The vibrational spectra, molecular structure and conformations of organic azides. I. A survey

Klæboe, P.; Nielsen, Claus J.; Priebe, H.; Schei, S.H.; Sjøgren, Carl E.

doi:10.1016/0022-2860(86)80320-9

Cited by 46 publications

(9 citation statements)

References 21 publications

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“…1.340 Å. The bond length obtained in our calculations is in agreement with the experimental values reported to be 1.243 Å [24–26] for hydrazoic acid, 1.216 Å [24] and 1.240 Å [26] for azidomethane, and 1.229 Å [27] for azidoethane. When comparing these values with the equivalent parameters in GAFF, the N1-N2 bond characteristics appears as a combination of the characteristics of the bonds represented by GAFF atom types n2-n1, n3-n1 and n2-n2, where n3 corresponds to sp 3 hybridized N atom, n2 to sp 2 , and n1 to sp .…”

Section: Resultssupporting

confidence: 91%

Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies

Pieffet

Petukhov

2009

J Mol Model

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The accuracy of molecular dynamics (MD) simulations is limited by the availability of parameters for the molecular system of interest. In most force fields parameters of common chemical groups are already present. With the development of novel small organic molecules as probes to study biological system more chemical groups require parameterization. An azide group is often used in studies of biological systems yet computational studies are impeded by the lack of parameters. In this paper we present a set of molecular mechanics (MM) parameters for aromatic and aliphatic azido groups and their application in MD simulations of a photoaffinity probe currently used in our laboratory for mapping the binding modes available in the active site of histone deacetylases. The parameters were developed for the Generalized Amber Force Field (GAFF) using density functional theory calculations (DFT) at B3LYP 6-311G(d) level. The parameters were validated by geometry optimization and MD simulations.

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Section: Resultssupporting

confidence: 91%

Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies

Pieffet

Petukhov

2009

J Mol Model

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“…distances are essen tially the same, as are the N^N,. distances [13]. From this information we can provide evidence of a bend in the NNN chain at N^.…”

Section: Discussionmentioning

confidence: 84%

“…They also predicted a tilt of the methyl group of 4.2 away from the CN bond. In collaboration with others [13] these workers carried out further calcu lations as well as electron diffraction studies on several other organic azides, and found bends of 6-8° in the NNN chain for all of them.…”

Section: Discussionmentioning

confidence: 99%

¹⁴N Nuclear Quadrupole Hyperfine Structure in the Microwave Spectrum of Methyl Azide, CH₃N₃

Heineking

Gerry

1989

Zeitschrift Für Naturforschung A

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The 14N nuclear quadrupole hyperfine structure in the rotational spectra of three isotopic species of methyl azide, CH314N3, CH315N14N2, and CH314N215N, has been resolved using microwave Fourier transform spectroscopy. The quadrupole coupling constants of 14N at all three positions have been evaluated and are compared with those from an ab initio calculation in the literature.Since the spectra of the substituted species have been obtained for the first time, they have provided new structural information: the rotational constants are consistent with a structure in which the NNN chain is slightly bent. I4N N u c le a r Q u a d r u p o le H y p e r fin e S tr u c tu r e

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“…The structures and conformational behavior of gaseous organic azides should therefore be of interest to better understand the chemistry of this class of compounds. Roughly 25 years ago, Klaeboe, Nielsen, Priebe, Schei, and co-workers synthesized several small organic azides and performed studies of their structural and conformational properties by electron diffraction, infrared spectroscopy, and theoretical calculations, as summarized in a review . It was established in these investigations that gaseous azides indeed have unique conformational and structural properties …”

Section: Introductionmentioning

confidence: 99%

Microwave Spectrum and Conformational Composition of (Azidomethyl)cyclopropane (C₃H₅CH₂N₃)

2014

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The microwave spectrum of (azidomethyl)cyclopropane, C3H5CH2N3, has been investigated in the 26-90 GHz spectral range at a temperature of about -30 °C. Five rotameric forms of this compound, whose spectra can be distinguished by microwave spectroscopy, may exist. The spectra of three of them denoted III, IV, and V were assigned. The ground vibrational state spectra of III and V were assigned, while the ground and six vibrationally excited states were assigned for IV. These three rotamers all have a synclinal orientation of the H-C-C-N chain of atoms, while the C-C-N-N link is either + or - synclinal or antiperiplanar. Conformer IV, having synclinal orientation of the two said dihedral angles, was found to have the lowest energy by relative intensity measurements. Rotamer V has an energy that is 1.6(6) kJ/mol higher than the energy of IV, while the energy of III is 2.1(6) kJ/mol higher than the energy of IV. Quantum chemical calculations were performed at the MP2/cc-pVTZ and CCSD/cc-pVTZ levels of theory. The rotational constants obtained in the CCSD calculations are in good agreement with the experimental rotational constants, while the MP2 centrifugal distortion constants are generally in poorer agreement with their experimental counterparts.

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The vibrational spectra, molecular structure and conformations of organic azides. I. A survey

Cited by 46 publications

References 21 publications

Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies

Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies

¹⁴N Nuclear Quadrupole Hyperfine Structure in the Microwave Spectrum of Methyl Azide, CH₃N₃

Microwave Spectrum and Conformational Composition of (Azidomethyl)cyclopropane (C₃H₅CH₂N₃)

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The vibrational spectra, molecular structure and conformations of organic azides. I. A survey

Cited by 46 publications

References 21 publications

Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies

Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies

14N Nuclear Quadrupole Hyperfine Structure in the Microwave Spectrum of Methyl Azide, CH3N3

Microwave Spectrum and Conformational Composition of (Azidomethyl)cyclopropane (C3H5CH2N3)

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¹⁴N Nuclear Quadrupole Hyperfine Structure in the Microwave Spectrum of Methyl Azide, CH₃N₃

Microwave Spectrum and Conformational Composition of (Azidomethyl)cyclopropane (C₃H₅CH₂N₃)