scholarly journals Geometries, interaction energies and complexation free energies of 18-crown-6 with neutral molecules

CrystEngComm ◽  
2016 ◽  
Vol 18 (44) ◽  
pp. 8653-8663 ◽  
Author(s):  
Ming W. Shi ◽  
Li-Juan Yu ◽  
Sajesh P. Thomas ◽  
Amir Karton ◽  
Mark A. Spackman
Keyword(s):  
Interaction Energies ◽  
Free Energies

Free energies of solvation with quantum mechanical interaction energies from classical mechanical simulations

1999 ◽  
Vol 110 (3) ◽  
pp. 1329-1337 ◽  
Author(s):  
Robert H. Wood ◽  
Eric M. Yezdimer ◽  
Shinichi Sakane ◽  
Jose A. Barriocanal ◽  
Douglas J. Doren
Keyword(s):  
Quantum Mechanical ◽  
Interaction Energies ◽  
Free Energies ◽  
Mechanical Interaction

Gas and solution phase thermochemistry and transition energies of NH2• and NH3•+, and their aquo complexes: an ab initio study

1994 ◽  
Vol 72 (3) ◽  
pp. 471-483 ◽  
Author(s):  
Dake Yu ◽  
Arvi Rauk ◽  
David A. Armstrong
Keyword(s):  
Ab Initio ◽  
Binding Energies ◽  
Solution Phase ◽  
Interaction Energies ◽  
Free Energies ◽  
Transition Energies ◽  
Bonding Interaction ◽  
Ab Initio Structure ◽  
Total Energies ◽  
Free Energy Of Solution

Ab initio calculations were performed on several aquo complexes of NH2•, and NH3•+, and on monomeric parent species. The geometries were optimized at the HF/6-31 + G* level and the vibrational frequencies were calculated. The total energies and the binding energies of complexes were evaluated at the MP2/6-31 + G* + ZPE level of theory. Gas and aqueous solution phase thermodynamic properites of NH2• and NH3•+ and several other species were calculated. The examination of solution phase properties of the radicals was facilitated by study of the structures and transition energies of aquo complexes. H-bonding interaction energies decreased in the order [Formula: see text] but were generally stronger than σ–σ* interactions involving the unpaired electron. From calculations with the CIS method, the weak absorption observed at 520 nm for aqueous NH2• is confirmed as a 2B1 → 2A1 transition, while the stronger NH2• absorption occurring below 250 nm and the absorption of NH3•+, which rises monotonically below 370 nm, are attributed to solvent-to-solute charge transfer bands. The solution free energies and related E0 values for NH2• and NH3•+ are in agreement with those of Stanbury. The ab initio structure studies show that water protons are bound to N, and proton transfer from solvent in reaction [18], NH2• + e− + H2O → NH3 + OH−, is likely to be the dominant redox reaction of NH2• in alkaline solution. The free energy of solution of NH3•+ is shown to be larger than that of [Formula: see text].

scholarly journals Theoretical Study on the Extraction of Alkaline Earth Salts by 18-Crown-6: Roles of Counterions, Solvent Types and Extraction Temperatures

2014 ◽  
Vol 14 (2) ◽  
pp. 199-208 ◽  
Author(s):  
Saprizal Hadisaputra ◽  
Lorenz R Canaval ◽  
Harno Dwi Pranowo ◽  
Ria Armunanto
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Alkaline Earth ◽  
Theoretical Study ◽  
Polar Solvent ◽  
Density Functional Method ◽  
Nitrate Anion ◽  
Interaction Energies ◽  
Free Energies ◽  
Solvent Phase

The roles of counterions, solvent types and extraction temperatures on the selectivity of 18-crown-6 (L) toward alkaline earth salts MX2 (M = Ca, Sr, Ba; X = Cl-, NO3-) have been studied by density functional method at B3LYP level of theory in gas and solvent phase. In gas phase, the chloride anion Cl- is the preference counterion than nitrate anion NO3-. This result is confirmed by the interaction energies, the second order interaction energies, charge transfers, energy difference between HOMO-LUMO and electrostatic potential maps. The presence of solvent reversed the gas phase trend. It is found that NO3- is the preference counterion in solvent phase. The calculated free energies demonstrate that the solvent types strongly change the strength of the complex formation. The free energies are exothermic in polar solvent while for the non polar solvent the free energies are endothermic. As the temperature changes the free energies also vary where the higher the temperatures the lower the free energy values. The calculated free energies are correlated well with the experimental stability constants. This theoretical study would have a strong contribution in planning the experimental conditions in terms of the preference counterions, solvent types and optimum extraction temperatures.

scholarly journals Regular Associated Solution Model for the Estimation of Free Energy of Mixing of Binary Liquid Alloys

