scholarly journals Local initiation conditions for water autoionization

2018 ◽  
Vol 115 (20) ◽  
pp. E4569-E4576 ◽  
Author(s):  
Mahmoud Moqadam ◽  
Anders Lervik ◽  
Enrico Riccardi ◽  
Vishwesh Venkatraman ◽  
Bjørn Kåre Alsberg ◽  
...  
Keyword(s):  
Rare Event ◽  
Water Structure ◽  
Ab Initio Molecular Dynamics ◽  
Local Order ◽  
Water Molecules ◽  
Hydronium Ions ◽  
Open Questions ◽  
Local Water ◽  
Ionization Of Water ◽  
Good Agreement

The pH of liquid water is determined by the infrequent process in which water molecules split into short-lived hydroxide and hydronium ions. This reaction is difficult to probe experimentally and challenging to simulate. One of the open questions is whether the local water structure around a slightly stretched OH bond is actually initiating the eventual breakage of this bond or whether this event is driven by a global ordering that involves many water molecules far away from the reaction center. Here, we investigated the self-ionization of water at room temperature by rare-event ab initio molecular dynamics and obtained autoionization rates and activation energies in good agreement with experiments. Based on the analysis of thousands of molecular trajectories, we identified a couple of local order parameters and show that if a bond stretch occurs when all these parameters are around their ideal range, the chance for the first dissociation step (double-proton jump) increases from 10−7 to 0.4. Understanding these initiation triggers might ultimately allow the steering of chemical reactions.

Neutral 4-phenyl-1-[phenyl(pyridin-2-yl)methylidene]semicarbazide and its salt forms with inorganic anions

2019 ◽  
Vol 75 (1) ◽  
pp. 1-7
Author(s):  
Vinicius Oliveira Araujo ◽  
Bárbara Tirloni ◽  
Lívia Streit ◽  
Vânia Denise Schwade
Keyword(s):  
Solid State ◽  
Spectroscopic Characterization ◽  
Water Molecules ◽  
Keto Form ◽  
Chloride Dihydrate ◽  
Ir And Nmr Spectroscopy ◽  
Tautomeric Forms ◽  
Counter Ions ◽  
Salt Forms ◽  
Good Agreement

Semicarbazones can exist in two tautomeric forms. In the solid state, they are found in the keto form. This work presents the synthesis, structures and spectroscopic characterization (IR and NMR spectroscopy) of four such compounds, namely the neutral molecule 4-phenyl-1-[phenyl(pyridin-2-yl)methylidene]semicarbazide, C19H16N4O, (I), abbreviated as HBzPyS, and three different hydrated salts, namely the chloride dihydrate, C19H17N4O+·Cl−·2H2O, (II), the nitrate dihydrate, C19H17N4O+·NO3 −·2H2O, (III), and the thiocyanate 2.5-hydrate, C19H17N4O+·SCN−·2.5H2O, (IV), of 2-[phenyl({[(phenylcarbamoyl)amino]imino})methyl]pyridinium, abbreviated as [H2BzPyS]+·X −·nH2O, with X = Cl− and n = 2 for (II), X = NO3 − and n = 2 for (III), and X = SCN− and n = 2.5 for (IV), showing the influence of the anionic form in the intermolecular interactions. Water molecules and counter-ions (chloride or nitrate) are involved in the formation of a two-dimensional arrangement by the establishment of hydrogen bonds with the N—H groups of the cation, stabilizing the E isomers in the solid state. The neutral HBzPyS molecule crystallized as the E isomer due to the existence of weak π–π interactions between pairs of molecules. The calculated IR spectrum of the hydrated [H2BzPyS]+ cation is in good agreement with the experimental results.

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 Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations

2020 ◽  
Vol 26 (42) ◽  
pp. 7598-7622 ◽  
Author(s):  
Xiao Hu ◽  
Irene Maffucci ◽  
Alessandro Contini
Keyword(s):  
Drug Discovery ◽  
Binding Free Energy ◽  
Docking Studies ◽  
Free Energy Calculations ◽  
Binding Energies ◽  
New Drugs ◽  
Water Molecules ◽  
Open Questions ◽  
Dynamics Simulations ◽  
Computational Drug Discovery

