scholarly journals Orthogonal halogen and hydrogen bonds involving a peptide bond model

CrystEngComm ◽  
2014 ◽  
Vol 16 (35) ◽  
pp. 8102-8105 ◽  
Author(s):  
Vera Vasylyeva ◽  
Susanta K. Nayak ◽  
Giancarlo Terraneo ◽  
Gabriella Cavallo ◽  
Pierangelo Metrangolo ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Peptide Bond ◽  
Carbonyl Oxygen ◽  
Carbonyl Oxygen Atom ◽  
Halogen Bonds ◽  
Bond Model

N-Methylacetamide, a well-known peptide bond model, and dihalotetrafluorobenzenes form co-crystals and show geometrically orthogonal hydrogen and halogen bonds sharing the same carbonyl oxygen atom.

Structure of the 2-Pyrrolidinone Monohydrate

1999 ◽  
Vol 54 (12) ◽  
pp. 1598-1601 ◽  
Author(s):  
Päivi Pirilä ◽  
Ilpo Mutikainen ◽  
Jouni Pursiainen
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Water Molecule ◽  
Carbonyl Oxygen ◽  
Carbonyl Oxygen Atom ◽  
Water Molecules ◽  
X Ray

The X-ray crystal structure of the 1:1 adduct shows a complicated network of water and 2-pyrrolidinone molecules where the carbonyl oxygen atom of 2-pyrrolidinone forms hydrogen bonds with protons of two separate water molecules and the NH proton of the 2- pyrrolidinone molecule interacts with the oxygen atom of a third water molecule.

Anchimeric assistance in hexosaminidases

2002 ◽  
Vol 80 (8) ◽  
pp. 1064-1074 ◽  
Author(s):  
Brian L Mark ◽  
Michael NG James
Keyword(s):  
Oxygen Atom ◽  
Active Site ◽  
Sequence Similarity ◽  
Carbonyl Oxygen ◽  
Carbonyl Oxygen Atom ◽  
Carboxyl Groups ◽  
Displacement Mechanism ◽  
Glycosidic Bonds ◽  
Anchimeric Assistance ◽  
Hydrolysis Of

Configuration retaining glycosidases catalyse the hydrolysis of glycosidic bonds via a double displacement mechanism, typically involving two key active site carboxyl groups (Glu or Asp). One of the enzymic carboxyl groups functions as a general acid–base catalyst, the other acts as a nucleophile. Alternatively, configuration-retaining hexosaminidases from the sequence-related glycosidase families 18, 20, and 56 lack a suitably positioned enzymic nucleophile; instead, they use the carbonyl oxygen atom of the neighbouring C2-acetamido group of the substrate. The carbonyl oxygen atom of the 2-acetamido group provides anchimeric assistance to the enzyme catalyzed reaction by acting as an intramolecular nucleophile, attacking the anomeric center and forming a cyclized oxazolinium ion intermediate that is stereochemically equivalent to the glycosyl–enzyme intermediate formed in the "normal" double displacement mechanism. Although there is little sequence similarity between families 18, 20, and 56 hexosaminidases, X-ray crystallographic studies demonstrate that they have evolved similar catalytic domains and active site architectures that are designed to distort the bound substrate so that the C2-acetamido group can become appropriately positioned to participate in catalysis. The substrate distortion allows for a substrate-assisted catalytic reaction that displays all the general characteristics of the classic double-displacement mechanism including the formation of a covalent intermediate.Key words: glycoside hydrolase, hexosaminidase, glycosidase, substrate-assisted catalysis, anchimeric assistance.

scholarly journals Hydrogen-bonding in enzyme catalysis. Fourier-transform infrared detection of ground-state electronic strain in acyl-chymotrypsins and analysis of the kinetic consequences

1990 ◽  
Vol 270 (3) ◽  
pp. 627-637 ◽  
Author(s):  
A J White ◽  
C W Wharton
Keyword(s):  
Hydrogen Bonding ◽  
Oxygen Atom ◽  
Difference Spectrum ◽  
Binding Mode ◽  
Carbonyl Oxygen ◽  
Carbonyl Oxygen Atom ◽  
Rate Theory ◽  
Active Centre ◽  
Ester Carbonyl ◽  
Bond Strengths

