scholarly journals Effects of Hydrogen Bonding on the Rotational Dynamics of Water-Like Molecules in Liquids: Insights from Molecular Dynamics Simulations

2020 ◽  
Vol 73 (8) ◽  
pp. 734
Author(s):  
W. A. Monika Madhavi ◽  
Samantha Weerasinghe ◽  
Konstantin I. Momot

Rotational motion of molecules plays an important role in determining NMR spin relaxation properties of liquids. The textbook theory of NMR spin relaxation predominantly uses the assumption that the reorientational dynamics of molecules is described by a continuous time rotational diffusion random walk with a single rotational diffusion coefficient. Previously we and others have shown that reorientation of water molecules on the timescales of picoseconds is not consistent with the Debye rotational-diffusion model. In particular, multiple timescales of molecular reorientation were observed in liquid water. This was attributed to the hydrogen bonding network in water and the consequent presence of collective rearrangements of the molecular network. In order to better understand the origins of the complex reorientational behaviour of water molecules, we carried out molecular dynamics (MD) simulations of a liquid that has a similar molecular geometry to water but does not form hydrogen bonds: hydrogen sulfide. These simulations were carried out at T=208K and p=1 atm (~5K below the boiling point). Ensemble-averaged Legendre polynomial functions of hydrogen sulfide exhibited a Gaussian decay on the sub-picosecond timescale but, unlike water, did not exhibit oscillatory behaviour. We attribute these differences to hydrogen sulfide’s absence of hydrogen bonding.

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.


2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.


1990 ◽  
Vol 45 (9-10) ◽  
pp. 1077-1084 ◽  
Author(s):  
D. Pusiol ◽  
F. Noack ◽  
C. Aguilera

Abstract Field-cycling and standard pulsed NMR techniques have been used to study the frequency dependence of the longitudinal proton spin relaxation time T x in the crystalline estradiol compound (+)3,1,7-ß-bis-(4n-butoxybenzoyloxy)-estra-1,3,5-(10)-trien or BET, which is a mesogenic material with a chiral molecular structure. From the measured Larmor frequency and temperature depen-dences we conclude that, at low NMR frequencies in the cholesteric phase, T1 reflects in addition to the relaxation process familiar from nematic liquid crystals (director fluctuation modes) another slow mechanism theoretically predicted for cholesteric systems, namely diffusion induced rotational molecular reorientation. These relaxation processes are not or much less effective in the crystalline and glassy state, where they are frozen. Also the high NMR frequency relaxation dispersion strongly differs between the cholesteric mesophase and the not liquid crystalline samples. This is interpreted by a change from essentially translational self-diffusion to rotational diffusion controlled proton relaxation.


Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5853
Author(s):  
Sulejman Skoko ◽  
Matteo Ambrosetti ◽  
Tommaso Giovannini ◽  
Chiara Cappelli

We present a detailed computational study of the UV/Vis spectra of four relevant flavonoids in aqueous solution, namely luteolin, kaempferol, quercetin, and myricetin. The absorption spectra are simulated by exploiting a fully polarizable quantum mechanical (QM)/molecular mechanics (MM) model, based on the fluctuating charge (FQ) force field. Such a model is coupled with configurational sampling obtained by performing classical molecular dynamics (MD) simulations. The calculated QM/FQ spectra are compared with the experiments. We show that an accurate reproduction of the UV/Vis spectra of the selected flavonoids can be obtained by appropriately taking into account the role of configurational sampling, polarization, and hydrogen bonding interactions.


Biochemistry ◽  
2003 ◽  
Vol 42 (47) ◽  
pp. 13856-13868 ◽  
Author(s):  
Hao Hu ◽  
Michael W. Clarkson ◽  
Jan Hermans ◽  
Andrew L. Lee

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