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ACS chemical biology, ISSN 1554-8929, 01/2013, Volume 8, Issue 1, pp. 71 - 81
Enzymes achieve their transition states by dynamic conformational searches on the femtosecond to picosecond time scale. Mimics of reactants at enzymatic... 
5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE | RICIN | PATHWAY | PURINE NUCLEOSIDE PHOSPHORYLASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | 5'-METHYLTHIOADENOSINE NUCLEOSIDASE | DYNAMICS | ATOMIC DETAIL | INHIBITORS | AMP NUCLEOSIDASE | Enzymes - chemistry | HIV Protease Inhibitors - pharmacology | HIV Protease - drug effects | Models, Biological | Drug Design | Indinavir - pharmacology | Models, Molecular | HIV Protease Inhibitors - chemistry | HIV Protease - chemistry | Kinetics | Indinavir - chemistry | Transition state analysis—the process of measuring intrinsic kinetic isotope effects at sufficient atomic positions to permit reconstruction of a transition state wave function by computational matching of all isotope effects to a quantum chemistry-derived transition state | Dynamic barrier crossing—reactants aligned in the catalytic site by the slow conformational change are subjected to local, fast interactions with catalytic site groups moving on the fsec time scale. When the interactions are optimized by simultaneous chance motion, the barrier to the reaction falls, the transition state is reached and barrier crossing (chemical reaction) can occur | Transition state—the traditional description is a one-dimensional energetic description: the point on the reaction coordinate profile of highest energy relative to substrate | Intrinsic kinetic isotope effects—kinetic isotope effects directly from the chemical step with all obscuring effects removed. Intrinsic kinetic isotope effects report on the bond vibrational status of the labeled reactant atom at the transition state | Transition state analogue—a chemically stable molecule with features of bond lengths, angles and electron density at the van der Waals surface to resemble the actual transition state more closely than it does the reactant. Faithful mimics of enzymatic transition states bind more tightly than substrates by orders of magnitude | Heavy enzyme—enzyme with isotopically substituted atoms to increase the protein mass and thereby decrease the bond vibrational frequency of the protein. Substitution with 2H, 13C and 15N alters mass but not electrostatics according to the Born-Oppenheimer approximation | Transition state structure—a static chemical model of the bond lengths, angles and electron density at the van der Waals surface of the reactant at the instant of the transition state. The transition state structure has a lifetime on the fsec timescale and has equal probability of partitioning to reactant or product | Kinetic isotope effects—the experimentally observed change in reaction rate caused by a specific isotopic substitution in a reactant substrate of the enzyme. Kinetic isotope effects are largest for atoms near the bonds being broken at the transition state but can be partly or fully hidden by kinetic effects obscuring the chemical step | Slow protein conformational changes—enzymes undergo loop, flap and domain motions to bind reactants and release products. These slow conformational changes are necessary steps in an enzymatic catalytic cycle but are too slow to couple to transition state formation
Journal Article
Angewandte Chemie (International ed.), ISSN 1433-7851, 2017, Volume 56, Issue 34, pp. 10070 - 10086
Journal Article
2009, IUCr monographs on crystallography, ISBN 9780199558964, Volume 23, xi, 317
Hydrogen bond (H-bond) effects are well known: it makes sea water liquid, joins cellulose microfibrils in sequoia trees, shapes DNA into chromosomes, and... 
Hydrogen bonding | Crystallography | Transition-state h-bond theory | H-bond puzzle | Equalization principle | Structural databases | Functional h-bonds | Charge-assisted h-bond | Thermodynamic databases | Electrostatic-covalent h-bond model | Resonance-assisted h-bond | Chemical leitmotifs
Book
Angewandte Chemie (International ed.), ISSN 1433-7851, 2013, Volume 52, Issue 38, pp. 9940 - 9943
The conclusion is inevitable: Increasing stabilization of an anionic transition state with increasing π‐acidity of the catalyst is observed; thus, anion–π... 
organocatalysis | molecular recognition | transition states | kinetics | noncovalent interactions
Journal Article
Angewandte Chemie International Edition, ISSN 1433-7851, 04/2016, Volume 55, Issue 17, pp. 5235 - 5237
The ab initio prediction of reaction rate constants for systems with hundreds of atoms with an accuracy that is comparable to experiment is a challenge for... 
ab initio calculations | zeolites | anharmonic vibrations | transition states | free energy calculations | Density functionals | Methylation | Zeolites | Force and energy | Communications | Communication
Journal Article
The journal of physical chemistry. B, ISSN 1520-6106, 05/2015, Volume 119, Issue 21, pp. 6349 - 6356
We examine the capabilities and foundations of three landmark rate theories: harmonic transition state theory, classical nucleation theory, and the Marcus... 
CHEMICAL-REACTIONS | KINETIC PATHWAYS | FOLDING PATHWAYS | ELECTRON-TRANSFER | REACTION COORDINATE | MOUNTAIN PASSES | FINDING SADDLE-POINTS | CHEMISTRY, PHYSICAL | FREE-ENERGY | ACTIVATED RATE-PROCESSES | TRANSITION-STATE THEORY | Nucleation | Research | Electron transport | Transition state (Chemistry)
Journal Article
International journal of chemical kinetics, ISSN 0538-8066
Journal
Journal of computational chemistry, ISSN 0192-8651, 2014, Volume 35, Issue 1, pp. 82 - 93
Kinetic and Statistical Thermodynamical Package (KiSThelP) is a cross‐platform free open‐source program developed to estimate molecular and reaction properties... 
quantum chemistry | RRKM | rate constant | thermochemistry | statistical mechanics | transition state theory | Transition state theory | Thermochemistry | Quantum chemistry | Rate constant | Statistical mechanics | PATH | STATES | WELL | CHEMISTRY, MULTIDISCIPLINARY
Journal Article