The C−H···O Hydrogen Bond:  Structural Implications and Supramolecular Design

Desiraju, Gautam R.

doi:10.1021/ar950135n

Cited by 1,824 publications

(1,109 citation statements)

References 56 publications

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“…C-H⋯O hydrogen bonds are weak, but biologically significant, interactions. 84,85 These features of the catalytic site suggest strategies for designing transition state inhibitors of diphtheria toxin. The transition state structure of the ribosyl group is similar to that for the hydrolysis of inosine catalyzed by nucleoside hydrolase from Crithidia fasiculata, 55 with a highly dissociative, oxocarbenium ion-like transition state.…”

Section: Binding Of the Transition Statementioning

confidence: 99%

Transition State Structure for the Hydrolysis of NAD⁺Catalyzed by Diphtheria Toxin

1997

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Diphtheria toxin (DTA) uses NAD + as an ADP-ribose donor to catalyze the ADP-ribosylation of eukaryotic elongation factor 2. This inhibits protein biosynthesis and ultimately leads to cell death. In the absence of its physiological acceptor, DTA catalyzes the slow hydrolysis of NAD + to ADPribose and nicotinamide, a reaction that can be exploited to measure kinetic isotope effects (KIEs) of isotopically labeled NAD + s. Competitive KIEs were measured by the radiolabel method for NAD + molecules labeled at the following positions: 1-15 N = 1.030 ± 0.004, 1′-14 C = 1.034 ± 0.004, (1-15 N,1′-14 C) = 1.062 ± 0.010, 1′-3 H = 1.200 ± 0.005, 2′-3 H = 1.142 ± 0.005, 4′-3 H = 0.990 ± 0.002, 5′-3 H = 1.032 ± 0.004, 4′-18 O = 0.986 ± 0.003. The ring oxygen, 4′-18 O, KIE was also measured by whole molecule mass spectrometry (0.991 ± 0.003) and found to be within experimental error of that measured by the radiolabel technique, giving an overall average of 0.988 ± 0.003. The transition state structure of NAD + hydrolysis was determined using a structure interpolation method to generate trial transition state structures and bond-energy/bond-order vibrational analysis to predict the KIEs of the trial structures. The predicted KIEs matched the experimental ones for a concerted, highly oxocarbenium ion-like transition state. The residual bond order to the leaving group was 0.02 (bond length = 2.65 Å), while the bond order to the approaching nucleophile was 0.03 (2.46 Å). This is an A N D N mechanism, with both leaving group and nucleophilic participation in the reaction coordinate. Fitting the transition state structure into the active site cleft of the X-ray crystallographic structure of DTA highlighted the mechanisms of enzymatic stabilization of the transition state. Desolvation of the nicotinamide ring, stabilization of the oxocarbenium ion by apposition of the side chain carboxylate of Glu148 with the anomeric carbon of the ribosyl moiety, and the placement of the substrate phosphate near the positively charged side chain of His21 are all consistent with the transition state features from KIE analysis.

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Section: Binding Of the Transition Statementioning

confidence: 99%

Transition State Structure for the Hydrolysis of NAD⁺Catalyzed by Diphtheria Toxin

1997

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“…Scientists exploit supramolecular chemistry (bottom-up strategy) to achieve this goal and control the organization of molecules into diverse 1D [2][3][4], 2D [5][6][7][8][9] or 3D shapes [10][11][12]. Owing to their directional potential, hydrogen bond [13][14][15][16][17][18][19][20][21][22][23] or halogen bond [24][25][26][27][28][29][30][31][32][33][34][35][36] are intermolecular forces that are often used to stick molecular building blocks together. Recently, in our laboratories, we exploited mainly H bonds to build supramolecular walls based on lactams [37] or proline derivatives [38].…”

