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1.
Environ Sci Technol ; 58(14): 6425-6434, 2024 Apr 09.
Artículo en Inglés | MEDLINE | ID: mdl-38554136

RESUMEN

Hydrated electron (eaq-) treatment processes show great potential in remediating recalcitrant water contaminants, including perfluoroalkyl and polyfluoroalkyl substances (PFAS). However, treatment efficacy depends upon many factors relating to source water composition, UV light source characteristics, and contaminant reactivity. Here, we provide critical insights into the complex roles of solution parameters on contaminant abatement through application of a UV-sulfite kinetic model that incorporates first-principles information on eaq- photogeneration and reactivity. The model accurately predicts decay profiles of short-chain perfluoroalkyl acids (PFAAs) during UV-sulfite treatment and facilitates quantitative interpretation of the effects of changing solution composition on PFAS degradation rates. Model results also confirm that the enhanced degradation of PFAAs observed under highly alkaline pH conditions results from changes in speciation of nontarget eaq- scavengers. Reverse application of the model to UV-sulfite data collected for longer chain PFAAs enabled estimation of bimolecular rate constants (k2, M-1 s-1), providing an alternative to laser flash photolysis (LFP) measurements that are not feasible due to the water solubility limitations of these compounds. The proposed model links the disparate means of investigating eaq- processes, namely, UV photolysis and LFP, and provides a framework to estimate UV-sulfite treatment efficacy of PFAS in diverse water sources.


Asunto(s)
Fluorocarburos , Contaminantes Químicos del Agua , Rayos Ultravioleta , Contaminantes Químicos del Agua/análisis , Sulfitos/química , Agua/química
2.
Environ Sci Technol ; 57(20): 7849-7857, 2023 05 23.
Artículo en Inglés | MEDLINE | ID: mdl-37170785

RESUMEN

Advanced reduction processes (ARPs) that generate hydrated electrons (eaq-; e.g., UV-sulfite) have emerged as a promising remediation technology for recalcitrant water contaminants, including per- and polyfluoroalkyl substances (PFASs). The effectiveness of ARPs in different natural water matrices is determined, in large part, by the presence of non-target water constituents that act to quench eaq- or shield incoming UV photons from the applied photosensitizer. This study examined the pH-dependent quenching of eaq- by ubiquitous dissolved carbonate species (H2CO3*, HCO3-, and CO32-) and quantified the relative importance of carbonate species to other abundant quenching agents (e.g., H2O, H+, HSO3-, and O2(aq)) during ARP applications. Analysis of laser flash photolysis kinetic data in relation to pH-dependent carbonate acid-base speciation yields species-specific bimolecular rate constants for eaq- quenching by H2CO3*, HCO3-, and CO32- (kH2CO3* = 2.23 ± 0.42 × 109 M-1 s-1, kHCO3- = 2.18 ± 0.73 × 106 M-1 s-1, and kCO32- = 1.05 ± 0.61 × 105 M-1 s-1), with quenching dominated by H2CO3* (which includes both CO2(aq) and H2CO3) at moderately alkaline pH conditions despite it being the minor species. Attempts to apply previously reported rate constants for eaq- quenching by CO2(aq), measured in acidic solutions equilibrated with CO2(g), overpredict quenching observed in this study at higher pH conditions typical of ARP applications. Moreover, kinetic simulations reveal that pH-dependent trends reported for UV-sulfite ARPs that have often been attributed to eaq- quenching by varying [H+] can instead be ascribed to variable acid-base speciation of dissolved carbonate and the sulfite sensitizer.


