scholarly journals Using Atomic Charges to Describe the pKa of Carboxylic Acids

2020 ◽  
Author(s):  
Zeynep Pinar Haslak ◽  
Sabrina Zareb ◽  
Viktorya Aviyente ◽  
Gerald Monard
Keyword(s):  
Linear Relationship ◽  
Carboxylic Acids ◽  
Atomic Charge ◽  
Basis Sets ◽  
Atomic Charges ◽  
Dft Methods ◽  
Solvent Models ◽  
Dynamics Simulations ◽  
Fast Prediction ◽  
Protein Environment

<div>In this study, we present an accurate protocol for the fast prediction of pKa's of carboxylic acids based on the linear relationship between computed atomic charges of the anionic form of the carboxylate fragment and their experimental pKa values. Five charge descriptors, three charge models, three solvent models, gas phase calculations and several DFT methods (combination of eight DFT functionals and fifteen basis sets) were tested. Among those, the best combination to reproduce experimental pKa's is to compute NPA atomic charge using the SMD model at the M06L/6-311G(d,p) level of theory and selecting the maximum atomic charge on carboxylic oxygen atoms (R^2 = 0.955). The applicability of the suggested protocol and its stability along geometrical changes are verified by molecular dynamics simulations performed for a set of aspartate, glutamate and alanine peptides. By reporting the calculated atomic charge of the carboxylate form into the linear relationship derived in this work, it will be possible to estimate accurately the amino acid’s pKa's in protein environment.</div><div><br></div>

scholarly journals Using Atomic Charges to Describe the pKa of Carboxylic Acids

2020 ◽  
Author(s):  
Zeynep Pinar Haslak ◽  
Sabrina Zareb ◽  
Viktorya Aviyente ◽  
Gerald Monard
Keyword(s):  
Linear Relationship ◽  
Carboxylic Acids ◽  
Atomic Charge ◽  
Basis Sets ◽  
Atomic Charges ◽  
Dft Methods ◽  
Solvent Models ◽  
Dynamics Simulations ◽  
Fast Prediction ◽  
Protein Environment

<div>In this study, we present an accurate protocol for the fast prediction of pKa's of carboxylic acids based on the linear relationship between computed atomic charges of the anionic form of the carboxylate fragment and their experimental pKa values. Five charge descriptors, three charge models, three solvent models, gas phase calculations and several DFT methods (combination of eight DFT functionals and fifteen basis sets) were tested. Among those, the best combination to reproduce experimental pKa's is to compute NPA atomic charge using the SMD model at the M06L/6-311G(d,p) level of theory and selecting the maximum atomic charge on carboxylic oxygen atoms (R^2 = 0.955). The applicability of the suggested protocol and its stability along geometrical changes are verified by molecular dynamics simulations performed for a set of aspartate, glutamate and alanine peptides. By reporting the calculated atomic charge of the carboxylate form into the linear relationship derived in this work, it will be possible to estimate accurately the amino acid’s pKa's in protein environment.</div><div><br></div>

scholarly journals Using Atomic Charges to Describe the pKa of Carboxylic Acids

2021 ◽  
Author(s):  
Zeynep Pinar Haslak ◽  
Sabrina Zareb ◽  
Ilknur Dogan ◽  
Viktorya Aviyente ◽  
Gerald Monard
Keyword(s):  
Linear Relationship ◽  
Carboxylic Acids ◽  
Atomic Charge ◽  
Basis Sets ◽  
Atomic Charges ◽  
Dft Methods ◽  
Solvent Models ◽  
Dynamics Simulations ◽  
Fast Prediction ◽  
Protein Environment

<div>In this study, we present an accurate protocol for the fast prediction of pKa's of carboxylic acids based on the linear relationship between computed atomic charges of the anionic form of the carboxylate fragment and their experimental pKa values. Five charge descriptors, three charge models, three solvent models, gas phase calculations and several DFT methods (combination of eight DFT functionals and fifteen basis sets) were tested. Among those, the best combination to reproduce experimental pKa's is to compute NPA atomic charge using the SMD model at the M06L/6-311G(d,p) level of theory and selecting the maximum atomic charge on carboxylic oxygen atoms (R^2 = 0.955). The applicability of the suggested protocol and its stability along geometrical changes are verified by molecular dynamics simulations performed for a set of aspartate, glutamate and alanine peptides. By reporting the calculated atomic charge of the carboxylate form into the linear relationship derived in this work, it will be possible to estimate accurately the amino acid’s pKa's in protein environment.</div><div><br></div>

scholarly journals COMPARAÇÃO ENTRE MÉTODOS PARA DETERMINAÇÃO DE CARGAS ATÔMICAS EM SISTEMAS MOLECULARES: A MOLÉCULA N-{N-(PTERINA-7-IL)CARBONILGLICIL}-L-TIROSINA (NNPT)

Química Nova ◽  
2020 ◽  
Author(s):  
Fernanda Botelho ◽  
Roberta Oliveira ◽  
Joyce Almeida ◽  
Tanos França ◽  
Itamar Borges
Keyword(s):  
Dipole Moment ◽  
Atomic Charge ◽  
Basis Sets ◽  
Atomic Charges ◽  
Resonance Effects ◽  
Molecular Systems ◽  
Moment Vector ◽  
Different Types ◽  
Partial Atomic Charges ◽  
Charge Calculations

