140 results on '"José R. Mora"'
Search Results
2. Analyzing coherent and incoherent optical susceptibilities in four-wave mixing: stochasticity, symmetry, and intramolecular coupling
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José L. Paz, Cristhian Davila, Marcos A. Loroño, Lenin González-Paz, Edgar Márquez, José R. Mora, and Ysaias J. Alvarado
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Nonlinear optical susceptibilities ,Propagation ,Coherent ,Incoherent ,Intramolecular coupling ,Physics ,QC1-999 - Abstract
The nonlinear optical susceptibilities are analyzed in their optical propagation length considering the incoherent-coherent contributions with the dependence on the relaxation times. In addition, some symmetry properties of the Four-Wave mixing (FWM) signal concerning the frequency detuning exchange are used in the study, without restricting ourselves to the maxima of population oscillations. We analyze the behaviors of these optical responses in a vibronic coupling scheme using a molecule model consisting of two coupled harmonic curves of electronic energies with displaced minima in position and nuclear energies. The solvent effect in our model is treated through the natural Bohr frequency shift to a time-dependent function, with explicit manifestations in its comparison as if the upper state were broadened. Our results for both FWM signal propagation and nonlinear optical susceptibilities are sensitive to the intramolecular coupling parameters, solvent stochasticity, and perturbation order for the treatment of the weak probe beam. The consideration of a second-order probe beam in FWM would not represent a significant contribution to the predicted results, since its percentage contribution is negligible within the model development framework; however, this contribution becomes important when increasing the ratio between longitudinal and transverse relaxation times.
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- 2024
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3. Photoelectrocatalytic degradation of high-density polyethylene microplastics on TiO2-modified boron-doped diamond photoanode
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Wendy Quilumbaquin, G. Xavier Castillo-Cabrera, Luis J. Borrero-González, José R. Mora, Vladimir Valle, Alexis Debut, Luis D. Loor-Urgilés, and Patricio J. Espinoza-Montero
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Materials chemistry ,Devices ,Science - Abstract
Summary: Microplastic (MP) accumulation in the environment is accelerating rapidly, which has led to their effects on both the ecosystem and human life garnering much attention. This study is the first to examine the degradation of high-density polyethylene (HDPE) MPs via photoelectrocatalysis (PEC) using a TiO2-modified boron-doped diamond (BDD/TiO2) photoanode. This study was divided into three stages: (i) preparation of the photoanode through electrophoretic deposition of synthetic TiO2 nanoparticles on a BDD electrode; (ii) characterization of the modified photoanode using electrochemical, structural, and optical techniques; and (iii) degradation of HDPE MPs by electrochemical oxidation and photoelectrocatalysis on bare and modified BDD electrodes under dark and UV light conditions. The results indicate that the PEC technique degraded 89.91 ± 0.08% of HDPE MPs in a 10-h reaction and was more efficient at a lower current density (6.89 mA cm−1) with the BDD/TiO2 photoanode compared to electrochemical oxidation on bare BDD.
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- 2024
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4. Stochastic Nature and Intramolecular Coupling in Optical Response Profiles: Critical Analysis through Semiclassical Models
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José Luis Paz, Marcos A. Loroño, Lenin A. González-Paz, Edgar Márquez, José R. Mora, and Ysaias J. Alvarado
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Chemistry ,QD1-999 - Published
- 2023
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5. Searching glycolate oxidase inhibitors based on QSAR, molecular docking, and molecular dynamic simulation approaches
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Nicolás Cabrera, Sebastián A. Cuesta, José R. Mora, José Luis Paz, Edgar A. Márquez, Patricio J. Espinoza-Montero, Yovani Marrero-Ponce, Noel Pérez, and Ernesto Contreras-Torres
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Medicine ,Science - Abstract
Abstract Primary hyperoxaluria type 1 (PHT1) treatment is mainly focused on inhibiting the enzyme glycolate oxidase, which plays a pivotal role in the production of glyoxylate, which undergoes oxidation to produce oxalate. When the renal secretion capacity exceeds, calcium oxalate forms stones that accumulate in the kidneys. In this respect, detailed QSAR analysis, molecular docking, and dynamics simulations of a series of inhibitors containing glycolic, glyoxylic, and salicylic acid groups have been performed employing different regression machine learning techniques. Three robust models with less than 9 descriptors—based on a tenfold cross (Q2 CV) and external (Q2 EXT) validation—were found i.e., MLR1 (Q2 CV = 0.893, Q2 EXT = 0.897), RF1 (Q2 CV = 0.889, Q2 EXT = 0.907), and IBK1 (Q2 CV = 0.891, Q2 EXT = 0.907). An ensemble model was built by averaging the predicted pIC50 of the three models, obtaining a Q2 EXT = 0.933. Physicochemical properties such as charge, electronegativity, hardness, softness, van der Waals volume, and polarizability were considered as attributes to build the models. To get more insight into the potential biological activity of the compouds studied herein, docking and dynamic analysis were carried out, finding the hydrophobic and polar residues show important interactions with the ligands. A screening of the DrugBank database V.5.1.7 was performed, leading to the proposal of seven commercial drugs within the applicability domain of the models, that can be suggested as possible PHT1 treatment.
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- 2022
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6. Elucidating the Racemization Mechanism of Aliphatic and Aromatic Amino Acids by In Silico Tools
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Mateo S. Andino, José R. Mora, José L. Paz, Edgar A. Márquez, Yunierkis Perez-Castillo, and Guillermin Agüero-Chapin
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racemization ,amino acids ,density functional theory ,intrinsic reaction coordinates ,natural bond orbital ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
The racemization of biomolecules in the active site can reduce the biological activity of drugs, and the mechanism involved in this process is still not fully comprehended. The present study investigates the impact of aromaticity on racemization using advanced theoretical techniques based on density functional theory. Calculations were performed at the ωb97xd/6-311++g(d,p) level of theory. A compelling explanation for the observed aromatic stabilization via resonance is put forward, involving a carbanion intermediate. The analysis, employing Hammett’s parameters, convincingly supports the presence of a negative charge within the transition state of aromatic compounds. Moreover, the combined utilization of natural bond orbital (NBO) analysis and intrinsic reaction coordinate (IRC) calculations confirms the pronounced stabilization of electron distribution within the carbanion intermediate. To enhance our understanding of the racemization process, a thorough examination of the evolution of NBO charges and Wiberg bond indices (WBIs) at all points along the IRC profile is performed. This approach offers valuable insights into the synchronicity parameters governing the racemization reactions.
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- 2023
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7. A kinetic model for the equilibrium dynamics of absorption and scattering processes in four-wave mixing spectroscopy
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Jose Luis Paz, Marcos Loroño, F. Javier Torres, Lenin A. González-Paz, Edgar Marquez, José R. Mora, Ysaias J. Alvarado, and Vladimiro Mujica
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Physics ,QC1-999 - Abstract
We construct a kinetic model, analogous to a simple chemical reaction, to describe the spatial propagation of the electromagnetic fields in four-wave mixing spectroscopy in a two-level molecular model, explicitly taking into account the stochastic effects of the solvent. We show that in this case, the nonlinear optics processes (absorption and scattering) along the optical path can be described using an analogy with the kinetic processes that occur in a chemical reaction. A key result is that it is possible to define an apparent equilibrium constant that regulates the competition of the photonic processes that take place, an idea conceptually similar to Einstein’s model for spontaneous emission and how it can be connected to induced emission in atoms and molecules but including an extension to nonlinear optical and relaxation processes. Our model can be generalized to describe a variety of phenomena in nano-photonics and plasmonic systems.
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- 2022
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8. Complex Networks Analyses of Antibiofilm Peptides: An Emerging Tool for Next-Generation Antimicrobials’ Discovery
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Guillermin Agüero-Chapin, Agostinho Antunes, José R. Mora, Noel Pérez, Ernesto Contreras-Torres, José R. Valdes-Martini, Felix Martinez-Rios, Cesar H. Zambrano, and Yovani Marrero-Ponce
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antibiofilm peptide ,chemical space ,StarPep toolbox ,complex network ,centrality measure ,motif discovery ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Microbial biofilms cause several environmental and industrial issues, even affecting human health. Although they have long represented a threat due to their resistance to antibiotics, there are currently no approved antibiofilm agents for clinical treatments. The multi-functionality of antimicrobial peptides (AMPs), including their antibiofilm activity and their potential to target multiple microbes, has motivated the synthesis of AMPs and their relatives for developing antibiofilm agents for clinical purposes. Antibiofilm peptides (ABFPs) have been organized in databases that have allowed the building of prediction tools which have assisted in the discovery/design of new antibiofilm agents. However, the complex network approach has not yet been explored as an assistant tool for this aim. Herein, a kind of similarity network called the half-space proximal network (HSPN) is applied to represent/analyze the chemical space of ABFPs, aiming to identify privileged scaffolds for the development of next-generation antimicrobials that are able to target both planktonic and biofilm microbial forms. Such analyses also considered the metadata associated with the ABFPs, such as origin, other activities, targets, etc., in which the relationships were projected by multilayer networks called metadata networks (METNs). From the complex networks’ mining, a reduced but informative set of 66 ABFPs was extracted, representing the original antibiofilm space. This subset contained the most central to atypical ABFPs, some of them having the desired properties for developing next-generation antimicrobials. Therefore, this subset is advisable for assisting the search for/design of both new antibiofilms and antimicrobial agents. The provided ABFP motifs list, discovered within the HSPN communities, is also useful for the same purpose.
