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1.
Proc Natl Acad Sci U S A ; 118(46)2021 11 16.
Artigo em Inglês | MEDLINE | ID: mdl-34750269

RESUMO

Antibiotic resistance is a major threat to global health; this problem can be addressed by the development of new antibacterial agents to keep pace with the evolutionary adaptation of pathogens. Computational approaches are essential tools to this end since their application enables fast and early strategical decisions in the drug development process. We present a rational design approach, in which acylide antibiotics were screened based on computational predictions of solubility, membrane permeability, and binding affinity toward the ribosome. To assess our design strategy, we tested all candidates for in vitro inhibitory activity and then evaluated them in vivo with several antibiotic-resistant strains to determine minimal inhibitory concentrations. The predicted best candidate is synthetically more accessible, exhibits higher solubility and binding affinity to the ribosome, and is up to 56 times more active against resistant pathogens than telithromycin. Notably, the best compounds designed by us show activity, especially when combined with the membrane-weakening drug colistin, against Acinetobacter baumanii, Pseudomonas aeruginosa, and Escherichia coli, which are the three most critical targets from the priority list of pathogens of the World Health Organization.


Assuntos
Antibacterianos/farmacologia , Bactérias/efeitos dos fármacos , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Macrolídeos/farmacologia , Colistina/farmacologia , Testes de Sensibilidade Microbiana/métodos
2.
J Comput Chem ; 40(21): 1902-1910, 2019 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-31062376

RESUMO

Combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the reaction mechanism of taxadiene synthase (TXS). TXS catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to taxadiene (T) and four minor cyclic products. All these products originate from the deprotonation of carbocation intermediates. The reaction profiles for the conversion of GGPP to T as well as to minor products were calculated for different configurations of relevant TXS carbocation complexes. The QM region was treated at the M06-2X/TZVP level, while the CHARMM27 force field was used to describe the MM region. The QM/MM calculations suggest a reaction pathway for the conversion of GGPP to T, which slightly differs from previous proposals regarding the number of reaction steps and the conformation of the carbocations. The QM/MM results also indicate that the formation of minor products via water-assisted deprotonation of the carbocations is highly exothermic, by about -7 to -23 kcal/mol. Curiously, however, the computed barriers and reaction energies indicate that the formation of some of the minor products is more facile than the formation of T. Thus, the present QM/MM calculations provide detailed insights into possible reaction pathways and into the origin of the promiscuity of TXS, but they do not reproduce the product distribution observed experimentally. © 2019 Wiley Periodicals, Inc.


Assuntos
Isomerases/química , Isomerases/metabolismo , Teoria Quântica , Alcenos/química , Alcenos/metabolismo , Biocatálise , Difosfatos/química , Difosfatos/metabolismo , Diterpenos/química , Diterpenos/metabolismo , Simulação de Dinâmica Molecular , Estrutura Molecular
3.
J Comput Chem ; 40(4): 638-649, 2019 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-30549072

RESUMO

Most modern semiempirical quantum-chemical (SQC) methods are based on the neglect of diatomic differential overlap (NDDO) approximation to ab initio molecular integrals. Here, we check the validity of this approximation by computing all relevant integrals for 32 typical organic molecules using Gaussian-type orbitals and various basis sets (from valence-only minimal to all-electron triple-ζ basis sets) covering in total more than 15.6 million one-electron (1-e) and 10.3 billion two-electron (2-e) integrals. The integrals are calculated in the nonorthogonal atomic basis and then transformed by symmetric orthogonalization to the Löwdin basis. In the case of the 1-e integrals, we find strong orthogonalization effects that need to be included in SQC models, for example, by strategies such as those adopted in the available OMx methods. For the valence-only minimal basis, we confirm that the 2-e Coulomb integrals in the Löwdin basis are quantitatively close to their counterparts in the atomic basis and that the 2-e exchange integrals can be safely neglected in line with the NDDO approximation. For larger all-electron basis sets, there are strong multishell orthogonalization effects that lead to more irregular patterns in the transformed 2-e integrals and thus cast doubt on the validity of the NDDO approximation for extended basis sets. Focusing on the valence-only minimal basis, we find that some of the NDDO-neglected integrals are reduced but remain sizable after the transformation to the Löwdin basis; this is true for the two-center 2-e hybrid integrals, the three-center 1-e nuclear attraction integrals, and the corresponding three-center 2-e hybrid integrals. We consider a scheme with a valence-only minimal basis that includes such terms as a possible strategy to go beyond the NDDO integral approximation in attempts to improve SQC methods. © 2018 Wiley Periodicals, Inc.

