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Journal ArticleDOI

Molecular Arrangement of a Mixture of Organosulfur Surfactants at the Aqueous Solution–Vapor Interface Studied by Photoelectron Intensity and Angular Distribution Measurements and Molecular Dynamics Simulations

TL;DR: In this article, the spatial arrangement of solute molecules at the solution-gas-phase interface is analyzed using electron angular distributions (PADs) from aqueous solution surfaces.
Abstract: Photoelectron angular distributions (PADs) from aqueous solution surfaces reveal details of the spatial arrangement of solute molecules at the solution–gas-phase interface. This is demonstrated her...
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TL;DR: X-ray photoelectron spectroscopy is an excellent method for the investigation of these interfaces due to its surface sensitivity, elemental and chemical specificity, and the possibility to obtain information on the depth distribution of solute and solvent species in the interfacial region as discussed by the authors.
Abstract: Liquid–vapor interfaces, particularly those between aqueous solutions and air, drive numerous important chemical and physical processes in the atmosphere and in the environment X-ray photoelectron spectroscopy is an excellent method for the investigation of these interfaces due to its surface sensitivity, elemental and chemical specificity, and the possibility to obtain information on the depth distribution of solute and solvent species in the interfacial region In this Perspective, we review the progress that was made in this field over the past decades and discuss the challenges that need to be overcome for investigations of heterogeneous reactions at liquid–vapor interfaces under close-to-realistic environmental conditions We close with an outlook on where some of the most exciting and promising developments might lie in this field

33 citations

Journal ArticleDOI
TL;DR: Hypobromous acid, a reaction intermediate in the oxidation process, is the only species showing surface propensity, which supports the idea of the complete bromide oxidation reaction sequence to bromine occurring at the interface.
Abstract: Multiphase reactions of halide ions in aqueous solutions exposed to the atmosphere initiate the formation of molecular halogen compounds in the gas phase. Their photolysis leads to halogen atoms, w...

20 citations

Journal ArticleDOI
TL;DR: In this paper, specific challenges associated with photoemission spectroscopy of bulk liquid water, aqueous solutions, water droplets and water clusters are discussed, and different energy referencing methods, including the application of a bias voltage to access absolute energy of solvent and solute.
Abstract: This perspective article reviews specific challenges associated with photoemission spectroscopy of bulk liquid water, aqueous solutions, water droplets and water clusters. The main focus lies on retrieving accurate energetics and photoelectron angular information from measured photoemission spectra, and on the question how these quantities differ in different aqueous environments. Measured photoelectron band shapes, vertical binding energies (ionization energies), and photoelectron angular distributions are influenced by various phenomena. We discuss the influences of multiple energy-dependent electron scattering in aqueous environments, and we discuss different energy referencing methods, including the application of a bias voltage to access absolute energetics of solvent and solute. Recommendations how to account for or minimize the influence of electron scattering are provided. The example of the hydrated electron in different aqueous environments illustrates how one can account for electron scattering, while reliable methods addressing parasitic potentials and proper energy referencing are demonstrated for ionization from the outermost valence orbital of neat liquid water.

15 citations

Journal ArticleDOI
TL;DR: In this article , an experimental X-ray photoelectron circular dichroism (PECD) study of liquid fenchone at the C 1s edge was performed on a liquid microjet.
Abstract: We present an experimental X-ray photoelectron circular dichroism (PECD) study of liquid fenchone at the C 1s edge. A novel setup to enable PECD measurements on a liquid microjet [Malerz et al., Rev. Sci. Instrum., 2022, 93, 015101] was used. For the C 1s line assigned to fenchone's carbonyl carbon, a non-vanishing asymmetry is found in the intensity of photoelectron spectra acquired under a fixed angle in the backward-scattering plane. This experiment paves the way towards an innovative probe of the chirality of organic/biological molecules in aqueous solution.

12 citations

Journal ArticleDOI
TL;DR: In this article , the authors used X-ray photoelectron spectroscopy to study the adsorption of a model surfactant, octanoic acid, at the water-gas interface.
Abstract: The characterization of liquid–vapor interfaces at the molecular level is an important underpinning for a basic understanding of fundamental heterogeneous processes in many areas, such as atmospheric science. Here we use X-ray photoelectron spectroscopy to study the adsorption of a model surfactant, octanoic acid, at the water–gas interface. In particular, we examine the information contained in photoelectron angular distributions and show that information about the relative depth of molecules and functional groups within molecules can be obtained from these measurements. Focusing on the relative location of carboxylate (COO−) and carboxylic acid (COOH) groups at different solution pH, the former is found to be immersed deeper into the liquid–vapor interface, which is confirmed by classical molecular dynamics simulations. These results help establish photoelectron angular distributions as a sensitive tool for the characterization of molecules at the liquid–vapor interface.

10 citations

References
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Journal ArticleDOI
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.

46,130 citations

Journal ArticleDOI
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
Abstract: Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.

33,683 citations

Journal ArticleDOI
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.

18,394 citations

Journal ArticleDOI
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

17,897 citations

Journal ArticleDOI
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

14,558 citations