Investigation of the Structure of Ethanol–Water Mixtures by Molecular Dynamics Simulation I: Analyses Concerning the Hydrogen-Bonded Pairs

Gereben, Orsolya; Pusztai, László

doi:10.1021/jp510490y

Cited by 82 publications

(102 citation statements)

References 49 publications

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“…A very similar conclusion could be obtained for water-ethanol mixtures from a recent MD study [27]. In that work, the main reason for this asymmetry was suggested to be the larger steric demands of the alcohol molecule; here, although to a lesser extent, the same reasoning may be applied.…”

Section: Some Features Of Hydrogen Bonds Statisticssupporting

confidence: 76%

“…Quite similar trends, in terms of the varying ratio of the first and secondary maxima of the X-ray TSF, were observed for ethanol-water mixtures [27], where also the OPLS/AA force field was applied for the description of alcohol molecules, and the SPC/E water model of water was made use of, too. The X-ray experimental data for ethanol solutions were recorded together with the ones reported here for water-methanol mixtures.…”

Section: Total Structure Factorssupporting

confidence: 59%

“…It is already known, see rather comprehensive discussion in Ref. [27,30] and documented here again, that for pure water both the SPC/E and TIP4P/Ew models provide appropriate descriptions of the X-ray diffraction data. The match between simulation and experiment may be called quantitative for the latter, the TIP4P/Ew, model that reproduces even the first maximum of the TSF, S(Q), within errors, Fig.…”

Section: Total Structure Factorsmentioning

confidence: 56%

“…It may therefore be speculated that the OPLS/AA-SPC/E combination with the geometric mean mixing rules works better in alcohol-water mixtures where the less hydrophilic the alcohol is. This conjecture would be interesting to check by complementing the two studies, the present one on water-methanol and the earlier one [27] on water-ethanol mixtures, by inspecting further alcohols with longer alkyl chains. Work in this direction is in progress, via the study of (1-and 2-)propanol-water solutions [31].…”

Section: Total Structure Factorsmentioning

confidence: 86%

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Microscopic structure of methanol–water mixtures: Synchrotron X-ray diffraction experiments and molecular dynamics simulations over the entire composition range

Galicia‐Andrés

Pusztai

Temleitner

et al. 2015

Journal of Molecular Liquids

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Section: Some Features Of Hydrogen Bonds Statisticssupporting

confidence: 76%

Section: Total Structure Factorssupporting

confidence: 59%

Section: Total Structure Factorsmentioning

confidence: 56%

Section: Total Structure Factorsmentioning

confidence: 86%

See 2 more Smart Citations

Microscopic structure of methanol–water mixtures: Synchrotron X-ray diffraction experiments and molecular dynamics simulations over the entire composition range

Galicia‐Andrés

Pusztai

Temleitner

et al. 2015

Journal of Molecular Liquids

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“…2. Compared with FA, both ethanol and DMSO have a much lower hydrogen bond capability, which is only roughly two bonds per molecules, whereas the water hydrogen bond capability lies between 3.5 and 4 per water molecule (30,31). Both aqueous mixtures show microheterogeneous structures at low concentration (31, 32), which are not formed in the case of FA/ water due to their almost equal ability to form hydrogen bonds.…”

Section: Resultsmentioning

confidence: 99%

Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

Niether

Afanasenkau

Dhont

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007) Proc Natl Acad Sci USA 104(22): 9346−9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of 10 −3 wt % that is typical for concentrations in shallow lakes on early Earth.concentration problem | hydrothermal vents | molecular evolution | origin-of-life problem | thermophoresis T hermophoresis has been suggested as an active transport mechanism to reach high concentrations of prebiotic molecules to culminate in the formation of RNA (1). A still open question is whether thermophoresis can also be a possible mechanism to form prebiotic nucleobases from simple molecules such as hydrogen cyanide (HCN) and formamide (FA). Already for almost 50 years, FA has been discussed as an important compound from which prebiotic molecules originate (2-7). It has been shown that all known nucleobases can be synthesized from aqueous FA solutions (4). In diluted HCN solutions, polymerization of HCN to form nucleobases becomes favored over hydrolysis of HCN at concentrations of 0.03-0.3 wt % (8). To our knowledge, there are no similar studies of diluted FA solutions. Taking into account the faster hydrolysis of FA (3), we estimated that a 100-timeshigher concentration between 3 wt % and 33 wt % should be sufficient for the synthesis of prebiotic molecules in aqueous solutions. In the ocean during the early stages of Earth, the natural occurring concentrations at a low temperature (10°C) and a pH between 6 and 8 are estimated to be only on the order of 10 −9 wt %, whereas, in shallow lakes (depth 10 m), due to vaporization and FA input from the atmosphere, higher concentrations of about 10 −3 wt % are possible (3). Still, these natural concentrations are far too small compared with those required for the formation of nucleobases.In this work, we perform numerical calculations ...

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Why different water models predict different structures under 2D confinement

2018

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Experiments of nanoconfined water between graphene sheets at high pressure suggest that it forms a square ice structure (Algara-Siller et al., Nature, 2015, 519, 443). Molecular dynamics (MD) simulations have been used to attempt to recreate this structure, but there have been discrepancies in the structure formed by the confined water depending on the simulation set-up that was employed and particularly on the choice of water model. Here, using classical molecular dynamics simulations, we have systematically investigated the effect that three different water models (SPC/E, TIP4P/2005 and TIP5P) have on the structure of water confined between two rigid graphene sheets with a 0.9 nm separation. We show that the TIP4P/2005 and the TIP5P water models form a hexagonal AA-stacked structure, whereas the SPC/E model forms a rhombic AB-stacked structure. Our work demonstrates that the formation of these structures is driven by differences in the strength of hydrogen bonds predicted by the three water models, and that the nature of the graphene/water interaction only mildly affects the phase diagram. Considering the available experimental data and first-principle simulations we conclude that, among the models tested, the TIP4P/2005 and TIP5P force fields are for now the most reliable when simulating water under confinement. © 2018 Wiley Periodicals, Inc.

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Investigation of the Structure of Ethanol–Water Mixtures by Molecular Dynamics Simulation I: Analyses Concerning the Hydrogen-Bonded Pairs

Cited by 82 publications

References 49 publications

Microscopic structure of methanol–water mixtures: Synchrotron X-ray diffraction experiments and molecular dynamics simulations over the entire composition range

Microscopic structure of methanol–water mixtures: Synchrotron X-ray diffraction experiments and molecular dynamics simulations over the entire composition range

Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

Why different water models predict different structures under 2D confinement

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