What happens to formamide during C—N bond rotation? Atomic and molecular energetics and molecular reactivity as a function of internal rotation

1993 ◽  
Vol 71 (6) ◽  
pp. 872-879 ◽  
Author(s):  
Keith E. Laidig ◽  
Lynn M. Cameron

We investigate the energetics of rotation about the C—N bond in formamide at the molecular and atomic levels using the HF/6-31G**//HF/6-31G** level of theory. At the molecular level, the barrier to rotation results from a decrease in overall attractive energies upon rotation away from the planar conformation, primarily due to the lengthening of the C—N bond. At the atomic level, the barrier is due to the loss in interatomic attraction between the nitrogen and its bonded neighbors. We investigate the susceptibility of formamide to electrophilic attack at nitrogen and oxygen as well as nucleophilic attack at carbonyl carbon as a function of C—N bond rotation using the Laplacian model of reactivity. The model predicts the susceptibility to nucleophilic attack at carbonyl carbon to reach a maximum with a O—C—N—H torsional angle of 60°. As a mimic of solvent fields, we investigate the effect of solvation upon these predictions with the application of homogeneous electric fields. This geometry–reactivity relationship is related to proposed models of activation in the enzymatic catalysis of peptides.

Author(s):  
Li Zhang ◽  
Ya‐Ling Ye ◽  
Xiao‐Ling Zhang ◽  
Xiang‐Hui Li ◽  
Qiao‐Hong Chen ◽  
...  

Two examples of catalysis by supported clusters are given that involve a molecular cluster frame during the catalytic cycle. (H)Os 3 (CO) 10 (OSi^) is able to hydrogenate ethylene between 343 and 373 K. The mechanism of this reaction, which involves the molecular cluster frame, requires the opening of the bridging three-electron oxygen ligand as the key step of the catalytic process. Rh 6 (CO) 16 adsorbed on alumina is a catalyst for the water-gas shift reaction carried out between 293 and 393 K. The mechanism of this reaction involves three steps: (i) electrophilic attack by surface protons on the metallic frame with formation of Rh I (CO) 2 and Rh III (H) (H) species; (ii) reductive elimination of H 2 favoured by CO coordination to the Rh III (H) (H) species; (iii) nucleophilic attack by molecular water on CO coordinated to Rh I with regeneration of the starting cluster, release of CO 2 and surface protons.


1979 ◽  
Vol 34 (9) ◽  
pp. 1130-1134 ◽  
Author(s):  
György Schultz ◽  
Mihály Bartók

Abstract A gas electron diffraction study of 2-methyloxacyclobutane has been carried out at room nozzle temperature. The four membered ring takes a planar conformation. The mean ra values for the O-C, C-C and C-H bonds are 1.448(5)A, 1.534(4)A and 1.118(3) Å, respectively. The endocyclic bond angles are C-C-C = 85.5(18)° and C-C-O=91.2 (15)°, while the angle C-O-C was assumed to be 92°. The position of exocyclic carbon atom was characterized, in addition by < Cexocyclic-C-O = 110.7(7)° and torsional angle Cexocyclic-C-O-C = 59.6(40)° (0° corresponds to the anti position of Cexocyclic-C and O-C bonds).


2021 ◽  
pp. 116883
Author(s):  
Linyang Dan ◽  
Kai Zhang ◽  
Zhengyong Huang ◽  
Feipeng Wang ◽  
Qiang Wang ◽  
...  

2000 ◽  
Vol 29 (10) ◽  
pp. 1130-1131 ◽  
Author(s):  
Seichi Okeya ◽  
Masato Hashimoto ◽  
Fumiko Nakamura ◽  
Yoshiaki Kusuyama ◽  
Mako Kobayashi ◽  
...  

2020 ◽  
Author(s):  
Yufan Wu ◽  
Stephen Fried ◽  
Steven Boxer

<div><p>Electrostatic interactions play a pivotal role in enzymatic catalysis and are increasingly modeled explicitly in computational enzyme design; nevertheless, they are challenging to measure experimentally. Using vibrational Stark effect (VSE) spectroscopy, we have measured electric fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have shown that these fields can be unusually large, but it has been unclear to what extent they specifically stabilize the transition state (TS) relative to a ground state (GS). In the following, we use crystallography and computational modeling to show that KSI’s intrinsic electric field is nearly perfectly oriented to stabilize the geometry of its reaction’s TS. Moreover, we find that this electric field adjusts the orientation of its substrate in the ground state so that the substrate needs to only undergo minimal structural changes upon activation to its TS. This work provides evidence that the active site electric field in KSI is preorganized to facilitate catalysis and provides a template for how electrostatic preorganization can be measured in enzymatic systems. <br></p></div>


2000 ◽  
Vol 78 (4) ◽  
pp. 508-515
Author(s):  
John Andraos ◽  
A Jerry Kresge

Rates of hydration of a number of ketenes were measured in neutral and basic solution using flash photolytic techniques, and rate constants for their uncatalyzed, kuc, and hydroxide-ion catalyzed, kHO, reactions were determined. These results, plus additional data from the literature, were found to provide the remarkably good correlation log kuc = -3.21 + 1.14 log kHO, which spans 10 orders of magnitude in reactivity and includes 31 ketenes. This good correlation implies that uncatalyzed and hydroxide-ion catalyzed ketene hydraton occur by similar reaction mechanisms, which for the hydroxide-ion catalyzed process is known to involve nucleophilic attack on the carbonyl carbon atom of the ketene. Rate constants for phenylhydroxyketene, on the other hand, do not fit this correlation, which suggests that the mechanistic assignment upon which these rate constants are based may not be correct. Solvent isotope effects on these uncatalyzed ketene hydrations are weak; most are less than kH/kD = 2. It is argued that these isotope effects are largely, if not entirely, secondary in nature and that they are consistent with both a reaction mechanism in which nucleophlic attack of a single water molecule on the ketene carbonyl carbon atom produces a zwitterionic intermediate and also a mechanism that avoids this intermediate by passing through a cyclic transition state involving several water molecules.Key words: ketene hydration, rate correlation, nucleophilic attack, solvent isotope effects, phenylhydroxyketene.


RSC Advances ◽  
2017 ◽  
Vol 7 (66) ◽  
pp. 41799-41811 ◽  
Author(s):  
Cheng Luo ◽  
Hongjie Wang ◽  
Wenyi Dong ◽  
Xianbing Zhang

The dual descriptor (Δf) data of azo form (a, RR2) and hydrazone form (b, HRR2) of RR2 dianion. For Δf> 0 (green), the site is favorable for nucleophilic attack, for Δf< 0 (blue), the site is favorable for electrophilic attack. Key bond lengths in Å.


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