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1.
J Phys Chem A ; 128(23): 4595-4604, 2024 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-38775015

RESUMO

This study uses computational means to explore the feasibility of N2 cleavage by frustrated Lewis pair (FLPs) species. The employed FLP systems are phosphane/borane (1) and carbene/borane (2). Previous studies show that 1 and 2 react with H2 and CO2 but do not activate N2. The present study demonstrates that N2 is indeed inert, and its activation requires augmentation of the FLPs by an external tool. As we demonstrate here, FLP-mediated N2 activation can be achieved by an external electric field oriented along the reaction axis of the FLP. Additionally, the study demonstrates that FLP -N2 activation generates useful nitrogen compound, e.g., hydrazine (H2N-NH2). In summary, we conclude that FLP effectively activates N2 in tandem with oriented external electric fields (OEEFs), which play a crucial role. This FLP/OEEF combination may serve as a general activator of inert molecules.

2.
Angew Chem Int Ed Engl ; 63(14): e202318629, 2024 04 02.
Artigo em Inglês | MEDLINE | ID: mdl-38299700

RESUMO

Flavoenzymes can mediate a large variety of oxidation reactions through the activation of oxygen. However, the O2 activation chemistry of flavin enzymes is not yet fully exploited. Normally, the O2 activation occurs at the C4a site of the flavin cofactor, yielding the flavin C4a-(hydro)hydroperoxyl species in monooxygenases or oxidases. Using extensive MD simulations, QM/MM calculations and QM calculations, our studies reveal the formation of the common nucleophilic species, Flavin-N5OOH, in two distinct flavoenzymes (RutA and EncM). Our studies show that Flavin-N5OOH acts as a powerful nucleophile that promotes C-N cleavage of uracil in RutA, and a powerful base in the deprotonation of substrates in EncM. We reason that Flavin-N5OOH can be a common reactive species in the superfamily of flavoenzymes, which accomplish generally selective general base catalysis and C-X (X=N, S, Cl, O) cleavage reactions that are otherwise challenging with solvated hydroxide ion base. These results expand our understanding of the chemistry and catalysis of flavoenzymes.


Assuntos
Flavinas , Oxigenases de Função Mista , Flavinas/metabolismo , Oxigenases de Função Mista/metabolismo , Oxirredução , Oxirredutases , Compostos Orgânicos
3.
J Am Chem Soc ; 145(36): 20132-20140, 2023 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-37664980

RESUMO

This paper describes the nature of the hydrogen bond (HB), B:---H-A, using valence bond theory (VBT). Our analysis shows that the most important HB interactions are polarization and charge transfer, and their corresponding sum displays a pattern that is identical for a variety of energy decomposition analysis (EDA) methods. Furthermore, the sum terms obtained with the different EDA methods correlate linearly with the corresponding VB quantities. The VBT analysis demonstrates that the total covalent-ionic resonance energy (RECS) of the HB portion (B---H in B:---H-A) correlates linearly with the dissociation energy of the HB, ΔEdiss. In principle, therefore, RECS(HB) can be determined by experiment. The VBT wavefunction reveals that the contributions of ionic structures to the HB increase the positive charge on the hydrogen of the corresponding external/free O-H bonds in, for example, the water dimer compared with a free water molecule. This increases the electric field of the external O-H bonds of water clusters and contributes to bringing about catalysis of reactions by water droplets and in water-hydrophobic interfaces.