Background: The inclusion of direct effects mediated by water during the ligandreceptor recognition is a hot-topic of modern computational chemistry applied to drug discovery and development. Docking or virtual screening with explicit hydration is still debatable, despite the successful cases that have been presented in the last years. Indeed, how to select the water molecules that will be included in the docking process or how the included waters should be treated remain open questions. Objective: In this review, we will discuss some of the most recent methods that can be used in computational drug discovery and drug development when the effect of a single water, or of a small network of interacting waters, needs to be explicitly considered. Results: Here, we analyse the software to aid the selection, or to predict the position, of water molecules that are going to be explicitly considered in later docking studies. We also present software and protocols able to efficiently treat flexible water molecules during docking, including examples of applications. Finally, we discuss methods based on molecular dynamics simulations that can be used to integrate docking studies or to reliably and efficiently compute binding energies of ligands in presence of interfacial or bridging water molecules. Conclusions: Software applications aiding the design of new drugs that exploit water molecules, either as displaceable residues or as bridges to the receptor, are constantly being developed. Although further validation is needed, workflows that explicitly consider water will probably become a standard for computational drug discovery soon.

scholarly journals Electron impact ionization of water molecules in ice and liquid phases

2007 ◽  
Vol 80 ◽  
pp. 012008 ◽  
Author(s):  
K N Joshipura ◽  
Sumona Gangopadhyay ◽  
C G Limbachiya ◽  
Minaxi Vinodkumar
Keyword(s):  
Electron Impact ◽  
Impact Ionization ◽  
Electron Impact Ionization ◽  
Water Molecules ◽  
Liquid Phases ◽  
Ionization Of Water

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

Complexation of the La(III) cation by p-sulfonatocalix[4]arene — A 139La NMR study

2002 ◽  
Vol 80 (2) ◽  
pp. 163-168 ◽  
Author(s):  
Yaël Israëli ◽  
Christine Bonal ◽  
Christian Detellier ◽  
Jean-Pierre Morel ◽  
Nicole Morel-Desrosiers
Keyword(s):  
Linear Relationship ◽  
Standard Enthalpy ◽  
Effective Radius ◽  
Water Soluble ◽  
Water Molecules ◽  
Standard Entropy ◽  
Nmr Data ◽  
Nmr Study ◽  
Good Agreement ◽  
Formation Of Complexes

The complexation of La(III) by the water-soluble p-sulfonatocalix[4]arene was thermodynamically characterized by 139La NMR. The 139La NMR data are consistent with the formation of a 1:1 complex resulting from electro static interactions between the sulfonato groups and La(III). The complexation is entropy-driven and is characterized by a positive standard enthalpy (ΔrH° = 11.0 ± 0.5 kJ mol–1) and a positive standard entropy (ΔrS° = 108 ± 2 J K–1 mol–1), which are in very good agreement with the ones determined previously by microcalorimetry. The linear relationship between the 139La NMR linewidth of the free and of the complexed cation, obtained at temperatures ranging from 290 to 340 K, excludes the formation of complexes or aggregates other than the 1:1 complex. It shows also that upon complexation, the effective radius of La(III) undergoes an increase of 50%, related to the replacement of water molecules of the hydrated cation by sulfonato groups of the ligand.Key words: complexation, water-soluble calixarene, p-sulfonatocalix[4]arene, 139La NMR, lanthanum.

scholarly journals VMC proper motions of the Magellanic Bridge

2018 ◽  
Vol 14 (S344) ◽  
pp. 130-133 ◽  
Author(s):  
Thomas Schmidt ◽  
Maria-Rosa Cioni ◽  
Florian Niederhofer ◽  
Jonathan Diaz ◽  
Gal Matijevic
Keyword(s):  
Galaxy Evolution ◽  
Milky Way ◽  
Dwarf Galaxy ◽  
Large Mass ◽  
Proper Motions ◽  
Dynamical Simulation ◽  
Open Questions ◽  
The Hierarchical Structure ◽  
The Universe ◽  
Good Agreement

AbstractDwarf galaxies enable us to study early phases of galaxy evolution and are key to many open questions about the hierarchical structure of the Universe. The Large and Small Magellanic Cloud (LMC and SMC) are the most luminous dwarf galaxy satellites of the Milky Way (MW). They are most likely gravitationally bound to each other, and their last interaction occurred about 200 Myr ago. Also, they are in an early phase of minor merging with the MW and will impact the Galactic structure in the future because of their relatively large mass. However, there are still major uncertainties regarding their origin and their interactions with one another and with the Milky Way. We cross-correlated the VMC and Gaia DR2 data to select a sample of stars that likely belong to the Magellanic Bridge, a feature formed of gas and stars which is connecting the LMC and the SMC. We removed potential MW foregound stars using a combination of parallax and colour-magnitude criteria and calculated the proper motions of the Bridge member stars. Our analysis supports a motion of star towards the LMC, which was found to be in good agreement with a dynamical simulation, of the SMC being stripped by the LMC.

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