We studied the energetics of the closed-ring mechanism of the acid-catalysed dehydration of d-fructose to 5-hydroxymethylfurfural (HMF) by carrying out canonical ensemble free-energy calculations using bias-sampling, hybrid Quantum Mechanics/Molecular Mechanics Molecular Dynamics simulations with explicit water solvent at 363 K. The quantum mechanical calculations are performed at the PM3 theor...

Allyl N-tosyloxycarbamates are found to be catalytically transformed into β-brominated oxazolidinones with FeBr(2)/n-Bu(4)NBr in t-BuOH.

Chain-of-state methods are becoming important tools in studying the chemical reaction mechanisms, especially for biomacromolecules. In this article, three chain-of-state methods, nudged elastic band (NEB) method and the replica path method with restraints or constraints, were tested and compared using three model systems with various sizes and at different levels of theory: alanine dipeptide is...

the nmr spectra of azo dyes, 5-arylazobarbituric (5a-g), 5-arylazo-1,3-dimethylbarbituric(6a-g) and 5-arylazothiobarbituric acids (7a-g) were studied in dmso-d6 in differentconcentrations. an intramolecular hydrogen bond was observed and indicating that thehydrazone forms is mostly predominant. the peak of the hydrazone proton was severelybroadened and its chemical shift appeared at down field ...

Energetically favourable conformations for simultaneous intramolecular rotations of both the 17 a ethyl side chain and the 17 ß hydroxyl group of a model steroid are calculated by MM2 molecular mechanics. In accordance with recent IR and NMR interpretations, the 17a substituent is found to preferably adopt conformations which may sterically hinder the formation of hydrogen bonds between the ste...

The vibrational motion of highly excited molecules is discussed in terms of exact quantum and classical mechanics calculations, employing global potential energy surfaces, as well as in terms of a spectroscopic Hamiltonian and its semiclassical limit. The main focus is saddle-node bifurcations and their influence on the spectrum. The general features are illustrated by three examples, which des...

In the present work, an extensive theoretical calculation study on Histidine-Histidine dipeptide in gas phase is done by using DFT method with Gaussian 98 program. Through investigations on the molecular geometries of this molecule it is found that there is six rings in the molecules not two rings. The presence of four intramolecular hydrogen bonds is responsible for the formation of additional...

Molecular structure, isomerism, conformational stability and intramolecular hydrogen bonding (IHB) of cis-enol forms of 1-(n-pyridyl)butane-1,3-diones (nPBD) (n = 2, 3, or 4) have been investigated by means of density functional theory (DFT) calculations. Energy differences for all possible nPBD cis-enol forms of isomers with respect to the most stable form of the correspondin...

Eukaryotic protein kinases regulate most cellular functions by phosphorylating targeted protein substrates through a highly conserved catalytic core. In the active state, the catalytic core oscillates between open, intermediate, and closed conformations. Currently, the intramolecular interactions that regulate the active state mechanics are not well understood. Here, using cAMP-dependent protei...

in the present work, an extensive theoretical calculation study on histidine-histidine dipeptide in gas phase is done by using dft method with gaussian 98 program. through investigations on the molecular geometries of this molecule it is found that there is six rings in the molecules not two rings. the presence of four intramolecular hydrogen bonds is responsible for the formation of additional...