4.
J Am Chem Soc ; 145(6): 3543-3553, 2023 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-36735972

RESUMO

Alzheimer's disease is one of the most common neurodegenerative conditions, which are ascribed to extracellular accumulation of ß-amyloid peptides into plaques. This phenomenon seems to typify other related neurodegenerative diseases. The present study uses classical molecular-dynamics simulations to decipher the aggregation-disintegration behavior of ß-amyloid peptide plaques in the presence of static and oscillating oriented external electric fields (OEEFs). A long-term disintegration of such plaques is highly desirable since this may improve the prospects of therapeutic treatments of Alzheimer's disease and of other neurodegenerative diseases typified by senile plaques. Our study illustrates the spontaneous aggregation of the ß-amyloid, its prevention and breakdown when OEEF is applied, and the fate of the broken aggregate when the OEEF is removed. Notably, we demonstrate that the usage of an oscillating OEEF on ß-amyloid aggregates appears to lead to an irreversible disintegration. Insight is provided into the root causes of the various modes of aggregation, as well as into the different fates of OEEF-induced disintegration in oscillating vs static fields. Finally, our simulation results are compared to the well-established TTFields and the Deep Brain Stimulation (DBS) therapies, which are currently used options for treatments of Alzheimer's disease and other related neurodegenerative diseases.


Assuntos
Doença de Alzheimer , Doenças Neurodegenerativas , Humanos , Doença de Alzheimer/metabolismo , Placa Amiloide/terapia , Peptídeos beta-Amiloides/metabolismo , Doenças Neurodegenerativas/tratamento farmacológico , Simulação de Dinâmica Molecular
5.
J Am Chem Soc ; 145(34): 18904-18911, 2023 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-37602827

RESUMO

This work reports that the octahedral hydrated Al3+ and Mg2+ ions operate within electrolytic cells as kosmotropic (long-range order-making) "ice makers" of supercooled water (SCW). 10-5 M solutions of hydrated Al3+ and Mg2+ ions each trigger, near the cathode (-20 ± 5 V), electro-freezing of SCW at -4 °C. The hydrated Al3+ ions do so with 100% efficiency, whereas the Mg2+ ions induce icing with 40% efficiency. In contrast, hydrated Na+ ions, under the same experimental conditions, do not induce icing differently than pure water. As such, our study shows that the role played by Al3+ and Mg2+ ions in water electro-freezing is impacted by two synchronous effects: (1) a geometric effect due to the octahedral packing of the coordinated water molecules around the metallic ions, and (2) the degree of polarization which these two ions induce and thereby acidify the coordinated water molecules, which in turn imparts them with an ice-like structure. Long-duration molecular dynamics (MD) simulations of the Al3+ and Mg2+ indeed reveal the formation of "ice-like" hexagons in the vicinity of these ions. Furthermore, the MD shows that these hexagons and the electric fields of the coordinate water molecules give rise to ultimate icing. As such, the MD simulations provide a rational explanation for the order-making properties of these ions during electro-freezing.

6.
J Am Chem Soc ; 145(13): 7252-7267, 2023 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-36943409

RESUMO

P450 TleB catalyzes the oxidative cyclization of the dipeptide N-methylvalyl-tryptophanol into indolactam V through selective intramolecular C-H bond amination at the indole C4 position. Understanding its catalytic mechanism is instrumental for the engineering or design of P450-catalyzed C-H amination reactions. Using multiscale computational methods, we show that the reaction proceeds through a diradical pathway, involving a hydrogen atom transfer (HAT) from N1-H to Cpd I, a conformational transformation of the substrate radical species, and a second HAT from N13-H to Cpd II. Intriguingly, the conformational transformation is found to be the key to enabling efficient and selective C-N coupling between N13 and C4 in the subsequent diradical coupling reaction. The underlined conformational transformation is triggered by the first HAT, which proceeds with an energy-demanding indole ring flip and is followed by the facile approach of the N13-H group to Cpd II. Detailed analysis shows that the internal electric field (IEF) from the protein environment plays key roles in the transformation process, which not only provides the driving force but also stabilizes the flipped conformation of the indole radical. Our simulations provide a clear picture of how the P450 enzyme can smartly modulate the selective C-N coupling reaction. The present findings are in line with all available experimental data, highlighting the crucial role of substrate dynamics in controlling this highly valuable reaction.


