A Co(III)-peroxo-arylboronate complex formed by nucleophilic reaction of a Co(III)-peroxo species.

In this work, we report the generation and characterization of two new Co(III)-peroxo complexes 2 and 3. 2 is best described as a mononuclear CoIII-(O2) complex that exhibits an 18O-isotope sensitive OO bond stretching vibration at 845(-49) cm-1, indicating a relatively weak peroxo moiety compared to those of other CoIII-(O2) complexes reported previously. Complex 3 is a CoIII-peroxo-arylboronate species having a rare {CoIIIOOBO} five-membered metallocycle, which is structurally characterized using X-ray crystallography. Investigations of the reaction mechanism using density functional theory calculations show that 2 likely undergoes a nucleophilic attack to an arylboronic acid, which is generated by hydrolysis of the BPh4- anion in wet acetonitrile solution, to first form a CoIII-peroxo-arylboronic acid adduct, followed by the loss of one benzene molecule to generate the five-membered metallocycle. The entire reaction is thermodynamically favorable. Taken together, the conversion of 2 to 3 represents the discovery of a novel nucleophilic reactivity that can be carried out by mononuclear Co(III)-peroxo complexes.

Direct Activation of the C(sp3)-NH2 Bond of Primary Aliphatic Alkylamines by a High-Valent CoIII,IV2(µ-O)2 Diamond Core Complex.

Aliphatic alkylamines are abundant feedstock and versatile building blocks for many organic transformations. While remarkable progress has been made to construct C-N bonds on aliphatic and aromatic carbon centers, the activation and functionalization of C(sp3)-NH2 bonds in primary alkylamines remain a challenging process. In the present work, we discovered an unprecedented method to directly activate the C(sp3)-NH2 bond of primary alkylamines by a high-valent dinuclear CoIII,IV2(µ-O)2 diamond core complex. This reaction results in the installation of other functional groups such as halides and alkenes onto the α-carbon center concomitant with the 2-e- oxidation of the nitrogen atom on the amino group to form NH2OH. These results shed light on future development enabling versatile functionalization of primary alkylamines based on the dinuclear cobalt system. Moreover, our work suggests that a related high-valent copper-oxo intermediate is likely generated in the ammonia monooxygenase catalytic cycle to affect the oxidation of NH3 to NH2OH.

Unusual In-plane Aromaticity Facilitates Intramolecular Hydrogen Transfer in Long-Bonded cis-Isonitrosyl Methoxide.

The hydrogen-atom transfer from methoxy radical to nitric oxide, leading to the formation of formaldehyde and nitroxyl, represents a secondary reaction of photodissociation of methyl nitrite, which is used as rocket fuel. In this study, we explored the potential energy profile of the hydrogen-atom transfer using the electronic structure calculations at the DLPNO-CCSD(T)/aug-cc-pVTZ level of theory for two isomeric forms (cis and trans) of the pre-reaction complex. The cis-oriented pre-reaction complex has a weak elongated O─O bond, which gets further elongated in the hydrogen transfer transition state. This O─O bond stabilizes the pre-reaction complex by 32.9 kJ/mol. The O─O-induced stabilization is even greater for the transition state (48.2 kJ/mol), which was unexpected because of the larger O─O distance in the transition state structure. To address this paradox, we performed the electronic structure analysis of the reaction participants using the valence bond (VB) theory, natural resonance theory, topological analysis of the electron density and its derivatives, and analysis of the electron localization function distribution. This combined analysis led to the conclusion that the cis-transition state for hydrogen transfer, instead of being directly stabilized by the O─O interaction, gained substantial stabilization from the in-plane five-center six-electron aromaticity.

Regioselectivity in the Scholl Reaction: Mono and Double [7]Helicenes.

We employed the density functionaly theory (DFT)-predicted regioselectivity of the intramolecular Scholl reaction in phenanthrene and dibenzo[g,p]chrysene frameworks to obtain π-extended mono and double [7]helicenes, respectively. The formation of these helical structures occurs despite the buildup of a large strain energy up to 30 kcal/mol compared with their most stable isomers. The twisted and strained structures were characterized and analyzed by experimental (NMR, UV-vis, emission, electrochemistry, and single-crystal X-ray diffraction) techniques and were further supported by DFT calculations.

Opening the CoIII,IV2(µ-O)2 Diamond Core by Lewis Bases Leads to Enhanced C-H Bond Cleaving Reactivity.