Asunto(s)
Electrones , Contaminantes Químicos del Agua , Contaminantes Químicos del Agua/análisis , Sulfitos/química , Carbonatos , Agua/química
3.
J Comput Chem ; 43(20): 1355-1361, 2022 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-35665946

RESUMEN

Per- and polyfluoroalkyl substances (PFAS) are robust "forever" chemicals that have become global environmental contaminants due to their inability to degrade using traditional techniques. In addition to the persistent nature of PFAS, the structural and functional diversity in PFAS creates a unique challenge in identification and remediation. Their identification is further complicated by the absence of standards for many PFAS. This work is aimed at developing a protocol for computing and establishing accurate 19 F NMR chemical shifts for PFAS using density functional theory (DFT), which can aid in the identification of PFAS. The impact of solvation and basis sets was evaluated by comparing the computed data with the experimental measurements. Results showed the addition of dispersion corrections in the methodology improve the accuracy of calculated NMR parameters within 4 ppm of the experimental values. Adding a second diffuse function and additional polarization did not improve the accuracy, likely because of the electronegativity of fluorine which does not allow the electron density of fluorine atoms to be polarized. The inclusion of various implicit solvation (DMSO, chloroform, and water) yielded negligible differences in accuracy, and were overall less accurate than the gas phase calculations. The most accurate methodology was then applied to more environmentally relevant PFAS, and the impact of helical nature on the NMR signatures was evaluated. The implication of this work is to be able to improve the identification of structurally diverse PFAS using the 19 F NMR.


Asunto(s)
Flúor , Fluorocarburos , Flúor/química , Espectroscopía de Resonancia Magnética/métodos
4.
J Comput Chem ; 43(24): 1656-1661, 2022 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-35869846

RESUMEN

Per- and polyfluoroalkyl substances (PFAS) have been widely used the past 70 years in numerous applications due to their chemical and thermal stability. Due to their robust stability, they are environmentally recalcitrant which made them one of the most persistent environmental contaminants. In addition to strong CF bond strength, oleophobicity, hydrophobicity, and high reduction-oxidation (redox) potential of PFAS has led to their inefficient degradation by traditional means. A characteristic of their structure is also their preference to adopt helical conformations along the carbon backbone, contrary to their hydrocarbon analogues. This work investigates the helical nature of perfluoroalkanes through their conformational distributions, especially as a benchmark for determining the impact of polar head groups, heteroatoms, and radical center on helical conformations. Since structure governs reactivity and molecular properties, it is important to assess if minor chemical perturbations in the structure will lead to changes in the conformations. Based on density functional theory calculations and comprehensive conformational distributions, it was concluded that the helicity is a local structural property which changes significantly with the presence of heteroatoms in the perfluoroalkyl chain as well as with the presence of radical centers.


Asunto(s)
Fluorocarburos , Fluorocarburos/química , Conformación Molecular
5.
Org Biomol Chem ; 20(5): 995-999, 2022 02 02.
Artículo en Inglés | MEDLINE | ID: mdl-35029270

RESUMEN

Reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) and peroxynitrite (ONOO-) oxidize arylboronic acids to their corresponding phenols. When used in molecular imaging probes and in ROS-responsive molecules, however, simple arylboronic acids struggle to discriminate between H2O2 and ONOO- because of their fast rate of reaction with both ROS. Here, we show that diazaborines (DABs) react slowly with H2O2 but rapidly with peroxynitrite in an aqueous buffer. In addition to their slow reaction with H2O2, the immediate product of DAB oxidation with H2O2 and ONOO- can yield a kinetically trapped CN Z-isomer that slowly equilibrates with its E-isomer. Taken together, our work shows that diazaborines exhibit enhanced kinetic discrimination between H2O2 and ONOO- compared to arylboronic acids, opening up new opportunities for diazaborine-based tools in chemical biology.