Assuntos
Sistema Enzimático do Citocromo P-450 , Simulação de Dinâmica Molecular , Sistema Enzimático do Citocromo P-450/metabolismo , Conformação Molecular , Oxirredução , Indóis
7.
Acc Chem Res ; 55(16): 2280-2290, 2022 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-35926175

RESUMO

This Account describes the manner whereby nature controls the Fenton-type reaction of O-O homolysis of hydrogen peroxide and harnesses it to carry out various useful oxidative transformations in metalloenzymes. H2O2 acts as the cosubstrate for the heme-dependent peroxidases, P450BM3, P450SPα, P450BSß, and the P450 decarboxylase OleT, as well as the nonheme enzymes HppE and the copper-dependent lytic polysaccharide monooxygenases (LPMOs). Whereas heme peroxidases use the Poulos-Kraut heterolytic mechanism for H2O2 activation, some heme enzymes prefer the alternative Fenton-type mechanism, which produces •OH radical intermediates. The fate of the •OH radical is controlled by the protein environment, using tight H-bonding networks around H2O2. The so-generated •OH radical is constrained by the surrounding H-bonding interactions, the orientation of which is targeted to perform H-abstraction from the Fe(III)-OH group and thereby leading to the formation of the active species, called Compound I (Cpd I), Por+•Fe(IV)═O, which performs oxidation of the substrate. Alternatively, for the nonheme HppE enzyme, the O-O homolysis catalyzed by the resting state Fe(II) generates an Fe(III)-OH species that effectively constrains the •OH radical species by a tight H-bonding network. The so-formed H-bonded •OH radical acts directly as the oxidant, since it is oriented to perform H-abstraction from the C-H bond of the substrate (S)-2-HPP. The Fenton-type H2O2 activation is strongly suggested by computations to occur also in copper-dependent LPMOs and pMMO. In LPMOs, the Cu(I)-catalyzed O-O homolysis of the H2O2 cosubstrate generates an •OH radical that abstracts a hydrogen atom from Cu(II)-OH and forms thereby the active species of the enzyme, Cu(II)-O•. Such Fenton-type O-O activation can be shared by both the O2-dependent activations of LPMOs and pMMOs, in which the O2 cosubstrate may be reduced to H2O2 by external reductants. Our studies show that, generally, the H2O2 activation is highly dependent on the protein environment, as well as on the presence/absence of substrates. Since H2O2 is a highly flexible and hydrophilic molecule, the absence of suitable substrates may lead to unproductive binding or even to the release of H2O2 from the active site, as has been suggested in P450cam and LPMOs, whereas the presence of the substrate seems to play a role in steering a Fenton-type H2O2 activation. In the absence of a substrate, the hydrophilic active site of P450BM3 disfavors the binding and activation of H2O2 and protects thereby the enzyme from the damage by the Fenton reaction. Due to the distinct coordination and reaction environment, the Fenton-type H2O2 activation mechanism by enzymes differs from the reaction in synthetic systems. In nonenzymatic reactions, the H-bonding networks are quite dynamic and flexible and the reactivity of H2O2 is not strategically constrained as in the enzymatic environment. As such, our Account describes the controlled Fenton-type mechanism in metalloenzymes, and the role of the protein environment in constraining the •OH radical against oxidative damage, while directing it to perform useful oxidative transformations.


Assuntos
Peróxido de Hidrogênio , Metaloproteínas , Cobre/química , Compostos Férricos , Heme/química , Peróxido de Hidrogênio/química , Metaloproteínas/metabolismo , Oxirredução , Peroxidases/metabolismo
8.
Chemistry ; 29(49): e202300977, 2023 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-37329272

RESUMO

The present work reports a DFT-based mechanistic investigation of aryl C-O bond activation in anisole catalysed by a Rh-Al pincer-type complex at room temperature. The study is extended to analogues Rh-E complexes based on Group 13 elements (E=B/Ga). Our results show a preference for the heterolytic cleavage pathway over oxidative addition in the C-O bond activation. The calculated barriers range from 16 to 36 kcal/mol, following the order: E=Al