The high-valent diiron(IV) intermediate Q is the key oxidant that cleaves strong C-H bonds of methane in the catalytic cycle of soluble methane monooxygenase (sMMO). sMMO-Q was previously reported as a bis-µ-oxo FeIV2(µ-O)2 diamond core but was recently described to have an open core with a long Fe···Fe distance. We recently reported a high-valent CoIII,IV2(µ-O)2 diamond core complex (1) that is highly reactive with sp3 C-H bonds. In this work, we demonstrated that the C-H bond cleaving reactivity of 1 can be further enhanced by introducing a Lewis base X, affording faster kinetic rate constants and the ability to cleave stronger C-H bonds compared to 1. We proposed that 1 first reacts with X in a fast equilibrium to form an open core species X-CoIII-O-CoIV-O (1-X). We were able to characterize 1-X using EPR spectroscopy and DFT calculations. 1-X exhibited an S = 1/2 EPR signal distinct from that of the parent complex 1. DFT calculations showed that 1-X has an open core with the spin density heavily delocalized in the CoIV-O unit. Moreover, 1-X has a more favorable thermodynamic driving force and a smaller activation barrier than 1 to carry out C-H bond activation reactions. Notably, 1-X is at least 4 orders of magnitude more reactive than its diiron open core analogues. Our findings indicate that the diamond core isomerization is likely a practical enzymatic strategy to unmask the strong oxidizing power of sMMO-Q necessary to attack the highly inert C-H bonds of methane.

Symmetry Effects in Photoinduced Electron Transfer in Chlorin-Quinone Dyads: Adiabatic Suppression in the Marcus Inverted Region.

In donor-acceptor dyads undergoing photoinduced electron transfer (PET), a direction or pathway for electron movement is usually dictated by the redox properties and the separation distance between the donor and acceptor subunits, while the effect of symmetry is less recognized. We have designed and synthesized two isomeric donor-acceptor assemblies in which electronic coupling between donor and acceptor is altered by the orbital symmetry control with the reorganization energy and charge transfer exothermicity being kept unchanged. Analysis of the optical absorption and luminescence spectra, supported by the DFT and TD-DFT calculations, showed that PET in these assemblies corresponds to the Marcus inverted region (MIR) and has larger rate for isomer with weaker electronic coupling. This surprising observation provides the first experimental evidence for theoretically predicted adiabatic suppression of PET in MIR, which unambiguously controlled solely by symmetry.

Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae.

Bacterial heme nitric oxide/oxygen (H-NOX) domains are nitric oxide (NO) or oxygen sensors. This activity is mediated through binding of the ligand to a heme cofactor. However, H-NOX from Vibrio cholerae (Vc H-NOX) can be easily purified in a heme-free state that is capable of reversibly responding to oxidation, suggesting a heme-independent function as a redox sensor. This occurs by oxidation of Cys residues at a zinc-binding site conserved in a subset of H-NOX homologs. Remarkably, zinc is not lost from the protein upon oxidation, although its ligation environment is significantly altered. Using a combination of computational and experimental approaches, we have characterized localized structural changes that accompany the formation of specific disulfide bonds between Cys residues upon oxidation. Furthermore, the larger-scale structural changes accompanying oxidation appear to mimic those changes observed upon NO binding to the heme-bound form. Thus, Vc H-NOX and its homologs may act as both redox and NO sensors by completely separate mechanisms.

Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?

Classical force fields are essential for computer simulations of proteins and are typically parameterized to reproduce secondary and tertiary structure of isolated proteins. However, while protein-protein interactions are ubiquitous in nature, they are not considered in parameterization efforts and are far less understood than isolated proteins. A better characterization of intermolecular interactions is widely recognized as a key to revolutionizing drug and therapeutic developments with high-throughput computational screening. Urgently needed is a critical assessment of the performance of modern protein force fields against first-principles electronic structure methods and experiments. In a daring step toward this goal, we here describe a comparison of peptide folding dynamics as predicted by a molecular mechanics force field on the one hand and by an approximate electronic structure quantum mechanical (QM) method based on density-functional tight-binding (DFTB) on the other. We further compare the dynamics from straightforward DFTB simulations with a near-linear scaling version of DFTB for massively parallel computation based on the fragment molecular orbital (FMO-DFTB) method. We illustrate differences between the phenomenology of the folding dynamics from these three methods for a small model peptide, as well as charge polarization and dynamic fluctuations, point out possible correlations and implications for force field developers, and discuss the lessons learned that might become applicable to future predictive high-throughput computer screening for personalized neoantigen cancer therapy.

Efficient newton-raphson/singular value decomposition-based optimization scheme with dynamically updated critical condition number for rapid convergence of weighted histogram analysis method equations.

