The performance of hybrid DFT for mechanisms involving transition metal complexes in enzymes

Comparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy

Molecular dynamics (MD) simulations are a powerful approach to studying the structure and dynamics of proteins related to health and disease. Advances in the MD field allow modeling proteins with high accuracy. However, modeling metal ions and their interactions with proteins is still challenging. NPL4 is a zinc-binding protein and works as a cofactor for p97 to regulate protein homeostasis. NPL4 is of biomedical importance and has been proposed as the target of disulfiram, a drug recently repurposed for cancer treatment. Experimental studies proposed that the disulfiram metabolites, bis-(diethyldithiocarbamate)‑copper and cupric ions, induce NPL4 misfolding and aggregation. However, the molecular details of their interactions with NPL4 and consequent structural effects are still elusive. Here, biomolecular simulations can help to shed light on the related structural details. To apply MD simulations to NPL4 and its interaction with copper the first important step is identifying a suitable force field to describe the protein in its zinc-bound states. We examined different sets of non-bonded parameters because we want to study the misfolding mechanism and cannot rule out that the zinc may detach from the protein during the process and copper replaces it. We investigated the force-field ability to model the coordination geometry of the metal ions by comparing the results from MD simulations with optimized geometries from quantum mechanics (QM) calculations using model systems of NPL4. Furthermore, we investigated the performance of a force field including bonded parameters to treat copper ions in NPL4 that we obtained based on QM calculations.

Theoretical Study of the Catalytic Mechanism of the Cu-Only Superoxide Dismutase

The catalytic mechanisms for the wild-type and the mutated Cu-only superoxide dismutase were studied using the hybrid density functional B3LYP and a quantum chemical cluster approach. Optimal protonation states of the active site were examined for each stage of the catalytic cycle. For both the reductive and the oxidative half-reactions, the arrival of the substrate O2•- was found to be accompanied by a charge-compensating H⁺ with exergonicities of -15.4 kcal·mol and -4.7 kcal·mol, respectively. The second-sphere Glu-110 and first-sphere His-93 were suggested to be the transient protonation site for the reductive and the oxidative half-reactions, respectively, which collaborates with the hydrogen bonding water chain to position the substrate near the redox-active copper center. For the reductive half-reaction, the rate-limiting step was found to be the inner-sphere electron transfer from the partially coordinated O2•- to Cu^II with a barrier of 8.1 kcal·mol. The formed O₂ is released from the active site with an exergonicity of -14.9 kcal·mol. For the oxidative half-reaction, the inner-sphere electron transfer from Cu^I to the partially coordinated O2•- was found to be accompanied by the proton transfer from the protonated His-93 and barrierless. The rate-limiting step was found to be the second proton transfer from the protonated Glu-110 to HO2- with a barrier of 7.3 kcal·mol. The barriers are reasonably consistent with experimental activities, and a proton-transfer rate-limiting step in the oxidative half-reaction could explain the experimentally observed pH-dependence. For the E110Q CuSOD, Asp-113 was suggested to be likely to serve as the transient protonation site in the reductive half-reaction. The rate-limiting barriers were found to be 8.0 and 8.6 kcal·mol, respectively, which could explain the slightly lower performance of E110X mutants. The results were found to be stable, with respect to the percentage of exact exchange in B3LYP.

Enzymatic Control over Reactive Intermediates Enables Direct Oxidation of Alkenes to Carbonyls by a P450 Iron-Oxo Species

The aerobic oxidation of alkenes to carbonyls is an important and challenging transformation in synthesis. Recently, a new P450-based enzyme (aMOx) has been evolved in the laboratory to directly oxidize styrenes to their corresponding aldehydes with high activity and selectivity. The enzyme utilizes a heme-based, high-valent iron-oxo species as a catalytic oxidant that normally epoxidizes alkenes, similar to other catalysts. How the evolved aMOx enzyme suppresses the commonly preferred epoxidation and catalyzes direct carbonyl formation is currently not well understood. Here, we combine computational modelling together with mechanistic experiments to study the reaction mechanism and unravel the molecular basis behind the selectivity achieved by aMOx. Our results describe that although both pathways are energetically accessible diverging from a common covalent radical intermediate, intrinsic dynamic effects determine the strong preference for epoxidation. We discovered that aMOx overrides these intrinsic preferences by controlling the accessible conformations of the covalent radical intermediate. This disfavors epoxidation and facilitates the formation of a carbocation intermediate that generates the aldehyde product through a fast 1,2-hydride migration. Electrostatic preorganization of the enzyme active site also contributes to the stabilization of the carbocation intermediate. Computations predicted that the hydride migration is stereoselective due to the enzymatic conformational control over the intermediate species. These predictions were corroborated by experiments using deuterated styrene substrates, which proved that the hydride migration is cis- and enantioselective. Our results demonstrate that directed evolution tailored a highly specific active site that imposes strong steric control over key fleeting biocatalytic intermediates, which is essential for accessing the carbonyl forming pathway and preventing competing epoxidation.

