement la condition de recouvrement difftrentiel zero, ce qui fourmit une base solide pour les thtories de la structure electronique moleculaire, qui se fondent sur I'approximation ZDO. Une theorie de type mtsomtrie avec des orbitales satisfaisant exactement I'approximation zDO peut fournir une description adequate de la liaison chimique. Verschiedene Berechnungen werden fur das Wasserstoffmolekulion und das Wasserstoffmolekul ausgefuhrt. Es wird gezeigt, dass ab-initio-Berechnungen fur Molekule ganz allgemein gemacht werden konnen mit einem Atomorbitalbasissatz, der exakt der Bedingung "Differentialuberlappung Null" (ZDO) genugt. Es wird weiter gezeigt, dass eine Valenzbindungsstheorie, die solche Orbitale verwendet, die exakt der zDo-Bedingung genugen, eine angemessene Beschreibung der chemischen Bindung geben kann.

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Cited by 7 publications

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Proton release pathway in bacteriorhodopsin: Molecular dynamics and electrostatic calculations

Proton release pathway in bacteriorhodopsin: Molecular dynamics and electrostatic calculations

Molecular modeling of the Wittig olefination reaction: Part 2: A molecular orbital approach at the MNDO‐PM3 level

Discontinuous approximate molecular electronic wave‐functions

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