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Extension of the AMBER force field to cyclic alpha,alpha dialkylated peptides
(Royal Soc Chemistry, Cambridge, 2012)
The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing alpha, alpha dialkylated residues with cyclic side chains. Together with the recent ...
How flexible is the water molecule structure? Analysis of crystal structures and the potential energy surface
(Royal Society of Chemistry, 2020)
Water molecules from crystal structures archived in the CSD show a relatively large range both in the bond angle and bond lengths. High level ab initio calculations at the CCSD(T)/CBS level predicted a possibility for ...
An improved AMBER force field for alpha,alpha-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems
(Royal Soc Chemistry, Cambridge, 2013)
alpha,alpha-Dialkylated amino acid residues have acquired considerable importance as effective means for introducing backbone conformation constraints in synthetic peptides. The prototype of such a class of residues, namely ...
in/out Isomerism of cyclophanes: a theoretical account of 2,6,15-trithia-[3(4,10)][7]metacyclophane and [3(4,10)][7]metacyclophane as well as their halogen substituted analogues
(Royal Soc Chemistry, Cambridge, 2017)
A detailed theoretical investigation of cyclophanes with a divergent set of methods ranging from molecular mechanics through semiempirical to ab initio is presented. Cyclophanes have attracted interest over the years due ...
Chain length, temperature and solvent effects on the structural properties of alpha-aminoisobutyric acid homooligopeptides
(Royal Soc Chemistry, Cambridge, 2016)
Non-coded alpha-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and ...
Intermittent chaos in the Bray-Liebhafsky oscillator. Temperature dependence
(Royal Soc Chemistry, Cambridge, 2016)
Intermittent oscillations as a chaotic mixture of large amplitude relaxation oscillations, grouped in bursts and small-amplitude sinusoidal ones or even quiescent parts between them known as gaps, were found and examined ...
The chaotic sequences in the Bray-Liebhafsky reaction in an open reactor
(Royal Soc Chemistry, Cambridge, 2008)
Attractor reconstruction is done from the time series obtained by experimental investigation and by deterministic and stochastic simulation of the Bray-Liebhafsky oscillatory reaction. The appearance of deterministic chaos ...
Malonic acid concentration as a control parameter in the kinetic analysis of the Belousov-Zhabotinsky reaction under batch conditions
(Royal Soc Chemistry, Cambridge, 2008)
The influence of the initial malonic acid concentration [MA](0) (8.00 x 10(-3) LT = [MA](0) LT = 4.30 x 10(-2) mol dm(-3)) in the presence of bromate (6.20 x 10(-2) mol dm(-3)), bromide (1.50 x 10(-5) mol dm(-3)), sulfuric ...
Structures of chaos in open reaction systems
(Royal Soc Chemistry, Cambridge, 2011)
By numerically simulating the Bray-Liebhafsky (BL) reaction (the hydrogen peroxide decomposition in the presence of hydrogen and iodate ions) in a continuously fed well stirred tank reactor (CSTR), we find "structured" ...