4.
Phys Chem Chem Phys ; 21(7): 3496-3505, 2019 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-29790517

RESUMO

Accurate ab initio calculations on the rotation-vibration spectrum of methyl fluoride (CH3F) are reported. A new nine-dimensional potential energy surface (PES) and dipole moment surface (DMS) have been generated using high-level electronic structure methods. Notably, the PES was constructed from explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and considered additional energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. The PES and DMS are evaluated through robust variational nuclear motion computations of pure rotational and vibrational energy levels, the equilibrium geometry of CH3F, vibrational transition moments, absolute line intensities of the ν6 band, and the rotation-vibration spectrum up to J = 40. The computed results show excellent agreement with a range of experimental sources, in particular the six fundamentals are reproduced with a root-mean-square error of 0.69 cm-1. This work represents the most accurate theoretical treatment of the rovibrational spectrum of CH3F to date.

5.
J Phys Chem A ; 123(26): 5600-5612, 2019 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-31181157

RESUMO

Among the title species, a reliable and accurate equilibrium geometry ( re structure) is available only for PF3, which has been determined experimentally more than 20 years ago. Here, we report accurate re structures for all title molecules, which were obtained using a composite computational approach based on explicitly correlated coupled-cluster theory (CCSD(T)-F12b) in conjunction with a large correlation-consistent basis set (cc-pCVQZ-F12) to take core-valence electron correlation into account. Additional terms were included to correct for the effects of iterative triple excitations (CCSDT), noniterative quadruple excitations (CCSDT(Q)), and scalar relativistic contributions (DKH2-CCSD(T)). The performance of this computational procedure was established through test calculations on selected small molecules (PH, PF, PCl, PH2, PF2, and PH3). For PF3, PCl3, PH3F2, and PF5 sufficiently accurate experimental ground-state rotational constants from the literature were used to determine semiexperimental re structures, which were found to be in excellent agreement with the corresponding best estimates from the current composite approach. The recommended equilibrium structural parameters are for PCl3, re(PCl) = 203.94 pm and θe(ClPCl) = 100.18°; for PH3F2, re(PHeq) = 138.38 pm and re(PFax) = 164.15 pm; for PF5, re(PFeq) = 153.10 pm and re(PFax) = 157.14 pm; for PCl3F2, re(PCleq) = 200.21 pm and re(PFax) = 159.37 pm; and for PCl5, re(PCleq) = 201.29 pm and re(PClax) = 211.83 pm. The associated uncertainties are estimated to be ±0.10 pm and ±0.10°, respectively.

6.
Proc Natl Acad Sci U S A ; 113(36): 10073-8, 2016 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-27551082

RESUMO

Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions.


Assuntos
Relógios Circadianos/genética , Criptocromos/química , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Proteínas do Olho/química , Histidina/química , Prótons , Motivos de Aminoácidos , Animais , Benzoquinonas/química , Benzoquinonas/metabolismo , Domínio Catalítico , Criptocromos/genética , Criptocromos/metabolismo , Cristalografia por Raios X , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/metabolismo , Proteínas do Olho/genética , Proteínas do Olho/metabolismo , Flavinas/química , Flavinas/metabolismo , Expressão Gênica , Histidina/metabolismo , Ligação de Hidrogênio , Concentração de Íons de Hidrogênio , Luz , Simulação de Dinâmica Molecular , Oxirredução , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
7.
J Am Chem Soc ; 140(44): 15099-15113, 2018 11 07.
Artigo em Inglês | MEDLINE | ID: mdl-30362731

