We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and β−sheets in protein, by including the constant force stretching at one end of molecules as in a typical single-molecule experiment. The conformations of double-stranded regions of the cha...

Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challengin...

The differences in the macrocyclic structures lead to different flexibilities, and yet effect of solvents on conformations is not clear so far. In this work, four representational molecules (pillar[5]arene, p-tert-butyl calix[6]arene, benzylic amide macrocycle dibenzo-18-crown-6) three with distinct polarity have been studied by all-atom molecular dynamics simulations. structural features macro...

NBO analysis and density functional theory (DFT: B3LYP/6-311+G**) based method were used to study the impacts of the anomeric effects (AE) on the conformational properties of 2-methoxy-1,2,4,5-tetrahydro-benzo[d]oxepine (1), -thiepine (2) and -selenepine (3). The Gibbs free energy difference (Geq–Gax) values (i.e. ΔGeq-ax) at 298.15 K and 1 atm between the axial and equatorial conformations inc...

The conformational behaviors of 2,3-bis(methylthio)-1,4-dioxane (1), 2,3-bis(methylthio)-1,4-dithiane (2) and 2,3-bis(methylthio)-1,4-diselenane (3) have been analyzed by means ofhybrid-density functional theory (B3LYP/Def2-TZVPP) based method and NBO interpretation.B3LYP/Def2-TZVPP results showed that the axial conformations of compounds 1-3 are morestable than their equatorial conformations. ...

The hybrid density functional theory (B3LYP) and ab initio molecular orbital (HF) based methods and Natural Bond Orbital (NBO) interpretation were used to analyze the conformational behaviors of 2,5,5-trimethyl-1,3,2-dioxaphosphinane 2-selenide (compound 1), 2,5,5-trimethyl-1,3,2-dithiaphosphinane 2-selenide (compound 2) and 2,5,5-trimethyl-1,3,2-diselena phosp...