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1.
Environ Sci Process Impacts ; 26(4): 734-750, 2024 Apr 24.
Artículo en Inglés | MEDLINE | ID: mdl-38426396

RESUMEN

To give a comprehensive account of the environmental acceptability of 1,1,2,3-tetrafluoropropene (CF2CF-CH2F) in the troposphere, we have examined the oxidation reaction pathways and kinetics of CF2CF-CH2F initiated by Cl-atoms using the second-order Møller-Plesset perturbation (MP2) theory along with the 6-31+G(d,p) basis set. We also performed single-point energy calculations to further refine the energies at the CCSD(T) level along with the basis sets 6-31+G(d,p) and 6-311++G(d,p). The estimation of the relative energies and thermodynamic parameters of the CF2CF-CH2F + Cl reaction clearly shows that Cl-atom addition reaction pathways are more dominant compared to H-abstraction reaction pathways. The value of the rate coefficient for each reaction channel is calculated using the conventional transition state theory (TST) over the temperature range of 200-1000 K at 1 atm. The estimated overall rate coefficients for the title reaction are found to be 1.10 × 10-12, 1.21 × 10-10, and 1.13 × 10-8 cm3 per molecule per s via the respective calculation methods viz. MP2/6-31+G(d,p), CCSD(T)//MP2/6-31+G(d,p), and CCSD(T)/6-311++G(d,p)//MP2/6-31+G(d,p), at 298.15 K. Moreover, the calculated rate coefficients and percentage branching ratio values suggest that the Cl-atom addition reaction at the ß-carbon atom is more preferable to that of the α-carbon addition to CF2CF-CH2F. Based on the rate coefficient values calculated by the three different methods, the atmospheric lifetime for the title reaction at 298.15 K is estimated. The radiative efficiency (RE) and Global Warming Potential (GWP) results of the title molecule show that its GWP would be negligible. Further, we have explored the degradation of its product radicals in the presence of O2 and NO. From the degradation results, we have found that CF2(Cl)COF, FCOCH2F, FCFO and FCOCl are formed as stable end products along with various radicals such as ˙CF2Cl and ˙CH2F. Therefore, these findings of kinetic and mechanistic data can be applied to the development and implementation of a novel CFC replacement.


Asunto(s)
Modelos Químicos , Oxidación-Reducción , Cinética , Contaminantes Atmosféricos/química , Contaminantes Atmosféricos/análisis , Fluorocarburos/química , Termodinámica , Atmósfera/química , Hidrocarburos Fluorados/química
2.
J Phys Chem A ; 127(41): 8508-8529, 2023 Oct 19.
Artículo en Inglés | MEDLINE | ID: mdl-37811794

RESUMEN

With the rapid growth of industrialization, deforestation, and burning of fossil fuels, undeniably there has been an incredible escalation of the CO2 concentration in the atmosphere. In order to mitigate the problem, the capture and utilization of CO2 in different value-added chemicals have thus remained topics of concerned research for more than a decade. Accordingly, we have performed molecular -level catalytic hydrogenation of CO2 to formic acid using bare [Cu2]0,±1 dimers as catalysts. The entire investigation has been performed using a density functional theory (DFT) method employing the Perdew-Burke-Ernzerhof (PBE) functional with the def2TZVPP basis set to explore the different possible routes and efficiency of the catalysts. Results reveal the feasibility of H2 dissociation on all three Cu2, Cu2+, and Cu2- dimers. The negatively charged hydride formed during H2 dissociation on Cu2 and Cu2+ dimers facilitates the formation of the HCOO* intermediate over COOH*, thereby providing product selectivity for HCOOH above CO. However, the reaction on the Cu2- dimer forms both HCOO* and COOH* intermediates, but HCOO*, being kinetically more favorable, results in HCOOH production. The free-energy change suggests that the complete reaction on Cu2 and Cu2+ dimers forms a stable product compared to the Cu2- dimer. Furthermore, H3COH production is studied using the title catalysts via the obtained HCOOH* intermediate from the reaction channel. Transition state theory (TST) has been considered to evaluate the rate constants for each step of the reaction. Overall results suggest Cu2 to be better compared to Cu2+ and Cu2- dimers for HCOOH formation and Cu2+ over Cu2 and Cu2- dimers to be more efficient for H3COH formation. This work opens the way for further investigation of the reaction mechanism and development of an efficient catalyst for CO2 hydrogenation.