RESUMO

A recent experimental study reported a visible-light-mediated aerobic oxidative coupling reaction of phenol with alkynes that produces hydroxyl-functionalized aryl ketones using inexpensive CuCl as catalyst under mild conditions. Here we apply the complete active space self-consistent field (CASSCF) method and multistate second-order perturbation (MS-CASPT2) theory in combination with density functional theory (DFT) to systematically explore the entire photocatalytic reaction between phenol and phenylacetylene in acetonitrile solution in the presence of molecular oxygen and CuCl. Our main findings are as follows: (1) The visible-light-driven conversion of phenylacetylene to PhCCCu(I) occurs thermally because of efficient excited-state deactivation to the S0 state. (2) The single electron transfer from PhCCCu(I) to molecular oxygen that leads to the PhCCCu(II) cation takes place in the T1 state after an efficient S1 → T1 intersystem crossing. (3) During the initial oxidation of phenol, molecular oxygen prefers to attack the para position of the phenol radical intermediate to produce 1,4-benzoquinone, which further reacts with PhCCCu(II) to generate para-hydroxyl-substituted aryl ketones; this is the origin of the experimentally observed regioselectivity. (4) The C≡C bond of the phenylacetylene moiety is not activated by the triplet-state single electron transfer from PhCCCu(I) to molecular oxygen but is cleaved at a later stage, in the [2+2] cycloaddition between PhCCCu(II) and 1,4-benzoquinone. (5) The substrate phenol plays an active role in several hydrogen transfer and decarboxylation reactions; the barriers to these phenol-assisted reactions are lower than those for the corresponding direct or water-assisted reactions, which explains the experimental finding that adding water does not enhance the photocatalytic reaction yield. In summary, while supporting the general features of the experimentally proposed mechanism, our computational study provides detailed mechanistic insights that should be useful for understanding and further improving visible-light-induced copper-catalyzed coupling reactions.

8.
J Am Chem Soc ; 140(8): 3156-3169, 2018 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-29429344

RESUMO

The hydrogenation of internal alkynes with [Cp*Ru]-based catalysts is distinguished by an unorthodox stereochemical course in that E-alkenes are formed by trans-delivery of the two H atoms of H2. A combined experimental and computational study now provides a comprehensive mechanistic picture: a metallacyclopropene (η2-vinyl complex) is primarily formed, which either evolves into the E-alkene via a concerted process or reacts to give a half-sandwich ruthenium carbene; in this case, one of the C atoms of the starting alkyne is converted into a methylene group. This transformation represents a formal gem-hydrogenation of a π-bond, which has hardly any precedent. The barriers for trans-hydrogenation and gem-hydrogenation are similar: whereas DFT predicts a preference for trans-hydrogenation, CCSD(T) finds gem-hydrogenation slightly more facile. The carbene, once formed, will bind a second H2 molecule and evolve to the desired E-alkene, a positional alkene isomer or the corresponding alkane; this associative pathway explains why double bond isomerization and over-reduction compete with trans-hydrogenation. The computed scenario concurs with para-hydrogen-induced polarization transfer (PHIP) NMR data, which confirm direct trans-delivery of H2, the formation of carbene intermediates by gem-hydrogenation, and their evolution into product and side products alike. Propargylic -OR (R = H, Me) groups exert a strong directing and stabilizing effect, such that several carbene intermediates could be isolated and characterized by X-ray diffraction. The gathered information spurred significant preparative advances: specifically, highly selective trans-hydrogenations of propargylic alcohols are reported, which are compatible with many other reducible functional groups. Moreover, the ability to generate metal carbenes by gem-hydrogenation paved the way for noncanonical hydrogenative cyclopropanations, ring expansions, and cycloadditions.

9.
J Comput Chem ; 39(19): 1215-1225, 2018 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-29450907

RESUMO

Molecular dynamics (MD) simulations have been performed to study the dynamic behavior of noncovalent enzyme carbocation complexes involved in the cyclization of geranylgeranyl diphosphate to taxadiene catalyzed by taxadiene synthase (TXS). Taxadiene and the observed four side products originate from the deprotonation of carbocation intermediates. The MD simulations of the TXS carbocation complexes provide insights into potential deprotonation mechanisms of such carbocations. The MD results do not support a previous hypothesis that carbocation tumbling is a key factor in the deprotonation of the carbocations by pyrophosphate. Instead water bridges are identified which may allow the formation of side products via multiple proton transfer reactions. A novel reaction path for taxadiene formation is proposed on the basis of the simulations. © 2018 Wiley Periodicals, Inc.