Asunto(s)
Compuestos Azo/química , Ácidos Borónicos/química , Peróxido de Hidrógeno/química , Ácido Peroxinitroso/química , Oxidación-Reducción , Estereoisomerismo
6.
J Phys Chem A ; 126(8): 1422-1428, 2022 Mar 03.
Artículo en Inglés | MEDLINE | ID: mdl-35171595

RESUMEN

Sulfate radical anion (SO4•-) is a potent oxidant capable of destroying recalcitrant environmental contaminants such as perfluoroalkyl carboxylic acids. In addition, it is thought to participate in important atmospheric reactions. Its standard reduction potential (E°) is fundamental to its reactivity. Using theoretical methods to accurately predict the aqueous phase E° requires solvation with explicit water molecules. Herein, using density functional theory, we calculated the aqueous E° of SO4•- and evaluated sensitivity to explicit water count. The E° increased considerably with more waters until ca. 24 were included, after which change in E° was small. When a proton was added to these systems, the E° was similar regardless of the explicit water count and this value was similar to the E° for systems with a large number of explicit waters but no proton. This result agrees with literature evidence that the E° is pH independent. Natural Bond Orbital natural population analysis indicated that in the case of both SO42- and SO4•-, considerable charge was donated from the SO4 center to the explicit solvation shells.


Asunto(s)
Agua , Aniones , Concentración de Iones de Hidrógeno , Oxidación-Reducción , Sulfatos , Agua/química
7.
J Org Chem ; 86(21): 14553-14562, 2021 11 05.
Artículo en Inglés | MEDLINE | ID: mdl-34582209

RESUMEN

Alloxan is an important toxic glucose analogue used to induce diabetes in lab test animals. Once regarded as a "problem structure," the condensed-phase structure of anhydrous alloxan has largely been settled, but literature inconsistencies remain for the structure of the typically employed reagent alloxan monohydrate. Due to the criticality of structure-function relationships, we have used 1H/13C{1H} NMR, IR spectroscopy, as well as quantum mechanical (QM) calculations to probe the liquid-phase structure and reactivity of alloxan monohydrate. In protic solvents (D2O and acetic acid-d4), hydration at the C5 carbonyl of alloxan monohydrate occurs quantitatively to form the C5 gem-diol (5,5'-dihydroxybarbituric acid). In the aprotic solvent dimethyl sulfoxide (DMSO)-d6, there exists a mixture of the C5 gem-diol and planar tetraketo form of alloxan monohydrate. QM calculations explain the solvent-dependent hydration reactivity, where a solvent-assisted H-atom transfer mechanism lowers the activation energy of water addition at the C5 carbonyl by ∼16 or 27 kcal/mol in water or acetic acid, respectively, compared to the unassisted hydration reaction. Prompt recrystallization of alloxan monohydrate from boiling water does not alter the structure of the reagent. These findings probe the exact structure of alloxan monohydrate to guide future research efforts in biological sciences and in organic synthesis.


Asunto(s)
Aloxano , Agua , Animales , Dimetilsulfóxido , Solventes , Termodinámica
8.
Environ Sci Technol ; 55(13): 8928-8936, 2021 07 06.
Artículo en Inglés | MEDLINE | ID: mdl-34170127

RESUMEN

Perfluoroalkyl carboxylic acids (PFCAs) are ubiquitous contaminants known for their bioaccumulation, toxicological harm, and resistance to degradation. Remediating PFCAs in water is an ongoing challenge with existing technologies being insufficient or requiring additional disposal. An emergent approach is using activated persulfate, which degrades PFCAs through sequential scission of CF2 equivalents yielding shorter-chain homologues, CO2 and F-. This transformation is thought to be initiated by single electron transfer (SET) from the PFCA to the activate oxidant, SO4•-. A pronounced pH effect has been observed for thermally activated persulfate PFCA transformation. To evaluate the role of pH during SET, we directly determined absolute rate constants for perfluorobutanoic acid and trifluoroacetic acid oxidation by SO4•- in the pH range of 0.5-4.0 using laser flash photolysis. The average of the rate constants for both substrates across all pH values was 9 ± 2 × 103 M-1 s-1 (±2σ), implying that acid catalysis of thermal persulfate activation may be the primary culprit of the observed pH effect, instead of pH influencing the SET step. In addition, density functional theory was used to investigate if SO4•-protonation might enhance PFCA transformation kinetics. We found that when calculations include explicit water molecules, direct SO4•- protonation does not occur.