Section: Introductionmentioning

confidence: 99%

Isomorphous Crystals from Diynes and Bromodiynes Involved in Hydrogen and Halogen Bonds

et al. 2016

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Isomorphous crystals of two diacetylene derivatives with carbamate functionality (BocNH-CH 2 -diyne-X, where X = H or Br) have been obtained. The main feature of these structures is the original 2D arrangement (as supramolecular sheets or walls) in which the H bond and halogen bond have a prominent effect on the whole architecture. The two diacetylene compounds harbor neighboring carbamate (Boc protected amine) and conjugated alkyne functionalities. They differ only by the nature of the atom located at the penultimate position of the diyne moiety, either a hydrogen atom or a bromine atom. Both of them adopt very similar 2D wall organizations with antiparallel carbamates (as in antiparallel beta pleated sheets). Additional weak interactions inside the same walls between molecular bricks are H bond interactions (diyne-H¨¨¨O=C) or halogen bond interactions (diyne-Br¨¨¨O=C), respectively. Based on crystallographic atom coordinates, DFT (B3LYP/6-31++G(d,p)) and DFT (M06-2X/6-31++G(d,p)) calculations were performed on these isostructural crystals to gain insight into the intermolecular interactions.

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“…Weak intra-chain C-HÁÁÁO hydrogen bonds within the chain are rather artefacts of the primary, strong interactions. Hereinafter, we will discuss the C-HÁÁÁO hydrogen bonds on the basis of both geometrical features and of their role on the crystal structure, either structure-directing or just mere secondary [35][36][37][38][39]. In the case of 1, the above-mentioned interactions are rather of secondary nature, but the interchain C-HÁÁÁO bonds (vide infra) are definitively playing important role in the building of crystal structure.…”

Section: Resultsmentioning

confidence: 99%

Even–odd effect in the co-crystals of pyrazine and dicarboxylic acids

Dutkiewicz

Kubicki

2014

Struct Chem

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The co-crystals of pyrazine with dicarboxylic acids of the form (COOH)-(CH 2 ) n -COOH: oxalic (n = 0), malonic (n = 1) succinic (n = 2), glutaric (n = 3), adipic (n = 4), and pimelic (n = 5) acid, were synthesized and structurally characterized by means of X-ray diffraction. There are two principal structural motifs, depending on the stoichiometry: for 1:1 co-crystals, there are chains of alternate pyrazine and acid molecules, connected by strong O-HÁÁÁN hydrogen bonds (ÁÁÁpyrÁÁÁacidÁÁÁpyrÁÁÁacidÁÁÁ) while for 2:1 stoichiometry the chains are made of pyrazine molecules and carboxylic acid centrosymmetric dimers (ÁÁÁpyrÁÁÁacidÁÁÁacidÁÁÁpyrÁÁÁ). The first possibility is observed for all acids in the series, while the second one only for these with odd numbers of methylene groups. The geometrical features of the acids do not show the clear indication for a reason of such behavior, the most probable reason can be connected with the possible symmetry of the acid molecule, C i for n even, and with the mutual orientation of terminal carbonyl and hydroxyl groups, defined by improper O=CÁÁÁC=O torsion angles, which are close to 180°for even and have much smaller values for odd n values.

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The C−H···O Hydrogen Bond: Structural Implications and Supramolecular Design

Cited by 1,824 publications

References 56 publications

Transition State Structure for the Hydrolysis of NAD⁺Catalyzed by Diphtheria Toxin

Transition State Structure for the Hydrolysis of NAD⁺Catalyzed by Diphtheria Toxin

Isomorphous Crystals from Diynes and Bromodiynes Involved in Hydrogen and Halogen Bonds

Even–odd effect in the co-crystals of pyrazine and dicarboxylic acids

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The C−H···O Hydrogen Bond: Structural Implications and Supramolecular Design

Cited by 1,824 publications

References 56 publications

Transition State Structure for the Hydrolysis of NAD+Catalyzed by Diphtheria Toxin

Transition State Structure for the Hydrolysis of NAD+Catalyzed by Diphtheria Toxin

Isomorphous Crystals from Diynes and Bromodiynes Involved in Hydrogen and Halogen Bonds

Even–odd effect in the co-crystals of pyrazine and dicarboxylic acids

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Transition State Structure for the Hydrolysis of NAD⁺Catalyzed by Diphtheria Toxin

Transition State Structure for the Hydrolysis of NAD⁺Catalyzed by Diphtheria Toxin