Quantum mechanical calculation of thermodynamic functions of solvation of ammonium ions in water

1985 ◽  
Vol 63 (7) ◽  
pp. 1746-1749 ◽  
Author(s):  
Renato Contreras ◽  
Gilles Klopman
Keyword(s):  
Quantum Mechanical ◽  
Free Energies ◽  
Enthalpy Of Solvation ◽  
Ammonium Ions ◽  
Generalized Born ◽  
Complete Set ◽  
Saturation Effects ◽  
Dielectric Saturation ◽  
Generalized Born Formula ◽  
Good Agreement

The application of an extended version of the generalized Born formula including dielectric saturation effects, implemented within the SCF-CNDO/2 approximation, provides a complete set of data concerning the thermodynamics of solvation of some ammonium ions in water. The calculated free energies of solvation are in good agreement with experimental data. An estimation of the entropy and enthalpy of solvation is also given and satisfactory qualitative trends are obtained.

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Electron Density ◽  
Partition Coefficients ◽  
Dna Bases ◽  
Atomic Charges ◽  
Free Energies ◽  
Solvation Model ◽  
Minimal Basis ◽  
Methylated Dna ◽  
Implicit Solvation Model ◽  
Good Agreement

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

THEORETICAL CALCULATION OF pKb VALUES FOR ANILINES AND SULFONAMIDE DRUGS IN AQUEOUS SOLUTION

2012 ◽  
Vol 11 (02) ◽  
pp. 283-295 ◽  
Author(s):  
BAHRAM GHALAMI-CHOOBAR ◽  
ALI GHIAMI-SHOMAMI ◽  
PARIA NIKPARSA
Keyword(s):  
Gas Phase ◽  
Continuum Model ◽  
Correlation Equation ◽  
Polarizable Continuum Model ◽  
Free Energies ◽  
Pcm Model ◽  
Solvation Models ◽  
Polarizable Continuum ◽  
Better Than ◽  
Good Agreement

In this work, calculations of p K b values have been performed for aniline and its substituted derivatives and sulfonamide drugs by using Gaussian 98 software package. Gas-phase energies were calculated with HF /6-31 G ** and B3LYP /6-31 G ** levels of theory. Free energies of solvation have been computed using the polarizable continuum model (PCM), conductor-like polarizable continuum model (CPCM) and the integral equation formalism-polarizable continuum model (IEFPCM) at the same levels which have been used for geometry determination in the gas-phase. The results show that the calculated p K b values using the B3LYP /6-31 G ** are better than those using the corresponding HF /6-31 G **. At first, the correlation equation was found to determine the p K b values of the investigated anilines. Then, this correlation equation was used to calculate the p K b values of the sulfonamide drugs. The results obtained indicate that the PCM model is a suitable solvation model for calculating p K b values in comparison to the other solvation models. For the investigated compounds a good agreement between the experimental and the calculated p K b values was also observed.

Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field

2004 ◽  
Vol 108 (41) ◽  
pp. 16264-16270 ◽  
Author(s):  
William L. Jorgensen ◽  
Jakob P. Ulmschneider ◽  
Julian Tirado-Rives
Keyword(s):  
Force Field ◽  
Free Energies ◽  
Generalized Born ◽  
Born Model ◽  
Generalized Born Model

A Semiempirical Quantum Mechanical Solvation Model for Solvation Free Energies in All Alkane Solvents

1995 ◽  
Vol 99 (18) ◽  
pp. 7137-7146 ◽  
Author(s):  
David J. Giesen ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Quantum Mechanical ◽  
Free Energies ◽  
Solvation Model ◽  
Alkane Solvents ◽  
Solvation Free Energies

scholarly journals A thermodynamic description of metastable c-TiAlZrN coatings with triple spinodally decomposed domains

2017 ◽  
Vol 53 (2) ◽  
pp. 85-93 ◽  
Author(s):  
J. Zhou ◽  
L. Zhang ◽  
L. Chen ◽  
Y. Du ◽  
Z.K. Liu
Keyword(s):  
Experimental Data ◽  
Phase Equilibria ◽  
First Principles ◽  
Thermodynamic Description ◽  
Quantitative Description ◽  
Experimental Phase Equilibria ◽  
Free Energies ◽  
Calphad Technique ◽  
Important Input ◽  
Good Agreement