9.
Chemistry ; 29(36): e202300992, 2023 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-37073808

RESUMO

We present here a valence bond analysis of structure and π-delocalization in Ge3 (NH)3 , which models germanazene that was prepared by Power et al. To get a broader perspective, we explore the entire E3 (NH)3 series (E=C, Si, Ge, Sn, Pb). Thus, while (4n+2)π systems of carbon rings are aromatic with cyclic π-delocalization, the E3 (NH)3 rings are dominated by a nonbonded structure, wherein π-lone pairs are localized on the N atoms. Nevertheless, these molecules enjoy large covalent-ionic resonance energies of 153.0, 86.6, 74.2, 61.2, and 58.9 kcal/mol, respectively, for E=C, Si, Ge, Sn, Pb. The covalent-ionic mixing in E3 (NH)3 creates π-systems, which are stabilized by charge-shift bonding. Thus, unlike in benzene, in Ge3 (NH)3 delocalization of π-electron pairs of the N atoms is primarily confined to the domains of their adjacent Ge atoms. These features carry over to the substituted germanazene, Ge3 (NAr)3 (Ar=Ph).

10.
Angew Chem Int Ed Engl ; 62(38): e202307579, 2023 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-37530131

RESUMO

Oriented external electric fields (EEFs) act as catalysts that can induce selectivity in chemical reactions. The responses of the Diels-Alder (DA) reaction between butadiene and ethylene (BDE-DA) as well as cyclopentadiene and ethylene (CPDE-DA) towards EEF stimuli are investigated here using density functional theory (B3LYP) calculations. EEF is a vector that catalyzes the reaction in one direction while inhibiting it in the opposite direction. Here we report that the inhibitive direction becomes rate-enhancing after some increase in the EEF. The EEF value that brings about the maximum possible inhibition for the reaction is defined as the electrostatic resistance point (ERP). The possibility of both normal and inverse electron-demand DA reactions causes catalytic activity in both directions of the EEF starting at a unique ERP value. The C5 substituents of cyclopentadiene control the ERP values depending upon the resistance power that the functional group provides against the EEF. The endo and exo diastereomeric transition states of the DA reaction have distinct ERP values and the difference (ΔERP) provides the through-space electrostatic contribution to the stereoselectivity on a relative scale. Thus, the ERP values can be used as a gauge for the electrostatic interactions between substituent groups and external stimuli.

11.
Angew Chem Int Ed Engl ; 62(7): e202212053, 2023 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-36545867

RESUMO

The copper-dependent formylglycine-generating enzyme (FGE) catalyzes the oxygen-dependent oxidation of specific peptidyl-cysteine residues to formylglycine. Our QM/MM calculations provide a very likely mechanism for this transformation. The reaction starts with dioxygen binding to the tris-thiolate CuI center to form a triplet CuII -superoxide complex. The rate-determining hydrogen atom abstraction involves a triplet-singlet crossing to form a CuII -OOH species that couples with the substrate radical, leading to a CuI -alkylperoxo intermediate. This is accompanied by proton transfer from the hydroperoxide to the S atom of the substrate via a nearby water molecule. The subsequent O-O bond cleavage is coupled with the C-S bond breaking that generates the formylglycine and a CuII -oxyl complex. Moreover, our results suggest that the aldehyde oxygen of the final product originates from O2 , which will be useful for future experimental work.


Assuntos
Cobre , Cisteína , Cobre/química , Cisteína/metabolismo , Oxirredução , Oxigênio/química
12.
J Am Chem Soc ; 144(32): 14607-14613, 2022 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-35925767

RESUMO

Valence-inverted reactivity (VIR) is discovered here through high-level computations of excited states of Ni(II) complexes that are generated by triplet energy transfer. For example, the so-generated 3[(Ar)(bpy)NiII(Br)] species possesses a valence-inverted occupancy, dxy1dxz1dx2-y22, wherein the uppermost dx2-y2 orbital is metal-ligand antibonding. This state promotes C-H bond activation of THF and its cross-coupling to the aryl ligand. Thus, due to the metal-ligand antibonding character of dx2-y2, the dxy1dx2-y22 subshell opens a Ni-coordination site by shifting the bidentate bipyridine ligand to monodentate plus a dangling pyridine. The tricoordinate Ni(II) intermediate inserts into a C-H bond of THF, transfers a proton to the dangling pyridine moiety, and eventually generates an arylated THF by reductive-coupling. The calculated high kinetic isotope effect is in accord with experiment, both revealing C-H activation. The VIR pattern is novel, its cross-coupling reaction is highly useful, and it is generally expected to occur in other d8 complexes.