3.
DNA Res ; 29(4)2022 Jun 25.
Artículo en Inglés | MEDLINE | ID: mdl-35920776

RESUMEN

A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons. In our study of SNPs in 586 genes across 156 Escherichia coli strains, synonymous polymorphism in 2-fold degenerate codons were higher in comparison to that in 4-fold degenerate codons, which could be attributed to the difference between transition (Ti) and transversion (Tv) substitution rates where the average rate of a transition is four times more than that of a transversion in general. We considered both the Ti/Tv ratio, and nonsense mutation in pretermination codons, to improve estimates of synonymous (S) and non-synonymous (NS) sites. The accuracy of estimating dN/dS has been improved by considering the Ti/Tv ratio and nonsense substitutions in pretermination codons. We showed that applying the modified approach based on Ti/Tv ratio and pretermination codons results in higher values of dN/dS in 29 common genes of equal reading-frames between E. coli and Salmonella enterica. This study emphasizes the robustness of amino acid composition with varying codon degeneracy, as well as the pretermination codons when calculating dN/dS values.


Asunto(s)
Proteínas de Escherichia coli , Selección Genética , Codón , Codón sin Sentido , Desoxirribonucleasa (Dímero de Pirimidina)/genética , Escherichia coli/genética , Evolución Molecular , Modelos Genéticos
4.
Front Plant Sci ; 13: 831589, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35677250

RESUMEN

The paper and pulp industry (PPI) is one of the largest industries that contribute to the growing economy of the world. While wood remains the primary raw material of the PPIs, the demand for paper has also grown alongside the expanding global population, leading to deforestation and ecological imbalance. Wood-based paper production is associated with enormous utilization of water resources and the release of different wastes and untreated sludge that degrades the quality of the environment and makes it unsafe for living creatures. In line with this, the indigenous handmade paper making from the bark of Daphne papyracea, Wall. ex G. Don by the Monpa tribe of Arunachal Pradesh, India is considered as a potential alternative to non-wood fiber. This study discusses the species distribution modeling of D. papyracea, community-based production of the paper, and glycome profiling of the paper by plant cell wall glycan-directed monoclonal antibodies. The algorithms used for ecological and geographical modeling indicated the maximum predictive distribution of the plant toward the western parts of Arunachal Pradesh. It was also found that the suitable distribution of D. papyracea was largely affected by the precipitation and temperature variables. Plant cell walls are primarily made up of cellulose, hemicellulose, lignin, pectin, and glycoproteins. Non-cellulosic cell wall glycans contribute significantly to various physical properties such as density, crystallinity, and tensile strength of plant cell walls. Therefore, a detailed analysis of non-cellulosic cell wall glycan through glycome profiling and glycosyl residue composition analysis is important for the polymeric composition and commercial processing of D. papyracea paper. ELISA-based glycome profiling results demonstrated that major classes of cell wall glycans such as xylan, arabinogalactans, and rhamnogalacturonan-I were present on D. papyracea paper. The presence of these polymers in the Himalayan Buddhist handmade paper of Arunachal Pradesh is correlated with its high tensile strength. The results of this study imply that non-cellulosic cell wall glycans are required for the production of high-quality paper. To summarize, immediate action is required to strengthen the centuries-old practice of handmade paper, which can be achieved through education, workshops, technical know-how, and effective marketing aid to entrepreneurs.