COMPARISON BETWEEN ATOMIC CHARGE METHODS FOR MOLECULAR SYSTEMS: THE N-{N-(PTERIN-7-YL) CARBONYLGLYCYL}-L-TYROSINE (NNPT) MOLECULE. Selecting a method to compute partial atomic charges is not trivial because different methods usually provide different charge values and there is no consensus on the most useful approach. In this work, Mulliken, MBS, Chelp, Chelpg, MK, Hirshfeld, NPA, DMA and AIM methods were selected to compute atomic charges and electric dipole moment vector of N-{N-(Pterin-7-yl)carbonylglycyl}-L-tyrosine molecule, a ricin inhibitor which has different types of bonds and chemical environments. While MBS and DMA methods provided the most chemically consistent charges according to atomic electronegativity and electron resonance effects criteria, Chelp, Chelpg and MK had the worst performances. Atomic charges and dipole moment calculated by the Hirshfeld method had the smallest magnitudes, a well-known behavior. Despite the differences among atomic charges predicted by all methods, the direction of the dipole moment vector was essentially the same. Further charge calculations using different basis sets and quantum methods indicated that the dependency on this aspect was the highest for Mulliken and Chelp and the lowest for MBS, Hirshfeld and DMA methods. Thus, results point to MBS and DMA as the most suitable methods for computing chemically consistent atomic charges and dipole moment vectors of similar systems for different applications; e.g., molecular dynamics.

A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

2018 ◽  
Author(s):  
Danilo Carmona ◽  
David Contreras ◽  
Oscar A. Douglas-Gallardo ◽  
Stefan Vogt-Geisse ◽  
Pablo Jaque ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Hydroxyl Radical ◽  
Ab Initio ◽  
Fenton Reaction ◽  
Basis Set ◽  
Basis Sets ◽  
Dft Methods ◽  
Elementary Steps ◽  
Oxygen Oxygen ◽  
Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

Using Atomic Charges to Model Molecular Polarization.

2022 ◽  
Author(s):  
Frank Jensen
Keyword(s):  
Force Fields ◽  
Atomic Charge ◽  
Electric Polarization ◽  
Special Focus ◽  
Atomic Charges ◽  
Electrical Polarization

We review different models for introducing electrical polarization in force fields, with special focus on methods where polarization is modelled at the atomic charge level. While electric polarization has been...

scholarly journals Analysis of the interaction of thermoacoustic modes with a Green’s function approach

2018 ◽  
Vol 10 (4) ◽  
pp. 326-336 ◽  
Author(s):  
Alessandra Bigongiari ◽  
Maria Heckl
Keyword(s):  
Green’S Function ◽  
Green's Function ◽  
Initial Perturbation ◽  
Time History ◽  
Function Approach ◽  
Stability Maps ◽  
Flame Describing Function ◽  
The Stability ◽  
Dynamics Simulations ◽  
Fast Prediction

In this paper, we will present a fast prediction tool based on a one-dimensional Green's function approach that can be used to bypass numerically expensive computational fluid dynamics simulations. The Green’s function approach has the advantage of providing a clear picture of the physics behind the generation and evolution of combustion instabilities. In addition, the method allows us to perform a modal analysis; single acoustic modes can be treated in isolation or in combination with other modes. In this article, we will investigate the role of higher-order modes in determining the stability of the system. We will initially produce the stability maps for the first and second mode separately. Then the time history of the perturbation will be computed, where both the modes are present. The flame will be modelled by a generic Flame Describing Function, i.e. by an amplitude-dependent Flame Transfer Function. The time-history calculations show the evolution of the two modes resulting from an initial perturbation; both transient and limit-cycle oscillations are revealed. Our study represents a first step towards the modelling of nonlinearity and non-normality in combustion processes.

scholarly journals Making Soup: Preparing and Validating Molecular Simulations of the Bacterial Cytoplasm

2019 ◽  
Author(s):  
Leandro Oliveira Bortot ◽  
Zahedeh Bashardanesh ◽  
David van der Spoel
Keyword(s):  
Large Scale ◽  
Biological Properties ◽  
Computational Power ◽  
E Coli ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Computational Modeling And Simulation ◽  
Dynamics Simulations ◽  
The Individual ◽  
Bacterial Cytoplasm

Biomolecular crowding affects the biophysical and biochemical behavior of macro- molecules when compared to the dilute environment present in experiments made with isolated proteins. Computational modeling and simulation are useful tools to study how crowding affects the structural dynamics and biological properties of macromolecules. As computational power increased, modeling and simulating large scale all-atom explicit solvent models of the prokaryote cytoplasm become possible. In this work, we build an atomistic model of the cytoplasm of Escherichia coli composed of 1.5 million atoms and submit it to a total of 3 μs of molecular dynamics simulations. The properties of biomolecules under crowding conditions are compared to those from simulations of the individual compounds under dilute conditions. The simulation model is found to be consistent with experimental data about the diffusion coefficient and stability of macromolecules under crowded conditions. In order to stimulate further work we provide a Python script and a set of files that enables other researchers to build their own E. coli cytoplasm models to address questions related to crowding.<br>

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