10.
Phys Chem Chem Phys ; 20(16): 11067-11080, 2018 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-29620123

RESUMO

We report quantum mechanical/molecular mechanical non-adiabatic molecular dynamics simulations on the electronically excited state of green fluorescent protein mutant S65T/H148D. We examine the driving force of the ultrafast (τ < 50 fs) excited-state proton transfer unleashed by absorption in the A band at 415 nm and propose an atomistic description of the two dynamical regimes experimentally observed [Stoner Ma et al., J. Am. Chem. Soc., 2008, 130, 1227]. These regimes are explained in terms of two sets of successive dynamical events: first the proton transfers quickly from the chromophore to the acceptor Asp148. Thereafter, on a slower time scale, there are geometrical changes in the cavity of the chromophore that involve the distance between the chromophore and Asp148, the planarity of the excited-state chromophore, and the distance between the chromophore and Tyr145. We find two different non-radiative relaxation channels that are operative for structures in the reactant region and that can explain the mismatch between the decay of the emission of A* and the rise of the emission of I*, as well as the temperature dependence of the non-radiative decay rate.


Assuntos
Proteínas de Fluorescência Verde/química , Ácido Aspártico/química , Fluorescência , Proteínas de Fluorescência Verde/efeitos da radiação , Proteínas de Fluorescência Verde/ultraestrutura , Modelos Químicos , Simulação de Dinâmica Molecular , Estrutura Molecular , Mutação , Conformação Proteica , Prótons , Teoria Quântica , Espectrometria de Fluorescência , Tirosina/química , Vibração
11.
J Chem Phys ; 148(15): 154103, 2018 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-29679961

RESUMO

We present an efficient implementation of configuration interaction with single excitations (CIS) for semiempirical orthogonalization-corrected OMx methods and standard modified neglect of diatomic overlap (MNDO)-type methods for the computation of vertical excitation energies as well as analytical gradients and nonadiabatic couplings. This CIS implementation is combined with Tully's fewest switches algorithm to enable surface hopping simulations of excited-state nonadiabatic dynamics. We introduce an accurate and efficient expression for the semiempirical evaluation of nonadiabatic couplings, which offers a significant speedup for medium-size molecules and is suitable for use in long nonadiabatic dynamics runs. As a pilot application, the semiempirical CIS implementation is employed to investigate ultrafast energy transfer processes in a phenylene ethynylene dendrimer model.

12.
J Chem Phys ; 148(24): 244108, 2018 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-29960378

RESUMO

We present the formalism of analytic gradients and derivative couplings for the spin-flip extended configuration interaction with single excitations (SF-XCIS) method. We report an efficient implementation of the SF-XCIS method in the framework of semiempirical quantum chemistry that allows fast excited-state calculations for large systems. The performance of the SF-XCIS method in combination with semiempirical orthogonalization-corrected models (OMx) is statistically evaluated for vertical singlet excitation energies. The SF-XCIS method treats the ground state and excited states in a fully balanced manner and properly describes conical intersections involving the ground state. It can thus be used in fewest switches surface hopping (FSSH) simulations of nonadiabatic dynamics processes. This is demonstrated in an OM2/SF-XCIS FSSH pilot study of excited-state proton transfer in 7-(2-pyridyl)indole.

13.
Molecules ; 23(10)2018 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-30347691

RESUMO

Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.


Assuntos
Entropia , Soluções/análise , Solventes/análise , Termodinâmica , Simulação de Dinâmica Molecular , Soluções/química , Solventes/química , Eletricidade Estática , Água/química
14.
J Am Chem Soc ; 139(8): 2972-2980, 2017 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-28145707

RESUMO

Light-oxygen-voltage (LOV) domains sense blue light through the photochemical formation of a cysteinyl-flavin covalent adduct. Concurrent protonation at the flavin N5 position alters the hydrogen bonding interactions of an invariant Gln residue that has been proposed to flip its amide side chain as a critical step in the propagation of conformational change. Traditional molecular dynamics (MD) and replica-exchange MD (REMD) simulations of the well-characterized LOV protein Vivid (VVD) demonstrate that the Gln182 amide indeed reorients by ∼180° in response to either adduct formation or reduction of the isoalloxazine ring to the neutral semiquinone, both of which involve N5 protonation. Free energy simulations reveal that the relative free energies of the flipped Gln conformation and the flipping barrier are significantly lower in the light-adapted state. The Gln182 flip stabilizes an important hinge-bß region between the PAS ß-sheet and the N-terminal cap helix that in turn destabilizes an N-terminal latch region against the PAS core. Release of the latch, observed both experimentally and in the simulations, is known to mediate light-induced VVD dimerization. This computational study of a LOV protein, unprecedented in its agreement with experiment, provides an atomistic view of long-range allosteric coupling in a photoreceptor.