1970 ◽  
Vol 8 (8) ◽  
pp. 30-33
Author(s):  
D Adhikari ◽  
BP Singh ◽  
IS Jha
Keyword(s):  
Free Energy ◽  
Equilibrium Constants ◽  
Solution Model ◽  
Interaction Energies ◽  
Free Energies ◽  
Scientific World ◽  
Energy Of Mixing ◽  
Free Energy Of Mixing ◽  
Associated Solution Model ◽  
Associated Solution

We have found the equilibrium constants and pairwise interaction energies between the species and the complexes of liquid CuSn, AgAl, FeSi, CdNa and HgNa alloys on the basis of regular associated solution model. These parameters are then used to estimate the free energies of mixing of each alloy. The observed asymmetry in the free energy of mixing of each alloy with respect to concentration is well explained. Key Words: Free energy of mixing; Asymmetry; Binary alloys; Interaction energy. DOI: 10.3126/sw.v8i8.3842 Scientific World Vol.8(8) 2010 pp.30-33

scholarly journals New methods for computational drug design

2015 ◽  
Author(s):  
Jimmy Charnley Kromann
Keyword(s):  
Hydrogen Bond ◽  
Vibrational Analysis ◽  
Attractive Alternative ◽  
Interaction Energies ◽  
Free Energies ◽  
Order Of Accuracy ◽  
Computational Drug Design ◽  
New Methods ◽  
Small Proteins ◽  
The University

This thesis describes the work that has been carried out in connection with my Masters at the University of Copenhagen. This work has led to new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. This work also included the implementation of the new HF-3c method in GAMESS and its interface with the fragmentation method FMO. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. HF-3c also shows interaction energies within the same order of accuracy as the PM6 based methods. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. PM6-D3H+ and FMO2-HF- 3c in GAMESS was used to optimize two small proteins which resulted in a much more reliable structure compared to the reference structures, than PM6-DH+ in MOPAC, most likely due to the different optimization algorithms associated with the programs. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.

GLYCOSIDATION OF SUGARS: II. METHANOLYSIS OF D-XYLOSE, D-ARABINOSE, D-LYXOSE, AND D-RIBOSE

1963 ◽  
Vol 41 (11) ◽  
pp. 2743-2758 ◽  
Author(s):  
C. T. Bishop ◽  
F. P. Cooper
Keyword(s):  
Conformational Analysis ◽  
Excellent Agreement ◽  
Transition States ◽  
Interaction Energies ◽  
Free Energies ◽  
Ionic Effects ◽  
Competing Reactions

Rates of methanolysis reactions of D-xylose, D-arabinose, D-lyxose, and D-ribose have been determined. It was found that methanolysis of a pentose proceeds to equilibrium through four distinguishable, competing reactions: (1) pentose → furanosides; (2) anomerization of furanosides; (3) furanosides → pyranosides; (4) anomerization of pyranosides. The glycoside compositions at equilibrium are interpreted in terms of stabilities of each of the four glycosides from each sugar as influenced by steric and ionic effects; a system of conformational analysis of furanoside rings is presented. The free energies of reaction in anomerization of pyranosides were in excellent agreement with values calculated from previously reported interaction energies in the pyranoid ring. The relative rates of the reactions were consistent with the view that non-bonded interactions in the methyl glycosides are relieved in the transition states for their interconversions.

Conformational analysis in carbohydrate chemistry. I. Conformational free energies. The conformations and α : β ratios of aldopyranoses in aqueous solution

1968 ◽  
Vol 21 (11) ◽  
pp. 2737 ◽  
Author(s):  
SJ Angyal
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Conformational Analysis ◽  
Reasonable Agreement ◽  
Anomeric Effect ◽  
Interaction Energies ◽  
Free Energies ◽  
Carbohydrate Chemistry ◽  
Predominant Conformation

The relative free energies of the aldopyranoses in aqueous solution have been calculated, taking non-bonded interaction energies and the anomeric effect into account. It is shown that the calculated free-energy values correctly predict the predominant conformation of the α- and β-pyranose forms of each aldose. The α- to β-pyranose ratios of the aldoses in aqueous solution, calculated from these values, are in reasonable agreement with those determined experimentally.

scholarly journals New methods for computational drug design

2015 ◽  
Author(s):  
Jimmy Charnley Kromann
Keyword(s):  
Hydrogen Bond ◽  
Vibrational Analysis ◽  
Attractive Alternative ◽  
Interaction Energies ◽  
Free Energies ◽  
Order Of Accuracy ◽  
Computational Drug Design ◽  
New Methods ◽  
Small Proteins ◽  
The University

This thesis describes the work that has been carried out in connection with my Masters at the University of Copenhagen. This work has led to new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. This work also included the implementation of the new HF-3c method in GAMESS and its interface with the fragmentation method FMO. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. HF-3c also shows interaction energies within the same order of accuracy as the PM6 based methods. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. PM6-D3H+ and FMO2-HF- 3c in GAMESS was used to optimize two small proteins which resulted in a much more reliable structure compared to the reference structures, than PM6-DH+ in MOPAC, most likely due to the different optimization algorithms associated with the programs. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.

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