β-cyclodextrine and Water: Semiempirical Calculations

1996 ◽  
Vol 51 (8) ◽  
pp. 950-956 ◽  
Author(s):  
C. Margheritis ◽  
C. Sinistri
Keyword(s):  
Electrostatic Interactions ◽  
Pure Water ◽  
Water Molecules ◽  
Atomic Charges ◽  
Compensation Mechanism ◽  
Interaction Energies ◽  
Water Interaction ◽  
Circular Arrangement ◽  
Unfavorable Condition ◽  
Consequent Increase

Abstract AM1 and PM3 calculations were carried out on ß-cyclodextrine (ß-CD) undecahydrate in the experimental conformation at 120 K. The calculated ß-CD/water interaction energies are very small and indicative for each water molecule of an unfavorable condition in respect to that of pure water. The conformationally optimized system was also studied: ß-CD appears highly symmetrical with negligible dipole moment, mainly because of the circular arrangement of the single vectors. Primary hydroxyls can easily rotate, while the secondary ones are stabilized by heteroannular hydrogen bonds and homoannular electrostatic interactions due to the consequent increase of the atomic charges. The ß-CD/water interaction energies in the optimized hydrated system are not significantly different from the experimental ones. This almost hydrophobic character is also shown by MM equilibrated solutions: all water molecules are rejected beyond 2.4 Å; between 2.4 and 2.9 Å highly structured water is present. From a purely enthalpic standpoint the molecule hydration appears highly improbable, thus the formation of ß-CD 11 H20 must involve a compensation mechanism.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

scholarly journals Entropy-driven binding of gut bacterial β-glucuronidase inhibitors ameliorates irinotecan-induced toxicity

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hsien-Ya Lin ◽  
Chia-Yu Chen ◽  
Ting-Chien Lin ◽  
Lun-Fu Yeh ◽  
Wei-Che Hsieh ◽  
...  
Keyword(s):  
Cancer Metabolism ◽  
Glucuronic Acid ◽  
Intestinal Epithelial Cells ◽  
Primary Treatment ◽  
Water Molecules ◽  
Intestinal Epithelial ◽  
E Coli ◽  
Severe Diarrhea ◽  
Coordinated Water ◽  
Consequent Increase

AbstractIrinotecan inhibits cell proliferation and thus is used for the primary treatment of colorectal cancer. Metabolism of irinotecan involves incorporation of β-glucuronic acid to facilitate excretion. During transit of the glucuronidated product through the gastrointestinal tract, an induced upregulation of gut microbial β-glucuronidase (GUS) activity may cause severe diarrhea and thus force many patients to stop treatment. We herein report the development of uronic isofagomine (UIFG) derivatives that act as general, potent inhibitors of bacterial GUSs, especially those of Escherichia coli and Clostridium perfringens. The best inhibitor, C6-nonyl UIFG, is 23,300-fold more selective for E. coli GUS than for human GUS (Ki = 0.0045 and 105 μM, respectively). Structural evidence indicated that the loss of coordinated water molecules, with the consequent increase in entropy, contributes to the high affinity and selectivity for bacterial GUSs. The inhibitors also effectively reduced irinotecan-induced diarrhea in mice without damaging intestinal epithelial cells.

CONDUCTANCES OF LITHIUM NITRATE SOLUTIONS IN ETHYL ALCOHOL AND ETHYL ALCOHOL - WATER MIXTURES AT 25.0 °C.

1956 ◽  
Vol 34 (9) ◽  
pp. 1232-1242 ◽  
Author(s):  
A. N. Campbell ◽  
G. H. Debus
Keyword(s):  
No Value ◽  
Ethyl Alcohol ◽  
Pure Water ◽  
Lithium Ion ◽  
Water Molecules ◽  
Lithium Nitrate ◽  
Absolute Alcohol ◽  
Pure Alcohol ◽  
Alcohol Water ◽  
Nitrate Solutions

The conductances of solutions of lithium nitrate in 30, 70, and 100 weight per cent ethyl alcohol have been determined at concentrations ranging from 0.01 molar up to saturation, at 25 °C. The densities and viscosities of these solutions have also been determined. The data have been compared with the calculated conductances obtained from the Wishaw–Stokes equation. The agreement is fairly good up to, say, 2 M, for all solvents except absolute alcohol. In the latter solvent there is no value of å, the distance of closest approach, which will give consistent values of the equivalent conductance. In passing from pure water to pure alcohol, the value of å increases progressively and this we attribute to a change in the solvation of the lithium ion from water molecules to alcohol molecules. Some further calculations incline us to the view that the nitrate ion, as well as the lithium ion, is solvated to some extent, at least in alcohol.