Assuntos
Amidas/metabolismo , Proteínas Fúngicas/metabolismo , Glutamina/metabolismo , Regulação Alostérica , Amidas/química , Proteínas Fúngicas/química , Glutamina/química , Conformação Molecular , Simulação de Dinâmica Molecular , Termodinâmica
15.
J Am Chem Soc ; 139(13): 4948-4953, 2017 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-28322057

RESUMO

A series of new P^P-chelating ligands constituted by a dicationic -[P(H2Im)2]+2 unit (H2Im = 1,3-dimethyl-4,5-dihydroimidazol-2-ylidene) and a -PPh2 group connected through structurally different backbones have been synthesized. Evaluation of their reactivity toward different metal centers provides evidence that the dicationic fragment, otherwise reluctant to coordinate metals, readily participates in the formation of chelates when embedded into such a scaffold. Moreover, it significantly enhances the Lewis acidity of the metals to which it coordinates. This property has been used to develop a Rh catalyst that efficiently triggers the hydroarylation of dienes with electron-rich aromatic molecules. Kinetic studies and deuterium-labeling experiments, as well as density functional theory calculations, were performed in order to rationalize these findings.

16.
J Am Chem Soc ; 139(6): 2443-2455, 2017 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-28169542

RESUMO

[Cp*RuCl]4 (1) has previously been shown to be the precatalyst of choice for stereochemically unorthodox trans-hydrometalations of internal alkynes. Experimental and computational data now prove that the alkyne primarily acts as a four-electron donor ligand to the catalytically active metal fragment [Cp*RuCl] but switches to adopt a two-electron donor character once the reagent R3MH (M = Si, Ge, Sn) enters the ligand sphere. In the stereodetermining step the resulting loaded complex evolves via an inner-sphere mechanism into a ruthenacyclopropene which swiftly transforms into the product. In accord with the low computed barriers, spectral and preparative data show that the reaction is not only possible but sometimes even favored at low temperatures. Importantly, such trans-hydrometalations are distinguished by excellent levels of regioselectivity when unsymmetrical alkynes are used that carry an -OH or -NHR group in vicinity of the triple bond. A nascent hydrogen bridge between the protic substituent and the polarized [Ru-Cl] unit imposes directionality onto the ligand sphere of the relevant intermediates, which ultimately accounts for the selective delivery of the R3M- group to the acetylene C-atom proximal to the steering substituent. The interligand hydrogen bonding also allows site-selectivity to be harnessed in reactions of polyunsaturated compounds, since propargylic substrates bind more tightly than ordinary alkynes; even the electronically coupled triple bonds of conjugated 1,3-diynes can be faithfully discriminated as long as one of them is propargylic. Finally, properly positioned protic sites lead to a substantially increased substrate scope in that they render even 1,3-enynes, arylalkynes, and electron-rich alkynylated heterocycles amenable to trans-hydrometalation which are otherwise catalyst poisons.

17.
Chemistry ; 23(50): 12353-12362, 2017 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-28574611

RESUMO

We describe the synthesis as well as the electronic and photophysical characterization of novel N-heterotriangulene derivatives decorated with methoxycarbonyl- and methyl-sulfanyl-substituted dithiafulvenyl moieties. The association of these electron-rich compounds with fullerene C60 as electron acceptor was investigated by means of photophysical, voltammetric, and mass spectrometric methods and rationalized by DFT calculations. Importantly, light-induced interactions between the dithiafulvene-substituted N-heterotriangulene bearing methoxycarbonyl substituents with C60 leads to cooperative fluorescence. Quantitative Job plot analyses by means of fluorescence spectroscopy and voltammetry confirm a 1:1 association with binding constants in the order of 104 m-1 . Supportive results for the supramolecular assembly of both N-heterotriangulenes with C60 were obtained by ESI mass spectrometric investigations in the gas phase.

