Proton costs

The main challenge in the present type of quantum mechanical modeling is to estimate the protonation cost The proton needed for the substrate reaction is ultimately provided by the solvent, a part that cannot be included in the model. To be able to work with a limited model, it is assumed that the resting state of the proton is the position of lowest energy in the quantum chemical model. For most models this position turns out to be the carboxyl-ate. This does not mean that the proton actually comes from the carboxylate or that the mechanism requires that the carboxylate is protonated in the reactant. The procedure simply gives a lower limit for the energy required to protonate the base. 

So far all models used for the base protonation mechanism have given total barriers for decarboxylation of more than 40 kcal/mol. In all those models, the amino acids added were chosen mainly to affect the C-C bond strength, but a large fraction of the total barrier comes from the protonation cost. The next step is therefore to discuss models that focus on the region around 02 and include residues that might affect the proton affinity of 02. In the X-ray... 

The final combined model should be the most balanced one, and it adds the 02 residues to Model 14, which has the charged network on the carboxylate side. In this model (Model 17), 02 protonation costs only 7 kcal/mol. This is surprisingly low, since by comparing the results for the Models 14... 

Calculating Protonation Costs for the Pyrimidine Ring Using QM/MM Models... 

The concerted nature of proton transfer contributes to its rapid rate. The energy cost of breaking the H—Cl bond is partially offset by the energy released in forming the new bond between the transfened proton and the oxygen of the alcohol. Thus, the activation energy is far- less than it would be for a hypothetical two-step process in which the H—Cl bond breaks first, followed by bond formation between FF and the alcohol. 

What is the cost of ATP-ADP exchange relative to the energy cost of ATP synthesis itselD We already noted that moving 1 ATP out and 1 ADP in is the equivalent of one proton moving from the cytosol to the matrix. Synthesis of an... 

A fuel cell is an electrochemical reactor with an anodic compartment for the fuel oxidation giving a proton and a cathodic compartment for the reaction of the proton with oxygen. Two scientific problems must be solved finding a low-cost efficient catalyst and finding a membrane for the separation of anodic and cathodic compartments. The membrane is a poly electrolyte allowing the transfer of hydrated proton but being barrier for the gases. 

For last few years, extensive studies have been carried out on proton conducting inorganic/organic hybrid membranes prepared by sol-gel process for PEMFC operating with either hydrogen or methanol as a fuel [23]. A major motivation for this intense interest on hybrid membranes is high cost, limitation in cell operation temperature, and methanol cross-... 

The electrocatalytic oxidation of methanol has been widely investigated for exploitation in the so-called direct methanol fuel cell (DMFC). The most likely type of DMFC to be commercialized in the near future seems to be the polymer electrolyte membrane DMFC using proton exchange membrane, a special form of low-temperature fuel cell based on PEM technology. In this cell, methanol (a liquid fuel available at low cost, easily handled, stored, and transported) is dissolved in an acid electrolyte and burned directly by air to carbon dioxide. The prominence of the DMFCs with respect to safety, simple device fabrication, and low cost has rendered them promising candidates for applications ranging from portable power sources to secondary cells for prospective electric vehicles. Notwithstanding, DMFCs were... 

The discrete protonation states methods employing implicit solvent models in both MD and MC steps have significantly lower computational cost. Dlugosz and... 

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