5.
Int J Biol Macromol ; 201: 298-307, 2022 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-34999043

RESUMEN

An integrated treatment coupling alkali, steam explosion and ammonia/chlorine-free bleaching with sequential mild acid pretreatment were performed to isolate and characterize cellulose from banana agrowastes followed by optimized enzymatic hydrolysis to glucose. The cellulose yield, compositional, microstructural, and morphological analysis initially obtained from three post-harvest banana agrowastes (peel, pseudostem, and peduncle) were surveyed. Isolation parameters for banana peduncle agrowastes, the most efficient precursor, were reconfigured for acid hydrolysis by applying an orthogonal L9 array of Taguchi design. Effects of solution-to-pulp ratio, acid concentration, temperature, and reaction time on physicochemical parameters were assessed resulting in ~81% cellulose recovery. Subsequently, cellulase driven enzymatic conversion to glucose was modelled using response surface methodology (RSM), where the mutual influences of incubation time, enzyme concentration, substrate concentration, and surfactant concentration were investigated. Artificial Neural Network (ANN) modelling further improved upon RSM optimizations ensuing ~97% optimized glucose yield, verified experimentally.


Asunto(s)
Celulasa , Musa , Celulosa/química , Hidrólisis , Musa/química , Vapor
6.
PLoS One ; 16(11): e0258645, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34780495

RESUMEN

All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.


Asunto(s)
Biología Computacional , Mapeo Epitopo , SARS-CoV-2/inmunología , Proteínas Estructurales Virales/inmunología , Secuencia de Aminoácidos , Vacunas contra la COVID-19/química , Vacunas contra la COVID-19/inmunología , Bases de Datos como Asunto , Epítopos de Linfocito B/química , Epítopos de Linfocito B/inmunología , Epítopos de Linfocito T/química , Epítopos de Linfocito T/inmunología , Antígenos de Histocompatibilidad Clase I/metabolismo , Humanos , Modelos Moleculares , Conformación Proteica , Reproducibilidad de los Resultados , Proteínas Estructurales Virales/química
7.
Chem Commun (Camb) ; 57(95): 12800-12803, 2021 Nov 30.
Artículo en Inglés | MEDLINE | ID: mdl-34783333

RESUMEN

The present work describes the first visible light-assisted, metal-free and organic base 1,1,3,3-tetramethyl guanidine (TMG) mediated synthesis of unsymmetrical methyl aryl/alkyl carbonates from the reaction of alcohols, methanol, and CO2 in high to excellent yields under atmospheric pressure and ambient temperature conditions.

8.
Environ Sci Pollut Res Int ; 28(33): 45646-45662, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-33876365

RESUMEN

Studies on primary gas-phase reactions of emitted saturated and unsaturated ethers with oxidants and subsequent secondary reactions of product radicals with O2 in the presence of NO are important in their atmospheric chemical processes. To accomplish these findings, we have examined the chemistry of OH-initiated oxidation of isopropenyl methyl ether (i-PME) CH3C(CH2)OCH3 by electronic structure ca using density functional theory. Our energetic calculations show that OH additions to carbon-carbon double bonds of i-PME are more favorable reaction pathways than H-abstraction reactions from the various CH sites of the titled molecule. The rate constant values which are obtained from the transition state theory also signify that OH-addition reactions have faster reaction rates than H-abstraction reactions. Our calculated total rate constant of the reaction is found 9.90 × 10-11 cm3 molecule-1 s-1. The percentage branching ratio calculations imply that OH-addition reactions have 98.09% contribution in the total rate constant. The atmospheric lifetime of i-PME is found to be 2.8 h. Further, we have identified 2-hydroxy-2-methoxypropanol, methyl acetate, methy-1,2-hydroxyacetate and 1-hydroxypropane-2-one, 1,2-dihydroxypropan-2-yl format, 2-hydroxyacetic acid, acetic acid, and formaldehyde from the secondary oxidation of product radicals.