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- 2023
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9. Hydrogel for the Controlled Delivery of Bioactive Components from Extracts of Eupatorium glutinosum Lam. Leaves
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Lizbeth Zamora-Mendoza, Santiago Nelson Vispo, Lola De Lima, José R. Mora, António Machado, and Frank Alexis
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controlled delivery system ,antioxidant activity ,anti-hemolytic activity ,antibacterial activity ,secondary metabolites ,Organic chemistry ,QD241-441 - Abstract
This research reported a hydrogel loaded with the ethanolic and methanolic extracts of Eupatorium glutinosum Lam. The E. glutinosum extracts were characterized by phytochemical screening, Fourier-transform infrared spectroscopy (FTIR), thin-layer chromatography (TLC), and UV/Vis profile identification. This research also evaluated the pharmacological activity of the extracts using antimicrobial, antioxidant, and anti-inflammatory assays prior to polymeric encapsulation. Results indicate that extracts inhibit the Escherichia colii DH5-α (Gram negative) growth; excellent antioxidant activity was evaluated by the ferric reducing power and total antioxidant activity assays, and extracts showed an anti-hemolytic effect. Moreover, the cotton and microcrystalline cellulose hydrogels demonstrate successful encapsulation based on characterization and kinetics studies such as FTIR, extract release, and swelling degree. Moreover, effective antibacterial activity was registered by the loaded hydrogel. The overall results encourage and show that Eupatorium glutinosum-loaded hydrogel may find a wide range of bandage and wound healing applications in the biomedical area.
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- 2023
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10. QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis
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Jhesua Valencia, Vivian Rubio, Gloria Puerto, Luisa Vasquez, Anthony Bernal, José R. Mora, Sebastian A. Cuesta, José Luis Paz, Braulio Insuasty, Rodrigo Abonia, Jairo Quiroga, Alberto Insuasty, Andres Coneo, Oscar Vidal, Edgar Márquez, and Daniel Insuasty
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Mycobacterium tuberculosis ,QSAR ,docking ,quinolinone ,thiosemicarbazone ,molecular dynamics and cytotoxicity ,Therapeutics. Pharmacology ,RM1-950 - Abstract
In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R2 = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a–e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2’-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of −71.3 to −12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a–e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.
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- 2022
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11. Propagation and Parametric Amplification in Four-Wave Mixing Processes: Intramolecular Coupling and High-Order Effects
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José Luis Paz, Patricio J. Espinoza-Montero, Marcos Loroño, Fernando Javier Torres, Lenin González-Paz, Edgar Márquez, Joan Vera-Villalobos, José R. Mora, Fernando Moncada, and Ysaias J. Alvarado
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intramolecular coupling ,propagation effects ,parametric amplification ,Mathematics ,QA1-939 - Abstract
A strong pump-power dependence of the four-wave mixing (FWM) signal for an aqueous solution of Malachite green is reported. The characteristics of the pump-power dependence of the nonlinear signal are reproduced by a theoretical model based on the coupling between pump-probe, considering signal fields and propagation effects. The effect of the intramolecular coupling on the nonlinear intensity of the FWM signal is studied using a model molecule consisting of two-coupled harmonic curves of electronic energies with minima displaced in energy and nuclear positions. Two-vibrational states are considered while including non-adiabatic effects for the two-state model. Moreover, the coupling among the field components, as well as the propagation effects, are studied by considering a constant pump-intensity. Our calculation scheme, considering both the intramolecular coupling effects in the description of the molecular structure and the effects produced by the propagation of the FWM signal along the optical length, allows the exponential dependence of the latter, as the intensity of the pumping beam increases. Our treatments do not require the inclusion of other non-resonant processes outside the RWA approximation, due to the consideration of an adiabatic basis.
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- 2022
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12. In Silico Searching for Alternative Lead Compounds to Treat Type 2 Diabetes through a QSAR and Molecular Dynamics Study
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Nicolás Cabrera, Sebastián A. Cuesta, José R. Mora, Luis Calle, Edgar A. Márquez, Roland Kaunas, and José Luis Paz
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free fatty acid receptor 1 ,type 2 diabetes ,molecular dynamics ,molecular docking ,agonits of FFA1 ,Pharmacy and materia medica ,RS1-441 - Abstract
Free fatty acid receptor 1 (FFA1) stimulates insulin secretion in pancreatic β-cells. An advantage of therapies that target FFA1 is their reduced risk of hypoglycemia relative to common type 2 diabetes treatments. In this work, quantitative structure–activity relationship (QSAR) approach was used to construct models to identify possible FFA1 agonists by applying four different machine-learning algorithms. The best model (M2) meets the Tropsha’s test requirements and has the statistics parameters R2 = 0.843, Q2CV = 0.785, and Q2ext = 0.855. Also, coverage of 100% of the test set based on the applicability domain analysis was obtained. Furthermore, a deep analysis based on the ADME predictions, molecular docking, and molecular dynamics simulations was performed. The lipophilicity and the residue interactions were used as relevant criteria for selecting a candidate from the screening of the DiaNat and DrugBank databases. Finally, the FDA-approved drugs bilastine, bromfenac, and fenofibric acid are suggested as potential and lead FFA1 agonists.
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- 2022
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13. Synthesis, In Vitro, and In Silico Analysis of the Antioxidative Activity of Dapsone Imine Derivatives
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Ricardo Guzmán-Ávila, Mayra Avelar, Edgar A. Márquez, Julio C. Rivera-Leyva, José R. Mora, Virginia Flores-Morales, and Jesús Rivera-Islas
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dapsone imines ,dapsone-derivatives ,antioxidant in vitro ,Organic chemistry ,QD241-441 - Abstract
Dapsone (DDS) is an antibacterial drug with well-known antioxidant properties. However, the antioxidant behavior of its derivatives has not been well explored. In the present work, the antioxidant activity of 10 dapsone derivatives 4-substituted was determined by an evaluation in two in vitro models (DPPH radical scavenging assay and ferric reducing antioxidant power). These imine derivatives 1–10 were obtained through condensation between DDS and the corresponding aromatic aldehydes 4-substuited. Three derivatives presented better results than DDS in the determination of DPPH (2, 9, and 10). Likewise, we have three compounds with better reducing activity than dapsone (4, 9, and 10). In order to be more insight, the redox process, a conceptual DFT analysis was carried out. Molecular descriptors such as electronic distribution, the total charge accepting/donating capacity (I/A), and the partial charge accepting/donating capacity (ω+/ω−) were calculated to analyze the relative donor-acceptor capacity through employing a donor acceptor map (DAM). The DFT calculation allowed us to establish a relationship between GAPHOMO-LUMO and DAM with the observed antioxidant effects. According to the results, we concluded that compounds 2 and 3 have the lowest Ra values, representing a good antioxidant behavior observed experimentally in DPPH radical capturing. On the other hand, derivatives 4, 9, and 10 display the best reducing capacity activity with the highest ω− and Rd values. Consequently, we propose these compounds as the best antireductants in our DDS imine derivative series.
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- 2021
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14. Effect of the Nucleophile’s Nature on Chloroacetanilide Herbicides Cleavage Reaction Mechanism. A DFT Study
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Sebastián A. Cuesta, F. Javier Torres, Luis Rincón, José Luis Paz, Edgar A. Márquez, and José R. Mora
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chloroacetanilide herbicides ,nucleophilic substitution ,reaction force ,electronic flux ,DFT calculations ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
In this study, the degradation mechanism of chloroacetanilide herbicides in the presence of four different nucleophiles, namely: Br−, I−, HS−, and S2O3−2, was theoretically evaluated using the dispersion-corrected hybrid functional wB97XD and the DGDZVP as a basis set. The comparison of computed activation energies with experimental data shows an excellent correlation (R2 = 0.98 for alachlor and 0.97 for propachlor). The results suggest that the best nucleophiles are those where a sulfur atom performs the nucleophilic attack, whereas the other species are less reactive. Furthermore, it was observed that the different R groups of chloroacetanilide herbicides have a negligible effect on the activation energy of the process. Further insights into the mechanism show that geometrical changes and electronic rearrangements contribute 60% and 40% of the activation energy, respectively. A deeper analysis of the reaction coordinate was conducted, employing the evolution chemical potential, hardness, and electrophilicity index, as well as the electronic flux. The charge analysis shows that the electron density of chlorine increases as the nucleophilic attack occurs. Finally, NBO analysis indicates that the nucleophilic substitution in chloroacetanilides is an asynchronous process with a late transition state for all models except for the case of the iodide attack, which occurs through an early transition state in the reaction.