Asunto(s)
Fluorocarburos , Contaminantes Químicos del Agua , Ácidos Carboxílicos , Electrones , Concentración de Iones de Hidrógeno , Oxidación-Reducción , Sulfatos , Contaminantes Químicos del Agua/análisis
9.
Org Biomol Chem ; 18(44): 9044-9049, 2020 11 28.
Artículo en Inglés | MEDLINE | ID: mdl-33150911

RESUMEN

A synthetic method towards fluorinated allylamines using allene precursors is reported. A variety of heterocyclic amines were employed as nucleophiles in a Selectfluor promoted intermolecular fluoroamination reaction. This strategy provides a novel synthetic route to access vinyl fluorides with a vicinal amine moiety.

10.
J Phys Chem A ; 124(21): 4193-4201, 2020 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-32337990

RESUMEN

Flavins are a diverse set of compounds with a wide variety of biological and nonbiological applications. Applications of flavins receiving attention recently consist of electro- and photocatalytic oxidation of substrates for organic synthesis, bioengineered nanotechnology, and water splitting catalysts, among others. While there is vast knowledge regarding the structure-property relationships of flavins and their electrochemistry, there is much less work elucidating the structure property relationships as they pertain to flavinium photochemistry. Herein, we report the effect of molecular tailoring on the molecular properties of N(5)-ethyl-flavinium cation (Et-Fl+), a derivative of the biocatalytic coenzyme riboflavin, by incorporating electron withdrawing and donating groups at the C7 and C8 position of the isoalloxazine ring. The presence of electron withdrawing groups at the C8 position caused a red shift in the absorption spectrum, while the electron donating groups caused a blue shift. Functionalization at the C7 position had the opposite effect on the absorption spectrum. The effects of single substitution were relatively negated with simultaneous functionalization at both the C8 and C7 positions. Difference density plots indicate no change in the nature of the S1 excited state, which was confirmed by optimization of the excited state geometries. The results presented in this study indicate that functionalization of the isoalloxazine unit affects the photophysical properties of N(5)-ethyl-flavinium cations.

11.
J Phys Chem A ; 124(21): 4290-4304, 2020 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-32364731

RESUMEN

Sooting tendencies of a series of nitrogen-containing hydrocarbons (NHCs) have been recently characterized experimentally using the yield sooting index (YSI) methodology. This work aims to identify soot-relevant reaction pathways for three selected C6H15N amines, namely, dipropylamine (DPA), diisopropylamine (DIPA), and 3,3-dimethylbutylamine (DMBA) using ReaxFF molecular dynamics (MD) simulations and quantum mechanical (QM) calculations and to interpret the experimentally observed trends. ReaxFF MD simulations are performed to determine the important intermediate species and radicals involved in the fuel decomposition and soot formation processes. QM calculations are employed to extensively search for chemical reactions involving these species and radicals based on the ReaxFF MD results and also to quantitatively characterize the potential energy surfaces. Specifically, ReaxFF simulations are carried out in the NVT ensemble at 1400, 1600, and 1800 K, where soot has been identified to form in the YSI experiment. These simulations account for the interactions among test fuel molecules and pre-existing radicals and intermediate species generated from rich methane combustion, using a recently proposed simulation framework. ReaxFF simulations predict that the reactivity of the amines decrease in the order DIPA > DPA > DMBA, independent of temperature. Both QM calculations and ReaxFF simulations predict that C2H4, C3H6, and C4H8 are the main nonaromatic soot precursors formed during the decomposition of DPA, DIPA, and DMBA, respectively, and the associated reaction pathways are identified for each amine. Both theoretical methods predict that sooting tendency increases in the order DPA, DIPA, and DMBA, consistent with the experimentally measured trend in YSI. This work demonstrates that sooting tendencies and soot-relevant reaction pathways of fuels with unknown chemical kinetics can be identified efficiently through combined ReaxFF and QM simulations. Overall, predictions from ReaxFF simulations and QM calculations are consistent, in terms of fuel reactivity, major intermediates, and major nonaromatic soot precursors.

