Molecular orientation near liquid–vapor interface of methanol: Simulational study

Matsumoto, Mitsuhiro; Kataoka, Yosuke

doi:10.1063/1.455982

Cited by 113 publications

(62 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…All PE bands exhibit a similar gas–liquid shift of −1.23 eV for MeOH and −1.10 eV for EtOH, which can be explained with polarization screening by the surrounding molecules; these values are somewhat smaller than for liquid water and attributed to the larger molecular size and thus distance of the alcohol molecules. We do not see any significant contribution to the gas–liquid shift from a present (polar) orientation of the alcohol molecules at the liquid’s surface, which agrees well with an orientation almost parallel to the liquid surface found in simulations . While a reasonable description of the inelastic scattering background could be achieved with a single Gaussian in the valence region, information of electron scattering in liquid alcohols is currently lacking.…”

Section: Discussionsupporting

confidence: 86%

“…No distinct dependence on the specific PE band was found, except the splitting caused by H-bonding for MeOH and strong overlapping bands of a−e for EtOH. Previously, MeOH has been found to show a strong molecular ordering at the liquid surface, with the CH 3 pointing out of the liquid surface; 60,61 however, its permanent dipole moment is aligned parallel to the liquid surface and the resulting electrostatic surface potential is only on the order of −0.03 V. 59 Therefore, the influence of surface dipole can be neglected. Orientation with the alkyl chain pointing away from the liquid surface has also been observed for higher order alcohols.…”

Section: The Journal Ofmentioning

confidence: 99%

“…We do not see any significant contribution to the gas−liquid shift from a present (polar) orientation of the alcohol molecules at the liquid's surface, which agrees well with an orientation almost parallel to the liquid surface found in simulations. 60 While a reasonable description of the inelastic scattering background could be achieved with a single Gaussian in the valence region, information of electron scattering in liquid alcohols is currently lacking. Comparison of the measured PE spectra with experimental and simulated X-ray emission spectra reveals that there is a good agreement (i.e., close match of the overall spectral shape) if nuclear dynamics in the core-hole state is omitted, which confirms involvement of nuclear dynamics in the X-ray emission process within its lifetime of several femtoseconds.…”

Section: ■ Conclusionmentioning

confidence: 99%

See 2 more Smart Citations

Valence Photoelectron Spectra of Liquid Methanol and Ethanol Measured Using He II Radiation

2021

View full text Add to dashboard Cite

High-resolution photoelectron (PE) spectra of liquid methanol and ethanol were measured using a liquid microjet and He IIα radiation (40.813 eV). The vertical ionization energy and the ionization threshold were determined as 9.70 ± 0.07 and 8.69 ± 0.07 eV for methanol and 9.52 ± 0.07 and 8.52 ± 0.07 eV for ethanol, respectively. Individual photoemission bands observed for the liquids are well correlated with those in PE spectra of the gaseous samples also measured in the present study, except that the liquid band positions were shifted on average by −1.23 eV for methanol and −1.10 eV for ethanol as compared to the gas. The 5a′ and 7a′ bands of liquid methanol exhibit specifically larger broadening than other bands, for which we attempted spectral fitting with two components, similarly with the case of the 3a1 band of liquid water. PE spectra of both liquid and gaseous ethanol are congested partly due to the presence of the trans and gauche isomers; however, the overall band positions are generally in good agreement with predictions based on quantum chemical calculations. Comparison of the measured PE spectra with experimental and simulated X-ray emission spectra indicate that spectral differences in the lowest ionization band of both methanol and ethanol originate from involvement of nuclear dynamics in the X-ray emission process.

show abstract

Section: Discussionsupporting

confidence: 86%

Section: The Journal Ofmentioning

confidence: 99%

Section: ■ Conclusionmentioning

confidence: 99%

See 1 more Smart Citation

Valence Photoelectron Spectra of Liquid Methanol and Ethanol Measured Using He II Radiation

2021

View full text Add to dashboard Cite

show abstract

“…The physical meaning of this discrete solvent effect has been matter of considerable debate in the classical simulation literature over the last two decades, in the context of ionic solvation free energies 22,44,45,[112][113][114][115][116][117][118][119][120][121] as well as in the context of surface potential calculations. 22,[122][123][124][125][126][127][128][129][130][131][132][133][134][135][136] The authors believe that this debate and its conclusions are appropriately summarized in Ref. 22 (see also Ref.…”

Section: Discussionmentioning

confidence: 99%

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

Rocklin¹,

Mobley²,

Dill³

et al. 2013

The Journal of Chemical Physics

222

368

View full text Add to dashboard Cite

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol(-1)) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

show abstract

“…methanol by MD simulations, and it was reported that methanol molecules in the interface have a tendency to project their methyl groups to the vapor phase. 15,29 We shall examine the molecular orientational distribution in the virtual vacuum evaporation states. According to Refs.…”

Section: ͑32͒mentioning

confidence: 99%

Molecular dynamics study of kinetic boundary condition at an interface between a polyatomic vapor and its condensed phase

2004

View full text Add to dashboard Cite

The kinetic boundary condition for the Boltzmann equation at an interface between a polyatomic vapor and its liquid phase is investigated by the numerical method of molecular dynamics, with particular emphasis on the functional form of the evaporation part of the boundary condition, including the evaporation coefficient. The present study is an extension of a previous one for argon [Ishiyama, Yano, and Fujikawa, Phys. Fluids 16, 2899 (2004)] to water and methanol, typical examples of polyatomic molecules. As in the previous study, molecular dynamics simulations of vapor-liquid equilibrium states and those of evaporation from liquid into a virtual vacuum are carried out for water and methanol. In spite of the formation of molecular clusters in the vapor phase and the presence of the preferential orientation of molecules at the interface, essentially the same results as in the previous study are obtained. When the bulk liquid temperature is relatively low, the evaporation part is the product of the half range Maxwellian for the translational velocity of molecules of saturated vapor at the temperature of the bulk liquid phase, the equilibrium distribution of rotational energy of molecules at the temperature, and the evaporation coefficient (or the condensation coefficient in the equilibrium state). The evaporation coefficients of water and methanol are determined without any ambiguity as decreasing functions of the temperature, and are found to approach unity with the decrease of the temperature.

show abstract

Molecular orientation near liquid–vapor interface of methanol: Simulational study

Cited by 113 publications

References 11 publications

Valence Photoelectron Spectra of Liquid Methanol and Ethanol Measured Using He II Radiation

Valence Photoelectron Spectra of Liquid Methanol and Ethanol Measured Using He II Radiation

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

Molecular dynamics study of kinetic boundary condition at an interface between a polyatomic vapor and its condensed phase

Contact Info

Product

Resources

About