Structural Aspects of Interatomic Charge-Transfer Bonding

Hassel, O.

doi:10.1126/science.170.3957.497

Cited by 437 publications

(334 citation statements)

References 9 publications

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“…The elongation effect arises also from major differences existing between the non-conventional C-H···O=C hydrogen bond [49] length (2.343 Å) and the C-Br···O=C halogen bond length (3.060 Å). In fact, this latter distance is 9% shorter than the sum of the van der Waals radii of Br and O [50][51][52], Looking along the b-axis ( Figure 3, top views of the supramolecular walls), there is no significant difference either. The repetitive unit along the c-axis is just a little bit longer in 2 (c = 12.274 Å) by comparison with 1 (c = 11.898 Å).…”

Section: Crystallographic Studiesmentioning

confidence: 93%

“…The elongation effect arises also from major differences existing between the non-conventional C-H¨¨¨O=C hydrogen bond [49] length (2.343 Å) and the C-Br¨¨¨O=C halogen bond length (3.060 Å). In fact, this latter distance is 9% shorter than the sum of the van der Waals radii of Br and O [50][51][52], strongly suggesting that there is more at stake than a simple van der Waals contact between the two heteroatoms. This is also supported by the alignment of the four atoms C-Br¨¨¨O=C matching that of the C-H¨¨¨O=C atoms involved in a hydrogen bond [53].…”

Section: Crystallographic Studiesmentioning

confidence: 96%

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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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Section: Crystallographic Studiesmentioning

confidence: 93%

Section: Crystallographic Studiesmentioning

confidence: 96%

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

et al. 2016

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“…Chlorines, bromines, and iodines in organic and inorganic compounds are known to polarize along their covalent bonds to generate an electropositive crown; the halogen thus acts as a Lewis acid to pair with Lewis bases, including oxygens and nitrogens. These electrostatic pairs, originally called charge-transfer bonds (1), are now known as halogen bonds (X-bonds), recognizing their similarities to hydrogen bonds (H-bonds) in their strength and directionality (2). In chemistry, X-bonds are being exploited in the design and engineering of supramolecular assemblies (3) and molecular crystals (for review, see ref.…”

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confidence: 99%

Directing macromolecular conformation through halogen bonds

Voth

Hays

2007

Proc. Natl. Acad. Sci. U.S.A.

329

310

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The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be Ϸ2-5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules.biomolecular engineering ͉ DNA structure ͉ molecular interactions H alogen bonds have recently seen a resurgence of interest as a tool for ''bottom-up'' molecular design. Chlorines, bromines, and iodines in organic and inorganic compounds are known to polarize along their covalent bonds to generate an electropositive crown; the halogen thus acts as a Lewis acid to pair with Lewis bases, including oxygens and nitrogens. These electrostatic pairs, originally called charge-transfer bonds (1), are now known as halogen bonds (X-bonds), recognizing their similarities to hydrogen bonds (H-bonds) in their strength and directionality (2). In chemistry, X-bonds are being exploited in the design and engineering of supramolecular assemblies (3) and molecular crystals (for review, see ref. 4), with an iodine X-bond estimated to be Ϸ3.5 kcal/mol more stable than an O-H⅐⅐⅐O H-bond in organic crystals (5).The X-bond, however, has not generally been a part of the biologist's lexicon. Although halogens are widely used in drug design and to probe molecular interactions, X-bonds have only recently been recognized as a distinct interaction in ligand recognition and molecular folding and in the assembly of proteins and nucleic acids (6, 7). With the growing application of biological molecules (biomolecule), particularly nucleic acids (for review, see ref. 8), in the design of nanomechanical devices, we ask here whether specific X-bonds can be engineered to direct conformational switching in a biomolecule.To compare X-and H-bonds in the complex environment of a biomolecule, we have designed a crystallographic assay to determine whether an intramolecular X-bond could be engineered to direct the conformational isomerization of a DNA Holliday junction by competing an X-bond against a classic H-bond and, consequently, we are able to compare the stabilization energies afforded by these two types of interactions. The stacked-X form of the DNA Holliday junction (Fig. 1), seen in high-salt solutions (9) and in crystal structures (10 -12), is a simple and well controlled biomolecular assay system that can isomerize between two nearly isoenergetic an...

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“…In the structures of 1 and 2 the driving force of the crystal architecture are quite strong C-HÁÁÁX halogen bonds (X=Br for 1, I for 2). This kind of interaction, postulated in the 1960s [34,35] and confirmed as an important player in the determination of the crystal structure (e.g. [36,37] and references therein), are in principle electrostatic interactions between a covalently bound halogen atom and the lone pair of the ''acceptor'' atom, and they should be quite directional.…”

Section: Resultsmentioning

confidence: 99%

The Role of Halogen Bonding in Crystal Structures of 3-Halogeno Cytisine Derivatives

Przybył

Kubicki

2012

J Chem Crystallogr

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The crystal structures of three 3-halogeno derivatives of 13N-substituted cytisine have been determined by X-ray diffraction. The two 13-acetyl substituted compounds, 3-bromo (1) and 3-iodo (2) are isostructural, with the isostructurality index as high as 99%. They both crystallize in monoclinic P2 1 space group, with unit cell parameters of a = 8.4709(10) Å , b = 9.2266(12) Å , c = 8.6051(10) Å , b = 98.528 (11)8 (1) and a = 8.2322(6) Å , b = 9.1724(7) Å , c = 8.5494(6) Å , b = 98.181 (7)8 (2). In turn, 3-bromo-13-t-butyl-carbonate derivative (3) crystallizes in orthorhombic P2 1 2 1 2 1 space group with a = 6.8171(3) Å , b = 7.8994(4) Å , c = 31.4657(15) Å . Conformation of the cytisine skeleton is similar in all three molecules, with almost planar A ring, sofa conformation of B-ring and C ring being an almost ideal chair. However, the orientations of the double C=O bonds in 13N-substituents are completely different: in 1 and 2 it is cis with respect to C12 (C12-N13-C14-O15 torsion angle is 3.3(4)8 in 1 and 1.3(6)8 in 2) while in 3 it is trans (-175.4(3)8). In the structures of 1 and 2 the driving force of the crystal architecture are quite strong C-HÁÁÁX halogen bonds with CÁÁÁX distances far shorter than the sums of van der Waals radii (CÁÁÁBr in 1 is 2.9430(19) Å and CÁÁÁI in 2 2.974(3)). In contrast in 3-partially as the consequence of different orientation of the substituent-there are no halogen bondings but instead some weak C-HÁÁÁO contacts organize the molecules into two-dimensional patterns.

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Structural Aspects of Interatomic Charge-Transfer Bonding

Cited by 437 publications

References 9 publications

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

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

Directing macromolecular conformation through halogen bonds

The Role of Halogen Bonding in Crystal Structures of 3-Halogeno Cytisine Derivatives

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