12.
Chemistry ; 25(21): 5337-5371, 2019 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-30444932

RESUMEN

Organophosphorus (OP) nerve agents and pesticides present significant threats to civilian and military populations. OP compounds include the nefarious G and V chemical nerve agents, but more commonly, civilians are exposed to less toxic OP pesticides, resulting in the same negative toxicological effects and thousands of deaths on an annual basis. After decades of research, no new therapeutics have been realized since the mid-1900s. Upon phosphylation of the catalytic serine residue, a process known as inhibition, there is an accumulation of acetylcholine (ACh) in the brain synapses and neuromuscular junctions, leading to a cholinergic crisis and eventually death. Oxime nucleophiles can reactivate select OP-inhibited acetylcholinesterase (AChE). Yet, the fields of reactivation of AChE and butyrylcholinesterase encounter additional challenges as broad-spectrum reactivation of either enzyme is difficult. Additional problems include the ability to cross the blood brain barrier (BBB) and to provide therapy in the central nervous system. Yet another complication arises in a competitive reaction, known as aging, whereby OP-inhibited AChE is converted to an inactive form, which until very recently, had been impossible to reverse to an active, functional form. Evaluations of uncharged oximes and other neutral nucleophiles have been made. Non-oxime reactivators, such as aromatic general bases and Mannich bases, have been developed. The issue of aging, which generates an anionic phosphylated serine residue, has been historically recalcitrant to recovery by any therapeutic approach-that is, until earlier this year. Mannich bases not only serve as reactivators of OP-inhibited AChE, but this class of compounds can also recover activity from the aged form of AChE, a process referred to as resurrection. This review covers the modern efforts to address all of these issues and notes the complexities of therapeutic development along these different lines of research.


Asunto(s)
Acetilcolinesterasa/metabolismo , Butirilcolinesterasa/metabolismo , Inhibidores de la Colinesterasa/metabolismo , Reactivadores de la Colinesterasa/metabolismo , Acetilcolinesterasa/química , Barrera Hematoencefálica/metabolismo , Butirilcolinesterasa/química , Inhibidores de la Colinesterasa/química , Reactivadores de la Colinesterasa/química , Humanos , Agentes Nerviosos/química , Agentes Nerviosos/metabolismo , Oximas/química , Oximas/metabolismo , Plaguicidas/química , Plaguicidas/metabolismo
13.
J Phys Chem A ; 123(2): 492-504, 2019 Jan 17.
Artículo en Inglés | MEDLINE | ID: mdl-30512957

RESUMEN

The rate constants for solvent-assisted 1,2-H atom rearrangements in para-substituted benzyloxyl radicals were studied with density functional theory. The rate of the radical rearrangement, calculated through transition state theory with Eckhart tunneling corrections, was shown to be drastically impacted by the presence of both implicit and explicit solvent molecules, with a quantitative agreement with laser flash photolysis studies for a variety of electron-donating and -withdrawing substituents. The rate of rearrangement was found to be correlated to the distance between the rearranging hydrogen atom and the α-carbon in the transition state, which could be modified through the para substituent and the type of assisting solvent molecule (e.g., water, ethanol, methanol, acetic acid, or a mixture of the latter). Natural bond orbital analysis showed that the rearrangement does not proceed through a hydrogen radical but through a quasi-proton exchange and charge transfer between the benzyl carbon and the adjacent oxygen atom. Energetic and spin population results indicated that electron-withdrawing groups induce faster rearrangement kinetics. Understanding 1,2-H atom shifts in benzyloxyl radicals are essential for tuning the rate of superoxide production in aqueous systems, as the resonance-stabilized carbon radical produced from the rearrangement can bind oxygen and decompose to produce superoxide radical anion, an important reactive intermediate in environmental and biological systems.

