Application of ab initio molecular orbital calculations to the structural moieties of carbohydrates. 5. The geometry of the hydrogen bonds

1979 ◽  
Vol 101 (8) ◽  
pp. 1997-2002 ◽  
Author(s):  
M. D. Newton ◽  
G. A. Jeffrey ◽  
Shozo Takagi
Keyword(s):  
Hydrogen Bonds ◽  
Ab Initio ◽  
Molecular Orbital ◽  
Molecular Orbital Calculations

Ab initio SCF study of the effect of Na+ and K+ ions and water on the local anaesthetic-phospholipid interaction

1989 ◽  
Vol 54 (4) ◽  
pp. 862-867 ◽  
Author(s):  
Milan Remko
Keyword(s):  
Hydrogen Bonds ◽  
Ab Initio ◽  
Molecular Orbital ◽  
Local Anaesthetic ◽  
Local Anaesthetics ◽  
Molecular Orbital Calculations ◽  
Model Substances ◽  
Insight Into ◽  
Gaining Insight

For gaining insight into the interactions of local anaesthetics with phospholipids, ab initio molecular orbital calculations were performed using trimethylamine and phosphate as model substances. The (OH)2OPO-···H+N(CH3)3 interaction was found comparable in strength to the (OH)2OPO-···M+ (M = Na, K) interaction and considerably stronger than the (OH)2OMPO···H2O interaction. This suggests that a major role of local anaesthetics may consist in their disturbing the P-O···H2O hydrogen bonds. Such interference may be one of the possible types of interaction between local anaesthetics and the biophase, leading to a measurable pharmacological effect.

Amino and cyano N atoms in competitive situations: which is the best hydrogen-bond acceptor? A crystallographic database investigation

2001 ◽  
Vol 57 (6) ◽  
pp. 850-858 ◽  
Author(s):  
Nahossé Ziao ◽  
Jérôme Graton ◽  
Christian Laurence ◽  
Jean-Yves Le Questel
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Molecular Orbital ◽  
Amino Nitrogen ◽  
Lone Pair ◽  
Molecular Surface ◽  
Molecular Orbital Calculations ◽  
Hydrogen Bond Acceptor

The relative hydrogen-bond acceptor abilities of amino and cyano N atoms have been investigated using data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. Surveys of the CSD for hydrogen bonds between HX (X = N, O) donors, N—T—C≡N (push–pull nitriles) and N—(Csp 3) n —C≡N molecular fragments  show that the hydrogen bonds are more abundant on the nitrile than on the amino nitrogen. In the push–pull family, in which T is a transmitter of resonance effects, the hydrogen-bonding ability of the cyano nitrogen is increased by conjugative interactions between the lone pair of the amino substituent and the C≡N group: a clear example of resonance-assisted hydrogen bonding. The strength of the hydrogen-bonds on the cyano nitrogen in this family follows the experimental order of hydrogen-bond basicity, as observed in solution through the pK HB scale. The number of hydrogen bonds established on the amino nitrogen is greater for aliphatic aminonitriles N—(Csp 3) n —C≡N, but remains low. This behaviour reflects the greater sensitivity of the amino nitrogen to steric hindrance and the electron-withdrawing inductive effect compared with the cyano nitrogen. Ab initio molecular orbital calculations (B3LYP/6-31+G** level) of electrostatic potentials on the molecular surface around each nitrogen confirm the experimental observations.

Carbonyl–Carbonyl Interactions can be Competitive with Hydrogen Bonds

1998 ◽  
Vol 54 (3) ◽  
pp. 320-329 ◽  
Author(s):  
F. H. Allen ◽  
C. A. Baalham ◽  
J. P. M. Lommerse ◽  
P. R. Raithby
Keyword(s):  
Hydrogen Bonds ◽  
Ab Initio ◽  
Interaction Energy ◽  
Molecular Orbital ◽  
Crystallographic Data ◽  
Basis Sets ◽  
Attractive Interaction ◽  
Molecular Orbital Calculations ◽  
Dimer Model ◽  
Intermolecular Perturbation Theory

The geometries and attractive energies of carbonyl–carbonyl interactions have been investigated using crystallographic data and ab initio molecular-orbital calculations. Analysis of crystallographic data for 9049 carbon-substituted >C=O groups shows that 1328 (15%) form contacts with other >C=O groups, in which d(C...O) < 3.6 Å. Three common interaction motifs are observed in crystal structures: (a) a slightly sheared antiparallel motif (650 instances) involving a pair of short C...O interactions, together with (b) a perpendicular motif (116 instances) and (c) a highly sheared parallel motif (130 instances), which both involve a single short C...O interaction. Together, these motifs account for 945 (71%) of the observed interactions. Ab-initio-based molecular-orbital calculations (6-31G** basis sets), using intermolecular perturbation theory (IMPT) applied to a bis-propanone dimer model, yield an attractive interaction energy of −22.3 kJ mol−1 for a perfect rectangular antiparallel dimer having both d(C...O) = 3.02 Å and attractive energies < −20 kJ mol−1 over the d(C...O) range 2.92–3.32 Å. These energies are comparable to those of medium-strength hydrogen bonds. The IMPT calculations indicate a slight shearing of the antiparallel motif with increasing d(C...O). For the perpendicular motif, IMPT yields an attractive interaction energy of −7.6 kJ mol−1, comparable in strength to a C—H...O hydrogen bond and with the single d(C...O) again at 3.02 Å.

