2014
DOI: 10.1080/00268976.2014.916822
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Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study

Abstract: The effects of trimethylamine-N-oxide (TMAO), urea and tetramethyl urea (TMU) on the hydrogen bonding structure and dynamics of aqueous solution of N-methylacetamide (NMA) are investigated by classical molecular dynamics simulations. The modification of the water's hydrogen bonding structure and interactions is calculated in presence of these co-solutes. It is observed that the number of four-hydrogen-bonded water molecules in the solution decreases significantly in the presence of TMAO rather than urea and TM… Show more

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Cited by 30 publications
(5 citation statements)
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“…The structural relaxation of hydrogen bonds is analyzed by using the intermittent hydrogen-bond correlation function C HB ( t ), and it is defined as , C normalH normalB ( t ) = h ( 0 ) h ( t ) / < h ( 0 ) 2 …”
Section: Resultsmentioning
confidence: 99%
“…The structural relaxation of hydrogen bonds is analyzed by using the intermittent hydrogen-bond correlation function C HB ( t ), and it is defined as , C normalH normalB ( t ) = h ( 0 ) h ( t ) / < h ( 0 ) 2 …”
Section: Resultsmentioning
confidence: 99%
“…Now we studied the dynamical properties [ [45] , [46] , [47] ]. We conducted molecular dynamics simulation analysis using the GROMACS software [ 48 ] CHARMM General force field (CGenFF) was used to perform ligand parameterization [ 49 ].…”
Section: Materials Methods and Computational Detailsmentioning
confidence: 99%
“…As a result, stabilizing osmolytes are excluded from the vicinity of proteins. ,, The surface of proteins is larger in the case of unfolded forms; thus, the equilibrium of the folding reaction is shifted toward the native state due to the entropy effect associated with the exclusion of the volume available for the osmolyte molecules. In turn, the driving force of protein unfolding by destabilizing osmolytes is the favorable enthalpy change, which results from a higher number of active binding centers accessible to denaturants in unfolded proteins. , Another hypothesis states that the stabilization or destabilization of proteins is the result of an indirect influence of osmolytes arising from the change in water properties in their solutions. ,,, Some research teams indicate that the real mechanism can be a mix of both direct and indirect mechanisms. , …”
Section: Introductionmentioning
confidence: 99%