14.
Phys Chem Chem Phys ; 20(14): 9671, 2018 04 04.
Artículo en Inglés | MEDLINE | ID: mdl-29616253

RESUMEN

Correction for 'Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism - a gas-phase ab initio study' by Vivek S. Bharadwaj et al., Phys. Chem. Chem. Phys., 2015, 17, 4054-4066.

15.
J Org Chem ; 82(11): 5731-5742, 2017 06 02.
Artículo en Inglés | MEDLINE | ID: mdl-28493696

RESUMEN

Resonantly stabilized radicals are some of the most investigated chemical species due to their preferential formation in a wide variety of chemical environments. Density functional theory and post-Hartree-Fock calculations were utilized to elucidate the chemical interactions that contribute to the stability of two ubiquitous, resonantly stabilized radicals, allyl and benzyl radicals. The relative stability of these radical species was quantified through bond dissociation energies and relative rotational energy barriers, with a difference of only 0.1 kcal/mol. To clarify and contextualize the energetic results, natural bond orbitals were used to evaluate the atomic spin density distribution in the given molecules. The benzyl radical was found to be ∼3 kcal/mol less stable than the allyl radical, which was attributed to the inability to efficiently delocalize the spin on a phenyl unit, starkly contrary to general chemistry knowledge. Increasing the degree of π-conjugation and hyperconjugation was shown to benefit allyl radicals to a greater degree than benzyl radicals, again due to more efficient radical delocalization in allyl radicals. This work highlights that more resonance structures do not always lead to a more stabilized radical species, and provides fundamental knowledge about how conjugation and hyperconjugation impact the stabilization of nonbonding electrons in these systems.

16.
J Org Chem ; 82(13): 6578-6585, 2017 07 07.
Artículo en Inglés | MEDLINE | ID: mdl-28548848

RESUMEN

Perfluorocyclobutyl polymers are thermally and chemically stable, may be produced without a catalyst via thermal 2π-2π cycloaddition, and can form block structures, making them suitable for commercialization of specialty polymers. Thermal 2π-2π cycloaddition is a rare reaction that begins in the singlet state and proceeds through a triplet intermediate to form an energetically stable four-membered ring in the singlet state. This reaction involves two changes in spin state and, thus, two spin-crossover transitions. Presented here are density functional theory calculations that evaluate the energetics and reaction mechanisms for the dimerizations of two different polyfluorinated precursors, 1,1,2-trifluoro-2-(trifluoromethoxy)ethane and hexafluoropropylene. The spin-crossover transition states are thoroughly investigated, revealing important kinetics steps and an activation energy for the gas-phase cycloaddition of two hexafluoropropene molecules of 36.9 kcal/mol, which is in good agreement with the experimentally determined value of 34.3 kcal/mol. It is found that the first carbon-carbon bond formation is the rate-limiting step, followed by a rotation about the newly formed bond in the triplet state that results in the formation of the second carbon-carbon bond. Targeting the rotation of the C-C bond, a set of parameters were obtained that best produce high molecular weight polymers using this chemistry.

17.
J Phys Chem A ; 121(45): 8675-8687, 2017 Nov 16.
Artículo en Inglés | MEDLINE | ID: mdl-29039951

RESUMEN

Devising effective degradation technologies for perfluoroalkyl substances (PFASs) is an active area of research, where the molecular mechanisms involving both oxidative and reductive pathways are still elusive. One commonly neglected pathway in PFAS degradation is fluorine atom migration in perfluoroalkyl radicals, which was largely assumed to be implausible because of the high C-F bond strength. Using density functional theory calculations, it was demonstrated that 1,2-F atom migrations are thermodynamically favored when the fluorine atom migrated from a less branched carbon center to a more branched carbon center. Activation barriers for these rearrangements were within 19-29 kcal/mol, which are possible to easily overcome at elevated temperatures or in photochemically activated species in the gas or aqueous phase. It was also found that the activation barriers for the 1,2-F atom migration are lowered as much as by 10 kcal/mol when common oxidative degradation products such as HF assisted the rearrangements or if the resulting radical center was stabilized by vicinal π-bonds. Natural bond orbital analyses showed that fluorine moves as a radical in a noncharge-separated state. These findings add an important reaction to the existing knowledge of mechanisms for PFAS degradation and highlights the fact that 1,2-F atom shifts may be a small channel for isomerization of these compounds, but upon availability of mineralization products, this isomerization process could become more prominent.

