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

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.

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.

Ultraviolet Absorption of Refractory Elements by a Dual Laser Plasma Method

1988 ◽  
Vol 102 ◽  
pp. 243-246
Author(s):  
J.T. Costello ◽  
W.G. Lynam ◽  
P.K. Carroll
Keyword(s):  
Absorption Spectra ◽  
Laser Plasma ◽  
Optical Pulse ◽  
Ionic Species ◽  
Neutral Species ◽  
Plasma Method ◽  
Plasma Technique ◽  
Refractory Elements ◽  
Delay Times ◽  
Dual Laser

AbstractThe dual laser-produced plasma technique for the study of ionic absorption spectra has been developed by the use of two Q-switched ruby lasers to enable independent generation of the absorbing and back-lighting plasmas. Optical pulse handling is used in the coupling cicuits to enable reproducible pulse delays from 250 nsec. to 10 msec, to be achieved. At delay times > 700 nsec. spectra of essentially pure neutral species are observed. The technique is valuable, not only for obtaining the neutral spectra of highly refractory and/or corrosive materials but also for studying behaviour of ionic species as a function of time. Typical spectra are shown in Fig. 1.

Effects of Electrical Discharges in Low Pressure Gases on the Morphology of Polyethylene Crystals

1974 ◽  
Vol 32 ◽  
pp. 544-545
Author(s):  
L.H. Bolz ◽  
D.H. Reneker
Keyword(s):  
Power Distribution ◽  
Electrical Discharge ◽  
Dielectric Breakdown ◽  
Ionic Species ◽  
Low Pressure ◽  
Polymer Surfaces ◽  
Electrical Discharges ◽  
Adhesive Bonds ◽  
Power Distribution Lines ◽  
Modification Of The Surface

The attack, on the surface of a polymer, by the atomic, molecular and ionic species that are created in a low pressure electrical discharge in a gas is interesting because: 1) significant interior morphological features may be revealed, 2) dielectric breakdown of polymeric insulation on high voltage power distribution lines involves the attack on the polymer of such species created in a corona discharge, 3) adhesive bonds formed between polymer surfaces subjected to such SDecies are much stronger than bonds between untreated surfaces, 4) the chemical modification of the surface creates a reactive surface to which a thin layer of another polymer may be bonded by glow discharge polymerization.

The observation of nano-voids in Au thin films

1987 ◽  
Vol 45 ◽  
pp. 366-367
Author(s):  
William Krakow
Keyword(s):  
Thin Films ◽  
Melting Point ◽  
Present Author ◽  
Stacking Faults ◽  
Damage Threshold ◽  
Ionic Species ◽  
Rare Gases ◽  
Chain Defects ◽  
Vacancy Chains ◽  
Au Thin Films

It has long been known that defects such as stacking faults and voids can be quenched from various alloyed metals heated to near their melting point. Today it is common practice to irradiate samples with various ionic species of rare gases which also form voids containing solidified phases of the same atomic species, e.g. ref. 3. Equivalently, electron irradiation has been used to produce damage events, e.g. ref. 4. Generally all of the above mentioned studies have relied on diffraction contrast to observe the defects produced down to a dimension of perhaps 10 to 20Å. Also all these studies have used ions or electrons which exceeded the damage threshold for knockon events. In the case of higher resolution studies the present author has identified vacancy and interstitial type chain defects in ion irradiated Si and was able to identify both di-interstitial and di-vacancy chains running through the foil.

Understanding Conformational Entropy in Small Molecules

2020 ◽  
Author(s):  
Lucian Chan ◽  
Garrett Morris ◽  
Geoffrey Hutchison
Keyword(s):  
Small Molecules ◽  
Degrees Of Freedom ◽  
Absolute Error ◽  
Low Energy ◽  
Standard Entropy ◽  
Free Energies ◽  
Conformational Entropy ◽  
Wide Range ◽  
High Degree ◽  
Empirical Corrections

The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers grows exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, including performing thermochemistry calculations with all possible stable conformations, and developing empirical corrections from experimental data. We have performed conformer sampling on over 120,000 small molecules generating some 12 million conformers, to develop models to predict conformational entropy across a wide range of molecules. Using insight into the nature of conformational disorder, our cross-validated physically-motivated statistical model can outperform common machine learning and deep learning methods, with a mean absolute error ≈4.8 J/mol•K, or under 0.4 kcal/mol at 300 K. Beyond predicting molecular entropies and free energies, the model implies a high degree of correlation between torsions in most molecules, often as- sumed to be independent. While individual dihedral rotations may have low energetic barriers, the shape and chemical functionality of most molecules necessarily correlate their torsional degrees of freedom, and hence restrict the number of low-energy conformations immensely. Our simple models capture these correlations, and advance our understanding of small molecule conformational entropy.

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>

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>

Molecular Docking Approaches to Suggest the Anti-Mycobacterial Targets of Natural Products

2020 ◽  
Author(s):  
Rafael Baptista ◽  
Sumana Bhowmick ◽  
Shen Jianying ◽  
Luis Mur
Keyword(s):  
Natural Products ◽  
Molecular Docking ◽  
Free Energies ◽  
Antibiotic Resistant ◽  
Drug Lead ◽  
Bisbenzylisoquinoline Alkaloids ◽  
Docking Approach ◽  
Global Threat ◽  
Physicochemical And Structural Properties

Tuberculosis (TB) is a major global threat mostly due to the development of antibiotic resistant forms of Mycobacterium tuberculosis, the causal agent of the disease. Driven by the pressing need for new anti-mycobacterial agents, several natural products (NPs) have been shown to have in vitro activities against M. tuberculosis. The utility of any NP as a drug lead is augmented when the anti-mycobacterial target(s) is unknown. To suggest these, we used a molecular docking approach to predict the interactions of 53 selected anti-mycobacterial NPs against known ‘druggable’ mycobacterial targets ClpP1P2, DprE1, InhA, KasA, PanK, PknB and Pks13. The docking scores / binding free energies were predicted and calculated using AutoDock Vina along with physicochemical and structural properties of the NPs, using PaDEL descriptors. These were compared to the established inhibitor (control) drugs for each mycobacterial target. The specific interactions of the bisbenzylisoquinoline alkaloids 2-nortiliacorinine, tiliacorine and 13’-bromotiliacorinine against the targets PknB and DprE1 (-11.4, -10.9 and -9.8 kcal.mol-1 ; -12.7, -10.9 and -10.3 kcal.mol-1 , respectively) and the lignan αcubebin and Pks13 (-11.0 kcal.mol-1 ) had significantly superior docking scores compared to controls. Our approach can be used to suggest predicted targets for the NP to be validated experimentally but these in silico steps are likely to facilitate drug optimisation.

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