I.r. difference spectra are presented for 3-(indol-3-yl)acryloyl-, cinnamoyl-, 3-(5-methylthien-2-yl)acryloyl-, dehydrocinnamoyl- and dihydrocinnamoyl-chymotrypsins at low pH, where the acyl-enzymes are catalytically inactive. At least two absorption bands are seen in each case in the ester carbonyl stretching region of the spectrum. Cinnamoyl-chymotrypsin substituted at the carbonyl carbon atom with 13C was prepared. A difference spectrum in which 13C-substituted acyl-enzyme was subtracted from [12C]acyl-enzyme shows two bands in the ester carbonyl region and thus confirms the assignment of the features to the single ester carbonyl group. The frequencies of the ester carbonyl bands are interpreted in terms of differential hydrogen-bonding. In each case a lower-frequency relatively narrow band is assigned to a productive potentially reactive binding mode in which the carbonyl oxygen atom is inserted in the oxyanion hole of the enzyme active centre. The higher-frequency band, which is broader, is assigned to a non-productive binding mode in each case, where a water molecule bridges from the carbonyl oxygen atom to His-57; this mode is equivalent to the crystallographically determined structure of 3-(indol-3-yl)acryloyl-chymotrypsin, i.e. the Henderson structure. A difference spectrum of dihydrocinnamoyl-chymotrypsin taken at higher pH shows resolution of a feature centred upon 1731 cm-1, which is assigned to a non-bonded conformer in which the carbonyl oxygen atom is not hydrogen-bonded. Perturbation of the protein spectrum in the presence of acyl groups is interpreted in terms of enhanced structural rigidity. It is reported that the ester carbonyl region of the difference spectrum of cinnamoyl-subtilisin is complicated by overlap of features that arise from protein perturbation. Measurements of carbonyl absorption frequencies in a number of solvents of the methyl esters of the acyl groups used to make acyl-enzymes have permitted determination of the apparent dielectric constants experienced by carbonyl groups in the enzyme active centre as well as a discussion of the effects of polarity. The ester carbonyl bond strengths of the various conformations were estimated by using simple harmonic oscillator theory and an empirical relation between the force constants and bond strengths. The fractional bond breaking induced by hydrogen-bonding was used to calculate rate enhancement factors by using absolute reaction rate theory.(ABSTRACT TRUNCATED AT 400 WORDS)

Host−Guest Chemistry of 1,2-Bis(chloromercurio)tetrafluorobenzene. Chelation of the Carbonyl Oxygen Atom of Acetone by a Bidentate Lewis Acid

1999 ◽  
Vol 18 (9) ◽  
pp. 1747-1753 ◽  
Author(s):  
Martin Tschinkl ◽  
Annette Schier ◽  
Jürgen Riede ◽  
François P. Gabbaï
Keyword(s):  
Oxygen Atom ◽  
Lewis Acid ◽  
Carbonyl Oxygen ◽  
Carbonyl Oxygen Atom ◽  
Guest Chemistry

MO study of molecular association of local anaesthetics of carbamate type

1983 ◽  
Vol 48 (2) ◽  
pp. 533-537 ◽  
Author(s):  
Milan Remko ◽  
Vladimír Frecer ◽  
Jozef Čižmárik
Keyword(s):  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Quantum Chemical ◽  
Local Anaesthetics ◽  
Carbonyl Oxygen ◽  
Molecular Association ◽  
Stable Complex ◽  
Intermolecular Hydrogen Bonds ◽  
Pcilo Method ◽  
Self Association

The quantum-chemical PCILO method has been used to study of molecular association of piperidinoethyl alkoxyphenylcarbamates. The self-association of this type of compounds has been studied with methyl phenylcarbamate as a simple model. The PCILO calculations indicate the open dimer with N-H...O=C hydrogen bond to be the most stable complex. Moreover, the PCILO method has been used fro study of intermolecular hydrogen bonds formed between oxygen and nitrogen atoms of -NH-COO- group of the title compounds and N-methylacetamide, N,N-dimethylacetamide, and phenol. The calculations have shown that the most stable hydrogen bonds are formed by carbonyl oxygen atom. Somewhat weaker hydrogen bonds are formed by N-H group. The weakest hydrogen bonds are formed by methoxyl oxygen atom of the -NH-COO- part of the drug.

Quadruple Coordination of the Carbonyl Oxygen Atom of an Amide by a Cyclic Tetradentate Lewis Acid

1998 ◽  
Vol 17 (6) ◽  
pp. 1215-1219 ◽  
Author(s):  
Jean Vaugeois ◽  
Michel Simard ◽  
James D. Wuest
Keyword(s):  
Oxygen Atom ◽  
Lewis Acid ◽  
Carbonyl Oxygen ◽  
Carbonyl Oxygen Atom

Restricted Internal Rotation in 1-Arylhydantoins, 3-Arylhydantoins, and 3-Aryl-2-Thiohydantoins: Reversal of the Effective Sizes of Methyl and Chlorine

1973 ◽  
Vol 51 (21) ◽  
pp. 3635-3639 ◽  
Author(s):  
Lawrence D. Colebrook ◽  
H. Gwynne Giles ◽  
Alessandro Granata ◽  
Siddik Icli ◽  
James R. Fehlner
Keyword(s):  
Oxygen Atom ◽  
Transition State ◽  
Internal Rotation ◽  
Chlorine Atom ◽  
Carbonyl Oxygen ◽  
Carbonyl Oxygen Atom ◽  
Reverse Order ◽  
Methyl Group ◽  
Torsional Transition

In 1-arylhydantoins an o-methyl group is effectively larger than an o-chloro substituent in restricting rotation about the aryl-C—N bond, whereas in 3-arylhydantoins and 3-aryl-2-thiohydantoins the reverse order of sizes is observed. This difference is attributed to repulsion between the chlorine atom and a carbonyl oxygen atom in the torsional transition state of the 3-aryl compounds.

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