Selection of the successful optimization strategy is an essential part of solving numerous practical problems yet often is a nontrivial task, especially when a function to be optimized is multidimensional and involves statistical data. Here we propose a robust optimization scheme, referred to as NR/SVD-Cdyn, which is based on a combination of the Newton-Raphson (NR) method along with singular value decomposition (SVD), and demonstrate its performance by numerically solving a system of the weighted histogram analysis method equations. Our results show significant improvement over the direct iteration and conventional NR optimization methods. The proposed scheme is universal and could be used for solving various optimization problems in the field of computational chemistry such as parameter fitting for the methods of molecular mechanics and semiempirical quantum-mechanical methods. © 2019 Wiley Periodicals, Inc.

Discovery and Characterization of Halogenated Xanthene Inhibitors of DUSP5 as Potential Photodynamic Therapeutics.

Dual specific phosphatases (DUSPs) are an important class of mitogen-activated protein kinase (MAPK) regulators, and are drug targets for treating vascular diseases. Previously we had shown that DUSP5 plays a role in embryonic vertebrate vascular patterning. Herein, we screened a library of FDA-approved drugs and related compounds, using a para-nitrophenylphosphate substrate (pNPP)-based assay. This assay identified merbromin (also known as mercurochrome) as targeting DUSP5; and, we subsequently identified xanthene-ring based merbromin analogs eosin Y, erythrosin B, and rose bengal, all of which inhibit DUSP5 in vitro. Inhibition was time-dependent for merbromin, eosin Y, 2',7'-dibromofluorescein, and 2',7'-dichlorofluorescein, with enzyme inhibition increasing over time. Reaction progress curve data fit best to a slow-binding model of irreversible enzyme inactivation. Potency of the time-dependent compounds, except for 2',7'-dichlorofluorescein, was diminished when dithiothreitol (DTT) was present, suggesting thiol reactivity. Two additional merbromin analogs, erythrosin B and rose bengal also inhibit DUSP5, but have the therapeutic advantage of being less sensitive to DTT and exhibiting little time dependence for inhibition. Inhibition potency is correlated with the xanthene dye's LUMO energy, which affects ability to form light-activated radical anions, a likely active inhibitor form. Consistent with this hypothesis, rose bengal inhibition is light-dependent and demonstrates the expected red shifted spectrum upon binding to DUSP5, with a Kd of 690 nM. These studies provide a mechanistic foundation for further development of xanthene dyes for treating vascular diseases that respond to DUSP5 inhibition, with the following relative potencies: rose bengal > merbromin > erythrosin B > eosin Y.

Highly Reactive CoIII,IV2(µ-O)2 Diamond Core Complex That Cleaves C-H Bonds.

The selective activation of strong sp3 C-H bonds at mild conditions is a key step in many biological and synthetic transformations and an unsolved challenge for synthetic chemists. In nature, soluble methane monooxygenase (sMMO) is one representative example of nonheme dinuclear iron-dependent enzymes that activate strong sp3 C-H bonds by a high-valent diiron(IV) intermediate Q. To date, synthetic model complexes of sMMO-Q have shown limited abilities to oxidize strong C-H bonds. In this work, we generated a high-valent CoIII,IV2(µ-O)2 complex 3 supported by a tetradentate tris(2-pyridylmethyl)amine (TPA) ligand via one-electron oxidation of its CoIII2(µ-O)2 precursor 2. Characterization of 2 and 3 using X-ray absorption spectroscopy and DFT calculations showed that both species possess a diamond core structure with a short Co···Co distance of 2.78 Å. Furthermore, 3 is an EPR active species showing an S = 1/2 signal with clearly observable hyperfine splittings originated from the coupling of the 59Co nuclear spin with the electronic spin. Importantly, 3 is a highly reactive oxidant for sp3 C-H bonds, and an oxygenation reagent. 3 has the highest rate constant (1.5 M-1 s-1 at -60 °C) for oxidizing 9,10-dihydroanthracene (DHA) compared to diamond core complexes of other first-row transition metals including Mn, Fe and Cu reported previously. Specifically, 3 is about 4-5 orders of magnitude more reactive than the diiron analogs FeIII,IV2(µ-O)2 and FeIV2(µ-O)2 supported by TPA and related ligands. These findings shed light on future development of more reactive approaches for C-H bond activation by bioinspired dicobalt complexes.

Exclusively Proton Conductive Membranes Based on Reduced Graphene Oxide Polymer Composites.