Asunto(s)
Radical Hidroxilo , Éteres Metílicos , Éteres , Cinética , Oxidación-Reducción
9.
Sci Rep ; 11(1): 4950, 2021 03 02.
Artículo en Inglés | MEDLINE | ID: mdl-33654109

RESUMEN

Density functional theory method combined with docking and molecular dynamics simulations are used to understand the interaction of carmustine with human glutathione reductase enzyme. The active site of the enzyme is evaluated by docking simulation is used for molecular dynamics simulation to deliver the carmustine molecule by (5,5) single walled carbon nanotube (SWCNT). Our model of carmustine in the active site of GR gives a negative binding energy that is further refined by QM/MM study in gas phase and solvent phase to confirm the stability of the drug molecule inside the active site. Once released from SWCNT, carmustine forms multiple polar and non-polar hydrogen bonding interactions with Tyr180, Phe209, Lys318, Ala319, Leu320, Leu321, Ile350, Thr352 and Val354 in the range of 2-4 Å. The SWCNT vehicle itself is held fix at its place due to multiple pi-pi stacking, pi-amide, pi-sigma interactions with the neighboring residues. These interactions in the range of 3-5 Å are crucial in holding the nanotube outside the drug binding region, hence, making an effective delivery. This study can be extended to envisage the potential applications of computational studies in the modification of known drugs to find newer targets and designing new and improved controlled drug delivery systems.


Asunto(s)
Antineoplásicos/química , Sistemas de Liberación de Medicamentos , Glutatión Reductasa/química , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Nanotubos de Carbono/química , Antineoplásicos/uso terapéutico , Glutatión Reductasa/uso terapéutico , Humanos
10.
J Phys Chem B ; 124(30): 6459-6474, 2020 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-32628490

RESUMEN

Density functional theory calculations have been carried out to observe the role of hydrogen bonding in hydrolysis and the coordination mechanism of three amino acid residues (histidine, cysteine, and alanine) with Ru-bis-DMSO complex via which the complex tends to interact with the HSA protein receptor. The interaction mechanism shows that ruthenium complexes prefer to bind protein receptor through cysteine and histidine residues rather than through alanine, which has been confirmed by DFT evaluated H-bonding and g-tensor analysis. The number of H-bonds plays a major role in stabilizing the intermediates and transition states involved in the Ru-bis-DMSO and amino acid residue interactions. Our theoretical g-tensor values are in good agreement with the available experimental results. Further QM/MM calculation on the Ru-bis-DMSO-HSA adducts reveals that the adduct is more stable when Ru gets coordinated with histidine imidazole rather than cysteine. These investigations helped us in understanding the type of amino acid residue responsible for binding the metal complex Ru-bis-DMSO with the carrier protein HSA.


Asunto(s)
Antineoplásicos , Rutenio , Aminoácidos , Dimetilsulfóxido , Humanos , Enlace de Hidrógeno , Albúmina Sérica Humana
11.
Int J Biol Macromol ; 154: 672-682, 2020 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-32198044

RESUMEN

In this study, microcrystalline cellulose (MCC) was isolated from Saccharum spontaneum by integrating alkaline delignification, chlorine-free bleaching, and acid hydrolysis treatments, through an environment friendly and sustainable method. To minimize acid concentrations, the acid hydrolysis conditions were optimized using Taguchi orthogonal L9 design that evaluated the influences of reaction time, temperature, acid concentration and solution to pulp ratio on the physical and chemical characteristics of MCC. The cellulose source at its different stages of processing was submitted to various analytical techniques for morphological and physiochemical investigations. The highest MCC yield optimized was 83%. This process is favorable due to the use of very low (5% H2SO4) acid concentration, low corrosivity, effluent reduction, and cost-effectiveness. Detailed analyses showed that the isolated MCC has good crystallinity and thermal stability and hence expected as a high-value precursor for the production of polymer biocomposites for diverse applications.


