Atom Condensed Fukui Function for Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

2019 ◽  
Author(s):  
Javier Oller ◽  
David A. Sáez ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Aqueous Solution ◽  
Molecular System ◽  
Chemical Reactivity ◽  
Nucleophilic Attack ◽  
Stable Conformation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Dynamics Simulations ◽  
Fixation Of Carbon Dioxide

<div><div><div><p>Local reactivity descriptors such as atom condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here, we propose to combine QM/MM Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann weighted atom condensed local reac- tivity descriptors based on conceptual DFT. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account allowing us to analyze the effect of changes in the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared to an aqueous solution. Our main result is that the protein en- vironment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α, β unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.</p></div></div></div>

Atom Condensed Fukui Function for Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

2019 ◽  
Author(s):  
Javier Oller ◽  
David A. Sáez ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Aqueous Solution ◽  
Molecular System ◽  
Chemical Reactivity ◽  
Nucleophilic Attack ◽  
Stable Conformation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Dynamics Simulations ◽  
Fixation Of Carbon Dioxide

<div><div><div><p>Local reactivity descriptors such as atom condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here, we propose to combine QM/MM Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann weighted atom condensed local reac- tivity descriptors based on conceptual DFT. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account allowing us to analyze the effect of macroscopic variables like temperature or changes in the molecular environment on reactivity. In this contribu- tion, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared to an aqueous solution. Our main result is that the protein en- vironment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α, β unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.</p></div></div></div>

scholarly journals Atom Condensed Fukui Function for Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

2019 ◽  
Author(s):  
Javier Oller ◽  
David A. Sáez ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Aqueous Solution ◽  
Molecular System ◽  
Chemical Reactivity ◽  
Nucleophilic Attack ◽  
Stable Conformation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Dynamics Simulations ◽  
Fixation Of Carbon Dioxide

<div><div><div><p>Local reactivity descriptors such as atom condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here, we propose to combine QM/MM Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann weighted atom condensed local reac- tivity descriptors based on conceptual DFT. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account allowing us to analyze the effect of changes in the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared to an aqueous solution. Our main result is that the protein en- vironment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α, β unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.</p></div></div></div>

scholarly journals DFT investigations on arylsulphonyl pyrazole derivatives as potential ligands of selected kinases

2020 ◽  
Vol 18 (1) ◽  
pp. 857-873
Author(s):  
Kornelia Czaja ◽  
Jacek Kujawski ◽  
Radosław Kujawski ◽  
Marek K. Bernard
Keyword(s):  
Free Energy ◽  
Molecular Orbital ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Chemical Hardness ◽  
Free Energy Of Solvation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Condensed Fukui Functions ◽  
Charge Partitioning

AbstractUsing the density functional theory (DFT) formalism, we have investigated the properties of some arylsulphonyl indazole derivatives that we studied previously for their biological activity and susceptibility to interactions of azoles. This study includes the following physicochemical properties of these derivatives: electronegativity and polarisability (Mulliken charges, adjusted charge partitioning, and iterative-adjusted charge partitioning approaches); free energy of solvation (solvation model based on density model and M062X functional); highest occupied molecular orbital (HOMO)–lowest occupied molecular orbital (LUMO) gap together with the corresponding condensed Fukui functions, time-dependent DFT along with the UV spectra simulations using B3LYP, CAM-B3LYP, MPW1PW91, and WB97XD functionals, as well as linear response polarisable continuum model; and estimation of global chemical reactivity descriptors, particularly the chemical hardness factor. The charges on pyrrolic and pyridinic nitrogen (the latter one in the quinolone ring of compound 8, as well as condensed Fukui functions) reveal a significant role of these atoms in potential interactions of azole ligand–protein binding pocket. The lowest negative value of free energy of solvation can be attributed to carbazole 6, whereas pyrazole 7 has the least negative value of this energy. Moreover, the HOMO–LUMO gap and chemical hardness show that carbazole 6 and indole 5 exist as soft molecules, while fused pyrazole 7 has hard character.