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- 2021
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15. Predicting the Adsorption of Amoxicillin and Ibuprofen on Chitosan and Graphene Oxide Materials: A Density Functional Theory Study
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Leonardo Anchique, Jackson J. Alcázar, Andrea Ramos-Hernandez, Maximiliano Méndez-López, José R. Mora, Norma Rangel, José Luis Paz, and Edgar Márquez
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emergent pollutants ,pharmaceuticals ,absorption ,density functional theory ,natural bond orbital ,Organic chemistry ,QD241-441 - Abstract
The occurrence, persistence, and accumulation of antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs) represent a new environmental problem due to their harmful effects on human and aquatic life. A suitable absorbent for a particular type of pollutant does not necessarily absorb other types of compounds, so knowing the compatibility between a particular pollutant and a potential absorbent before experimentation seems to be fundamental. In this work, the molecular interactions between some pharmaceuticals (amoxicillin, ibuprofen, and tetracycline derivatives) with two potential absorbers, chitosan and graphene oxide models (pyrene, GO-1, and coronene, GO-2), were studied using the ωB97X-D/6-311G(2d,p) level of theory. The energetic interaction order found was amoxicillin/chitosan > amoxicillin/GO-1 > amoxicillin/GO-2 > ibuprofen/chitosan > ibuprofen/GO-2 > ibuprofen/GO-1, the negative sign for the interaction energy in all complex formations confirms good compatibility, while the size of Eint between 24–34 kcal/mol indicates physisorption processes. Moreover, the free energies of complex formation were negative, confirming the spontaneity of the processes. The larger interaction of amoxicillin Gos, compared to ibuprofen Gos, is consistent with previously reported experimental results, demonstrating the exceptional predictability of these methods. The second-order perturbation theory analysis shows that the amoxicillin complexes are mainly driven by hydrogen bonds, while van der Waals interactions with chitosan and hydrophobic interactions with graphene oxides are modelled for the ibuprofen complexes. Energy decomposition analysis (EDA) shows that electrostatic energy is a major contributor to the stabilization energy in all cases. The results obtained in this work promote the use of graphene oxides and chitosan as potential adsorbents for the removal of these emerging pollutants from water.
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- 2021
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16. In Silico Screening of the DrugBank Database to Search for Possible Drugs against SARS-CoV-2
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Sebastián A. Cuesta, José R. Mora, and Edgar A. Márquez
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SARS-CoV-2 ,QSAR ,docking analysis ,DrugBank ,molecular dynamics ,Organic chemistry ,QD241-441 - Abstract
Coronavirus desease 2019 (COVID-19) is responsible for more than 1.80 M deaths worldwide. A Quantitative Structure-Activity Relationships (QSAR) model is developed based on experimental pIC50 values reported for a structurally diverse dataset. A robust model with only five descriptors is found, with values of R2 = 0.897, Q2LOO = 0.854, and Q2ext = 0.876 and complying with all the parameters established in the validation Tropsha’s test. The analysis of the applicability domain (AD) reveals coverage of about 90% for the external test set. Docking and molecular dynamic analysis are performed on the three most relevant biological targets for SARS-CoV-2: main protease, papain-like protease, and RNA-dependent RNA polymerase. A screening of the DrugBank database is executed, predicting the pIC50 value of 6664 drugs, which are IN the AD of the model (coverage = 79%). Fifty-seven possible potent anti-COVID-19 candidates with pIC50 values > 6.6 are identified, and based on a pharmacophore modelling analysis, four compounds of this set can be suggested as potent candidates to be potential inhibitors of SARS-CoV-2. Finally, the biological activity of the compounds was related to the frontier molecular orbitals shapes.
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- 2021
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17. Classical QSAR and Docking Simulation of 4-Pyridone Derivatives for Their Antimalarial Activity
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Máryury Flores-Sumoza, Jackson J. Alcázar, Edgar Márquez, José R. Mora, Jesús Lezama, and Esneyder Puello
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computational study ,DFT ,nitrogen compounds ,molecular descriptors ,Organic chemistry ,QD241-441 - Abstract
In this work, the minimum energy structures of 22 4-pyridone derivatives have been optimized at Density Functional Theory level, and several quantum molecular, including electronic and thermodynamic descriptors, were computed for these substrates in order to obtain a statistical and meaningful QSAR equation. In this sense, by using multiple linear regressions, five mathematical models have been obtained. The best model with only four descriptors (r2 = 0.86, Q2 = 0.92, S.E.P = 0.38) was validated by the leave-one-out cross-validation method. The antimalarial activity can be explained by the combination of the four mentioned descriptors e.g., electronic potential, dipolar momentum, partition coefficient and molar refractivity. The statistical parameters of this model suggest that it is robust enough to predict the antimalarial activity of new possible compounds; consequently, three small chemical modifications into the structural core of these compounds were performed specifically on the most active compound of the series (compound 13). These three new suggested compounds were leveled as 13A, 13B and 13C, and the predicted biological antimalarial activity is 0.02 µM, 0.03 µM, and 0.07 µM, respectively. In order to complement these results focused on the possible action mechanism of the substrates, a docking simulation was included for these new structures as well as for the compound 13 and the docking scores (binding affinity) obtained for the interaction of these substrates with the cytochrome bc1, were −7.5, −7.2, −6.9 and −7.5 kcal/mol for 13A, 13B, 13C and compound 13, respectively, which suggests that these compounds are good candidates for its biological application in this illness.
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- 2018
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18. New Insight into the Chloroacetanilide Herbicide Degradation Mechanism through a Nucleophilic Attack of Hydrogen Sulfide
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José R. Mora, Cristian Cervantes, and Edgar Marquez
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density functional theory ,computational modeling ,transition state ,herbicides ,reaction mechanism ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
The nucleophilic attack of hydrogen sulfide (HS−) on six different chloroacetanilide herbicides was evaluated theoretically using the dispersion-corrected hybrid functional wB97XD and the 6-311++G(2d,2p) Pople basis sets. The six evaluated substrates were propachlor (A), alachlor (B), metolachlor (C), tioacetanilide (D), β-anilide (E), and methylene (F). Three possible mechanisms were considered: (a) bimolecular nucleophilic substitution (SN2) reaction mechanism, (b) oxygen assistance, and (c) nitrogen assistance. Mechanisms based on O- and N-assistance were discarded due to a very high activation barrier in comparison with the corresponding SN2 mechanism, with the exception of compound F. The N-assistance mechanism for compound F had a free activation energy of 23.52 kcal/mol, which was close to the value for the corresponding SN2 mechanism (23.94 kcal/mol), as these two mechanisms could occur in parallel reactions with almost 50% of each one. In compounds A to D, an important electron-withdrawing effect of the C=O and C=S groups was seen, and consequently, the activation free energies in these SN2 reactions were smaller, with a value of approximately 18 kcal/mol. Instead, compounds E and F, which have a CH2 group in the β-position, presented a higher activation free energy (≈22 kcal/mol). Good agreement was found between experimental and theoretical values for all cases, and a reaction force analysis was performed on the intrinsic reaction coordinate profile in order to gain more details about the reaction mechanism. Finally, from the natural bond orbital (NBO) analysis, it was possible to evaluate the electronic reorganization through the reaction pathway where all the transition states were early in nature in the reaction coordinate (δBav < 50%); the transition states corresponding to compounds A to D turned out to be more synchronous than those for compounds E and F.
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- 2018
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19. ElectroPredictor: An Application to Predict Mayr’s Electrophilicity E through Implementation of an Ensemble Model Based on Machine Learning Algorithms
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Sebastián A. Cuesta, Martín Moreno, Romina A. López, José R. Mora, José Luis Paz, and Edgar A. Márquez
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General Chemical Engineering ,General Chemistry ,Library and Information Sciences ,Computer Science Applications - Published
- 2023
20. Air pollution exposure when cooking with electricity compared to gas
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Carlos F. Gould, Lissete Dávila, M. Lorena Bejarano, Marshall Burke, Darby W. Jack, Samuel B. Schlesinger, José R. Mora, and Alfredo Valarezo
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We report small-sample evidence from a randomized experiment among a set of urban Ecuadorian households who owned both electric induction and gas stoves. We randomly assigned households to cook only with one stove during a prescribed two-day monitoring period, and then cook only with the other stove in a subsequent two-day period. The order of stove use was randomized, and air pollution was measured during each period. We found that mean 48-hour personal NO2exposure was 9.9 ppb higher (95% CI, 4.5-15.3) — a 50% increase over the 48-hour induction mean — when households were randomized to gas as compared to induction. Mean kitchen area NO2concentrations were 1 ppb higher (95% CI, 0.4-2.1) (a 6% increase) and mean personal PM2.5exposure was 11μgm−3higher (95% CI, -0.1-22.8) (a 44% increase) during study periods when randomized to gas. We use time-resolved cooking and pollution data to illustrate that these differences are driven by LPG cooking, which was associated with a 5.0 ppb increase in 5-minute average NO2kitchen area concentrations (95% CI, 3.4-6.7) and a 20.8μgm−3increase in 5-minute average personal PM2.5exposure (95% CI 8.9-32.6). In contrast, cooking with induction was not associated with changes to short-term NO2kitchen area concentrations, though it was associated with short-term increased personal PM2.5exposure (10.8, 95% CI, 5.7-15.9).