Asunto(s)
Celulosa/biosíntesis , Tecnología Química Verde , Saccharum/metabolismo , Hidrólisis
12.
Environ Sci Pollut Res Int ; 27(1): 907-920, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31820248

RESUMEN

To understand the atmospheric chemistry of hydrofluoroethers, we have studied the oxidation of a highly fluorinated compound n-C2F5CF(OCH3)CF(CF3)2 (HFE-7300) by OH/Cl oxidants. Here, we have employed M06-2X functional along with a 6-31 + G(d,p) basis set to obtain the optimized structures, various forms of energies, and different modes of frequencies for all species. We have characterized energies of all species on the potential energy surface, and it indicates that H-abstraction from n-C2F5CF(OCH3)CF(CF3)2 by Cl atom is kinetically more dominant than the H-abstraction reaction initiated by OH radical. In contrast, the calculated energy change (ΔrH°298 and ΔrG°298) results govern that OH-initiated H-abstraction reaction is highly exothermic and spontaneous compared to the Cl-initiated H-abstraction reaction. Rate constants are estimated using transition state theory as well as canonical variation transition state theory at the temperature range 200-1000 K and 1 atm pressure. The calculated rate constants of the H-abstraction channels are found to be in good agreement with the reported experimental rate constant at 298 K. Moreover, we have estimated the atmospheric lifetimes of HFE-7300 for the reaction with OH radical and Cl atom and are found to be 1.75 and 153.93 years, respectively. Additionally, the global warming potentials for HFE-7300 molecule are also estimated for 20-, 100-, and 500-year time horizons. Further, subsequent aerial oxidation of product radical (n-C2F5CF(OCH2)CF(CF3)2) in the presence of NO radical is performed, and it produced alkoxy radical via formation of peroxy radical. This alkoxy radical undergoes unimolecular decompositions via two different ways and formed n-C2F5CF(OCHO)CF(CF3)2 and n-C2F5CF(OH) CF(CF3)2 products.


Asunto(s)
Contaminantes Atmosféricos/química , Éteres/química , Oxidantes/química , Atmósfera/química , Calentamiento Global , Radical Hidroxilo/química , Cinética , Modelos Químicos , Oxidación-Reducción , Termodinámica
13.
Chemphyschem ; 20(5): 680-686, 2019 03 04.
Artículo en Inglés | MEDLINE | ID: mdl-30648792

RESUMEN

Capture of CO2 and its conversion into organic feedstocks are increasingly needed as society moves towards a renewable energy economy. Here, a hydride-assisted selective reduction pathway is proposed for the conversion of CO2 to formic acid (FA) over SnO2 monomers and dimers. Our density functional theory calculations infer a strong chemisorption of CO2 on SnO2 clusters forming a carbonate structure, whereas heterolytic cleavage of H2 provides a new pathway for the selective reduction of CO2 to formic acid at low overpotential. Among the two investigated pathways for reduction of CO2 to HCOOH, the hydride pinning pathway is found promising with a unique selectivity for HCOOH. The negatively-charged hydride forms on the cluster during the dissociation of H2 and facilitates the formation of a formate intermediate, which determines the selectivity for FA over the alternative CO and H2 evolution reaction. It is confirmed that SnO2 clusters exhibit a different catalytic behaviour from their surface equivalents, thus offering promise for future work investigating the reduction of CO2 to FA via a hydride pinning pathway at low overpotential and CO2 capturing.

14.
J Mol Model ; 25(2): 43, 2019 Jan 24.
Artículo en Inglés | MEDLINE | ID: mdl-30675641

RESUMEN

The oxidation of bis(2-chloroethyl) ether (ClCH2CH2OCH2CH2Cl) in the atmosphere, as initiated by various oxidants (OH and NO3 radicals and Cl atoms), was examined using the functional M06-2X in conjunction with the basis set 6-31 + G(d,p). We explored the oxidation pathways and reaction energies (enthalpies and Gibb's free energies) for the abstraction of H from the -CH2Cl and -OCH2 sites of ClCH2CH2OCH2CH2Cl by oxidants. The energy profile shows that H abstraction from the -OCH2 site of the title molecule by each atmospheric oxidant is more likely than H abstraction from the other site. The resulting radical ClCH2C•HOCH2CH2Cl was found to more stable than any other product, as shown by their reaction energies. The rate constants of the oxidation reactions were also calculated using canonical transition state theory in the temperature range 298-400 K. The calculated total rate constant at 298 K is consistent with the reported experimental rate constant. The branching ratio percentages and global atmospheric lifetime of the title molecule are also reported herein.

