Identification and computational characterization of isomers with cis and trans amide bonds in folate and its analogues

2018 ◽  
Vol 20 (45) ◽  
pp. 28818-28831 ◽  
Author(s):  
Stoyan Iliev ◽  
Gergana Gocheva ◽  
Nikoleta Ivanova ◽  
Boyana Atanasova ◽  
Jasmina Petrova ◽  
...  
Keyword(s):  
Electronic Structure ◽  
First Principles ◽  
Md Simulations ◽  
Electronic Structure Calculations ◽  
Amide Bond ◽  
Amide Bonds ◽  
Cis And Trans ◽  
Configurational Isomerism ◽  
Structure Calculations

MD simulations and first-principles electronic structure calculations reveal viable configurational isomerism of a peptide-like amide bond in folate and its analogues.

Molecular Dynamics Study Of Si/Si3N4 Interface

1996 ◽  
Vol 446 ◽  
Author(s):  
Martina E. Bachlechner ◽  
Ingvar Ebbsjö ◽  
Rajiv K. Kalia ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Charge Transfer ◽  
Md Simulations ◽  
Electronic Structure Calculations ◽  
Interface Structure ◽  
Bond Bending ◽  
Three Body ◽  
Structure Calculations ◽  
Weber Potential

AbstractStructural correlations at the Si(111)/Si3N4(0001) interface are studied using the molecular dynamics (MD) method. In the bulk, Si is described by the Stillinger-Weber potential and Si3N4 by an interaction potential which contains two-body (steric, Coulomb, electronic polarizabilities) and three-body (bond bending and stretching) terms. At the interface, the charge transfer from silicon to nitrogen is taken from LCAO electronic structure calculations. Using these Si, Si3N4 and interface interactions in MD simulations, the interface structure (atomic positions, bond lengths, and bond angles) is determined. Results for fracture in silicon are also presented.

Effect of Boron and Hydrogen on the Electronic Structure of Ni3Al

1993 ◽  
Vol 319 ◽  
Author(s):  
N. Kioussis ◽  
H. Watanabe ◽  
R.G. Hemker ◽  
W. Gourdin ◽  
A. Gonis ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Charge Density ◽  
First Principles ◽  
Electronic Structure Calculations ◽  
Interstitial Site ◽  
Octahedral Interstitial Site ◽  
Interstitial Region ◽  
Ordered Intermetallic ◽  
Lmto Method ◽  
Structure Calculations

AbstractUsing first-principles electronic structure calculations based on the Linear-Muffin-Tin Orbital (LMTO) method, we have investigated the effects of interstitial boron and hydrogen on the electronic structure of the L12 ordered intermetallic Ni3A1. When it occupies an octahedral interstitial site entirely coordinated by six Ni atoms, we find that boron enhances the charge distribution found in the strongly-bound “pure” Ni3AI crystal: Charge is depleted at Ni and Al sites and enhanced in interstitial region. Substitution of Al atoms for two of the Ni atoms coordinating the boron, however, reduces the interstitial charge density between certain atomic planes. In contrast to boron, hydrogen appears to deplete the interstitial charge, even when fully coordinated by Ni atoms. We suggest that these results are broadly consistent with the notion of boron as a cohesion enhancer and hydrogen as an embrittler.

scholarly journals First principles methods using CASTEP

2005 ◽  
Vol 220 (5/6) ◽  
Author(s):  
Stewart J. Clark ◽  
Matthew D. Segall ◽  
Chris J. Pickard ◽  
Phil J. Hasnip ◽  
Matt I. J. Probert ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Future Development ◽  
First Principles ◽  
Electronic Structure Calculations ◽  
Development Plans ◽  
Near Future ◽  
Structure Calculations

AbstractThe CASTEP code for first principles electronic structure calculations will be described. A brief, non-technical overview will be given and some of the features and capabilities highlighted. Some features which are unique to CASTEP will be described and near-future development plans outlined.

Studies of structure and dynamics in a nominally symmetric twisted amide by NMR and electronic structure calculations

2006 ◽  
Vol 84 (3) ◽  
pp. 421-428 ◽  
Author(s):  
Alex D Bain ◽  
Hao Chen ◽  
Paul H.M Harrison
Keyword(s):  
Electronic Structure ◽  
Nmr Spectra ◽  
Chemical Exchange ◽  
Electronic Structure Calculations ◽  
Amide Bond ◽  
Electronic Effects ◽  
H Nmr ◽  
Line Shape Analysis ◽  
Structure Calculations ◽  
C Nmr

Amides that are twisted around the C—N bond show unusual spectroscopy and reactivity when compared with planar amides. The diacyl derivatives of 3,4,7,8-tetramethyl-2,5-dithioglycoluril are intriguing examples of this class, since the crystal structures show that the two acyl groups are twisted by different amounts on either side of the molecule owing to a combination of steric and electronic effects. However, the 1H NMR spectra in solution at room temperature exhibit only one acyl resonance, so there must be fast interconversion among pairs of equivalent structures of each compound. We have prepared a number of derivatives with different acyl groups, both on the glycoluril framework as well as on its dithio analogue. The chemical exchange in solution was slowed down sufficiently by cooling to see individual sites for only two compounds: the dithiodipivaloyl and the dithiodiadamantyl derivatives. The barriers were estimated at 41 kJ mol–1 for the dipivaloyl derivative and 45 kJ mol–1 for diadamantyl derivative. The results show that rotation around the twisted amide bond is slowed by both the steric size of the acyl group and the presence of the thioureido group vs. the ureido group in the glycoluril core. In the solid-state 13C NMR spectra, there is no evidence for any dynamics, even for the diacetyl derivative at ambient temperature. Electronic structure calculations predict a geometry for the dipivaloyl derivative very close to that observed in the crystal structure. These results indicate that the crystal confines, but does not distort the molecule. A mechanism for the exchange is proposed. The relevance of these results to the mechanism of Claisen-like condensations in diacylglycolurils is also discussed.Key words: 1H and 13C NMR, exchange, dynamics, CP/MAS, solids, line shape analysis, amides, twisted amides, atropisomers, glycoluril.

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