18.
J Org Chem ; 82(24): 13563-13571, 2017 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-29131960

RESUMO

The enzyme SpnF, involved in the biosynthesis of spinosyn A, catalyzes a formal [4+2] cycloaddition of a 22-membered macrolactone, which may proceed as a concerted [4+2] Diels-Alder reaction or a stepwise [6+4] cycloaddition followed by a Cope rearrangement. Quantum mechanics/molecular mechanics (QM/MM) calculations combined with free energy simulations show that the Diels-Alder pathway is favored in the enzyme environment. OM2/CHARMM free energy simulations for the SpnF-catalyzed reaction predict a free energy barrier of 22 kcal/mol for the concerted Diels-Alder process and provide no evidence of a competitive stepwise pathway. Compared with the gas phase, the enzyme lowers the Diels-Alder barrier significantly, consistent with experimental observations. Inspection of the optimized geometries indicates that the enzyme may prearrange the substrate within the active site to accelerate the [4+2] cycloaddition and impede the [6+4] cycloaddition through interactions with active-site residues. Judging from partial charge analysis, we find that the hydrogen bond between the Thr196 residue of SpnF and the substrate C15 carbonyl group contributes to the enhancement of the rate of the Diels-Alder reaction. QM/MM simulations show that the substrate can easily adopt a reactive conformation in the active site of SpnF because interconversion between the C5-C6 s-trans and s-cis conformers is facile. Our QM/MM study suggests that the enzyme SpnF does behave as a Diels-Alderase.

19.
Phys Chem Chem Phys ; 19(45): 30316-30331, 2017 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-28951896

RESUMO

Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly formed N-terminus (amine) and C-terminus (carboxylate) protein fragments from the site of catalysis coupled with the inclusion of one or more solvent waters. Here we report a novel crystal structure of membrane type I MMP (MT1-MMP or MMP-14), which includes a small peptide bound at the catalytic Zn site via its C-terminus. This structure models the initial product state formed immediately after peptide cleavage but before the final proton transfer to the bound amine; the amine is not present in our system and as such proton transfer cannot occur. Modeling of the protein, including earlier structural data of Bertini and coworkers [I. Bertini, et al., Angew. Chem., Int. Ed., 2006, 45, 7952-7955], suggests that the C-terminus of the peptide is positioned to form an H-bond network to the amine site, which is mediated by a single oxygen of the functionally important Glu240 residue, facilitating efficient proton transfer. Additional quantum chemical calculations complemented with magneto-optical and magnetic resonance spectroscopies clarify the role of two additional, non-catalytic first coordination sphere waters identified in the crystal structure. One of these auxiliary waters acts to stabilize key intermediates of the reaction, while the second is proposed to facilitate C-fragment release, triggered by protonation of the amine. Together these results complete the enzymatic cycle of MMPs and provide new design criteria for inhibitors with improved efficacy.


Assuntos
Metaloproteinase 14 da Matriz/química , Inibidores de Metaloproteinases de Matriz/química , Modelos Moleculares , Conformação Proteica , Sítios de Ligação , Catálise , Domínio Catalítico , Metaloproteinase 14 da Matriz/metabolismo , Solventes
20.
J Phys Chem A ; 121(13): 2572-2579, 2017 Apr 06.
Artigo em Inglês | MEDLINE | ID: mdl-28318255

RESUMO

The photophysical properties of tetraphenylethene (TPE) compounds may differ widely depending on the substitution pattern, for example, with regard to the fluorescence quantum yield ϕf and the propensity to exhibit aggregation-induced emission (AIE). We report combined electronic structure calculations and nonadiabatic dynamics simulations to study the excited-state decay mechanisms of two TPE derivatives with four methyl substituents, either in the meta position (TPE-4mM, ϕf = 0.1%) or in the ortho position (TPE-4oM, ϕf = 64.3%). In both cases, two excited-state decay pathways may be relevant, namely, photoisomerization around the central ethylenic double bond and photocyclization involving two adjacent phenyl rings. In TPE-4mM, the barrierless S1 cyclization is favored; it is responsible for the ultralow fluorescence quantum yield observed experimentally. In TPE-4oM, both the S1 photocyclization and photoisomerization paths are blocked by non-negligible barriers, and fluorescence is thus feasible. Nonadiabatic dynamics simulations with more than 1000 surface hopping trajectories show ultrafast cyclization upon photoexcitation of TPE-4mM, whereas TPE-4oM remains unreactive during the 1 ps simulations. We discuss the chances for spectroscopic detection of the postulated cyclic photoproduct of TPE-4mM and the relevance of our findings for the AIE process.

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