Molecular proton-exchanged

In molecular mechanics and molecular dynamics studies of proteins, assig-ment of standard, non-dynamical ionization states of protein titratable groups is a common practice. This assumption seems to be well justified because proton exchange times between protein and solution usually far exceed the time range of the MD simulations. We investigated to what extent the assumed protonation state of a protein influences its molecular dynamics trajectory, and how often our titration algorithm predicted ionization states identical to those imposed on the groups, when applied to a set of structures derived from a molecular dynamics trajectory [34]. As a model we took the bovine... 

Consider a nucleus that can partition between two magnetically nonequivalent sites. Examples would be protons or carbon atoms involved in cis-trans isomerization, rotation about the carbon—nitrogen atom in amides, proton exchange between solute and solvent or between two conjugate acid-base pairs, or molecular complex formation. In the NMR context the nucleus is said to undergo chemical exchange between the sites. Chemical exchange is a relaxation mechanism, because it is a means by which the nucleus in one site (state) is enabled to leave that state. 

Dlugosz M, Antosiewicz JM (2005) Effects of solute-solvent proton exchange on polypeptide chain dynamics A constant-pH molecular dynamics study. J Phys Chem B 109 13777-13784. 

Due to rapid proton exchange between forms 22, 23, and 24 (Scheme 1), benzotriazole exhibits at room temperature just two C-H signals, each for two protons, in its 111 NMR spectra. However, when the temperature is lowered, the signals broaden and finally split into four separate resonances of the four individual C-H protons. The results of such study for an acetone solution of benzotriazole are given in Table 3 <2002T9089>. The situation is additionally complicated by formation of adducts 25 and 26, which at — 90 °C contribute 25% and 5%, respectively, to the total molecular population. 

In previous sections we have shown clearly that intramolecular dihydrogen bonds X-H- H-Y, with X and Y representing various chemical elements, can exist in both the solid state and in solution. In addition, the bonds can be a critical factor in the control of molecular conformational states or effects on rapid and reversible hydride-proton exchanges related to the process shown in Scheme 5.1, or the well-known H-D isotope exchanges in similar subsystems [23]. Such bonds could also play an important role in the stabilization of transition states, appearing as a reaction coordinate in many transformations. This is particularly... 

According to a recent ab initio molecular dynamic simulation study639 formation of formyl cation 328 is optimally favored in the 1 1 HF-SbF5 solution. No evidence, however, was found for the formation of the isoformyl cation 329 and diprotonated CO. The fast proton exchange observed earlier was suggested to occur between HCO+ and HF(HF) or SbF6. ... 

Methyl-substituted malonaldehyde (a-methyl-/3-hydroxyacrolein) provides an opportunity to study the role of asymmetry of the potential profile in the proton exchange. In the initial and final states, one of the C-H bonds of the methyl group is in the molecular plane and directed toward the proton position. The double well potential becomes symmetric only due to methyl group rotation over tt/6, when the C-H bond lies in the plane perpendicular to the molecular one. As a result, proton tunneling occurs in combination with CH3 hindered rotation and the... 

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