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- 2023
21. Molecular Docking and Molecular Dynamics Studies of SARS-CoV-2 Inhibitors: Crocin, Digitoxigenin, Beta-Eudesmol and Favipiravir: Comparative Study
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G. C. Lorena, José R. Mora, L. H. Mendoza-Huizar, G. S. Morán, Sebastián Cuesta, Assia Belhassan, Tahar Lakhlifi, P. F. Carlos, and Mohammed Bouachrine
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Protease ,biology ,Chemistry ,Stereochemistry ,medicine.medical_treatment ,Protein Data Bank (RCSB PDB) ,Active site ,Favipiravir ,Biochemistry ,Crocin ,chemistry.chemical_compound ,Digitoxigenin ,Docking (molecular) ,biology.protein ,medicine ,Molecular Medicine ,Binding site ,Molecular Biology ,Biotechnology - Abstract
In this study, Crocin, Digitoxigenin, Beta-Eudesmol, and Favipiravir were docked in the active site of SARS-CoV-2 main protease (PDB code: 6LU7). The docking study was followed by Molecular Dynamics simulation. The result indicates that Crocin and Digitoxigenin are the structures with the best affinity in the studied enzyme's binding site. Still, Molecular Dynamics simulation showed that Digitoxigenin is the molecule that fits better in the active site of the main protease. Therefore, this molecule could have a more potent antiviral treatment of COVID-19 than the other three studied compounds. © 2021 by the authors.
- Published
- 2021
22. Fast Pyrolysis as a Valorization Mechanism for Banana Rachis and Low‐Density Polyethylene Waste
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Daniela Almeida Streitwieser, Sebastián Salazar, María L. Bejarano, Daniela Oña Villamil, José R. Mora, and Erika Gutierrez
- Subjects
Low-density polyethylene ,Materials science ,Residual biomass ,General Chemical Engineering ,General Chemistry ,Pulp and paper industry ,Pyrolysis ,Industrial and Manufacturing Engineering ,Mechanism (sociology) - Published
- 2021
23. Solvent randomness and intramolecular considerations of optical responses in four-wave mixing
- Author
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Patricio Espinoza-Montero, Lenin A. González-Paz, Edgar Marquez, Marcos Loroño, Joan Vera-Villalobos, José R. Mora, Ysaias J. Alvarado, and José Luis Paz
- Subjects
Coupling ,Physics::Biological Physics ,Quantitative Biology::Biomolecules ,Materials science ,Molecular physics ,Atomic and Molecular Physics, and Optics ,Condensed Matter::Soft Condensed Matter ,Solvent ,Four-wave mixing ,Intramolecular force ,Thermal ,Physics::Chemical Physics ,Solvent effects ,Random variable ,Randomness - Abstract
We determined the optical profiles of a molecular system coupled with a thermal bath in presence of intramolecular coupling. Solvent effects were explicitly considered as a random variable by model...
- Published
- 2021
24. Molecular simulation of the (GPx)-like antioxidant activity of ebselen derivatives through machine learning techniques
- Author
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Luis Calle, Yovani Marrero-Ponce, and José R. Mora
- Subjects
chemistry.chemical_classification ,Antioxidant ,Chemistry ,Ebselen ,General Chemical Engineering ,medicine.medical_treatment ,Glutathione peroxidase ,Molecular simulation ,General Chemistry ,Condensed Matter Physics ,Redox ,chemistry.chemical_compound ,Biochemistry ,Organoselenium Compound ,Modeling and Simulation ,medicine ,General Materials Science ,Information Systems ,Initial rate - Abstract
The selenoenzyme glutathione peroxidase (GPx) like activity of stable organoselenium compounds has been evaluated through the initial rate (ν0) of the reduction reaction of H2O2, Cum-OOH, and t-BuO...
- Published
- 2021
25. Study of potential inhibition of the estrogen receptor α by cannabinoids using an in silico approach: Agonist vs antagonist mechanism
- Author
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Cristian Rocha-Roa, Eliceo Cortes, Sebastián A. Cuesta, José R. Mora, José L. Paz, Máryury Flores-Sumoza, and Edgar A. Márquez
- Subjects
Health Informatics ,Computer Science Applications - Abstract
Breast cancer is the main cancer type with more than 2.2 million cases in 2020, and is the principal cause of death in women; with 685000 deaths in 2020 worldwide. The estrogen receptor is involved at least in 70% of breast cancer diagnoses, and the agonist and antagonist properties of the drug in this receptor play a pivotal role in the control of this illness. This work evaluated the agonist and antagonist mechanisms of 30 cannabinoids by employing molecular docking and dynamic simulations. Compounds with docking scores -8 kcal/mol were analyzed by molecular dynamic simulation at 300 ns, and relevant insights are given about the protein's structural changes, centered on the helicity in alpha-helices H3, H8, H11, and H12. Cannabicitran was the cannabinoid that presented the best relative binding-free energy (-34.96 kcal/mol), and based on rational modification, we found a new natural-based compound with relative binding-free energy (-44.83 kcal/mol) better than the controls hydroxytamoxifen and acolbifen. Structure modifications that could increase biological activity are suggested.
- Published
- 2022
26. Metal Oxide/Sulphide-Based Nanocatalysts in Biodiesel Synthesis
- Author
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Juan S. Villarreal and José R. Mora
- Published
- 2022
27. A computational study of the reaction mechanism involved in the fast cleavage of an unconstrained amide bond assisted by an amine intramolecular nucleophilic attack
- Author
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F. Javier Torres, Vladimir Rodriguez, José R. Mora, Sebastián Cuesta, and Luis Rincón
- Subjects
Reaction mechanism ,010304 chemical physics ,Proton ,Chemistry ,General Chemistry ,010402 general chemistry ,Cleavage (embryo) ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,Computational Mathematics ,Nucleophile ,Intramolecular force ,0103 physical sciences ,Molecule ,Peptide bond ,Amine gas treating - Abstract
In the present work, the fast amide bond cleavage of [3-((1R,5S,7s)-3-azabicyclo[3.3.1]nonane-7-carbonyl)-3-azabicyclo[3.3.1]nonane-7-carboxylic acid (bi-ATDO)], through an intramolecular nucleophilic attack of an amine group is evaluated. First, six possible peptide bond cleavage mechanisms, two of them including a water molecule, are described at the ωB97XD/6-311 + G(d,p)//MP2/6-311 + G(d,p) level of theory. The reaction consisting of an intramolecular nitrogen nucleophilic attack followed by a proton transfer and the amide bond cleavage is determined as the most favorable mechanism. The activation free energy computed for the latter is 20.5 kcal mol-1 , which agrees with the reported experimental result of 24.8 kcal mol-1 . Inclusion of a water molecule to assist the first step of the reaction results in an activation free energy increase of about 17 kcal mol-1 . All the steps in the most favorable mechanism are studied more in detail employing intrinsic reaction coordinate as well as the reaction force and reaction electronic flux analysis.
- Published
- 2021
28. Synthesis, characterization, and photophysical properties of a new 2,5-di(aryl)phosphole derivative and their trigonal copper–phosphole complexes
- Author
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Neskarlys Rios, Juan M. Garcia-Garfido, Deivi Oliveros, Yomaira Otero, José R. Mora, and Franmerly Fuentes
- Subjects
Aryl ,Phosphole ,chemistry.chemical_element ,Trigonal crystal system ,010402 general chemistry ,010403 inorganic & nuclear chemistry ,01 natural sciences ,Copper ,0104 chemical sciences ,Characterization (materials science) ,chemistry.chemical_compound ,chemistry ,Yield (chemistry) ,Polymer chemistry ,Materials Chemistry ,Physical and Theoretical Chemistry ,Derivative (chemistry) - Abstract
A new phosphole derivative, 2,5-di(2-quinolyl)-1-phenylphosphole (1), was synthesized by using the Fagan–Nugent method. Phosphole 1 was obtained as an air-stable solid in high yield (73%). Addition...
