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 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>

Proton Transfer in Bulk Water by 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 ◽  
Adaptive Methods ◽  
Bulk Water ◽  
Water Molecules ◽  
Computational Costs ◽  
Adaptive Treatment ◽  
Grotthuss Mechanism ◽  
Hydronium Ion ◽  
Method Integration ◽  
Large Systems

The quantum mechanical/molecular mechanical (QM/MM) method is a hybrid molecular simulation technique that makes local electronic structures of large systems accessible.<br>It has the strengths of accuracy found in the QM method as well as the strengths of small<br>computational costs found in the MM method. However, it is severe to directly apply the<br>QM/MM method to dynamics of solution systems, particularly to proton transfer. As explained in the Grotthuss mechanism, proton transfer is a structural interconversion between hydronium ion and solvent water molecules. 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. Although there have been several solvent-adaptive methods proposed, a full adaptive framework, an approach that also takes into account of adaptation for solutes, still remains untapped. In this paper, we propose a new numerical expression for the coordinate of the excess proton and its control algorithm. Furthermore, we confirmed that this method can stably and accurately simulate proton transfer dynamics in bulk water.

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

2020 ◽  
Author(s):  
Hiroshi Watanabe ◽  
Masayuki Yamada ◽  
Yohichi Suzuki
Keyword(s):  
Proton Transfer ◽  
Adaptive Methods ◽  
Bulk Water ◽  
Water Molecules ◽  
Computational Costs ◽  
Adaptive Treatment ◽  
Grotthuss Mechanism ◽  
Hydronium Ion ◽  
Method Integration ◽  
Large Systems

The quantum mechanical/molecular mechanical (QM/MM) method is a hybrid molecular simulation technique that makes local electronic structures of large systems accessible.<br>It has the strengths of accuracy found in the QM method as well as the strengths of small<br>computational costs found in the MM method. However, it is severe to directly apply the<br>QM/MM method to dynamics of solution systems, particularly to proton transfer. As explained in the Grotthuss mechanism, proton transfer is a structural interconversion between hydronium ion and solvent water molecules. 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. Although there have been several solvent-adaptive methods proposed, a full adaptive framework, an approach that also takes into account of adaptation for solutes, still remains untapped. In this paper, we propose a new numerical expression for the coordinate of the excess proton and its control algorithm. Furthermore, we confirmed that this method can stably and accurately simulate proton transfer dynamics in bulk water.

scholarly journals Phosphinate MOF formed from tetratopic ligands as proton conductive materials

2021 ◽  
Author(s):  
Matouš Kloda ◽  
Tomáš Plecháček ◽  
Soňa Ondrušová ◽  
Petr Brázda ◽  
Petr Chalupský ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Proton Transfer ◽  
Rational Design ◽  
Metal Organic Frameworks ◽  
Adsorbed Water ◽  
Proton Conductors ◽  
Water Molecules ◽  
Conductive Materials ◽  
Grotthuss Mechanism ◽  
Metal Organic

Metal organic frameworks (MOFs) are attracting attention as potential proton conductors. There are two main advantages of MOFs in this application: the possibility of rational design and tuning of the properties, and clear conduction pathways given by their crystalline structure. We hereby present two new MOF structures, ICR-10 and ICR-11, based on tetratopic phosphinate ligands. The structures of both MOFs were determined by 3D electron diffraction. They both crystallize in the P-3 space group and contain arrays of parallel linear pores lined with hydrophilic non-coordinated phosphinate groups. This, together with the adsorbed water molecules, facilitates proton transfer via the Grotthuss mechanism, leading to the proton conductivity up to 4.26∙10-4 S cm-1 for ICR-11.

scholarly journals Proton transfer in bulk water using the full adaptive QM/MM method: integration of solute- and solvent-adaptive approaches

2021 ◽  
Author(s):  
Hiroshi C. Watanabe ◽  
Masayuki Yamada ◽  
Yohichi Suzuki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Proton Transfer ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Adaptive Approach ◽  
Hydronium Ion ◽  
Method Integration ◽  
Adaptive Approaches

The full adaptive approach achieved an accurate and stable molecular dynamics simulation of hydronium ion in bulk.

scholarly journals Ein Wasserstoffisotopieeffekt im CuSO4 * 5H2O

1969 ◽  
Vol 24 (10) ◽  
pp. 1502-1511
Author(s):  
Karl Heinzinger
Keyword(s):  
Water Vapor ◽  
Aqueous Solutions ◽  
Separation Factor ◽  
Room Temperature ◽  
Copper Ion ◽  
Hydrogen Isotopes ◽  
Bulk Water ◽  
Water Molecules ◽  
Hydration Water ◽  
Sulfate Solutions

Abstract There are two kinds of water in CuSO4·5H2O differing by their binding in the crystal. The oxygen of four water molecules is bonded to the copper ion, that of the fifth molecule is hydrogen bonded. It is shown that the D/H ratios of these two kinds of water differ by 5.7%, the light isotope being enriched in the water molecules coordinated with the copper ion. The results show that there is no exchange of the hydrogen isotopes during the time needed for dehydration at room temperature which takes several days. The assumption has been confirmed that the water coordinated with the copper ion leaves the crystal first on dehydration at temperatures below 50 °C. Additional measurements of the separation factor for the hydrogen isotopes between water vapor and copper sulfate solutions allow conclusions on the fractionation of the hydrogen isotopes between bulk water and hydration water in aqueous solutions.

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.

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.

Calculation of the proton transfer between water molecules

1970 ◽  
Vol 6 (2) ◽  
pp. 117-120 ◽  
Author(s):  
Yeong Fang ◽  
Jose R. De La Vega
Keyword(s):  
Proton Transfer ◽  
Water Molecules
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