Amide I Vibrational Dynamics ofN-Methylacetamide in Polar Solvents:  The Role of Electrostatic Interactions

2005 ◽  
Vol 109 (21) ◽  
pp. 11016-11026 ◽  
Author(s):  
M. F. DeCamp ◽  
L. DeFlores ◽  
J. M. McCracken ◽  
A. Tokmakoff ◽  
K. Kwac ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Polar Solvents ◽  
Vibrational Dynamics

The Role of Electrostatic Interactions in Protease Surface Diffusion and the Consequence for Interfacial Biocatalysis

Langmuir ◽  
2010 ◽  
Vol 26 (24) ◽  
pp. 18916-18925 ◽  
Author(s):  
Bob E. Feller ◽  
James T. Kellis ◽  
Luis G. Cascão-Pereira ◽  
Channing R. Robertson ◽  
Curtis W. Frank
Keyword(s):  
Surface Diffusion ◽  
Electrostatic Interactions

scholarly journals Role of Dispersion Attraction in Differential Geometry Based Nonpolar Solvation Models

2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Zhan Chen
Keyword(s):  
Differential Geometry ◽  
Electrostatic Interactions ◽  
Polar Component ◽  
Great Success ◽  
Free Energies ◽  
Dispersion Interactions ◽  
Solvation Models ◽  
Nonpolar Solvation ◽  
Solvation Analysis

AbstractDifferential geometry (DG) based solvation models have shown their great success in solvation analysis by avoiding the use of ad hoc surface definitions, coupling the polar and nonpolar free energies, and generating solvent-solute boundary in a physically self-consistent fashion. Parameter optimization is a key factor for their accuracy, predictive ability of solvation free energies, and other applications. Recently, a series of efforts have been made to improve the parameterization of these new implicit solvent models. In thiswork, we aim at studying the role of dispersion attraction in the parameterization of our DG based solvation models. To this end, we first investigate the necessity of van derWaals (vdW) dispersion interactions in the model and then carry out systematic parameterization for the model in the absence of electrostatic interactions. In particular, we explore how the changes in Lennard-Jones (L-J) potential expression, its decomposition scheme, and choices of some fixed parameter values affect the optimal values of other parameters as well as the overall modeling error. Our study on nonpolar solvation analysis offers insights into the parameterization of nonpolar components for the full DG based models by eliminating uncertainties from the electrostatic polar component. Therefore, it can be regarded as a step towards better parameterization for the full DG based model.

scholarly journals Efficient utilization of renewable feedstocks: the role of catalysis and process design

2017 ◽  
Vol 376 (2110) ◽  
pp. 20170064 ◽  
Author(s):  
Regina Palkovits ◽  
Irina Delidovich
Keyword(s):  
Elevated Temperature ◽  
Gas Phase ◽  
Process Design ◽  
Circular Economy ◽  
Paradigm Shift ◽  
Efficient Utilization ◽  
Polar Solvents ◽  
Platform Chemicals ◽  
Renewable Feedstocks

Renewable carbon feedstocks such as biomass and CO 2 present an important element of future circular economy. Especially biomass as highly functionalized feedstock provides manifold opportunities for the transformation into attractive platform chemicals. However, this change of the resources requires a paradigm shift in refinery design. Fossil feedstocks are processed in gas phase at elevated temperature. In contrast, biorefineries are based on processes in polar solvents at moderate conditions to selectively deoxygenate the polar, often thermally instable and high-boiling molecules. Here, challenges of catalytic deoxygenation, novel strategies for separation and opportunities provided at the interface to biotechnology are discussed in form of showcases. This article is part of a discussion meeting issue ‘Providing sustainable catalytic solutions for a rapidly changing world’.

Solvent effect on the conformational behavior of substituted spiro[4.5]decanes and spiro[5.5]undecanes

1995 ◽  
Vol 73 (5) ◽  
pp. 703-709 ◽  
Author(s):  
S. Sağ Erdem ◽  
T. Varnali ◽  
V. Aviyente ◽  
M.F. Ruiz-Lopez
Keyword(s):  
Solvent Effect ◽  
Electrostatic Interactions ◽  
Multipole Moment ◽  
Semiempirical Methods ◽  
Main Role ◽  
Solvent Interactions ◽  
Reaction Field ◽  
Solvent Models ◽  
Conformational Equilibria

We studied the relatively complex polar systems 6-substituted-1,4-dioxospiro[4.5]decanes and 7-substituted-1,5-dioxospiro[5.5]undecanes with substituents X = CH3, F, Cl, CN, OH, OCH3, and NO2. Solvent effects on the equilibrium have been analysed by means of a Self-Consistent-Reaction-Field model and the PM3 method. Complete geometry optimizations have been carried out for all the structures in the gas phase and in solution. For some substituents, a set of rotamers have been separately optimized. The discussion of the results is focussed on the effects arising from structural aspects and from steric and electrostatic interactions on the axial/equatorial relative stability. The role played by multipole moment is considered. In general, good agreement with available experimental data and with previous theoretical studies has been obtained. Though the use of semiempirical methods and simple solvent models prevents us from reaching definitive conclusions, this approach seems to be very useful in predicting the main role of solute–solvent interactions in conformational equilibria of complex systems for which ab initio calculations cannot be performed. Keywords: conformational equilibria, spiro decanes and undecanes, cavity model, SCRF, solvent effect, PM3 calculations.

scholarly journals Thermodynamics of primary antioxidant action of flavonols in polar solvents

2019 ◽  
Vol 12 (1) ◽  
pp. 108-118 ◽  
Author(s):  
Martin Michalík ◽  
Ján Rimarčík ◽  
Vladimír Lukeš ◽  
Erik Klein
Keyword(s):  
Reaction Pathway ◽  
Hydrogen Atom Transfer ◽  
Antioxidant Effect ◽  
Antioxidant Action ◽  
Polar Solvents ◽  
Polar Media ◽  
Primary Antioxidant ◽  
Intramolecular Hydrogen

Abstract Very recently, a report on the antioxidant activity of flavonoids has appeared, where authors concluded that Hydrogen Atom Transfer mechanism represents the thermodynamically preferred mechanism in polar media (https://doi.org/10.1016/j.foodres.2018.11.018). Unfortunately, serious errors in the theoretical part of the paper led to incorrect conclusions. For six flavonols (galangin, kaempferol, quercetin, morin, myricetin, and fisetin), reaction enthalpies related to three mechanisms of the primary antioxidant action were computed. Based on the obtained results, the role of intramolecular hydrogen bonds (IHB) in the thermodynamics of the antioxidant effect is presented. Calculations and the role of solvation enthalpies of proton and electron in the determination of thermodynamically preferred mechanism is also briefly explained and discussed. The obtained results are in accordance with published works considering the Sequential Proton-Loss Electron-Transfer thermodynamically preferred reaction pathway.

scholarly journals Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall

2018 ◽  
Author(s):  
Alister T. Boags ◽  
Firdaus Samsudin ◽  
Syma Khalid
Keyword(s):  
Cell Wall ◽  
Electrostatic Interactions ◽  
Cell Envelope ◽  
Binding Domain ◽  
Gram Negative Bacteria ◽  
Inner Membrane ◽  
E Coli ◽  
Non Covalent Interactions ◽  
Covalent Interactions

SUMMARYWe present a molecular modeling and simulation study of the of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. We show that non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. When OmpA is truncated to remove the peptidoglycan binding domain, TolR is able to pull the cell wall down towards the inner membrane. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria.

Sign in / Sign up

Export Citation Format

Share Document