scholarly journals Theoretical Studies of the Transition-State Structures and Free Energy Barriers for Base-Catalyzed Hydrolysis of Amides

2006 ◽  
Vol 110 (46) ◽  
pp. 12644-12652 ◽  
Author(s):  
Ying Xiong ◽  
Chang-Guo Zhan
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Theoretical Studies ◽  
Energy Barriers ◽  
Hydrolysis Of ◽  
Transition State Structures

scholarly journals Application of rate-equilibrium free energy relationship analysis to nonequilibrium ion channel gating mechanisms

2009 ◽  
Vol 134 (2) ◽  
pp. 129-136 ◽  
Author(s):  
László Csanády
Keyword(s):  
Free Energy ◽  
Ion Channels ◽  
Transition State ◽  
Ion Channel ◽  
Conformational Transition ◽  
Limited Information ◽  
Relationship Analysis ◽  
Gating Mechanisms ◽  
Gating Mechanism ◽  
Transition State Structures

Rate-equilibrium free energy relationship (REFER) analysis provides information on transition-state structures and has been applied to reveal the temporal sequence in which the different regions of an ion channel protein move during a closed–open conformational transition. To date, the theory used to interpret REFER relationships has been developed only for equilibrium mechanisms. Gating of most ion channels is an equilibrium process, but recently several ion channels have been identified to have retained nonequilibrium traits in their gating cycles, inherited from transporter-like ancestors. So far it has not been examined to what extent REFER analysis is applicable to such systems. By deriving the REFER relationships for a simple nonequilibrium mechanism, this paper addresses whether an equilibrium mechanism can be distinguished from a nonequilibrium one by the characteristics of their REFER plots, and whether information on the transition-state structures can be obtained from REFER plots for gating mechanisms that are known to be nonequilibrium cycles. The results show that REFER plots do not carry information on the equilibrium nature of the underlying gating mechanism. Both equilibrium and nonequilibrium mechanisms can result in linear or nonlinear REFER plots, and complementarity of REFER slopes for opening and closing transitions is a trivial feature true for any mechanism. Additionally, REFER analysis provides limited information about the transition-state structures for gating schemes that are known to be nonequilibrium cycles.

Kinetics and mechanism of the hydrolysis of a (5,6)-spirophosphorane. Thermodynamics of the hydrolysis of cyclic five-membered and six-membered phosphonium ions

1991 ◽  
Vol 69 (12) ◽  
pp. 2064-2074 ◽  
Author(s):  
Glenn H. McGall ◽  
Robert A. McClelland
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Rate Constants ◽  
Strong Acid ◽  
Membered Ring ◽  
Phosphate Esters ◽  
Hydrolysis Rate ◽  
Activation Free Energy ◽  
Stabilizing Effect ◽  
Hydrolysis Of

The cyclic five-membered phosphonium ion 2b (2-(2′-hydroxyethoxy)-2-phenyl-1,3,2-dioxaphospholan-2-ylium) derived from ring-opening of the (5,5)-spirophosphorane 1b (5-phenyl-1,4,6,9-tetraoxa-5-phosphaspiro[4,4]nonane) has been observed in neat CF3SO3H and at >85% H2SO4. The cation undergoes hydrolysis in the latter solutions, and an extrapolation has been carried out to obtain an estimate for reactivity in 100% water. Hydrolysis rate constants for phenyltrialkoxyphosphonium ions in water are 107, 100, and 5 × 10−3 s−1 for cyclic five-membered, cyclic six-membered, and acyclic derivatives respectively; these show an excellent correlation with rate constants for a similar series of phosphate esters. An investigation of the hydrolysis of the (5,6)-spirophosphorane 5 (5-phenyl-8,8-dimethyl-1,4,6,10-tetraoxa-5-phosphaspiro[4,5]decane) provides a clue as to the origins of these rate differences. This phosphorane can in principle hydrolyze via two isomeric cyclic phosphonium ions, the six-membered 14 and the five-membered 15. The former is thermodynamically more stable, being the only cation observed under equilibrating conditions of strong acid. However, the hydrolysis of the spirophosphorane, as well as the hydrolysis of fully formed 14, channels through the cyclic five-membered 15. A thermodynamic breakdown reveals that the 9.5 kcal mol−1 difference in activation free energy for the hydrolysis of five- and six-membered cyclic phosphonium ions is due to a combination of a higher free energy (2.5–4.5 kcal mol−1) for the five-membered cation, and a lower free energy (7–5 kcal mol−1) for the pentacoordinate transition state with the five-membered ring. This analysis also shows that a (5,6)-spirophosphorane is 6–8 kcal mol−1 more stable than a (6,6)-spirophosphorane. Thus, a five-membered ring has a significant stabilizing effect on a pentacoordinated phosphorus structure. The accelerated hydrolysis of cyclic phosphonium ions and phosphate esters with five-membered rings is caused by a combination of this stabilizing effect in the transition state and a destabilizing effect in the ground state associated with ring strain. Key words: phosphorane, hydrolysis, phosphate, phosphonium.

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