Feasible Cluster Model Method for Simulating the Redox Potentials of Laccase CueO and Its Variant

Laccases are regarded as versatile green biocatalysts, and recent scientific research has focused on improving their redox potential for broader industrial and environmental applications. The density functional theory (DFT) quantum mechanics approach, sufficiently rigorous and efficient for the calculation of electronic structures, is conducted to better comprehend the connection between the redox potential and the atomic structural feature of laccases. According to the crystal structure of wild type laccase CueO and its variant, a truncated miniature cluster model method was established in this research. On the basic of thermodynamic cycle, the overall Gibbs free energy variations before and after the one-electron reduction were calculated. It turned out that the trends of redox potentials to increase after variant predicted by the theoretical calculations correlated well with those obtained by experiments, thereby validating the feasibility of this cluster model method for simulating the redox potentials of laccases.

Reversible Structural Isomerization of Nature's Water Oxidation Catalyst Prior to O-O Bond Formation

Photosynthetic water oxidation is catalyzed by a manganese–calcium oxide cluster, which experiences five “S-states” during a light-driven reaction cycle. The unique “distorted chair”-like geometry of the Mn₄CaO₅₍₆₎ cluster shows structural flexibility that has been frequently proposed to involve “open” and “closed”-cubane forms from the S₁ to S₃ states. The isomers are interconvertible in the S₁ and S₂ states, while in the S₃ state, the open-cubane structure is observed to dominate inThermosynechococcus elongatus (cyanobacteria) samples. In this work, using density functional theory calculations, we go beyond the S₃⁺Y_z state to the S₃ⁿY_z^• → S₄⁺Y_z step, and report for the first time that the reversible isomerism, which is suppressed in the S₃⁺Y_z state, is fully recovered in the ensuing S₃ⁿY_z^• state due to the proton release from a manganese-bound water ligand. The altered coordination strength of the manganese–ligand facilitates formation of the closed-cubane form, in a dynamic equilibrium with the open-cubane form. This tautomerism immediately preceding dioxygen formation may constitute the rate limiting step for O₂ formation, and exert a significant influence on the water oxidation mechanism in photosystem II.

A Reactive, Photogenerated High-Spin (S = 2) FeIV(O) Complex via O2 Activation

Addition of dioxygen at low temperature to the non-heme ferrous complex Fe^II(Me₃TACN)((OSi^Ph2)₂O) (1) in 2-MeTHF produces a peroxo-bridged diferric complex Fe₂^III(μ-O₂)(Me₃TACN)₂((OSi^Ph2)₂O)₂ (2), which was characterized by UV-vis, resonance Raman, and variable field Mössbauer spectroscopies. Illumination of a frozen solution of 2 in THF with white light leads to homolytic O-O bond cleavage and generation of a Fe^IV(O) complex 4 (ν(Fe=O) = 818 cm^-1; δ = 0.22 mm s^-1, ΔE_Q = 0.23 mm s^-1). Variable field Mössbauer spectroscopy measurements show that 4 is a rare example of a high-spin S = 2 Fe^IV(O) complex and the first synthetic example to be generated directly from O₂. Complex 4 is highly reactive, as expected for a high-spin ferryl, and decays rapidly in fluid solution at cryogenic temperatures. This decay process in 2-MeTHF involves C-H cleavage of the solvent. However, the controlled photolysis of 2 in situ with visible light and excess phenol substrate leads to competitive phenol oxidation, via the proposed transient generation of 4 as the active oxidant.

Nonheme Iron Imido Complexes Bearing a Non-Innocent Ligand: A Synthetic Chameleon Species in Oxidation Reactions

High-valent iron-imido complexes can perform C-H activation and sulfimidation reactions, but are far less studied than the more ubiquitous iron-oxo species. As case studies, we have looked at a recently published iron(V)-imido ligand π-cation radical complex, which is formally an iron(VI)-imido complex [Fe^V (NTs)(TAML^+. )] (1; NTs=tosylimido), and an iron(V)-imido complex [Fe^V (NTs)(TAML)]^- (2). Using a theoretical approach, we found that they have multiple energetically close-lying electromers, sometimes even without changing spin states, reminiscent of the so-called Compound I in Cytochrome P450. When studying their reactivity theoretically, it is indeed found that their electronic structures may change to perform efficient oxidations, emulating the multi-spin state reactivity in Fe^IV O systems. This is actually in contrast to the known [Fe^V (O)(TAML)]^- species (3), where the reactions occur only on the ground spin state. We also looked into the whole reaction pathway for the C-H bond activation of 1,4-cyclohexadiene by these intermediates to reproduce the experimentally observed products, including steps that usually attract no interest (neither theoretically nor experimentally) due to their non-rate-limiting status and fast reactivity. A new "clustering non-rebound mechanism" is presented for this C-H activation reaction.

