A theoretical study of the C–H⋯N hydrogen bond in the methane–ammonia complex

Wong, Ning‐Bew; Cheung, Y. H.; Wu, DY; Ren, Yuan; Wang, X; Tian, Anmin; Li, Wai‐Kee

doi:10.1016/s0166-1280(99)00386-3

Cited by 28 publications

(13 citation statements)

References 13 publications

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“…In accordance with the NBO theory the formation of hydrogen bond is accompanied by charge transfer (CT) from the lone pair of proton acceptor to the vacant antibonding orbitals of the D-H bond of proton donor. Energy of this interaction can be estimated by E(2) values derived from second order perturbation theory analysis of Fock matrix in NBO basis [12][13][14][15]. All calculations were performed using NBO 5.0 program package [16].…”

Section: Methodsmentioning

confidence: 99%

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

et al. 2009

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Investigation of characteristics of hydrogen bonding between pyridine and water by MP2/aug-cc-pvdz method reveals that these two molecules may form three types of hydrogen bonds depending on nature of proton withdrawal site of pyridine. Change of orientation of water with respect to plane of aromatic ring leads to transformation of the O-HÁÁÁN bond to O-HÁÁÁp bond via wide region of the potential energy surface where both lone pair of the nitrogen atom and p-system make significant contribution into hydrogen bonding. Hydrogen bond in this intermediate region may be considered as mixed O-HÁÁÁN/ O-HÁÁÁp bond representing new type of H bonds.

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Section: Methodsmentioning

confidence: 99%

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

et al. 2009

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“…In accordance with the NBO theory the formation of hydrogen bond is accompanied by charge transfer (CT) from the lone pair of proton acceptor to the vacant antibonding orbitals of the D-H bond of proton donor. Energy of this interaction can be estimated by E(2) values derived from second order perturbation theory analysis of Fock matrix in NBO basis [38][39][40][41]. For each donor NBO (i) and acceptor NBO (j), the stabilization energy E(2) associated with delocalization (''2e-stabilization'') may be estimated as:…”

Section: Methods Of Calculationmentioning

confidence: 99%

Structure and hydrogen bonding in polyhydrated complexes of guanine

et al. 2007

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Molecular structure of complexes of guanine with 12, 13, 16, and 17 water molecules were calculated using B3LYP/6-311G(d,p) level of theory. Interaction with water results in some deformation of geometrical parameters of guanine, which can be described as contribution of zwitter-ionic resonant form into the structure of DNA base. Saturation of water binding sites within guanine creates possibilities for the formation of the NÁÁÁH-O hydrogen bond where the nitrogen atom of amino group acts as proton acceptor. The NBO analysis of guanine-water interactions reveals that hydrogen bonds involving the N(3) and N(7) atoms of guanine represent a case of mixed NÁÁÁH-O/pÁÁÁH-O hydrogen bonds where contribution of p-system into total energy of interaction varies from 3% to 41%. This contribution significantly depends on orientation of the hydrogen atom of water molecule with respect to plane of purine bicycle and influence of neighboring water molecules.

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“…It should be noted that this is only model for description of interactions within this theory and it does not imply real CT between atoms or bonds. Energy of this interaction can be estimated by the E(2) values derived from secondorder perturbation theory analysis of Fock matrix in NBO basis [42][43][44][45]. All calculations were performed using NBO 5.0 program package [46].…”

Section: Synthesis and Crystal Preparationmentioning

confidence: 99%

Intramolecular S···O chalcogen bond in thioindirubin

et al. 2010

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Results of X-ray diffraction study and quantumchemical calculations revealed that molecular conformation of thioindirubin molecule creates suitable conditions for formation of intramolecular C-HÁÁÁO and SÁÁÁO interactions. Analysis of molecular electrostatic potential (MEP) demonstrates existence of two areas of positive MEP (r-holes) in the outermost part of the sulfur atom on the continuation of the lines of the C-S bonds. One of these r-holes is oriented toward region of negative MEP around the oxygen atom of carbonyl group. Such situation corresponds to formation of r-hole or chalcogen bond. Existence of both types of bonding interactions is confirmed by topological analysis of electron density distribution using ''Atoms in Molecules'' (AIM) theory. Energies of the C-HÁÁÁO hydrogen bond and the SÁÁÁO r-hole bond derived from AIM and NBO theories are very close.Keywords Thioindirubin Á X-ray diffraction study Á r-hole bonding Á AIM Á NBO Á MEP

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A theoretical study of the C–H⋯N hydrogen bond in the methane–ammonia complex

Cited by 28 publications

References 13 publications

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Structure and hydrogen bonding in polyhydrated complexes of guanine

Intramolecular S···O chalcogen bond in thioindirubin

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