Assuntos
Níquel , Prótons , Ligantes , Modelos Moleculares , Níquel/química , Piridinas
13.
J Am Chem Soc ; 144(44): 20484-20494, 2022 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-36282048

RESUMO

Nature has devised intrinsic electric fields (IEFs) that are engaged in electrostatic catalysis of enzymes. But, how does the IEF target its function in enzymes that involve several reaction steps in catalytic cycles? To decipher the impact of the IEF on the catalytic cycle of an enzyme system, we have performed molecular dynamics and quantum-mechanical/molecular-mechanical (QM/MM) simulations on tyrosine hydroxylase (TyrH). The catalytic cycle of TyrH involves two reaction stages: the activation of H2O2 to form the active species of compound I (Cpd I), in the first stage, and the Cpd I-mediated hydroxylation of l-tyrosine to l-DOPA, in the second stage. For the first stage, the QM/MM calculations show that a heme-propionate group functions as a base to catalyze the O-O heterolysis reaction. For the second stage, the study reveals that the reaction is initiated by the His88-mediated proton-coupled electron transfer followed by the oxygen atom transfer from compound II (Cpd II) to the l-Tyr substrate. Importantly, our calculations demonstrate that the IEF in TyrH is optimized to promote the O-O bond heterolysis that generates the active species of the enzyme, Cpd I. However, the same IEF slows down the subsequent aromatic hydroxylation. Thus, the IEF in the TyrH enzymes does not catalyze the product formation step, but will selectively boost one or more challenging steps in the catalytic cycle. These findings have general implications on O2/H2O2-dependent metalloenzymes, which can expand our understanding of how nature has used electric fields as "smart reagents" in modulating the catalytic reactivity.


Assuntos
Teoria Quântica , Tirosina 3-Mono-Oxigenase , Tirosina 3-Mono-Oxigenase/química , Peróxido de Hidrogênio/química , Catálise , Heme/química
14.
J Chem Inf Model ; 62(4): 1025-1035, 2022 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-35129977

RESUMO

Cytochrome P450 peroxygenases use hydrogen peroxide to hydroxylate long-chain fatty acids by bypassing the use of O2 and a redox partner. Among the peroxygenases, P450OleT uniquely performs decarboxylation of fatty acids and production of terminal olefins. This route taken by P450OleT is intriguing, and its importance is augmented by the practical importance of olefin production. As such, this mechanistic choice merits elucidation. To address this puzzle, we use hybrid QM/MM calculations and MD simulations for the OleT enzyme as well as for the structurally analogous enzyme, P450BSß. The study of P450OleT reveals that the protonated His85 in the wild-type P450OleT plays a crucial role in steering decarboxylation activity by stabilizing the corresponding hydroxoiron(IV) intermediate (Cpd II). In contrast, for P450BSß in which Q85 replaces H85, the respective Cpd II species is unstable and it reacts readily with the substrate radical by rebound, producing hydroxylation products. As shown, this single-site difference creates in P450OleT a local electric field (LEF), which is significantly higher than that in P450BSß. In turn, these LEF differences are responsible for the different stabilities of the respective Cpd II/radical intermediates and hence for different functions of the two enzymes. P450BSß uses the common rebound mechanism and leads to hydroxylation, whereas P450OleT proceeds via decarboxylation and generates terminal olefins. Olefin production projects the power of a single residue to alter the LEF and the enzyme's function.


