Towards accurate ab inito QM/MM calculations of free-energy profiles of enzymatic reactions

Article Abstract:

The evaluation of ab inito QM/MM free-energy surfaces and activation free energies of reactions in enzymes and in solutions is carried out by using the empirical valence bond (EVB) method as a reference potential and then using linear response approximation (LRA). This new method evaluates the free energy associated with both the substrate and the solvent and helps in obtaining a free-energy barrier that reflects the solute entropy properly.

Science & research, Research, Chemistry, Analytic, Entropy (Physics), Entropy (Thermodynamics), Valence, Valence (Chemistry), Qualitative chemical analysis

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Energetics and dynamics of enzymatic reactions

Article Abstract:

The search of the origin of the catalytic power of enzymes must involve dissection of partial energy contribution, which is accomplished by computer simulation approaches is emphasized. The catalytic proposals are examined by two examples: the popular proposal that enzymes catalyze reaction by special dynamic effects is considered and the effectiveness of simulation approaches is demonstrated.

Enzyme kinetics, Computer simulation, Computer-generated environments, Atomic properties, Catalytic antibodies

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On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

Article Abstract:

Reliable studies of enzymatic reactions by combined quantum mechanics/molecular mechanics (QM/MM) approaches, with an ab initio description of the quantum region, presents a major challenge to computational chemists. The hypothetical reaction of a metaphosphate ion with water in the Ras. GAP complex was chosen, to examine the problems with energy minimization QM/MM approaches.

Phosphates, Quantum theory, Quantum mechanics, Mechanical properties, Enzymatic analysis, Properties

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