The affinity of HGGG, GHGG, GGHG, and GGGH peptides for copper(II) and the structures of their complexes — An ab initio study

2009 ◽  
Vol 87 (7) ◽  
pp. 942-953 ◽  
Author(s):  
Stephen D. Barry ◽  
Gail A. Rickard ◽  
M. Jake Pushie ◽  
Arvi Rauk
Keyword(s):  
Geometry Optimization ◽  
Forward Direction ◽  
Ionic Species ◽  
Abundant Species ◽  
Coordination Pattern ◽  
Free Energies ◽  
Solvation Model ◽  
Model Free ◽  
C Terminus ◽  
Peptide Complexes

The structures and relative free energies in aqueous solution of the Cu(II) complexes of the “histidine walk” peptides, AcHGGGNH2, AcGHGGNH2, AcGGHGNH2, and AcGGGHNH2, were determined as a function of pH. Numerous structures of each species were found by gaseous- and solution-phase geometry optimization at the B3LYP/6–31G(d) level, and the effect of solvation estimated by the IEFPCM continuum solvation model. Free energies of solvation of the ionic species are large and favour structures with an extended peptide chain. In all Cu(II)–peptide complexes, deprotonation of two amide groups occurs readily at or below pH 7. In each system, the most abundant species at pH 7 is a neutral 1:1 complex with N3O1 coordination pattern. Binding in the forward direction toward the C terminus is preferred. The results are compared to recent experimental spectroscopic and potentiometric studies on related systems. Alternative explanations are offered for some of the experimental observations.

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>

MINDO-Forces Study on Substituted Nitromethane ⇋ aci-Nitromethane Tautomerism

2005 ◽  
Vol 60 (1-2) ◽  
pp. 47-53
Author(s):  
Bareehan M. Salim ◽  
Salim M. Khalil
Keyword(s):  
Theoretical Calculations ◽  
Geometry Optimization ◽  
Heats Of Formation ◽  
Geometrical Parameters ◽  
Free Energies ◽  
Electron Densities ◽  
Isodesmic Reactions ◽  
Complete Geometry Optimization

MINDO-Forces calculations with complete geometry optimization have been performed on nitromethane, aci-nitromethane and X-substituted nitromethane and aci-nitromethane (X = F, OH, NH2, CH3, CN, CF3, NO2, CHO). It is found that nitromethane is more stable than aci-nitromethane by 9.337 kcal/mol. This agrees with theoretical calculations. Thermodynamically, substituted aci-nitro tautomers are more stable than the corresponding nitromethane, except in case of the substituent F. Geometrical parameters, heats of formation, electron densities, Gibbs free energies and isodesmic reactions are reported.

scholarly journals Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3293
Author(s):  
Mateusz Zalewski ◽  
Sebastian Kmiecik ◽  
Michał Koliński
Keyword(s):  
Molecular Dynamics ◽  
Geometry Optimization ◽  
Computational Prediction ◽  
Md Simulations ◽  
Coarse Grained ◽  
Ligand Interaction ◽  
Vast Number ◽  
Docking Simulations ◽  
Peptide Models ◽  
Peptide Complexes

One of the major challenges in the computational prediction of protein–peptide complexes is the scoring of predicted models. Usually, it is very difficult to find the most accurate solutions out of the vast number of sometimes very different and potentially plausible predictions. In this work, we tested the protocol for Molecular Dynamics (MD)-based scoring of protein–peptide complex models obtained from coarse-grained (CG) docking simulations. In the first step of the scoring procedure, all models generated by CABS-dock were reconstructed starting from their original C-alpha trace representations to all-atom (AA) structures. The second step included geometry optimization of the reconstructed complexes followed by model scoring based on receptor–ligand interaction energy estimated from short MD simulations in explicit water. We used two well-known AA MD force fields, CHARMM and AMBER, and a CG MARTINI force field. Scoring results for 66 different protein–peptide complexes show that the proposed MD-based scoring approach can be used to identify protein–peptide models of high accuracy. The results also indicate that the scoring accuracy may be significantly affected by the quality of the reconstructed protein receptor structures.

Mindo-Forces Study on the Keto-Enol Tautomerism of α-Substituted Acetaldehydes XCH2CH=O (X = H, F, Oh, Cn, NH2, NO2, CH3, CF3, OCH3): Comparison with Acetyl Derivatives

2004 ◽  
Vol 59 (12) ◽  
pp. 980-986
Author(s):  
Wasim F. Al-Halasah ◽  
Salim M. Khalil
Keyword(s):  
Theoretical Calculations ◽  
Geometry Optimization ◽  
Substituent Effects ◽  
Geometrical Parameters ◽  
Free Energies ◽  
Electron Densities ◽  
The Stability ◽  
Complete Geometry Optimization

MINDO-Forces calculations with complete geometry optimization have been performed on α- substituted acetaldehydes XCH2CH=O and their enols (X = H, F, OH, CN, NH2, NO2, CH3, CF3, OCH3). All substituents were found to decrease the stability of the acetaldehyde and mostly in the case of electron withdrawing capacity (e. g NO2 and CF3). This agrees with theoretical calculations, except in the case of F. The substituent effects on the stabilities in this study are compared with results obtained from our previous theoretical calculations on acetyl derivatives. Geometrical parameters, electron densities, and Gibbs free energies are reported.

MST Continuum Study of the Hydration Free Energies of Monovalent Ionic Species

2005 ◽  
Vol 109 (8) ◽  
pp. 3565-3574 ◽  
Author(s):  
Carles Curutchet ◽  
Axel Bidon-Chanal ◽  
Ignaci Soteras ◽  
Modesto Orozco ◽  
F. Javier Luque
Keyword(s):  
Ionic Species ◽  
Free Energies

Precise estimation of transfer free energies for ionic species between similar media

2018 ◽  
Vol 20 (42) ◽  
pp. 27003-27010
Author(s):  
Carmen Esposito ◽  
Andreas Vitalis
Keyword(s):  
Molecular Dynamics ◽  
Ionic Species ◽  
Umbrella Sampling ◽  
Two Dimensional ◽  
Free Energies ◽  
Precise Estimation ◽  
Transfer Properties

Two-dimensional umbrella sampling is combined with molecular dynamics to calculate correction-free estimates of transfer properties for individual ions.

Sign in / Sign up

Export Citation Format

Share Document