- Published
- 2021
29. Optimization of a Gas Chromatography Methodology for Biodiesel Analysis
- Author
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Erika L. Ponce A, José R. Mora, David A. Egas, Francisco Quintanilla, and Valeria Ochoa-Herrera
- Subjects
Biodiesel ,Chemistry ,business.industry ,Calibration curve ,010401 analytical chemistry ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Reduction (complexity) ,Gas chromatography ,Process engineering ,business ,Renewable resource - Abstract
Biodiesel from four different renewable resources was produced. An optimization of the reference methodology by gas chromatography was conducted based on the construction of calibration curves for each biodiesel during fatty acid methyl esters (FAME) quantification. Therefore, in the proposed optimized methodology, pure commercial standards are not necessary. Consequently, a reduction in the research expenses is achieved, making this methodology a cost-effective alternative for FAME quantification. The calibration curves obtained for each biodiesel presented slope values between 0.5–0.7 and regression coefficients (R2) > 0.98 in all cases. These results were compared to those obtained by the conventional methodology. With respect to the validation of the optimized methodology, a comparison of the results obtained by this proposed methodology and the reference one is presented. Finally, a robust and promising technique to quantify FAME present in biodiesel was successfully developed in this study.
- Published
- 2021
30. Highly Active MgP Catalyst for Biodiesel Production and Polyethylene Terephthalate Depolymerization
- Author
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Pablo A. Gangotena, Sebastian Ponce, Álvaro Gallo‐Córdova, Daniela Almeida Streitwieser, and José R. Mora
- Subjects
General Chemistry - Published
- 2022
31. Unveiling the structure‐reactivity relationship involved in the reaction mechanism of the <scp>HCl</scp> ‐catalyzed alkyl t ‐butyl ethers thermal decomposition. A computational study
- Author
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Sebastián A. Cuesta, José R. Mora, Lorena M. Meneses, Edgar A. Márquez, Virginia Flores‐Morales, Luis Rincón, Fernando J. Torres, and Cesar H. Zambrano
- Subjects
Physical and Theoretical Chemistry ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics - Published
- 2022
32. Sulfonylation of Five‐Membered Aromatic Heterocycles Compounds through Nucleophilic Aromatic Substitution: Concerted or Stepwise Mechanism?
- Author
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José R. Mora, Tania Cordova-Sintjago, and Sebastián Cuesta
- Subjects
Reaction mechanism ,Chemistry ,Nucleophilic aromatic substitution ,General Chemistry ,Medicinal chemistry ,Meisenheimer complex ,Mechanism (sociology) - Published
- 2020
33. Quantitative structure–property relationship analysis of the spectrochemical series by employing electronic descriptors from DFT calculations
- Author
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Deivi A. Oliveros R., Rubén A. Machado, and José R. Mora
- Subjects
Biophysics ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Molecular Biology - Abstract
Correlations among Shimura’s parameter (dCo) from spectrochemical series for 34 ligands and electronic descriptors from density functional theory calculations are reported. Simple and multiple linear regression models were constructed. The best results were obtained with the descriptors estimated with MN15 functional, obtaining a multiple linear regression model based on a quantitative structure–property relationship (QSPR) approach, with four attributes and the statistical parameters: R2 = 0.8543, Q2LOO = 0.8050, and Q2LMO = 0.7977. The four molecular descriptors are ligand field splitting (Δ), dipole moment (χC), enthalpy of the metal complex (HC) and the ligand HOMO energy (EHO_L). This model obtained for the Ni(0) complexes represents a novel approach to the spectroscopic series description based on computational tools also revising the models proposed from Werner’s description until modern recompilations carried out across the spectroscopic series developments. The applicability of the model was evaluated on cooper complexes and good prediction of the dCo values for some ligands was also obtained.
- Published
- 2022
- Full Text
- View/download PDF
34. Reaction Mechanism of the Gas-Phase Pyrolysis of N – Acetylthiourea and N, N’–Diacetylthiourea: A Theoretical Study Based in Density Functional Theory
- Author
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Ivan Mendoza, José Luis Paz, Lenin A. González-Paz, Edgar A. Márquez, Joan Vera-Villalobos, José R. Mora, Ysaias J. Alvarado, Tania Cordova-Sintjago, and Marcos A. Loroño G.
- Subjects
Physical and Theoretical Chemistry ,Condensed Matter Physics ,Biochemistry - Published
- 2022
35. Na⋯B bond in NaBH: An induced spin‐polarized bond
- Author
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F. Javier Torres, José R. Mora, Vladimir Rodriguez, and Luis Rincón
- Subjects
Delocalized electron ,Crystallography ,Materials science ,Spin polarization ,Electric field ,Electronic structure ,Physical and Theoretical Chemistry ,Valence electron ,Induced polarization ,Atomic and Molecular Physics, and Optics ,Electron localization function ,Ion - Abstract
The nature of the Na⋯B bond, in the recently synthesized NaBH 3- adduct, is analyzed on the light of the Na- propensity to polarize along the bond axis as a consequence of the electric field produced by the BH3 fragment. The observed induced polarization has two consequences: (i) the energetic stabilization of the Na- , and (ii) the split of its valence electrons into two opposite lobes along the bond axis. Additionally, an analysis of the electron localization is presented using the information content of the correlated conditional pair density that reveals a significant delocalization between one lobe of the polarized Na- anion and the BH3 fragment at the equilibrium distance. Our findings reported here complement previous works on this system.
- Published
- 2021
36. Nonlinear optical responses of molecular systems with vibronic coupling in fluctuating environments
- Author
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José Luis Paz, Lenin A. González-Paz, Ysaias Alvarado, Joan Vera-Villalobos, José R. Mora, Edgar Marquez, and Marcos Loroño
- Subjects
Coupling (electronics) ,Physics ,Vibronic coupling ,Four-wave mixing ,Nonlinear optical ,Physics and Astronomy (miscellaneous) ,Thermal reservoir ,Intramolecular force ,Physics::Chemical Physics ,Molecular systems ,Molecular physics ,Atomic and Molecular Physics, and Optics ,Electronic, Optical and Magnetic Materials - Abstract
The topological profiles of the nonlinear optical properties of a two-level molecular system involving simplified versions of intramolecular coupling immersed in a thermal reservoir have been studied in four-wave mixing (FWM) spectroscopy. Solvent effects have been explicitly considered by modeling the nonradiative interaction with the solute as a random variable. To formulate a solution, it is necessary to introduce stochastic considerations. We assume that system–solvent interactions induce random shifts in the Bohr frequency of the adiabatic states, and their manifestation corresponds to the broadening of the upper level. The Born–Oppenheimer (BO) electronic energy curves for this molecular model consist of two intertwined harmonic oscillator potentials shifted in both their position and their minimum equilibrium energy. The critical quantities for this analysis are the transition and permanent dipole moments, which depend strongly on intramolecular coupling. Our results show how absorption and refractive index are affected by vibronic coupling and solvent stochasticity.
- Published
- 2021
37. Predicting the Adsorption of Amoxicillin and Ibuprofen on Chitosan and Graphene Oxide Materials: A Density Functional Theory Study
- Author
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Jackson J. Alcázar, José Luis Paz, Leonardo Anchique, Andrea Ramos-Hernandez, José R. Mora, Edgar Marquez, Maximiliano Méndez-López, and Norma Rangel
- Subjects
Polymers and Plastics ,Organic chemistry ,02 engineering and technology ,010501 environmental sciences ,pharmaceuticals ,01 natural sciences ,Article ,law.invention ,Chitosan ,Hydrophobic effect ,chemistry.chemical_compound ,symbols.namesake ,Adsorption ,QD241-441 ,Physisorption ,law ,emergent pollutants ,density functional theory ,0105 earth and related environmental sciences ,Graphene ,Hydrogen bond ,General Chemistry ,Interaction energy ,021001 nanoscience & nanotechnology ,natural bond orbital ,chemistry ,Chemical engineering ,symbols ,van der Waals force ,0210 nano-technology ,absorption - Abstract
The occurrence, persistence, and accumulation of antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs) represent a new environmental problem due to their harmful effects on human and aquatic life. A suitable absorbent for a particular type of pollutant does not necessarily absorb other types of compounds, so knowing the compatibility between a particular pollutant and a potential absorbent before experimentation seems to be fundamental. In this work, the molecular interactions between some pharmaceuticals (amoxicillin, ibuprofen, and tetracycline derivatives) with two potential absorbers, chitosan and graphene oxide models (pyrene, GO-1, and coronene, GO-2), were studied using the ωB97X-D/6-311G(2d,p) level of theory. The energetic interaction order found was amoxicillin/chitosan >, amoxicillin/GO-1 >, amoxicillin/GO-2 >, ibuprofen/chitosan >, ibuprofen/GO-2 >, ibuprofen/GO-1, the negative sign for the interaction energy in all complex formations confirms good compatibility, while the size of Eint between 24–34 kcal/mol indicates physisorption processes. moreover, the free energies of complex formation were negative, confirming the spontaneity of the processes. The larger interaction of amoxicillin GOs, compared to ibuprofen GOs, is consistent with previously reported experimental results, demonstrating the exceptional predictability of these methods. The second-order perturbation theory analysis shows that the amoxicillin complexes are mainly driven by hydrogen bonds, while van der Waals interactions with chitosan and hydrophobic interactions with graphene oxides are modelled for the ibuprofen complexes. Energy decomposition analysis (EDA) shows that electrostatic energy is a major contributor to the stabilization energy in all cases. The results obtained in this work promote the use of graphene oxides and chitosan as potential adsorbents for the removal of these emerging pollutants from water.