18.
Phys Chem Chem Phys ; 17(6): 4054-66, 2015 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-25566585

RESUMEN

The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter-molecular non-covalent interactions.


Asunto(s)
Butanos/química , Fumaratos/química , Tolueno/química , Biocatálisis , Enzimas/química , Radicales Libres/química , Cinética , Teoría Cuántica , Estereoisomerismo , Succinatos/química , Temperatura , Termodinámica
19.
J Biol Chem ; 288(9): 6498-510, 2013 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-23322772

RESUMEN

Vaccinia VH1-related (VHR) is a dual specificity phosphatase that consists of only a single catalytic domain. Although several protein substrates have been identified for VHR, the elements that control the in vivo substrate specificity of this enzyme remain unclear. In this work, the in vitro substrate specificity of VHR was systematically profiled by screening combinatorial peptide libraries. VHR exhibits more stringent substrate specificity than classical protein-tyrosine phosphatases and recognizes two distinct classes of Tyr(P) peptides. The class I substrates are similar to the Tyr(P) motifs derived from the VHR protein substrates, having sequences of (D/E/ϕ)(D/S/N/T/E)(P/I/M/S/A/V)pY(G/A/S/Q) or (D/E/ϕ)(T/S)(D/E)pY(G/A/S/Q) (where ϕ is a hydrophobic amino acid and pY is phosphotyrosine). The class II substrates have the consensus sequence of (V/A)P(I/L/M/V/F)X1-6pY (where X is any amino acid) with V/A preferably at the N terminus of the peptide. Site-directed mutagenesis and molecular modeling studies suggest that the class II peptides bind to VHR in an opposite orientation relative to the canonical binding mode of the class I substrates. In this alternative binding mode, the Tyr(P) side chain binds to the active site pocket, but the N terminus of the peptide interacts with the carboxylate side chain of Asp(164), which normally interacts with the Tyr(P) + 3 residue of a class I substrate. Proteins containing the class II motifs are efficient VHR substrates in vitro, suggesting that VHR may act on a novel class of yet unidentified Tyr(P) proteins in vivo.


Asunto(s)
Fosfatasa 3 de Especificidad Dual/química , Secuencias de Aminoácidos , Fosfatasa 3 de Especificidad Dual/genética , Fosfatasa 3 de Especificidad Dual/metabolismo , Humanos , Mutagénesis Sitio-Dirigida , Biblioteca de Péptidos , Unión Proteica , Especificidad por Sustrato/fisiología
20.
J Phys Chem A ; 118(34): 6873-82, 2014 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-25083824

RESUMEN

Electronic and structural properties of the room temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulonyl)imide are studied using density functional theory (DFT) methods in addition to infrared and UV-vis spectroscopy. The DFT methods were conducted for both gas phase and solution phase using the integral equation formalism polarizable continuum model, while optical absorption experiments were conducted using neat and dilute methanol solutions. Three energetically similar conformers were obtained for each of the gas phase and solution phase DFT calculations. These multiple configurations were considered when analyzing the molecular interactions between the ion pair and for a molecular-level interpretation of the experimental IR and UV-vis spectroscopy data. Excitation energies of low-lying singlet excited states of the conformers were calculated with time-dependent DFT and experimentally with UV-vis absorption spectra. Difference density plots and excited-state calculations in the gas phase are found to be in good agreement with the experimental findings, while the implicit solvation model calculations adversely impacted the accuracy of the predicted spectra.

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