New molecular target insights about protein kinases of the Plasmodium falciparum. Using molecular docking and DFT-based reactivity descriptors

2017 ◽  
Vol 16 (08) ◽  
pp. 1750076 ◽  
Author(s):  
Alejandro Morales-Bayuelo
Keyword(s):  
Plasmodium Falciparum ◽  
Protein Kinases ◽  
Density Functional ◽  
Chemical Potential ◽  
Chemical Reactivity ◽  
Binding Pocket ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Chemical Reactivity Descriptors ◽  
Hinge Zone

Currently, there is increasing interest in the potential of malaria inhibitors in Plasmodium falciparum activity. In this work, is propose a possible alternative to classifying 154 antimalarials, with P. falciparum activity. These antimalarials were synthesized by the Chibale’s group ( http://www.kellychibaleresearch.uct.ac.za/ ), with the goal of finding new insights on the binding pocket of the protein kinase PfPK5, PfPK7, PfCDPK1, PfCDPK4, PfMAP1, and PfPK6 of the malaria parasite. However, there is only information about crystallography of PfPK5 and PfPK7. The protein kinases PfCDPK1, PfCDPK4, PfMAP1, and PfPK6 were modeled using molecular homology. The validation used shows that our homology models can be an alternative for the protein kinases from P. falciparum, unknown today. The antimalarials were classified by taking into account the interactions in the hinge zone. These ligands bind to the kinase through the formation of one of two hydrogen bonds, with the backbone residues of the hinge region connecting the kinase N- and C-terminal loops. These interactions were supported by a reactivity chemistry analysis, using global chemical reactivity descriptors such as chemical potential, hardness, softness, electrophilicity, and the Fukui functions as local reactivity descriptors, within the Density Functional Theory (DFT) context.

scholarly journals A Theoretical Study of Chemical Reactivity of Tartrazine Through DFT Reactivity Descriptors

2017 ◽  
Vol 58 (4) ◽  
Author(s):  
Luis Humberto Mendoza Huizar
Keyword(s):  
Free Radicals ◽  
Theoretical Study ◽  
Chemical Reactivity ◽  
Nucleophilic Attack ◽  
Initial Attack ◽  
Reactivity Descriptors ◽  
Pcm Model ◽  
Total Energies ◽  
Global And Local ◽  
Global Reactivity Descriptors

<p>In this work we have calculated global and local DFT reactivity descriptors for tartrazine at B3LYP/6-311++G (2d,2p) level. Global reactivity descriptors such as ionization energy, molecular hardness, electrophilicity, and total energies were calculated to evaluate the tartrazine reactivity in aqueous and gas conditions. Local reactivity was evaluated through the Fukui function. The influence of the solvent was taken into account with the PCM model. The results indicate that the solvation process modifies the reactivity descriptors values. From our results, it was found that an electrophilic attack allows a direct cleavage of the N=N bond. If a nucleophilic attack is considered as initial attack, it is necessary a second attack by free radicals or electrophiles to cleave the N=N bond. In the case of an initial attack by free radicals, tartrazine requires a subsequent nucleophilic attack to cleave the N=N bond.</p>

Global and Local Reactivity Descriptors Based on Quadratic and Linear Energy Models for α,β-Unsaturated Organic Compounds

2018 ◽  
Author(s):  
Javier Oller ◽  
Patricia Perez ◽  
Paul W. Ayers ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Fukui Function ◽  
Nucleophilic Attack ◽  
Quadratic Model ◽  
Molecular Response ◽  
Local Descriptors ◽  
Unsaturated Ketones ◽  
Global And Local

<div>Global and local descriptors of chemical reactivity can be derived from conceptual density functional theory. Their explicit form, however, depends on how the energy is defined as a function of the number of electrons. Within the existing interpolation models, here, the quadratic and the linear energy model were used to derive global descriptors as the electrophilicity and nucleophilicity (defined as the negative of the ionization potential) and local descriptors employing either the corresponding condensed fukui function in the linear model or the local response of the global descriptor in the quadratic model. The ability of these descriptors to predict the reactivity of molecules with more than one reactive site was first studied on a set of α ,β -unsaturated ketones, where experimental rate constants for the nucleophilic attack is known. With the validated descriptors the reactivity of α ,β -unsaturated carboxylic compounds with different heteroatoms as α ,β -unsaturated thioesters, esters and amides as alternative substrates for the enzymatic CO<sub>2</sub> fixation studied experimentally by Erb <i>et al.</i> was addressed. The carbon dioxide fixation involves the reduction of the neutral α ,β -unsaturated carboxylic compounds by a nucleophilic attack of a hydride anion from NADPH and the following electrophilic attack by carbon dioxide. It was found that condensed values of the linear fukui function within the fragment of molecular response approximation describe best the reactivity of α ,β -unsaturated ketones. For the two relevant processes involved in CO<sub>2</sub> fixation the amides present the largest reactivity in vacuum and in aqueous solution compared to the esters and thioesters and may, therefore, serve as alternative sustrates of carboxylases.</div>

