ELECTRONIC STRUCTURE AND STABILITY OF NH4(NH3)n AND NH4(NH3)m(H2O)n

1996 ◽  
Vol 03 (01) ◽  
pp. 353-357 ◽  
Author(s):  
R. TAKASU ◽  
K. FUKE ◽  
F. MISAIZU
Keyword(s):  
Alkali Atom ◽  
Binding Energies ◽  
Water Molecules ◽  
Clear Trend ◽  
Photoionization Process ◽  
Large Binding Energy ◽  
Ammonia Clusters ◽  
Mixed Clusters ◽  
Limiting Value ◽  
Photoemission Threshold

The photoionization process of NH 4( NH 3)n and NH 4( NH 3)m( H 2 O )n radicals produced by an ArF excimer laser photolysis of ammonia clusters and ammonia–water mixed clusters are examined using time-of-flight mass spectroscopy. The ionization potentials (IPs) of NH 4( NH 3)n (n=0−35) and NH 4( NH 3)m( H 2 O )n (m=0−4, n=0−3) are determined by the photoionization threshold measurements. The binding energies of NH 4( NH 3)n−1− NH 3 (n=1−6) are estimated from IPs. The results indicate that the bonding between NH 4 and NH 3 is semi-ionic. The IPs for the large ammoniated NH 4 clusters decrease with increasing n up to 35. The limiting value (n→∞) is found to be 1.33 eV, which coincides with the photoemission threshold of liquid NH 3. This feature is similar to those found recently for alkali-atom–ammonia clusters. A clear trend is found for the IPs of NH 4( NH 3)m( H 2 O )n; the clusters containing more water molecules have higher IP. This trend is ascribed to the large binding energy of [Formula: see text] comparing with that of [Formula: see text].

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 Chemical Energetics and Atomic Charges Distribution of Variably Sized Hydrated Sulfate Clusters in the light of Density Functional Theory

2021 ◽  
Vol 25 (1) ◽  
pp. 595
Author(s):  
Anant Babu Marahatta
Keyword(s):  
Structural Stability ◽  
Density Functional ◽  
Hydration Number ◽  
Binding Energies ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Atomic Charges ◽  
Electronic Interactions ◽  
Hydrogen Bond Formation ◽  
Depth Analysis

Among the ions classified in the Hofmeister series, the firstly ranked divalent sulfate anion has the strongest hydrating and water-structure making propensity. This unique characteristic actually makes it kosmotropic which causes water molecules to interact each other and contributes to gain structural stability of its hydrated clusters [SO42−(H2O)n]n = 1−40. In this study, few variably sized microhydrated sulfate clusters [SO42−(H2O)n]n = 1−4, 16 are considered separately, and inquired their chemical energetics and atomic charge distributions through ab initio based theoretical model. The main objective of this insight is to specify and interpret their thermodynamic stabilities, binding energies, and specific bonding and electronic interactions quantum mechanically. An in-depth analysis of their change in relative ground state electronic energy with respect to hydration number indicates stronger affinity of the sulfate ion towards water molecules while attaining structural stability in any aqueous type solutions. The mathematically determined values of their binding energy (DE) almost holds up the same with this structural stability order: [SO42−(H2O)16] > [SO42−(H2O)4] > [SO42−(H2O)3] > [SO42−(H2O)2] > [SO42−(H2O)], as reliable as experimentally and molecular dynamics simulation predicted trend. Moreover, the Mulliken derived partial atomic charges feature qualitative charge distribution in them which not only depicts electronic interactions between the specific atoms but also exemplifies the involvement of central sulfate units in hydrogen bond formation with surrounding water molecules.

The mobility of alkali ions in gases III. The mobility of alkali ions in water vapour

1939 ◽  
Vol 172 (948) ◽  
pp. 51-54 ◽  
Keyword(s):  
Water Vapour ◽  
Infinite Dilution ◽  
Pure Water ◽  
Atomic Weight ◽  
Alkali Atom ◽  
Water Molecules ◽  
Degree Of Hydration ◽  
Alkali Ions ◽  
Alkali Ion

It is known that in electrolytes at infinite dilution the mobility of an alkali ion increases with its mass and this has been attributed by some to a decrease in its degree of hydration as the size of the alkali atom increases. In Part I evidence was obtained, at least in helium and neon, that the average number of water molecules which are attached to an alkali ion when water is present as an impurity also decreases as the atomic weight of the ion increases. As a natural corollary to this work a determination of the mobility of the alkali ions in pure water vapour has been undertaken and is here described. The method and apparatus of Part I was used. The nature of the ion from the source was first verified by running it in a pure gas which was then pumped off and water vapour introduced. The results are shown in fig. 1, where the mobility of the ion is plotted with E/p . For the sake of clearness the results for Rb + are excluded from the graph except at low values of E/p . The remainder of the Rb + graph follows more or less that for Na + .