Assuntos
Sistema Enzimático do Citocromo P-450 , Ácidos Graxos , Sistema Enzimático do Citocromo P-450/metabolismo , Ácidos Graxos/química , Hidroxilação , Oxigenases de Função Mista , Oxirredução
15.
J Chem Phys ; 157(9): 090901, 2022 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-36075734

RESUMO

This Perspective outlines a panoramic description of the nature of the chemical bond according to valence bond theory. It describes single bonds and demonstrates the existence of a "forgotten family" of charge-shift bonds (CSBs) in which the entire/most of the bond energy arises from the resonance between the covalent and ionic structures of the bond. Many of the CSBs are homonuclear bonds. Hypervalent molecules (e.g., XeF2) are CSBs. This Perspective proceeds to describe multiple bonded molecules with an emphasis on C2 and 3O2. C2 has four electron pairs in its valence shell and, hence, 14 covalent structures and 1750 ionic structures. This Perspective outlines an effective methodology of peeling the electronic structure to the minimal and important number of structures: a dominant structure that displays a quadruple bond and two minor structures with π + σ bonds, which stabilize the quadruple bond by resonance. 3O2 is chosen because it is a diradical, which is persistent and life-sustaining. It is shown that the persistence of this diradical is due to the charge-shift bonding of the π-3-electron bonds. This section ends with a discussion of the roles of π vs σ in the geometric preferences of benzene, acetylene, ethene, and their Si-based analogs. Subsequently, this Perspective discusses bonding in clusters of univalent metal atoms, which possess only parallel spins (n+1Mn), and are nevertheless bonded due to the resonance interactions that stabilize the repulsive elementary structure (all spins are up). The bond energy reaches ∼40 kcal/mol for a pair of atoms (in n+1Cun; n ∼ 10-12). The final subsection discusses singlet excited states in ethene, ozone, and SO2. It demonstrates the capability of the breathing-orbital VB method to yield an accurate description of a variety of excited states using merely 10 or few VB structures. Furthermore, the method underscores covalent structures that play a key role in the correct description and bonding of these excited states.

16.
Molecules ; 27(2)2022 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-35056805

RESUMO

This article analyzes the nature of the chemical bond in coinage metal halides using high-level ab initio Valence Bond (VB) theory. It is shown that these bonds display a large Charge-Shift Bonding character, which is traced back to the large Pauli pressure arising from the interaction between the bond pair with the filled semicore d shell of the metal. The gold-halide bonds turn out to be pure Charge-Shift Bonds (CSBs), while the copper halides are polar-covalent bonds and silver halides borderline cases. Among the different halogens, the largest CSB character is found for fluorine, which experiences the largest Pauli pressure from its σ lone pair. Additionally, all these bonds display a secondary but non-negligible π bonding character, which is also quantified in the VB calculations.

17.
Angew Chem Int Ed Engl ; 61(50): e202214235, 2022 12 12.
Artigo em Inglês | MEDLINE | ID: mdl-36259368

RESUMO

The non-heme iron ergothioneine synthase (EgtB) is a sulfoxide synthase that catalyzes oxidative C-S bond formation in the synthesis of ergothioneine, which plays roles against oxidative stress in cells. Despite extensive experimental and computational studies of the catalytic mechanisms of EgtB, the root causes for the selective C-S bond formation remain elusive. Using quantum mechanics/molecular mechanics (QM/MM) calculations, we show herein that a coordination switch of the sulfoxide intermediate is involved in the catalysis of the non-heme iron EgtB. This coordination switch from the S to the O atom is driven by the S/π electrostatic interactions, which efficiently promotes the observed stereoselective C-S bond formation while bypassing cysteine dioxygenation. The present mechanism is in agreement with all available experimental data, including regioselectivity, stereoselectivity and KIE results. This match underscores the critical role of coordination switching in the catalysis of non-heme enzymes.


