Femtosecond Real-Time Probing of Reactions. 19. Nonlinear (DFWM) Techniques for Probing Transition States of Uni- and Bimolecular Reactions

1996 ◽  
Vol 100 (14) ◽  
pp. 5620-5633 ◽  
Author(s):  
M. Motzkus ◽  
S. Pedersen ◽  
A. H. Zewail
Keyword(s):  
Real Time ◽  
Transition States ◽  
Bimolecular Reactions

scholarly journals Real‐time femtosecond probing of ‘‘transition states’’ in chemical reactions

1987 ◽  
Vol 87 (4) ◽  
pp. 2395-2397 ◽  
Author(s):  
Marcos Dantus ◽  
Mark J. Rosker ◽  
Ahmed H. Zewail
Keyword(s):  
Real Time ◽  
Chemical Reactions ◽  
Transition States

Real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization

Nature ◽  
2001 ◽  
Vol 414 (6863) ◽  
pp. 531-534 ◽  
Author(s):  
Takayoshi Kobayashi ◽  
Takashi Saito ◽  
Hiroyuki Ohtani
Keyword(s):  
Real Time ◽  
Transition States

scholarly journals Morse bifurcations of transition states in bimolecular reactions

Nonlinearity ◽  
2015 ◽  
Vol 28 (12) ◽  
pp. 4303-4329 ◽  
Author(s):  
R S MacKay ◽  
D C Strub
Keyword(s):  
Transition States ◽  
Bimolecular Reactions

scholarly journals Femtosecond real-time probing of reactions. 12. Vectorial dynamics of transition states

1993 ◽  
Vol 97 (48) ◽  
pp. 12447-12459 ◽  
Author(s):  
T. Baumert ◽  
S. Pedersen ◽  
A. H. Zewail
Keyword(s):  
Real Time ◽  
Transition States

Force-activated catalytic pathway accelerates bacterial adhesion against flow

2018 ◽  
Vol 475 (16) ◽  
pp. 2611-2620 ◽  
Author(s):  
Jagadish P. Hazra ◽  
Nisha Arora ◽  
Amin Sagar ◽  
Shwetha Srinivasan ◽  
Abhishek Chaudhuri ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Bacterial Adhesion ◽  
Rational Design ◽  
Enzymatic Reaction ◽  
Transition States ◽  
Factors Affecting ◽  
The Real ◽  
Time Dynamics ◽  
Dynamics Simulations

Mechanical cues often influence the factors affecting the transition states of catalytic reactions and alter the activation pathway. However, tracking the real-time dynamics of such activation pathways is limited. Using single-molecule trapping of reaction intermediates, we developed a method that enabled us to perform one reaction at one site and simultaneously study the real-time dynamics of the catalytic pathway. Using this, we showed single-molecule calligraphy at nanometer resolution and deciphered the mechanism of the sortase A enzymatic reaction that, counter-intuitively, accelerates bacterial adhesion under shear tension. Our method captured a force-induced dissociation of the enzyme–substrate bond that accelerates the forward reaction 100×, proposing a new mechano-activated catalytic pathway. In corroboration, our molecular dynamics simulations in the presence of force identified a force-induced conformational switch in the enzyme that accelerates proton transfer between CYS184 (acceptor) and HIS120 (donor) catalytic dyads by reducing the inter-residue distances. Overall, the present study opens up the possibility of studying the influence of factors affecting transition states in real time and paves the way for the rational design of enzymes with enhanced efficiency.

scholarly journals Real‐time clocking of bimolecular reactions: Application to H+CO2

1990 ◽  
Vol 92 (9) ◽  
pp. 5239-5259 ◽  
Author(s):  
N. F. Scherer ◽  
C. Sipes ◽  
R. B. Bernstein ◽  
A. H. Zewail
Keyword(s):  
Real Time ◽  
Bimolecular Reactions

Organic reactions in liquid crystalline solvents. 2. An investigation into the use of liquid crystalline solvents to effect stereochemical control in the Diels–Alder reaction

1985 ◽  
Vol 63 (10) ◽  
pp. 2736-2741 ◽  
Author(s):  
William J. Leigh
Keyword(s):  
Liquid Crystalline ◽  
Transition States ◽  
Alder Reaction ◽  
Diels Alder ◽  
Shape Transition ◽  
Bimolecular Reactions ◽  
Solvent Phase ◽  
Stereochemical Control ◽  
Diels Alder Reaction ◽  
Liquid Crystalline Phases

The possibility of using liquid crystalline solvents to control the stereospecificity of bimolecular reactions as a result of differences in liquid crystalline solvation of the various possible transition states has been examined. The Diels–Alder reactions of 2,5-dimethyl-3,4-diphenylcyclopentadienone with four dienophiles of varying steric size (cyclopentene, cycloheptene, indene, and acenaphthylene) have been carried out in benzene, cholesteryl nonanoate (isotropic), cholesteryl propionate (cholesteric), and 4-ethyl-4′-(4-pentylcyclohexyl)biphenyl (smectic) at 105 °C. In spite of very large differences in steric solvation requirements for the endo- (globular in shape) and exo- (plate-like in shape) transition states in these reactions, no variation in product ratio with solvent phase is observed in any case.The inability of the ordered liquid crystalline phases to differentiate between endo- and exo-transition states in the Diels–Alder reactions investigated is rationalized as being the possible result of several factors. The most important of these are believed to be free volume effects, owing to both inefficient steric solvation of the bulky diene and volume contraction in the transition states for cycloaddition.

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