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.

scholarly journals Separation of water–ethanol solutions with carbon nanotubes and electric fields

2016 ◽  
Vol 18 (48) ◽  
pp. 33310-33319 ◽  
Author(s):  
Winarto Winarto ◽  
Daisuke Takaiwa ◽  
Eiji Yamamoto ◽  
Kenji Yasuoka
Keyword(s):  
Carbon Nanotubes ◽  
Electric Field ◽  
Electric Fields ◽  
Electrostatic Interactions ◽  
Water Molecules ◽  
Ordered Structure

Under an electric field, water prefers to fill CNTs over ethanol, and electrostatic interactions within the ordered structure of the water molecules determine the separation effects.

A Molecular Dynamics Study of Aqueous Solutions II. Cesium Chloride in H2O

1975 ◽  
Vol 30 (6-7) ◽  
pp. 789-796 ◽  
Author(s):  
P. C. Vogel ◽  
K. Heinzinger
Keyword(s):  
Molecular Dynamics ◽  
Elevated Temperatures ◽  
Pure Water ◽  
Pair Correlation ◽  
Cesium Chloride ◽  
Pair Interaction ◽  
Chloride Ions ◽  
Water Molecules ◽  
Static Properties ◽  
Average Potential Energy

Abstract Results of a molecular dynamics study of an aqueous CsCl solution are reported. The system consisted of 216 particles, 200 water molecules, 8 cesium ions and 8 chloride ions and was run over 8000 time steps equivalent of 9 · 10-13 sec. On the basis of radial pair correlation functions, average potential energy of the water molecules and pair interaction energy distribution the static properties of the first hydration shells of the ions are discussed in detail. The self diffusion coefficient for the water molecules is calculated and compared with NMR measurement as well as with molecular dynamics calculations for pure water at elevated temperatures and pressures.

Fractionation of Hydrogen Isotopes in Aqueous Lithium Chloride Solutions

1988 ◽  
Vol 43 (5) ◽  
pp. 449-453 ◽  
Author(s):  
Masahisa Kakiuchi
Keyword(s):  
Oxygen Isotope ◽  
Isotope Effect ◽  
Lithium Chloride ◽  
Structural Changes ◽  
Platinum Catalyst ◽  
Pure Water ◽  
Free Water ◽  
Hydrogen Gas ◽  
Water Molecules ◽  
Chloride Solutions

The D/H ratio of hydrogen gas in equilibrium with water vapor over aqueous lithium chloride solutions was measured at 25 °C, using a hydrophobic platinum catalyst. Experimental details are described. The hydrogen isotope effect between the solution and pure water depends linearly on the LiCl concentration up to ca. 12 m, and at higher concentrations a marked deviation from linearity takes place, as was also observed for the oxygen isotope effect measured by Bopp et al. On the basis of these hydrogen and oxygen isotope effects it is concluded that H218O is enriched in the water molecules coordinated to Li+ ions and HD16O is enriched in the free water molecules of the solution. The observed deviation from linearity for concentrations higher than ca. 12m is interpreted in terms of structural changes in the hydration sphere of the Li+ ions.

Infrared spectrum of HDO in aqueous solutions of perchlorates and tetrafluoroborates

1970 ◽  
Vol 48 (19) ◽  
pp. 3019-3025 ◽  
Author(s):  
George Brink ◽  
Michael Falk
Keyword(s):  
Aqueous Solutions ◽  
Pure Water ◽  
Ion Pairs ◽  
Low Frequency ◽  
Frequency Component ◽  
High Frequency Component ◽  
Water Molecules ◽  
Oh Groups ◽  
Cation Effect ◽  
Crystalline Hydrates

The OH and OD stretching bands of HDO in aqueous solutions containing the ions ClO4− and BF4− are split into two components. The high-frequency component, A, does not shift with temperature. It is interpreted as due to OH groups involved in weak [Formula: see text] or [Formula: see text] hydrogen bonds. This interpretation is in line with the corresponding OH frequencies of other systems containing ClO4− ions, such as methanolic solutions and crystalline hydrates. Solvent-separated ion pairs may account for the observed cation effect on band A. The low-frequency component, B, varies with temperature almost exactly like the corresponding band of pure water. It is interpreted to be due to those OH groups which are not associated with the anion. Components A and B are not resolved in solutions of most electrolytes because the distribution of strengths of interactions of OH groups with most anions overlaps that of [Formula: see text] interactions between 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 + .

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