- Published
- 2021
- Full Text
- View/download PDF
38. Novel copper(I) complex of 2,5-Bis(2-pyridyl)phosphole: Synthesis, Characterization, Catalytic Activity and DFT Calculations
- Author
-
Juan Manuel Garcia Garfido, Yomaira Otero, Edward Ávila, Andreas Reiber, José R. Mora, Deivi Oliveros, Rocío Rivera-Campos, Franmerly Fuentes, and Jeremy Guaramato
- Abstract
A copper(I) complex [CuCl{k1(P)-1a}{k2(P,N)-1a}] (1a = 2,5-bis(2-pyridyl)-1-phenylphosphole) with pseudo tetrahedral geometry was synthesized. In solution, 1a displays a hemilabile behaviour leading to a dynamic equilibrium between four and three-coordinate specie. Its catalytic potential was tested in synthesis of propargylamines and 1,2,3-triazoles via three-component reactions. Experimental results discussed on base to DFT calculations.
- Published
- 2021
39. In Silico Screening of the DrugBank Database to Search for Possible Drugs against SARS-CoV-2
- Author
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José R. Mora, Sebastián Cuesta, and Edgar Marquez
- Subjects
Quantitative structure–activity relationship ,Antagonists & inhibitors ,In silico ,Drug Evaluation, Preclinical ,Pharmaceutical Science ,Quantitative Structure-Activity Relationship ,Cysteine Proteinase Inhibitors ,Molecular Dynamics Simulation ,computer.software_genre ,01 natural sciences ,Molecular Docking Simulation ,Antiviral Agents ,Article ,Analytical Chemistry ,lcsh:QD241-441 ,03 medical and health sciences ,Docking (dog) ,lcsh:Organic chemistry ,Drug Discovery ,Physical and Theoretical Chemistry ,DrugBank ,Coronavirus 3C Proteases ,030304 developmental biology ,0303 health sciences ,Database ,010405 organic chemistry ,QSAR ,SARS-CoV-2 ,Organic Chemistry ,COVID-19 ,RNA-Dependent RNA Polymerase ,molecular dynamics ,0104 chemical sciences ,COVID-19 Drug Treatment ,Chemistry (miscellaneous) ,Molecular Medicine ,Pharmacophore ,computer ,docking analysis ,Databases, Chemical ,Applicability domain - Abstract
Coronavirus desease 2019 (COVID-19) is responsible for more than 1.80 M deaths worldwide. A Quantitative Structure-Activity Relationships (QSAR) model is developed based on experimental pIC50 values reported for a structurally diverse dataset. A robust model with only five descriptors is found, with values of R2 = 0.897, Q2LOO = 0.854, and Q2ext = 0.876 and complying with all the parameters established in the validation Tropsha’s test. The analysis of the applicability domain (AD) reveals coverage of about 90% for the external test set. Docking and molecular dynamic analysis are performed on the three most relevant biological targets for SARS-CoV-2: main protease, papain-like protease, and RNA-dependent RNA polymerase. A screening of the DrugBank database is executed, predicting the pIC50 value of 6664 drugs, which are IN the AD of the model (coverage = 79%). Fifty-seven possible potent anti-COVID-19 candidates with pIC50 values >, 6.6 are identified, and based on a pharmacophore modelling analysis, four compounds of this set can be suggested as potent candidates to be potential inhibitors of SARS-CoV-2. Finally, the biological activity of the compounds was related to the frontier molecular orbitals shapes.
- Published
- 2021
40. Designing an efficient and recoverable magnetic nanocatalyst based on Ca, Fe and pectin for biodiesel production
- Author
-
Paula I. Acosta, Alvaro Gallo-Cordova, Santiago A. Carrera, José R. Mora, José F. Noboa, and Juan S. Villarreal
- Subjects
Biodiesel ,food.ingredient ,Pectin ,Chemistry ,General Chemical Engineering ,Organic Chemistry ,Energy Engineering and Power Technology ,engineering.material ,Catalysis ,law.invention ,chemistry.chemical_compound ,Fuel Technology ,food ,law ,Biodiesel production ,engineering ,Calcination ,Biopolymer ,Methanol ,Nuclear chemistry ,Superparamagnetism - Abstract
Magnetic catalysts containing Fe and Ca synthesized in the presence of pectin have demonstrated to be highly efficient in the transesterification reaction for biodiesel production. Catalysts were prepared by the co-precipitation method under a N2 atmosphere with Na2CO3 from a mixture of FeSO4, FeCl3, Ca(NO3)2, and pectin followed by calcination at 550 ˚C/6h. The influence of the Fe:Ca molar ratio in the catalytic activity on the transesterification reaction with methanol was evaluated in the presence or absence of pectin. The most efficient catalyst was prepared in the presence of pectin with a Fe:Ca molar ratio of 4.5:2 (FCP2), and the best experimental conditions were at 3 % wt catalyst, 14:1 of methanol: soybean oil molar ration and 7.5 h of reaction time, which resulted in a methyl ester yield of 96.3%. It was shown that the presence of the biopolymer in the synthesis enhances the catalytic activity of the material from 20% to 99% of biodiesel production. All materials were fully characterized by TEM, FTIR, TGA, BET, XRD and DC magnetometry. It was found that catalysts present high surface areas with a nanometer size (∼20 nm), giving rise to a superparamagnetic state with a magnetic saturation high enough for separation by means of a magnet. In contrast, catalysts prepared in the absence of pectin demonstrated poor performance in the transesterification reaction of biodiesel in the optimized experimental conditions. The magnetic properties and the biopolymer role are discussed.
- Published
- 2022
41. Modelling the Anti-Methicillin-Resistant Staphylococcus Aureus (MRSA) Activity of Cannabinoids: A QSAR and Docking Study
- Author
-
Eliceo Eliceo Cortes, José R. Mora, and Edgar Marquez
- Subjects
Quantitative structure–activity relationship ,General Chemical Engineering ,medicine.medical_treatment ,Anti-MRSA ,010402 general chemistry ,01 natural sciences ,DNA gyrase ,DFT ,Inorganic Chemistry ,cannabinoids ,Molecular descriptor ,anti-MRSA ,medicine ,lcsh:QD901-999 ,General Materials Science ,biology ,010405 organic chemistry ,Chemistry ,Cannabinoids ,QSAR ,Active site ,Biological activity ,molecular docking ,Condensed Matter Physics ,Antimicrobial ,0104 chemical sciences ,Biochemistry ,Docking (molecular) ,Molecular docking ,biology.protein ,Cannabinoid ,lcsh:Crystallography - Abstract
Twenty-four cannabinoids active against MRSA SA1199B and XU212 were optimized at WB97XD/6-31G(d,p), and several molecular descriptors were obtained. Using a multiple linear regression method, several mathematical models with statistical significance were obtained. The robustness of the models was validated, employing the leave-one-out cross-validation and Y-scrambling methods. The entire data set was docked against penicillin-binding protein, iso-tyrosyl tRNA synthetase, and DNA gyrase. The most active cannabinoids had high affinity to penicillin-binding protein (PBP), whereas the least active compounds had low affinities for all of the targets. Among the cannabinoid compounds, Cannabinoid 2 was highlighted due to its suitable combination of both antimicrobial activity and higher scoring values against the selected target, therefore, its docking performance was compared to that of oxacillin, a commercial PBP inhibitor. The 2D figures reveal that both compounds hit the protein in the active site with a similar type of molecular interaction, where the hydroxyl groups in the aromatic ring of cannabinoids play a pivotal role in the biological activity. These results provide some evidence that the anti-Staphylococcus aureus activity of these cannabinoids may be related to the inhibition of the PBP protein, besides, the robustness of the models along with the docking and Quantitative Structure&ndash, Activity Relationship (QSAR) results allow the proposal of three new compounds, the predicted activity combined with the scoring values against PBP should encourage future synthesis and experimental testing.
- Published
- 2020
- Full Text
- View/download PDF
42. Stabilization of ZnO quantum dots by preferred 1:2 interaction with a liquid crystal molecule
- Author
-
Juliana Eccher, Wallison Chaves Costa, Harald Bock, Samara de Quadros, Lizandra M. Zimmermann, Crislaine Sandri, José R. Mora, Ivan H. Bechtold, Ana L.E.P. Silva, Departamento de Física [Universidade Federal de Santa Catarina], Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC), Departamento de Quimica [Universidade Federal de Santa Catarina], Departamento de Quimica [Blumenau] (FURB), Universidade Regional de Blumenau (FURB), Universidad San Francisco de Quito, Departamento de Ingenieria Quimica, Centre de Recherche Paul Pascal (CRPP), and Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Materials science ,Supramolecular chemistry ,Nanoparticle ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Colloid ,chemistry.chemical_compound ,Liquid crystal ,Materials Chemistry ,Molecule ,Physical and Theoretical Chemistry ,Spectroscopy ,ComputingMilieux_MISCELLANEOUS ,[CHIM.MATE]Chemical Sciences/Material chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Electronic, Optical and Magnetic Materials ,Chemical engineering ,chemistry ,Quantum dot ,0210 nano-technology ,Stoichiometry ,Perylene - Abstract
Zinc oxide (ZnO) quantum dots were synthesized in the presence of a columnar liquid crystalline perylene derivative. The liquid crystal molecules did not influence the nanoparticles' growth, and surprisingly they were efficient in stabilizing the colloidal dispersion over several months. For the first time, the quantity of ZnO units present in the ~4 nm sized ZnO nanoparticles was determined from the supramolecular interaction between the nanoparticles and the liquid crystal molecules as well as by analyzing the stoichiometry of the mixture. The quantity of ZnO units was also confirmed by theoretical studies performed by means of DFT calculations. The mixture was efficiently applied for methylene blue photodegradation.