15.
Environ Sci Pollut Res Int ; 25(26): 26144-26156, 2018 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-29971745

RESUMEN

In the present investigation, the oxidation of HFO-1234yf (2,3,3,3-tetrafluoropropene) with O3 molecule and NO3 radical is studied by quantum chemical methods. The possible reaction pathways of the titled molecule with O3 molecule and NO3 radical are analyzed using M06-2X meta-hybrid density functional with the 6-311++G(d,p) basis set. We have further employed a series of single-point energy calculations by using a potentially high-level couple cluster method with single and double excitations, including perturbative corrections ((CCSD(T)) at the same basis set. The addition reaction of HFO-1234yf with O3 molecule is initiated by the formation of primary ozonide complex, which leads to the formation of various carbonyl compounds and Criegee intermediates. The calculated energy barriers and thermochemical parameters inferred that decomposition of C˙H2OO˙ and CF3CFO is slightly more preferred over the formation of CF3C˙FOO˙ and CH2O. Further, the NO3 radical addition at α- and ß-sits of CF3CF〓CH2 molecule is analyzed in details. The individual and overall rate constants for each reaction pathways are calculated by using canonical transition state theory over the temperature range of 250-450 K. We have observed that the computed rate constants are in good agreement with the available experimental data. Atmospheric lifetimes and global warming potentials of the HFO-1234yf are also reported in this manuscript.


Asunto(s)
Fluorocarburos/química , Calentamiento Global , Nitratos/química , Ozono/química , Cinética , Oxidación-Reducción
16.
Environ Sci Pollut Res Int ; 25(3): 2147-2156, 2018 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-29116529

RESUMEN

Present manuscript represents the DFT studies on the oxidation reaction of camphene initiated by OH radical and fate of product radicals using M06-2X functional along with 6-31+G(d,p) basis set. Intrinsic reaction calculation is done for transition states involving OH-addition reactions which proceed via reaction complexes proceeding to the formation of transition states. The rate constant calculated by using canonical transition state theory at 298 K and 1 atm is found to be 5.67 × 10-11 cm3 molecule-1 s-1 which is in good agreement with the experimental rate constant. The atmospheric lifetime of the titled molecule has also been reported in our work.


Asunto(s)
Radical Hidroxilo/química , Terpenos/química , Contaminación del Aire , Atmósfera , Monoterpenos Bicíclicos , Cinética , Modelos Químicos , Oxidación-Reducción
17.
J Mol Graph Model ; 62: 56-68, 2015 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-26386453

RESUMEN

InhA is an attractive target to combat tuberculosis (TB), which is targeted by many pro-drugs (isoniazid, etc.) and drugs such as triclosan. However, triclosan is less useful as an antitubercular drug due to its low bioavailability and therefore, in order to overcome this difficulty, many derivatives of triclosan were prepared. Here, we have combined various computational techniques to virtually screen out four potential triclosan derivatives. Molecular docking methods have been employed to screen out 32 out of 62 triclosan derivatives considering the mode of binding and the top re-rank scores. A comparative study on the chemical properties of triclosan and some of its derivatives has been performed using density functional theory (DFT) calculations. DFT based global reactivity descriptors (GRD), such as hardness, chemical potential, chemical softness, electrophilicity index, Fukui function, and local philicity calculated at the optimized geometries were used to investigate the usefulness of these descriptors for understanding the reactive nature and sites of the molecules. QSAR equations were built using these descriptors considering these 32 compounds. Four common compounds showing the best correlation and the best docking scores were considered for the ADMET property calculations and their dynamical movements have been studied using molecular dynamics simulations. Our results showed that these four compounds are chemically more active than triclosan and have the potential to inhibit the Mycobacterium tuberculosis enoyl acyl carrier protein reductase. This work shows that combination of different computational techniques may help to screen out potential drug candidates from a list of possible ones.