Hydrogen-Bond Acceptor Properties of Nitro-O Atoms: A Combined Crystallographic Database and Ab Initio Molecular Orbital Study

1997 ◽  
Vol 53 (6) ◽  
pp. 1017-1024 ◽  
Author(s):  
F. H. Allen ◽  
C. A. Baalham ◽  
J. P. M. Lommerse ◽  
P. R. Raithby ◽  
E. Sparr
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Molecular Orbital ◽  
Lone Pair ◽  
Basis Set ◽  
Molecular Orbital Calculations ◽  
Hydrogen Bond Energy ◽  
Hydrogen Bond Acceptor ◽  
Model Dimer

Crystallographic data for 620 C—nitro-O...H—N,O hydrogen bonds, involving 560 unique H atoms, have been investigated to the van der Waals limit of 2.62 Å. The overall mean nitro-O...H bond length is 2.30 (1) Å, which is much longer (weaker) than comparable hydrogen bonds involving >C=O acceptors in ketones, carboxylic acids and amides. The donor hydrogen prefers to approach the nitro-O atoms in the C—NO2 plane and there is an approximate 3:2 preference for hydrogen approach between the two nitro-O atoms, rather than between the C and O substituents. However, hydrogen approach between the two O acceptors is usually strongly asymmetric, the H atom being more closely associated with one of the O atoms: only 60 H atoms have both O...H distances \leq 2.62 Å. The approach of hydrogen along putative O-atom lone-pair directions is clearly observed. Ab-initio-based molecular orbital calculations (6-31G** basis set level), using intermolecular perturbation theory (IMPT) applied to the nitromethane–methanol model dimer, agree with the experimental observations. IMPT calculations yield an attractive hydrogen-bond energy of ca −15 kJ mol−1, about half as strong as the >C=O...H bonds noted above.

A pairwise additivity scheme for conformational energies of substituted ethanes

1975 ◽  
Vol 343 (1632) ◽  
pp. 1-10 ◽  
Keyword(s):  
Large Deviations ◽  
Ab Initio ◽  
Dihedral Angle ◽  
Molecular Orbital ◽  
Methyl Groups ◽  
Molecular Orbital Calculations ◽  
Linear Combinations ◽  
Strongly Interacting ◽  
Conformational Energies

Ab initio molecular orbital calculations are used to explore additivity in the conformational energies of poly-substituted ethanes in terms of conformational energies of ethane and appropriate mono- and 1,2-di-substituted derivatives. Such relations would allow complex calculations for poly-substituted ethanes to be replaced by much simpler ones on a small number of parent molecules. General expressions for the linear combinations are derived from the assumption that interactions between vicinal substituents are pairwise additive and depend only on the vicinal dihedral angle. The additivity scheme is tested for 15 ethanes, di-, tri- or tetrasubstituted by cyano and methyl groups and for a smaller number of fluoroethanes. Additivity applies to within 0.1- 0.3 k J mol -1 in the methylethanes and mostly to within about 0.7- 0.8 kJ mol -1 in cyanoethanes. Large deviations are found among the geminally substituted fluoroethanes. It is suggested that the additivity approximation is most successful in the absence of strongly interacting geminal groups. Predictions are made of conformational energies of ten hexa(cyano- and methyl-) substituted ethanes.

Gas-Phase Tautomerism in the Triazoles and Tetrazoles: A Study by Photoelectron Spectroscopy and ab Initio Molecular Orbital Calculations

1981 ◽  
Vol 36 (11) ◽  
pp. 1246-1252 ◽  
Author(s):  
Michael H. Palmer ◽  
Isobel Simpson ◽  
J. Ross Wheeler
Keyword(s):  
Ab Initio ◽  
Gas Phase ◽  
Molecular Orbital ◽  
Photoelectron Spectroscopy ◽  
Relative Stability ◽  
Photoelectron Spectra ◽  
Equilibrium Geometry ◽  
Molecular Orbital Calculations ◽  
Methyl Derivatives

The photoelectron spectra of the tautomeric 1,2,3,- and 1,2,4-triazole and 1,2,3,4-tetrazole systems have been compared with the corresponding N-methyl derivatives. The dominant tautomers in the gas phase have been identified as 2 H-1,2,3-triazole, 1 H-1,2,4-triazole and 2H-tetrazole.Full optimisation of the equilibrium geometry by ab initio molecular orbital methods leads to the same conclusions, for relative stability of the tautomers in each of the triazoles, but the calculations wrongly predict the tetrazole tautomerism.

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