Proton exchange membranes are at the heart of various technologies utilizing electrochemical storage of intermittent energy sources and powering electrical devices. Current state of the art membranes are based on perfluorosulfonic acid, introduced more than a half century ago. Low specificity to protons accompanied by permeance by other species is one of the main impediments for various promising applications in green technologies in an energy sustainable economy. Here we present composite membranes that are exclusively proton selective and do not allow crossover of any ionic or molecular species other than protons. Membranes have high proton conductivity and exceptional mechanical and chemical stability and thus may significantly improve performance of hydrogen-based technologies such as electrolyzers, various kinds of fuel cells, and flow batteries in the future.

Coexistence of structurally similar but electronically distinct isomers of delocalized cation radicals as a basis for the development of functional materials.

Certain low-symmetry aromatic molecules with a small HOMO/HOMO-1 energy gap might co-exist as electronic isomers in their cation radical states that differ only in bond lengths yet have distinct optical and electronic properties. These electronic isomers are sensitive to the environment and might be used for the development of novel functional materials.

Bimolecular Cross-Metathesis of a Tetrasubstituted Alkene with Allylic Sulfones.

Exquisite control of catalytic metathesis reactivity is possible through ligand-based variation of ruthenium carbene complexes. Sterically hindered alkenes, however, remain a generally recalcitrant class of substrates for intermolecular cross-metathesis. Allylic chalcogenides (sulfides and selenides) have emerged as "privileged" substrates that exhibit enhanced turnover rates with the commercially available second-generation ruthenium catalyst. Increased turnover rates are advantageous when competing catalyst degradation is limiting, although specific mechanisms have not been defined. Herein, we describe facile cross-metathesis of allylic sulfone reagents with sterically hindered isoprenoid alkene substrates. Furthermore, we demonstrate the first example of intermolecular cross-metathesis of ruthenium carbenes with a tetrasubstituted alkene. Computational analysis by combined coupled cluster/DFT calculations exposes a favorable energetic profile for metallacyclobutane formation from chelating ruthenium ß-chalcogenide carbene intermediates. These results establish allylic sulfones as privileged reagents for a substrate-based strategy of cross-metathesis derivatization.

Role of Conserved Histidine and Serine in the HCXXXXXRS Motif of Human Dual-Specificity Phosphatase 5.

BACKGROUND: The mitogen-activated protein kinase (MAPK) pathway is functionally generic and critical in maintaining physiological homeostasis and normal tissue development. This pathway is under tight regulation, which is in part mediated by dual-specific phosphatases (DUSPs), which dephosphorylate serine, threonine, and tyrosine residues of the ERK family of proteins. DUSP5 is of high clinical interest because of mutations we identified in this protein in patients with vascular anomalies. Unlike other DUSPs, DUSP5 has unique specificity toward substrate pERK1/2. Using molecular docking and simulation strategies, we previously showed that DUSP5 has two pockets, which are utilized in a specific fashion to facilitate specificity toward catalysis of its substrate pERK1/2. Remarkably, most DUSPs share high similarity in their catalytic sites. Studying the catalytic domain of DUSP5 and identifying amino acid residues that are important for dephosphorylating pERK1/2 could be critical in developing small molecules for therapies targeting DUSP5. RESULTS: In this study, we utilized computational modeling to identify and predict the importance of two conserved amino acid residues, H262 and S270, in the DUSP5 catalytic site. Modeling studies predicted that catalytic activity of DUSP5 would be altered if these critical conserved residues were mutated. We next generated independent Glutathione-S-Transferase (GST)-tagged full-length DUSP5 mutant proteins carrying specific mutations H262F and S270A in the phosphatase domain. Biochemical analysis was performed on these purified proteins, and consistent with our computational prediction, we observed altered enzyme activity kinetic profiles for both mutants with a synthetic small molecule substrate (pNPP) and the physiological relevant substrate (pERK) when compared to wild type GST-DUSP5 protein. CONCLUSION: Our molecular modeling and biochemical studies combined demonstrate that enzymatic activity of phosphatases can be manipulated by mutating specific conserved amino acid residues in the catalytic site (phosphatase domain). This strategy could facilitate generation of small molecules that will serve as agonists/antagonists of DUSP5 activity.

Molecular Actuators in Action: Electron-Transfer-Induced Conformation Transformation in Cofacially Arrayed Polyfluorenes.