Asunto(s)
Antituberculosos/química , Proteínas Bacterianas/química , Sitios de Unión , Descubrimiento de Drogas , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , NAD/química , Oxidorreductasas/química , Unión Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Relación Estructura-Actividad Cuantitativa
18.
J Org Chem ; 80(13): 6776-83, 2015 Jul 02.
Artículo en Inglés | MEDLINE | ID: mdl-26036359

RESUMEN

Iron(III)-mediated radical nitration of bisarylsulfonyl hydrazones is described. In this protocol, the nontoxic and inexpensive Fe(NO3)3·9H2O plays a dual role as catalyst as well as nitro source. The mild conditions, broad substrate scope, and the functional group compatibility are the significant features. The reaction pathway has been demonstrated using DFT calculations, and the products can be subsequently converted into oximes using SnCl2·2H2O in high yields.

19.
J Mol Model ; 21(4): 69, 2015 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-25750024

RESUMEN

In the present work, theoretical study on the mechanism and kinetics of the gas-phase reactions of CF3CF2CH2OCH3 (HFE-365mcf3) with the OH radicals have been performed using meta-hybrid modern density functional M06-2X in conjunction with 6-31+G(d,p) basis set. Reaction profiles for OH-initiated hydrogen abstraction are modeled including the formation of pre-reactive and post-reactive complexes at entrance and exit channels. Our calculations reveal that hydrogen abstraction from the -CH2 group is thermodynamically more facile than that from the -CH3 group. This is further ascertained by the calculated C-H bond dissociation energy of CF3CF2CH2OCH3 molecule. The rate constants of the titled reactions are computed over the temperature range of 250-450 K. The calculated rate constant value at 298 K is found to be in reasonable agreement with the experimental results. The atmospheric life time of HFE-365mcf3 is estimated to be 42 days. The atmospheric fate of the alkoxy radicals, CF3CF2CH(O(•))OCH3 and CF3CF2CH2OCH2O(•) are also investigated for the first time using the same level of theory. Out of three plausible decomposition channels, our results clearly point out that reaction with O2 is the dominant atmospheric sink for the decomposition of CF3CF2CH(O(•))OCH3 radical in the atmosphere.

20.
J Phys Chem A ; 118(38): 8779-86, 2014 Sep 25.
Artículo en Inglés | MEDLINE | ID: mdl-25170971

RESUMEN

We theoretically investigated OH-initiated hydrogen abstraction reactions of methyl fluoroacetate (MFA) CH2FC(O)OCH3 at the MPWB1K level of theory in conjunction with the 6-31+G(d,p) basis set. Thermodynamic and kinetic data are computed using the comparatively accurate G2(MP2) method. Two most stable conformers of MFA are identified, and the energy difference between them is found to be only 0.32 kcal mol(-1). Both of them are considered for rate coefficient calculations, and the contribution from each of the conformers is found to be quite significant. We propose an indirect mechanism due to validation of pre- and post-reactive complexes. The rate parameters are determined using canonical transition state theory and energetics at the G2(MP2) level. The temperature dependence of the rate constant can be described by the Arrhenius expressions: k = 8.79 × 10(-13) exp[(-377.27 ± 64)/T] cm(3) molecule(-1) s(-1) over a temperature range of 250-450 K. The ΔfH°298 for CH2FC(O)OCH3, CH2FC(O)OC(•)H2, and C(•)HFC(O)OCH3 are also computed using an isodesmic procedure. The OH-driven atmospheric lifetime of MFA was estimated to be 24 days. A mechanistic study to shed light on the atmospheric degradation and the sole fate for the consumption of CH2FC(O)OCH2O(•) radical has also been reported.

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