Global and Local Reactivity Descriptors Based on Quadratic and Linear Energy Models for α,β-Unsaturated Organic Compounds

2018 ◽  
Author(s):  
Javier Oller ◽  
Patricia Perez ◽  
Paul W. Ayers ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Fukui Function ◽  
Nucleophilic Attack ◽  
Quadratic Model ◽  
Molecular Response ◽  
Local Descriptors ◽  
Unsaturated Ketones ◽  
Global And Local

<div>Global and local descriptors of chemical reactivity can be derived from conceptual density functional theory. Their explicit form, however, depends on how the energy is defined as a function of the number of electrons. Within the existing interpolation models, here, the quadratic and the linear energy model were used to derive global descriptors as the electrophilicity and nucleophilicity (defined as the negative of the ionization potential) and local descriptors employing either the corresponding condensed fukui function in the linear model or the local response of the global descriptor in the quadratic model. The ability of these descriptors to predict the reactivity of molecules with more than one reactive site was first studied on a set of α ,β -unsaturated ketones, where experimental rate constants for the nucleophilic attack is known. With the validated descriptors the reactivity of α ,β -unsaturated carboxylic compounds with different heteroatoms as α ,β -unsaturated thioesters, esters and amides as alternative substrates for the enzymatic CO<sub>2</sub> fixation studied experimentally by Erb <i>et al.</i> was addressed. The carbon dioxide fixation involves the reduction of the neutral α ,β -unsaturated carboxylic compounds by a nucleophilic attack of a hydride anion from NADPH and the following electrophilic attack by carbon dioxide. It was found that condensed values of the linear fukui function within the fragment of molecular response approximation describe best the reactivity of α ,β -unsaturated ketones. For the two relevant processes involved in CO<sub>2</sub> fixation the amides present the largest reactivity in vacuum and in aqueous solution compared to the esters and thioesters and may, therefore, serve as alternative sustrates of carboxylases.</div>

scholarly journals Conceptual DFT as a Novel Chemoinformatics Tool for Studying the Chemical Reactivity Properties of the Amatoxin Family of Fungal Peptides

2019 ◽  
Vol 17 (1) ◽  
pp. 1133-1139 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional ◽  
Chemical Reactivity ◽  
Active Regions ◽  
Chemical Hardness ◽  
Conceptual Density Functional Theory ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Molecular Systems ◽  
Chemical Structures ◽  
Simple Protocol

AbstractThe chemical structures and molecular reactivities of the Amatoxin group of fungi-derived peptides have been determined by means of the consideration of a model chemistry that has been previously validated as well-behaved for our purposes. The reactivity descriptors were calculated on the basis of a methodological framework built around the concepts that are the outcome of the so called Conceptual Density Functional Theory (CDFT). This procedure in connection with the different Fukui functions allowed to identify the chemically active regions within the molecules. By considering a simple protocol designed by our research group for the estimation of the pKa of peptides through the information coming from the chemical hardness, these property has been established for the different molecular systems explored in this research. The information reported through this work could be of interest for medicinal chemistry researchers in using this knowledge for the design of new medicines based on the studied peptides or as a help for the understanding of the toxicity mechanisms exerted by them.

scholarly journals Chemical-Reactivity Properties, Drug Likeness, and Bioactivity Scores of Seragamides A–F Anticancer Marine Peptides: Conceptual Density Functional Theory Viewpoint

Computation ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 52 ◽  
Author(s):  
Norma Flores-Holguín ◽  
Juan Frau ◽  
Daniel Glossman-Mitnik
Keyword(s):  
Density Functional Theory ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Drug Repurposing ◽  
Chemical Hardness ◽  
Conceptual Density Functional Theory ◽  
Functional Theory ◽  
Fukui Functions ◽  
Reactivity Descriptors

A methodology based on concepts that arose from Density Functional Theory (CDFT) was chosen for the calculation of global and local reactivity descriptors of the Seragamide family of marine anticancer peptides. Determination of active sites for the molecules was achieved by resorting to some descriptors within Molecular Electron Density Theory (MEDT) such as Fukui functions. The pKas of the six studied peptides were established using a proposed relationship between this property and calculated chemical hardness. The drug likenesses and bioactivity properties of the peptides considered in this study were obtained by resorting to a homology model by comparison with the bioactivity of related molecules in their interaction with different receptors. With the object of analyzing the concept of drug repurposing, a study of potential AGE-inhibition abilities of Seragamides peptides was pursued by comparison with well-known drugs that are already available as pharmaceuticals.

Sign in / Sign up

Export Citation Format

Share Document