Ultrafast fragmentation of small alkali atom-ammonia clusters

1995 ◽  
Vol 239 (1-3) ◽  
pp. 18-24 ◽  
Author(s):  
C.P. Schulz ◽  
J. Höhndorf ◽  
P. Brockhaus ◽  
F. Noack ◽  
I.V. Hertel
Keyword(s):  
Alkali Atom ◽  
Ammonia Clusters

scholarly journals Visualization of magnesium and rubidium ion hydration in sulfocationite using quantum chemical calculation

2021 ◽  
Vol 65 (6) ◽  
pp. 692-701
Author(s):  
V. S. Soldatov ◽  
T. V. Bezyazychnaya ◽  
E. G. Kosandrovich
Keyword(s):  
Binding Energy ◽  
Ab Initio Calculation ◽  
Molecular Layer ◽  
Binding Energies ◽  
Magnesium Ion ◽  
Water Molecules ◽  
Chemical Calculation ◽  
Ion Hydration ◽  
Coordination Numbers ◽  
Comparable Size

Based on the data of ab initio calculation of the structure of (RSO3)2Mg (H2O)18 and (RSO3Rb)2(H2O)16 clusters, which simulate the structure of swollen sulfostyrene ion exchangers in the corresponding ionic forms and a water cluster of comparable size, the numbers of water molecules directly bound to cations and their coordination numbers, including the oxygen atoms of the sulfonic groups linked to the cation, were calculated. It is shown that the first molecular layer around the magnesium ion is formed from water molecules with the highest binding energy with the cluster, and around the rubidium ion – from the molecules of the nearest environment with the lowest binding energies. This is explained by the fact that the transfer of water molecules from its volume to magnesium hydrate is energetically favorable, but not to rubidium hydrate. Therefore, the magnesium ion builds its hydrate mainly from water molecules with the highest binding energy in order to obtain the greatest energy gain, and the rubidium ion – from molecules with the lowest energy, which provides the smallest energy loss.

scholarly journals Dual Geometry Schemes in Tetrel Bonds: Complexes between TF4 (T = Si, Ge, Sn) and Pyridine Derivatives

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 376 ◽  
Author(s):  
Wiktor Zierkiewicz ◽  
Mariusz Michalczyk ◽  
Rafał Wysokiński ◽  
Steve Scheiner
Keyword(s):  
Deformation Energy ◽  
Binding Energies ◽  
The Other ◽  
Equatorial Position ◽  
Interaction Energies ◽  
Pyridine Derivatives ◽  
Clear Trend ◽  
Tetrahedral Structure ◽  
Equilibrium Geometries ◽  
Tetrel Bonds

When an N-base approaches the tetrel atom of TF4 (T = Si, Ge, Sn) the latter molecule deforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situate itself at either an axial or equatorial position, leading to two different equilibrium geometries. The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol, which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform the tetrahedral monomer into the equatorial structure is much higher than the equivalent deformation energy in the axial dimer. When these two opposite trends are combined, it is the axial geometry which is somewhat more stable than the equatorial, yielding binding energies in the 8–34 kcal/mol range. There is a clear trend of increasing interaction energy as the tetrel atom grows larger: Si < Ge < Sn, a pattern which is accentuated for the binding energies.

Fission of charged nano-hydrated ammonia clusters – microscopic insights into the nucleation processes

2019 ◽  
Vol 21 (46) ◽  
pp. 25749-25762
Author(s):  
Bart Oostenrijk ◽  
Darío Barreiro ◽  
Noelle Walsh ◽  
Anna Sankari ◽  
Erik P. Månsson ◽  
...  
Keyword(s):  
Atmospheric Aerosols ◽  
Theoretical Study ◽  
Model System ◽  
Water Molecules ◽  
Ammonia Clusters ◽  
Hydrogen Bonded

The dynamics of nucleation and fission in atmospheric aerosols is tackled in a joint experimental–theoretical study using a model system that consists of hydrogen-bonded ammonia and water molecules.

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