A critical thermodynamic assessment of the metastable c-TiAlZrN coatings, which are reported to spinodally decompose into triple domains, i.e., c-TiN, c-AlN, and c-ZrN, was performed via the CALculation of PHAse Diagram (CALPHAD) technique based on the limited experimental data as well as the first-principles computed free energies. The metastable c-TiAlZrN coatings were modeled as a pseudo-ternary phase consisting of c-TiN, c-AlN and c-ZrN species, and described using the substitutional solution model. The thermodynamic descriptions for the three boundary binaries were directly taken from either the CALPHAD assessment or the first-principles results available in the literature except for a re-adjustment of the pseudo-binary c-AlN/c-ZrN system based on the experimental phase equilibria in the pseudo-ternary system. The good agreement between the calculated phase equilibria and the experimental data over the wide temperature range was obtained, validating the reliability of the presently obtained thermodynamic descriptions for the c-TiAlZrN system. Based on the present thermodynamic description, different phase diagrams and thermodynamic properties can be easily predicted. It is anticipated that the present thermodynamic description of the metastable c-TiAlZrN coatings can serve as the important input for the later quantitative description of the microstructure evolution during service life.

scholarly journals Novel Pyrazolo[3,4-c]pyridine Antagonists with Nanomolar affinity for A1 / A3 Adenosine Receptors: Binding Kinetics and Exploration of their Binding Profile Using Mutagenesis Experiments, MD simulations and TI/MD calculations

2021 ◽  
Author(s):  
Margarita Stampelou ◽  
Anna Suchankova ◽  
Eva Tzortzini ◽  
Lakshiv Dhingra ◽  
Kerry Barkan ◽  
...  
Keyword(s):  
Drug Design ◽  
Transmembrane Helix ◽  
Rank Correlation ◽  
Membrane System ◽  
Md Simulations ◽  
Dissociation Rate ◽  
The Novel ◽  
Free Energies ◽  
Electronegative Group ◽  
Good Agreement

Drugs targeting the four adenosine receptor (AR) subtypes can provide “soft" treatment of various significant diseases. Even for the two experimentally resolved AR subtypes the description of the orthosteric binding area and structure-activity relationships of ligands remains a demanding task due to the high similar amino acids sequence but also the broadness and flexibility of the ARs binding area. The identification of new pharmacophoric moieties and nanomolar leads and the exploration of their binding area with mutagenesis and state-of-the-art computational methods useful also for drug design purposes remains a challenging aim for all ARs. Here, we identified several low nanomolar ligands and potent competitive antagonists against A1R / A3R, containing the novel pyrazolo[3,4-c]pyridine pharmacophore for ARs, from a screen of an in-house library of only 52 compounds, originally designed for anti-proliferative activity. We identified L2-L10, A15, A17 with 3-aryl, 7-anilino and a electronegative group at 5-position as low micromolar to low nanomolar A1R / A3R antagonists. A17 has for A1R Kd = 5.62 nM and a residence time (RT) 41.33 min and for A3R Kd = 13.5 nM, RT = 47.23 min. The kinetic data showed that compared to the not potent or mediocre congeners the active compounds have similar association, for example at A1R Kon = 13.97 x106 M-1 (A17) vs Kon = 3.36 x106 M-1 (A26) but much lower dissociation rate Koff = 0.024 min-1 (A17) vs 0.134 min-1 (A26). Using molecular dynamics (MD) simulations and mutagenesis experiments we investigated the binding site of A17 showing that it can interact with an array of residues in transmembrane helix 5 (TM5), TM6, TM7 of A1R or A3R including residues E5.30, E5.28, T7.35 in A1R instead of Q5.28, V5.30 , L7.35 in A3R. A striking observation for drug design purposes is that for L2506.51A the binding affinity of A17 significantly increased at A1R. A17 provides a lead representative of a promising series and by means of the Thermodynamics Integration coupled with MD simulations (TI/MD) method, first applied here on whole GPCR- membrane system and showing a very good agreement between calculated and experimental relative binding free energies for A1R and A3R (spearman rank correlation p = 0.82 and 0.84, respectively), and kinetic experiments can lead to ligands with improved profile against ARs.

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
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