There is much current interest in the design of molecular actuators, which undergo reversible, controlled motion in response to an external stimulus (light, heat, oxidation, etc.). Here we describe the design and synthesis of a series of cofacially arrayed polyfluorenes (MeF nH m) with varied end-capping groups, which undergo redox-controlled electromechanical actuation. Such cofacially arrayed polyfluorenes are a model molecular scaffold to investigate fundamental processes of charge and energy transfer across a π-stacked assembly, and we show with the aid of NMR and optical spectroscopies, X-ray crystallography and DFT calculations that in the neutral state the conformation of MeF nH1 and MeF nH2 is open rather than cofacial, with a conformational dependence that is highly influenced by the local environment. Upon (electro)chemical oxidation, these systems undergo a reversible transformation into a closed fully π-stacked conformation, driven by charge-resonance stabilization of the cationic charge. These findings are expected to aid the design of novel wire-like cofacially arrayed systems capable of undergo redox-controlled actuation.

Ab Initio Study Predicts That Enigmatic Isonitrosyl Fluoride Should Be Stable at Low Temperatures yet Unnoticeable Due to Its Photoreactivity.

Isonitrosyl fluoride F-ON remains an undetected molecule despite multiple attempts to generate it and successful identification of other isonitrosyl halides (X-ONs) via phototransformations of corresponding X-NOs. We investigated this problem using ab initio methods and found no evidence of instability of F-ON at low temperatures of 8-10 K. Instead, experimental observation of F-ON is likely challenged by the (1) different nature of photoexcitation of F-NO and its quantum yield being lower than those of other X-NOs and (2) the presence of a bright charge-transfer transition in the F-ON spectrum that likely overlaps with the weak band of F-NO used for photoexcitation. Formation of F-ON via symmetry-prohibited photoexcitation of F-NO is followed by its immediate photodecomposition to the charge-transfer excited state and its conversion to F-NO upon de-excitation. Thus, F-ON should be readily observable using non-photochemistry methods such as microwave spectroscopy.

Acid-facilitated product release from a Mo(IV) center: relevance to oxygen atom transfer reactivity of molybdenum oxotransferases.

We report that pyridinium ions (HPyr+) accelerate the conversion of [Tp*MoIVOCl(OPMe3)] (1) to [Tp*MoIVOCl(NCCH3)] (2) by 103-fold, affording 2 in near-quantitative yield; Tp* = hydrotris(3,5-dimethyl-1-pyrazolyl)borate. This novel reactivity and the mechanism of this reaction were investigated in detail. The formation of 2 followed pseudo-first-order kinetics, with the observed pseudo-first-order rate constant (k obs) linearly correlated with [HPyr+]. An Eyring plot revealed that this HPyr+-facilitated reaction has a small positive value of ∆S ‡ indicative of a dissociative interchange (Id) mechanism, different from the slower associative interchange (Ia) mechanism in the absence of HPyr+ marked with a negative ∆S ‡. Interestingly, log(k obs) was found to be linearly correlated to the acidity of substituted pyridinium ions. This novel reactivity is further investigated using combined DFT and ab initio coupled cluster methods. Different reaction pathways, including Id, Ia, and possible alternative routes in the absence or presence of HPyr+, were considered, and enthalpy and free energies were calculated for each pathway. Our computational results further underscored that the Id route is energetically favored in the presence of HPyr+, in contrast with the preferred Ia-NNO pathway in the absence of HPyr+. Our computational results also revealed molecular-level details for the HPyr+-facilitated Id route. Specifically, HPyr+ initially becomes hydrogen-bonded to the oxygen atom of the Mo(IV)-OPMe3 moiety, which lowers the activation barrier for the Mo-OPMe3 bond cleavage in a rate-limiting step to dissociate the OPMe3 product. The implications of our results were discussed in the context of molybdoenzymes, particularly the reductive half-reaction of sulfite oxidase.

Dual Specificity Phosphatase 5-Substrate Interaction: A Mechanistic Perspective.

The mammalian genome contains approximately 200 phosphatases that are responsible for catalytically removing phosphate groups from proteins. In this review, we discuss dual specificity phosphatase 5 (DUSP5). DUSP5 belongs to the dual specificity phosphatase (DUSP) family, so named after the family members' abilities to remove phosphate groups from serine/threonine and tyrosine residues. We provide a comparison of DUSP5's structure to other DUSPs and, using molecular modeling studies, provide an explanation for DUSP5's mechanistic interaction and specificity toward phospho-extracellular regulated kinase, its only known substrate. We also discuss new insights from molecular modeling studies that will influence our current thinking of mitogen-activated protein kinase signaling. Finally, we discuss the lessons learned from identifying small molecules that target DUSP5, which might benefit targeting efforts for other phosphatases. © 2017 American Physiological Society. Compr Physiol 7:1449-1461, 2017.