- Published
- 2020
43. Ensemble Models Based on QuBiLS-MAS Features and Shallow Learning for the Prediction of Drug-Induced Liver Toxicity: Improving Deep Learning and Traditional Approaches
- Author
-
César R. García-Jacas, Yovani Marrero-Ponce, José R. Mora, and Amileth Suarez Causado
- Subjects
Drug ,Liver toxicity ,Computer science ,media_common.quotation_subject ,In silico ,Quantitative Structure-Activity Relationship ,Computational biology ,010501 environmental sciences ,Toxicology ,01 natural sciences ,Models, Biological ,Machine Learning ,03 medical and health sciences ,Drug Discovery ,030304 developmental biology ,0105 earth and related environmental sciences ,media_common ,0303 health sciences ,Ensemble forecasting ,Drug discovery ,business.industry ,Deep learning ,General Medicine ,Pipeline (software) ,Key (cryptography) ,Artificial intelligence ,Chemical and Drug Induced Liver Injury ,business ,Software - Abstract
Drug-induced liver injury (DILI) is a key safety issue in the drug discovery pipeline and a regulatory concern. Thus, many in silico tools have been proposed to improve the hepatotoxicity predictio...
- Published
- 2020
44. Theoretical Description of R–X⋯NH3 Halogen Bond Complexes: Effect of the R Group on the Complex Stability and Sigma-Hole Electron Depletion
- Author
-
Cesar H. Zambrano, José R. Mora, F. Javier Torres, Luis Rincón, Vladimir Rodriguez, and Juan Esteban Zurita
- Subjects
fermi-hole ,Binding energy ,Substituent ,Pharmaceutical Science ,Kullback–Leibler divergence ,010402 general chemistry ,01 natural sciences ,Analytical Chemistry ,lcsh:QD241-441 ,conditional pair density ,Delocalized electron ,chemistry.chemical_compound ,lcsh:Organic chemistry ,0103 physical sciences ,Drug Discovery ,Molecule ,Physical and Theoretical Chemistry ,Halogen bond ,010304 chemical physics ,Electronic correlation ,Chemistry ,Organic Chemistry ,sigma-hole ,Electron localization function ,0104 chemical sciences ,Crystallography ,Chemistry (miscellaneous) ,Halogen ,Molecular Medicine ,halogen bond - Abstract
In the present work, a number of R&ndash, X⋯NH3 (X = Cl, Br, and I) halogen bonded systems were theoretical studied by means of DFT calculations performed at the &omega, B97XD/6-31+G(d,p) level of theory in order to get insights on the effect of the electron-donating or electron-withdrawing character of the different R substituent groups (R = halogen, methyl, partially fluorinated methyl, perfluoro-methyl, ethyl, vinyl, and acetyl) on the stability of the halogen bond. The results indicate that the relative stability of the halogen bond follows the Cl <, Br <, I trend considering the same R substituent whereas the more electron-withdrawing character of the R substituent the more stable the halogen bond. Refinement of the latter results, performed at the MP2/6-31+G(d,p) level showed that the DFT and the MP2 binding energies correlate remarkably well, suggesting that the Grimme&rsquo, s type dispersion-corrected functional produces reasonable structural and energetic features of halogen bond systems. DFT results were also observed to agree with more refined calculations performed at the CCSD(T) level. In a further stage, a more thorough analysis of the R&ndash, Br⋯NH3 complexes was performed by means of a novel electron localization/delocalization tool, defined in terms of an Information Theory, IT, based quantity obtained from the conditional pair density. For the latter, our in-house developed C++/CUDA program, called KLD (acronym of Kullback&ndash, Leibler divergence), was employed. KLD results mapped onto the one-electron density plotted at a 0.04 a.u. isovalue, showed that (i) as expected, the localized electron depletion of the Br sigma-hole is largely affected by the electron-withdrawing character of the R substituent group and (ii) the R&ndash, X bond is significantly polarized due to the presence of the NH3 molecule in the complexes. The afore-mentioned constitutes a clear indication of the dominant character of electrostatics on the stabilization of halogen bonds in agreement with a number of studies reported in the main literature. Finally, the cooperative effects on the [Br&mdash, CN]n system (n = 1&ndash, 8) was evaluated at the MP2/6-31+G(d,p) level, where it was observed that an increase of about ~14.2% on the complex stability is obtained when going from n = 2 to n = 8. The latter results were corroborated by the analysis of the changes on the Fermi-hole localization pattern on the halogen bond zones, which suggests an also important contribution of the electron correlation in the stabilization of these systems.
- Published
- 2020
- Full Text
- View/download PDF
45. Experimental and theoretical study of the thermal decomposition of ethyl acetate during fast pyrolysis
- Author
-
Sebastián Salazar, José R. Mora, Daniela Almeida Streitwieser, Diana Cristina Vargas, and Kevin Van Geem
- Subjects
Materials science ,020209 energy ,General Chemical Engineering ,Ethyl acetate ,Analytical chemistry ,02 engineering and technology ,Activation energy ,MECHANISMS ,Reaction rate ,Acetic acid ,chemistry.chemical_compound ,symbols.namesake ,GAS-PHASE ELIMINATION ,Arrhenius equation ,0202 electrical engineering, electronic engineering, information engineering ,Thermal decomposition ,BIOMASS PYROLYSIS ,KINETICS ,RENEWABLE ENERGY ,CHALLENGES ,Concerted reaction ,General Chemistry ,021001 nanoscience & nanotechnology ,Unimolecular decomposition ,Chemistry ,chemistry ,symbols ,0210 nano-technology ,Pyrolysis - Abstract
The thermal decomposition of ethyl acetate was experimentally studied in a newly designed fast pyrolysis set-up. The results were compared to theoretical calculations and literature values in order to proof the experimental concept. The reaction was carried out in a free fall tubular reactor with a residence time of 0.15 s. The identification and quantification of products stream composition was performed online using a GC-TCD/FID. First, an overview of the reaction rate at feed volumes of 0.25, 0.50 and 0.75 mL was obtained at reaction temperature between 400 to 600 degrees C in intervals of 50 degrees C. As a result mass transfer limitation for feeds larger than 0.5 mL were identified. For the second approach, a constant feed volume of 0.25 mL and temperatures between 420 to 550 degrees C were investigated. Using the experimental results, a global kinetic model is proposed for the thermal decomposition of ethyl acetate into ethylene and acetic acid through a first order unimolecular reaction. Also, theoretical calculations were performed at wB97XD/6-311++G(d,p) level. A concerted mechanism through a six-membered transition state was identified in the reaction path. The theoretical and experimental activation energy values lie within the literature values between 193 and 213 kJ/mol. 2020 The Authors. Published by Elsevier B.V. on behalf of Institution of Chemical Engineers. This is an open access article under the CC BY-NC -ND license (http://creativecommons.orgilicenseseby-nc-nd/450/).
- Published
- 2020
46. A valence bond perspective of the reaction force formalism
- Author
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José R. Mora, Luis Rincón, Vladimir Rodriguez, F. Javier Torres, and Cesar H. Zambrano
- Subjects
Physics ,Crystallography ,Formalism (philosophy of mathematics) ,010304 chemical physics ,Reaction ,Reaction step ,0103 physical sciences ,Valence bond theory ,Reaction path ,Physical and Theoretical Chemistry ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences - Abstract
The reaction force formalism represents a convenient approach to analyze the course of a reaction step. From this analysis, the reaction path can be separated in a number of regions that are associated to either structural changes or electronic reorganization. This empirical observation is rationalized in this work on the basis of a simple two-state valence bond correlation diagram. We demonstrate that the ratio between the integrated reaction force and the region of interest ($$w_{\text{ii}}/w_{\text{i}}$$ for the forward reaction and $$w_{\text{iii}}/w_{\text{iv}}$$ for the backward reaction) increases with the ratio between the quantum mechanical resonance energy and the energy required to reach the crossing point at the transition state, we call to this ratio the strength of the resonance. This observation means that the size of the transition region (region ii and iii), that includes the transition state, depends on the strength of the resonance, and the structural zones (region i and iv), that are regions associated with the pure valence bond state curves (no resonance). We propose a simple analytical relationship for $$w_{\text{ii}}/w_{\text{i}}$$ and $$w_{\text{iii}}/w_{\text{iv}}$$ based on three parameters: (i) the quantum mechanical resonance energy, (ii) the energy of the reaction and (iii) the overlap between the VB structures at the transition state. The previous conclusions were supported by a reaction force analysis of a $${\text{S}}_{N}2$$ reactions, $${\text{X}}^{-} + {\text{CH}}_{3}{-}{\text{Y}} \rightarrow {{\text{X}}{-}{\text{CH}}}_{3} + {\text{Y}}^{-} ({\text{X}} = {\text{F}}, {\text{Cl}}, {\text{Br}})$$. The valence bond parameters for these reactions are estimated from empirical considerations. A very good agreement is found between the computed reaction force ratios and the predicted one.