Assuntos
Ergotioneína , Catálise , Simulação de Dinâmica Molecular , Ferro , Sulfóxidos
18.
J Am Chem Soc ; 143(11): 4367-4378, 2021 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-33689334

RESUMO

To develop an approach to pre-emptively predict the existence of major reaction modes associated with a chemical system, based on exclusive consideration of reactant properties, we build herein on the valence bond perspective of chemical reactivity. In this perspective, elementary chemical reactions are conceptualized as crossovers between individual diabatic/semilocalized states. As demonstrated, the spacings between the main diabatic states in the reactant geometries-the so-called promotion energies-contain predictive information about which types of crossings are likely to occur on a potential energy surface, facilitating the identification of potential transition states and products. As an added bonus, promotion energy analysis provides direct insight into the impact of environmental effects, e.g., the presence of (polar) solvents and/or (local) electric fields, on a mechanistic landscape. We illustrate the usefulness of our approach by focusing on model nucleophilic and electrophilic aromatic substitution reactions. Overall, we envision our analysis to be useful not only as a tool for conceptualizing individual mechanistic landscapes but also as a facilitator of systematic reaction-network exploration efforts. Because the emerging VB descriptors are computationally inexpensive (and can alternatively be inferred through machine learning), they could be evaluated on-the-fly as part of an exploration algorithm. The so-predicted reaction modes could subsequently be examined in detail through computationally more-demanding methods.

19.
J Am Chem Soc ; 143(2): 1005-1016, 2021 01 20.
Artigo em Inglês | MEDLINE | ID: mdl-33426875

RESUMO

Cytochrome P450 monooxygenases (P450s) are versatile biocatalysts used in natural products biosynthesis, xenobiotic metabolisms, and biotechnologies. In P450s, the electrons required for O2 activation are supplied by NAD(P)H through stepwise electron transfers (ETs) mediated by redox partners. While much is known about the machinery of the catalytic cycle of P450s, the mechanisms of long-range ET are largely unknown. Very recently, the first crystal structure of full-length P450TT was solved. This enables us to decipher the interdomain ET mechanism between the [2Fe-2S]-containing ferredoxin and the heme, by use of molecular dynamics simulations. In contrast to the "distal" conformation characterized in the crystal structure where the [2Fe-2S] cluster is ∼28 Šaway from heme-Fe, our simulations demonstrated a "proximal" conformation of [2Fe-2S] that is ∼17 Š[and 13.7 Šedge-to-edge] away from heme-Fe, which may enable the interdomain ET. Key residues involved in ET pathways and interdomain complexation were identified, some of which have already been verified by recent mutation studies. The conformational transit of ferredoxin between "distal" and "proximal" was found to be controlled mostly by the long-range electrostatic interactions between the ferredoxin domain and the other two domains. Furthermore, our simulations show that the full-length P450TT utilizes a flexible ET pathway that resembles either P450Scc or P450cam. Thus, this study provides a uniform picture of the ET process between reductase domains and heme domain.


Assuntos
Sistema Enzimático do Citocromo P-450/metabolismo , Ferredoxinas/metabolismo , Heme/metabolismo , Biocatálise , Sistema Enzimático do Citocromo P-450/química , Transporte de Elétrons , Ferredoxinas/química , Heme/química , Modelos Moleculares , Conformação Molecular , Simulação de Dinâmica Molecular
20.
J Org Chem ; 86(13): 9030-9039, 2021 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-34152765

RESUMO

In this study, we explore strategies to resolve entangled reactivity modes. More specifically, we consider the competition between SN2 and E2 reaction pathways for alkyl halides and nucleophiles/bases. We first demonstrate that the emergence of an E2-preference is associated with an enhancement of the magnitude of the resonance stabilization in the transition-state (TS) region, resulting from the improved mixing of electrostatically stabilized valence bond structures into the TS wavefunction. Subsequently, we show that the TS resonance energy can be tuned selectively and rationally either through the application of an oriented external electric field directed along the C-C axis of the alkyl halide or through a regular substitution approach of the C-C moiety. We end our study by demonstrating that the insights gained from our analysis enable one to rationalize the main reactivity trends emerging from a recently published large database of competing SN2 and E2 reaction pathways.

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