ChemInform Abstract: Transition States for N-Acetylneuraminic Acid Glycosyl Transfer: Catalysis via a Transition State Hydrogen Bond

ChemInform ◽  
2010 ◽  
Vol 30 (31) ◽  
pp. no-no
Author(s):  
Benjamin A. Horenstein
2012 ◽  
Vol 11 (05) ◽  
pp. 965-995 ◽  
Author(s):  
MOSTAFA M. H. ELLABAAN ◽  
YEW SOON ONG ◽  
Q. C. NGUYEN ◽  
JER-LAI KUO

As a basic Aristotle element, water is the most abundant and more importantly crucial substance on earth. Without water, there would not be any form of life as we know. Understanding many phenomena in water such as water evaporation and ice melting and formation requires a deep understanding of hydrogen bond breaking and formation. In particular transition states play a key role in the understanding of such hydrogen bond behavior. Transition states, unlike other metastable states, are energy maxima along the minimum energy path connecting two isomers of molecular clusters. Geometry optimization of transition state structures, however, is a difficult task, and becomes even more arduous, especially when dealing with complex biochemical systems using first-principles calculations. In this paper, a novel molecular memetic algorithm (MOL-MA) composing of specially designed molecular-based water evolutionary operators coupled with a transition-state-local search solver and valley adaptive clearing scheme for the discovery of multiple precise transition states structures is proposed. The transition states of water clusters up to four water molecules uncovered using MOL-MA are reported. MOL-MA is shown not only to reproduce previously found transition states in water clusters, but also established newly discovered transition states for sizes 2–4 water molecules. The search performance of MOL-MA is also shown to outperform its compeers when pitted against those reported in the literature for finding transition states as well as recent advances in niching algorithms in terms of solution precision, computational effort, and number of transition states uncovered.


1994 ◽  
Vol 47 (8) ◽  
pp. 1523 ◽  
Author(s):  
MR Haque ◽  
M Rasmussen

The N1/N3-alkylation patterns of 4-amino-, 4-methyl- and 4-nitro-benzimidazole anions, and their 2-methyl analogues, with a standard set of primary alkyl halides (in dimethylformamide, 30°) have been determined and compared. The observed regioselectivities are dominated by proximal effects-electrostatic field, non-bonded steric and in some cases specific association (hydrogen bonding)-the interplay of which is critically dependent on the (variable) geometries of the SN2 transition states involved, in particular on the N---C distance of the developing N-alkyl bonds. The presence of a symmetrically placed 2-methyl group produces an enhanced N1/N3 site selectivity, very sensitive to the loose-tight nature of the transition state. Halide leaving group effects on butylation regioselectivities of 2-unsubstituted, 2-ethoxy-, 2-methyl- and 2-chloro-4-methylbenzimidazole anions, whilst small, are consistent with a Bell-Evans-Polanyi analysis of SN2 transition state variations, with the earlier transition states of CH3(CH2)3I leading to reduced regioselectivities.


1976 ◽  
Vol 54 (5) ◽  
pp. 678-684 ◽  
Author(s):  
Sujit Banerjee ◽  
Nick Henry Werstiuk

Rate data for the acetolysis of exo-norbornyl-sulfonates have been correlated with those for the corresponding endo isomers. It is shown that the slopes of the log kexovs. log kendo plots reflect the difference in delocalization between the transition states derived from the exo and endo isomers, respectively. The log kexovs. log kendo plot, which is comprised of the parent norbornyl sufonate and its derivatives substituted at the 5, 6, and 7 positions, has a slope of 1.11 ± 0.08, which establishes that σ bridging is absent in the transition state obtained from the exo isomer. A similar analysis of base-catalyzed hydrogen–deuterium exchange rates of norbornanones reveals that exo proton exchange is more sensitive to substituent effects than the corresponding endo process.


2020 ◽  
Vol 56 (88) ◽  
pp. 13661-13664
Author(s):  
Piers A. Townsend ◽  
Matthew N. Grayson

This work demonstrates a novel method for aza-Michael reactivity prediction using easily calculable intermediate structures instead of time-consuming transition states.


2017 ◽  
Vol 197 ◽  
pp. 9-39 ◽  
Author(s):  
Shuai Wang ◽  
Iker Agirrezabal-Telleria ◽  
Aditya Bhan ◽  
Dante Simonetti ◽  
Kazuhiro Takanabe ◽  
...  

This account illustrates concepts in chemical kinetics underpinned by the formalism of transition state theory using catalytic processes that enable the synthesis of molecules suitable as fuels from C1 and oxygenate reactants. Such feedstocks provide an essential bridge towards a carbon-free energy future, but their volatility and low energy density require the formation of new C–C bonds and the removal of oxygen. These transformations are described here through recent advances in our understanding of the mechanisms and site requirements in catalysis by surfaces, with emphasis on enabling concepts that tackle ubiquitous reactivity and selectivity challenges. The hurdles in forming the first C–C bond from C1 molecules are illustrated by the oxidative coupling of methane, in which surface O-atoms form OH radicals from O2 and H2O molecules. These gaseous OH species act as strong H-abstractors and activate C–H bonds with earlier transition states than oxide surfaces, thus rendering activation rates less sensitive to the weaker C–H bonds in larger alkane products than in CH4 reactants. Anhydrous carbonylation of dimethyl ether forms a single C–C bond on protons residing within inorganic voids that preferentially stabilize the kinetically-relevant transition state through van der Waals interactions that compensate for the weak CO nucleophile. Similar solvation effects, but by intrapore liquids instead of inorganic hosts, also become evident as alkenes condense within MCM-41 channels containing isolated Ni2+ active sites during dimerization reactions. Intrapore liquids preferentially stabilize transition states for C–C bond formation and product desorption, leading to unprecedented reactivity and site stability at sub-ambient temperatures and to 1-alkene dimer selectivities previously achieved only on organometallic systems with co-catalysts or activators. C1 homologation selectively forms C4 and C7 chains with a specific backbone (isobutane, triptane) on solid acids, because of methylative growth and hydride transfer rates that reflect the stability of their carbenium ion transition states and are unperturbed by side reactions at low temperatures. Aldol condensation of carbonyl compounds and ketonization of carboxylic acids form new C–C bonds concurrently with O-removal. These reactions involve analogous elementary steps and occur on acid–base site pairs on TiO2 and ZrO2 catalysts. Condensations are limited by α-H abstraction to form enolates via concerted interactions with predominantly unoccupied acid–base pairs. Ketonization is mediated instead by C–C bond formation between hydroxy-enolates and monodentate carboxylates on site pairs nearly saturated by carboxylates. Both reactions are rendered practical through bifunctional strategies, in which H2 and a Cu catalyst function scavenge unreactive intermediates, prevent sequential reactions and concomitant deactivation, and remove thermodynamic bottlenecks. Alkanal–alkene Prins condensations on solid acids occur concurrently with alkene dimerization and form molecules with new C–C bonds as skeletal isomers unattainable by other routes. Their respective transition states are of similar size, leading to selectivities that cannot sense the presence of a confining host. Prins condensation reactions benefit from weaker acid sites because their transition states are less charged than those for oligomerization and consequently less sensitive to conjugate anions that become less stable as acids weaken.


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