Water-assisted ground state intra-molecular proton transfer in 2,5-dihydroxy-substituted azobenzenes: experimental and computational studies

CrystEngComm ◽  
2019 ◽  
Vol 21 (14) ◽  
pp. 2373-2380 ◽  
Author(s):  
Dhiraj Das ◽  
Angshuman Roy Choudhury
Keyword(s):  
Proton Transfer ◽  
Theoretical Calculation ◽  
Ground State ◽  
Water Molecules ◽  
Computational Studies ◽  
Azobenzene Derivatives

The phenomenon of ground-state proton transfer in a series of 2,5-dihydroxy azobenzene derivatives has been studied. In addition, the effect of the substitutions and water molecules has been investigated by the theoretical calculation.

scholarly journals Proton Transfer in Bulk Water using the Full Adaptive QM/MM Method: Integration of Solute- and Solvent-Adaptive Approaches

2020 ◽  
Author(s):  
Hiroshi C. Watanabe ◽  
Masayuki Yamada ◽  
Yohichi Suzuki
Keyword(s):  
Proton Transfer ◽  
Control Algorithm ◽  
Adaptive Methods ◽  
Bulk Water ◽  
Water Molecules ◽  
Adaptive Treatment ◽  
Grotthuss Mechanism ◽  
Hydronium Ions ◽  
Method Integration ◽  
Large Systems

<div><div>The quantum mechanical/molecular mechanical (QM/MM) method is a hybrid molecular simulation technique that increases the accessibility of local electronic structures of large systems.</div><div> The technique combines the benefit of accuracy found in the QM method and that of cost efficiency found in the MM method.</div><div> However, it is difficult to directly apply the QM/MM method to the dynamics of solution systems, particularly for proton transfer. </div><div> As explained in the Grotthuss mechanism, proton transfer is a structural interconversion between hydronium ions and solvent water molecules. </div><div> Hence, when the QM/MM method is applied, an adaptive treatment, namely on-the-fly revisions on molecular definitions, is required for both the solute and solvent. </div><div> Although several solvent-adaptive methods have been proposed, a full adaptive framework, which is an approach that also considers adaptation for solutes, remains untapped. In this paper, we propose a new numerical expression for the coordinates of the excess proton and its control algorithm.</div><div> Furthermore, we confirm that this method can stably and accurately simulate proton transfer dynamics in bulk water.</div></div>

scholarly journals Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate

2016 ◽  
Vol 72 (5) ◽  
pp. 751-755 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Network Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Arsanilic Acid ◽  
Dimensional Network

In the structure of the brucinium salt of 4-aminophenylarsonic acid (p-arsanilic acid), systematically 2,3-dimethoxy-10-oxostrychnidinium 4-aminophenylarsonate tetrahydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water molecules of solvation are accommodated between the layers and are linked to them through a primary cation N—H...O(anion) hydrogen bond, as well as through water O—H...O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

Molecular dissociation and proton transfer in aqueous methane solution under electric field.

2021 ◽  
Author(s):  
Giuseppe Cassone ◽  
Jiri Sponer ◽  
Franz Saija
Keyword(s):  
Solar System ◽  
Electric Field ◽  
Proton Transfer ◽  
Computational Studies ◽  
Molecular Dissociation ◽  
The Subject

Methane-water mixtures are ubiquitous in our Solar System and they have been the subject of a wide variety of experimental, theoretical, and computational studies aimed at understanding their behaviour under...

Theoretical Calculation of Hyperfine Structures and g-factors of Ground State of Mercuric Fluoride Molecule

2017 ◽  
Vol 37 (9) ◽  
pp. 0902001
Author(s):  
郝 美 Hao Mei ◽  
汪海玲 Wang Hailing ◽  
印建平 Yin Jianping
Keyword(s):  
Theoretical Calculation ◽  
Ground State ◽  
Hyperfine Structures ◽  
G Factors

scholarly journals Validity and limitations of simple reaction kinetics to calculate concentrations of organic compounds from ion counts in PTR-MS

2019 ◽  
Vol 12 (11) ◽  
pp. 6193-6208 ◽  
Author(s):  
Rupert Holzinger ◽  
W. Joe F. Acton ◽  
William J. Bloss ◽  
Martin Breitenlechner ◽  
Leigh R. Crilley ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Reaction Kinetics ◽  
Transfer Reaction ◽  
Performance Status ◽  
Calibration Method ◽  
Proton Transfer Reaction ◽  
Rural Site ◽  
Water Molecules ◽  
Simple Reaction ◽  
Wide Range

Abstract. In September 2017, we conducted a proton-transfer-reaction mass-spectrometry (PTR-MS) intercomparison campaign at the CESAR observatory, a rural site in the central Netherlands near the village of Cabauw. Nine research groups deployed a total of 11 instruments covering a wide range of instrument types and performance. We applied a new calibration method based on fast injection of a gas standard through a sample loop. This approach allows calibrations on timescales of seconds, and within a few minutes an automated sequence can be run allowing one to retrieve diagnostic parameters that indicate the performance status. We developed a method to retrieve the mass-dependent transmission from the fast calibrations, which is an essential characteristic of PTR-MS instruments, limiting the potential to calculate concentrations based on counting statistics and simple reaction kinetics in the reactor/drift tube. Our measurements show that PTR-MS instruments follow the simple reaction kinetics if operated in the standard range for pressures and temperature of the reaction chamber (i.e. 1–4 mbar, 30–120∘, respectively), as well as a reduced field strength E∕N in the range of 100–160 Td. If artefacts can be ruled out, it becomes possible to quantify the signals of uncalibrated organics with accuracies better than ±30 %. The simple reaction kinetics approach produces less accurate results at E∕N levels below 100 Td, because significant fractions of primary ions form water hydronium clusters. Deprotonation through reactive collisions of protonated organics with water molecules needs to be considered when the collision energy is a substantial fraction of the exoergicity of the proton transfer reaction and/or if protonated organics undergo many collisions with water molecules.

scholarly journals Rigidly hydrogen-bonded water molecules facilitate proton transfer in photosystem II

2020 ◽  
Vol 22 (28) ◽  
pp. 15831-15841
Author(s):  
Naoki Sakashita ◽  
Hiroshi Ishikita ◽  
Keisuke Saito
Keyword(s):  
Photosystem Ii ◽  
Proton Transfer ◽  
Water Molecules ◽  
Hydrogen Bonded

In the channel of photosystem II, rigidly hydrogen-bonded water molecules facilitate the Grotthuss-like proton transfer, whereas flexible water molecules prevent proton transfer in the channel of aquaporin.

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