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- 2019
47. Computational molecular modelling of N-cinnamoyl and hydroxycinnamoyl amides as potential α-glucosidase inhibitors
- Author
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José R. Mora, Luis Calle, and Edgar Marquez
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chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Value (computer science) ,Atom (order theory) ,Biological activity ,01 natural sciences ,0104 chemical sciences ,Polar surface area ,Amino acid ,010404 medicinal & biomolecular chemistry ,symbols.namesake ,Computational chemistry ,Linear regression ,symbols ,Density functional theory ,General Pharmacology, Toxicology and Pharmaceutics ,van der Waals force - Abstract
In the present work, a molecular modelling has been performed on a total of 17 cinnamic acids, derived with different amino acids. These have recently been evaluated as potential α-glucosidase inhibitors. Consequently, we proposed a quantitative 3D structure–activity relationships in order to obtain predictive models of the biological activity. Two types of descriptors were used for the modelling: quantum chemical and multi-linear algebraic maps. The first one was obtained by using Density Functional Theory (DFT) at the M06/6-311++G(d,p) level, while for the second, attribute sets were obtained by using 3D molecular topology, atom weighed by physicochemical properties including the polar surface area, hardness, softness, van der Waals volume and charges. A genetic algorithm scheme was employed to determine the best subset of attributes for the application of the multiple linear regression. The most robust model (M4R_TD) was obtained with four multi-linear algebraic map descriptors (R2 = 0.946, Q2 = 0.901, F = 85.70), which indicate a good correlation between experimental and calculated results. Seven new simple structural modifications in the molecular core were suggested specifically for the three most active compounds (1, 2 and 5). The modifications to compound 1 appear to lead to an increase in the predicted activity from a pIC50 value of 9.872 to 10.656 in compound 1.3. The modifications to compound 2 do not affect an increase in the biological activity, and finally the modifications to compound 5 seem to increase the activity with a predicted pIC50= log[10/(10−6×IC50)]IC50 value of 10.094 for compound 5.1.
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- 2018
48. Theoretical Calculations of the Multistep Reaction Mechanism Involved in Asparagine Pyrolysis Supported by Degree of Rate Control and Thermodynamic Control Analyses
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José R. Mora, Cristian Cervantes, Luis Rincón, Javier Torres, Jackson J. Alcázar, Edgar Marquez, and Miguel Angel Mendez
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Reaction mechanism ,010402 general chemistry ,01 natural sciences ,chemistry.chemical_compound ,symbols.namesake ,Condensed Matter::Materials Science ,Succinimide ,Computational chemistry ,Physics::Atomic and Molecular Clusters ,General Materials Science ,Asparagine ,Physics::Chemical Physics ,Instrumentation ,Maleimide ,Fluid Flow and Transfer Processes ,010405 organic chemistry ,Process Chemistry and Technology ,General Engineering ,asparagine ,pyrolysis ,biomass pyrolysis ,0104 chemical sciences ,Computer Science Applications ,Gibbs free energy ,chemistry ,Polymerization ,symbols ,Density functional theory ,reaction mechanism ,Pyrolysis - Abstract
A computational study on the mechanisms of reaction for the pyrolysis of asparagine is presented. A density functional theory (DFT) study at the &omega, B97XD/6-311G(d,p) level was performed to analyze the differences in two reaction mechanisms: (i) the formation of five-membered cyclic products: maleimide and succinimide, and (ii) the more classical, six-membered cyclic products (diketopiperazine species) which are common in the pyrolysis of many other amino acids. The effect of temperature was included in the calculations at 300 °, C or 625 °, C, as required. Moreover, a detailed study based on the degree of rate control and thermodynamic control of the proposed mechanism for the formation of maleimide and succinimide is also presented. Results show that, for asparagine, the five-membered ring formation is the preferred process instead of the six-membered cycle (32 kJ/mol of Gibbs free energy difference between them at the first cyclization step), therefore, the polymerization is favored. On the other hand, the rupture of the polymer represents the highest energetic barrier (&Delta, G&Dagger, = 281 kJ/mol) and the most influential process in the overall rate of the reaction. These results are in good agreement with the experimental evidence.
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- 2019
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49. Synthesis, In Vitro, and In Silico Analysis of the Antioxidative Activity of Dapsone Imine Derivatives
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Julio Cesar Rivera-Leyva, Edgar Marquez, Ricardo Guzmán-Ávila, Mayra Avelar, José R. Mora, Virginia Flores-Morales, and Jesús Rivera-Islas
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Antioxidant ,DPPH ,medicine.medical_treatment ,Imine ,Pharmaceutical Science ,antioxidant in vitro ,Redox ,Article ,Antioxidants ,Analytical Chemistry ,Structure-Activity Relationship ,Partial charge ,chemistry.chemical_compound ,QD241-441 ,Molecular descriptor ,Drug Discovery ,medicine ,Computer Simulation ,Physical and Theoretical Chemistry ,Density Functional Theory ,Molecular Structure ,Chemistry ,Organic Chemistry ,Combinatorial chemistry ,In vitro ,dapsone imines ,Chemistry (miscellaneous) ,Molecular Medicine ,Ferric ,dapsone-derivatives ,Imines ,Dapsone ,medicine.drug - Abstract
Dapsone (DDS) is an antibacterial drug with well-known antioxidant properties. However, the antioxidant behavior of its derivatives has not been well explored. In the present work, the antioxidant activity of 10 dapsone derivatives 4-substituted was determined by an evaluation in two in vitro models (DPPH radical scavenging assay and ferric reducing antioxidant power). These imine derivatives 1–10 were obtained through condensation between DDS and the corresponding aromatic aldehydes 4-substuited. Three derivatives presented better results than DDS in the determination of DPPH (2, 9, and 10). Likewise, we have three compounds with better reducing activity than dapsone (4, 9, and 10). In order to be more insight, the redox process, a conceptual DFT analysis was carried out. Molecular descriptors such as electronic distribution, the total charge accepting/donating capacity (I/A), and the partial charge accepting/donating capacity (ω+/ω−) were calculated to analyze the relative donor-acceptor capacity through employing a donor acceptor map (DAM). The DFT calculation allowed us to establish a relationship between GAPHOMO-LUMO and DAM with the observed antioxidant effects. According to the results, we concluded that compounds 2 and 3 have the lowest Ra values, representing a good antioxidant behavior observed experimentally in DPPH radical capturing. On the other hand, derivatives 4, 9, and 10 display the best reducing capacity activity with the highest ω− and Rd values. Consequently, we propose these compounds as the best antireductants in our DDS imine derivative series.
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- 2021
50. Theoretical study on the flash vacuum gas-phase pyrolysis reaction mechanism of 2-(2-benzylidenehydrazinyl)pyridine and analogous
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Sebastián Cuesta, José R. Mora, Edgar Marquez, Marcos Loroño, and José Luis Paz
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Reaction mechanism ,010304 chemical physics ,Flash vacuum pyrolysis ,Bond strength ,Substituent ,Activation energy ,010402 general chemistry ,Condensed Matter Physics ,Ring (chemistry) ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,0103 physical sciences ,Pyridine ,Physical chemistry ,Reactivity (chemistry) ,Physical and Theoretical Chemistry - Abstract
In the present study, the most favourable reaction mechanism in the flash vacuum pyrolysis of 2-[(2E)-2-benzylidenehydrazinyl]pyridine and analogous was theoretically studied using B3LYP-D3/6-311G(d,p) level. The influence of different substituents on the phenyl ring in the para position is evaluated at 500 K. A deep analysis of the mechanisms reveals the influence of the substituents in the activation energy, where the reactivity order OCH3 > CH3 > H > Cl > NO2 is found, following Hammet parameters (σp). To reach the transition state, geometric changes contribute more than 70% of the energy in agreement with the reaction force analysis. A recent independent gradient model (IGM) is also applied to establish an influence between the substituent and the strength of the bonds involved in the mechanism, through an intrinsic bond strength index (IBSI). Furthermore, the influence of the substituent was also evaluated in terms of interatomic distances and evolution percentages, finding high correlations with Hammet σp values.
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- 2021
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