Dependence of Tyrosine Oxidation in Highly Oxidizing Bacterial Reaction Centers on pH and Free-Energy Difference†

Biochemistry ◽  
2004 ◽  
Vol 43 (40) ◽  
pp. 12905-12912 ◽  
Author(s):  
L. Kálmán ◽  
A. J. Narváez ◽  
R. LoBrutto ◽  
J. C. Williams ◽  
J. P. Allen
Keyword(s):  
Free Energy ◽  
Energy Difference ◽  
Reaction Centers ◽  
Free Energy Difference ◽  
Bacterial Reaction Centers ◽  
Tyrosine Oxidation

Reduction of the oxidized bacteriochlorophyll dimer in reaction centers by ferrocene is dependent upon the driving force

2007 ◽  
Vol 11 (03) ◽  
pp. 205-211 ◽  
Author(s):  
László Kálmán ◽  
Arlene L. M. Haffa ◽  
JoAnn C. Williams ◽  
Neal W. Woodbury ◽  
James P. Allen
Keyword(s):  
Electron Transfer ◽  
Rate Constants ◽  
Ph Dependence ◽  
Photosynthetic Bacterium ◽  
Energy Difference ◽  
Reaction Centers ◽  
Free Energy Difference ◽  
Midpoint Potential ◽  
Bacteriochlorophyll Dimer ◽  
Purple Photosynthetic Bacterium

The rates of electron transfer from ferrocene to the oxidized bacteriochlorophyll dimer, P , in reaction centers from the purple photosynthetic bacterium Rhodobacter sphaeroides, were measured for a series of mutants in which the P / P + midpoint potentials range from 410 to 765 mV (Lin et al. Proc. Natl. Acad. Sci. USA 1994; 91: 10265-10269). The observed rate constant for each mutant was found to be linearly dependent upon the ferrocene concentration up to 50 μM. The electron transfer is described as a second order reaction with rate constants increasing from 1.5 to 35 × 106 M -1. s -1 with increasing P / P + midpoint potential. This dependence was tested for three additional mutants, each of which exhibits a pH dependence of the P / P + midpoint potential due to an electrostatic interaction with an introduced carboxylic group (Williams et al. Biochemistry 2001; 40: 15403-15407). For these mutants, the pH dependence of the bimolecular rate constants followed a sigmoidal pattern that could be described with a Henderson-Hasselbalch equation, attributable to the change of the free energy difference for the reaction due to deprotonation of the introduced carboxylic side chains.

Computer simulation results for the free-energy difference between B-DNA and Z-DNA

2000 ◽  
Vol 12 (8A) ◽  
pp. A327-A332 ◽  
Author(s):  
José L F Abascal ◽  
Juan Carlos Gil Montoro
Keyword(s):  
Computer Simulation ◽  
Free Energy ◽  
Energy Difference ◽  
Free Energy Difference ◽  
Simulation Results ◽  
Z Dna

Conformational analysis of 1,4-disubstituted cyclohexanes. III. trans-1,4-Di(trifluoroacetoxy)cyclohexane

1969 ◽  
Vol 47 (3) ◽  
pp. 429-431 ◽  
Author(s):  
Gordon Wood ◽  
E. P. Woo ◽  
M. H. Miskow
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Free Energy ◽  
Magnetic Resonance ◽  
Low Temperature ◽  
Conformational Analysis ◽  
Integration Method ◽  
Standard Free Energy ◽  
Energy Difference ◽  
Free Energy Difference ◽  
Conformational Free Energy

By the low temperature nuclear magnetic resonance integration method the standard free energy difference between the diequatorial and the diaxial forms of 1-H,4-H-trans-1,4-di(trifluoroacetoxy)-cyclohexane-d8 was found to be 77 ± 5 cal/mole. The conformational free energy (−ΔG0) of the trifluoroacetoxy group in the monosubstituted cyclohexane was 485 ± 4 cal/mole at the same temperature. The non-additivity of the −ΔG0 values is discussed in terms of transannular electrostatic interaction.

A comprehensive computational examination of transannular Diels–Alder reactions of unsubstituted C14 trienes — Barriers, template effects, and the Curtin–Hammett principle

2001 ◽  
Vol 79 (8) ◽  
pp. 1284-1292 ◽  
Author(s):  
Saul Wolfe ◽  
Anthony V Buckley ◽  
Noham Weinberg
Keyword(s):  
Free Energy ◽  
Energy Difference ◽  
Diels Alder ◽  
Molecular Orbital Calculations ◽  
Free Energy Difference ◽  
Molecular Mechanics Calculations ◽  
Geometrical Isomers ◽  
Free Energy Of Activation ◽  
Transition Structures ◽  
Cyclic Compounds

A combination of MM3-level molecular mechanics calculations and PM3-level semiempirical molecular orbital calculations has been employed, in conjunction with an algorithm for the comprehensive conformational analysis of cyclic compounds, to obtain 1202 unique 1,3,9-cyclotetradecatriene conformations, distributed over the six possible geometrical isomers, and 70 unique transannular Diels–Alder transition structures leading to the six possible stereoisomeric tricyclic olefins. A kinetic analysis that takes into account all minima of a given geometrical isomer and all transition structures leading to the same tricyclic product leads to a free energy of activation that is almost the same as the free energy difference between the lowest minimum and the lowest transition structure (the Curtin–Hammett principle). A substantial template effect, mainly entropic in origin, is found when the transannular reactions are compared to the Diels–Alder reactions of the cognate 2,4-hexatrienes with the 2-butenes. Although the cyclization of the trans-cis-trans triene favours the cis-anti-cis over the trans-anti-trans product by more than 20 kcal mol–1, the situation is reversed in the acyclic reaction. A cyclic triene that can cyclize directly to a trans-anti-trans tricycle can therefore be proposed.Key words: molecular models, Deslongchamps, Takahashi, trans-anti-trans tricycle, MM3, PM3, transition states.

Sign in / Sign up

Export Citation Format

Share Document