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European Journal of Organic Chemistry, ISSN 1434-193X, 10/2019, Volume 2019, Issue 38, pp. 6486 - 6495
Viral RNA 2′‐O‐methyltransferases play a crucial role for luring the host cell innate antiviral response during a viral infection by catalyzing either the... 
Transition states | Nucleosides | Viral RNA methyltransferases | RNA 2′‐O‐methylation | Bisubstrate | RNA 2 '-O-methylation | DESIGN | RECOGNITION | CHEMISTRY, ORGANIC | SELF | PROBES | STRUCTURAL BASIS | DNA | INHIBITORS | BINDING | Organic chemistry | Chemical Sciences
Journal Article
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... 
HUMAN THYMIDINE PHOSPHORYLASE | 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE | PURINE NUCLEOSIDE PHOSPHORYLASE | PSEUDOMONAS-AERUGINOSA | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | 5'-METHYLTHIOADENOSINE NUCLEOSIDASE | HIV-1 PROTEASE | ENZYMATIC-REACTION | ADENOSINE DEAMINASE | 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 Edition, ISSN 1433-7851, 11/2017, Volume 56, Issue 45, pp. 14154 - 14158
Journal Article
The Journal of Organic Chemistry, ISSN 0022-3263, 03/2017, Volume 82, Issue 5, pp. 2436 - 2449
The Ni–Pd catalyzed addition–cyclization of sulfanyl 1,6-diynes 2–9 with nucleobases is described. The reactions of N-tethered 1,6-diynes with N... 
PROTOZOAN NUCLEOSIDE HYDROLASES | CROSS-METATHESIS | IN-VITRO | NUCLEIC-ACID | REVERSE-TRANSCRIPTASE | CHEMISTRY, ORGANIC | STEREOSELECTIVE-SYNTHESIS | INHIBITORS | TRANSITION-STATE ANALOG | ANTIVIRAL DRUGS | DERIVATIVES
Journal Article
European Journal of Medicinal Chemistry, ISSN 0223-5234, 08/2016, Volume 118, pp. 121 - 142
Journal Article
The Journal of Organic Chemistry, ISSN 0022-3263, 02/2008, Volume 73, Issue 4, pp. 1403 - 1412
Journal Article
ChemPhysChem, ISSN 1439-4235, 11/2018, Volume 19, Issue 21, pp. 2839 - 2842
We report herein a gas‐phase reactivity study on a para‐benzyne cation and its three cyano‐substituted, isomeric derivatives performed using a dual‐linear... 
electron affinities | mass spectrometry | gas-phase reactions | Biradical | para-benzyne | P-BENZYNE | DESIGN | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | REACTION EFFICIENCIES | QUADRUPOLE ION-TRAP | CHEMISTRY | ISOMERS | AFFINITIES | Nitriles | Mass spectrometry | Free radicals (Chemistry)
Journal Article
Current Opinion in Chemical Biology, ISSN 1367-5931, 08/2014, Volume 21, pp. 63 - 72
Journal Article
Journal Article
Current Medicinal Chemistry, ISSN 0929-8673, 2015, Volume 22, Issue 34, pp. 3897 - 3909
Transition-state analysis based on kinetic isotope effects and computational chemistry provides electrostatic potential maps to serve as blueprints for the... 
Transition-state theory | Deaminases | N-ribosyltransferases | Iminoribitols | Nucleoside analogues | Transition-state analogues