Catalysis of Thermal Isomerization of Methyl Yellow by Salts

Cu²⁺ ions are reported to catalyze the thermal isomerization (TI) of cis-azobenzene. It was found that some alkali halides (NaCl, KCl, NaBr, and KBr) also catalyze the TI of 4-dimethylamino-azobenzene in ethanol. These tendencies were attributed to the interaction between the azo group and the cation based on experimental data and density functional theory (DFT) calculations. Some Na salts (CH₃COONa, Na₂HPO₄, and Na₂SO₃) were found to inhibit the TI of 4-dimethylamino-azobenzene in ethanol. It is inferred that the weak acid ions in these salts decrease the concentration of H⁺ ions that catalyze the TI process.

Quantum Chemical and QM/MM Models in Biochemistry

Quantum chemical (QC) calculations provide a basis for deriving a microscopic understanding of enzymes and photobiological systems. Here we describe how QC models can be used to explore the electronic structure, dynamics, and energetics of biomolecules. We introduce the hybrid quantum mechanics/classical mechanics (QM/MM) approach, where a quantum mechanically described system of interest is embedded in a classically described force field representation of the biochemical surroundings. We also discuss the QM cluster model approach, as well as embedding theories, that provide complementary methodologies to model quantum mechanical effects in biomolecules. The chapter also provides some practical guides for building quantum biochemical models using the quinone reduction catalysis in respiratory complex I and a model reaction in solution as examples.

Mechanistic insights into the allylic oxidation of aliphatic compounds by tetraamido iron(v) species: A C–H vs. O–H bond activation

This work is based on a deep insight into a comparative study of C–H vs. O–H bond activation of allylic compound by the high valent iron complex. Our theoretical findings can help to design catalysts with better efficiency for catalytic reactions.

Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation

The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out. Based on the results, a branched mechanism was proposed. An FeII-peroxysuccinate complex with a dissociated CO2 generated through the nucleophilic attack of the superoxo moiety of the Fe-O2 species on the keto carbon of 2OG is the key common intermediate in both reactions. A competition between the subsequent CO2 insertion (a key step in the ethylene-forming pathway) and the O-O bond cleavage (leading to the formation of succinate) governs the product selectivity. The calculated reaction barriers suggested that the CO2 insertion is favored over the O-O bond cleavage. This is consistent with the product preference observed in experiments. By comparison with the results of AsqJ (an Fe/2OG oxygenase that leads to substrate oxidation exclusively), the protein environment was found to be crucial for the selectivity. Further calculations demonstrated that the local electric field of the protein environment in EFE promotes ethylene formation by acting as a charge template, exemplifying the importance of the electrostatic interaction in enzyme catalysis. These findings offer mechanistic insights into the EFE catalysis and provide important clues for better understanding the unique ethylene-forming capability of EFE compared with other Fe/2OG oxygenases.

A Nonheme Thiolate-Ligated Cobalt Superoxo Complex: Synthesis and Spectroscopic Characterization, Computational Studies, and Hydrogen Atom Abstraction Reactivity

The synthesis and characterization of a Co(II) dithiolato complex Co(Me₃TACN)(S₂SiMe₂) (1) are reported. Reaction of 1 with O₂ generates a rare thiolate-ligated cobalt-superoxo species Co(O₂)(Me₃TACN)(S₂SiMe₂) (2) that was characterized spectroscopically and structurally by resonance Raman, EPR, and X-ray absorption spectroscopies as well as density functional theory. Metal-superoxo species are proposed to S-oxygenate metal-bound thiolate donors in nonheme thiol dioxygenases, but 2 does not lead to S-oxygenation of the intramolecular thiolate donors and does not react with exogenous sulfur donors. However, complex 2 is capable of oxidizing the O-H bonds of 2,2,6,6-tetramethylpiperidin-1-ol derivatives via H atom abstraction. Complementary proton-coupled electron-transfer reactivity is seen for 2 with separated proton/reductant pairs. The reactivity studies indicate that 2 can abstract H atoms from weak X-H bonds with bond dissociation free energy (BDFE) ≤ 70 kcal mol^-1. DFT calculations predict that the putative Co(OOH) product has an O-H BDFE = 67 kcal mol^-1, which matches the observed pattern of reactivity seen for 2. These data provide new information regarding the selectivity of S-oxygenation versus H atom abstraction in thiolate-ligated nonheme metalloenzymes that react with O₂.

Computational study of acylphloroglucinols: an investigation with many branches

Acylphloroglucinols (ACPLs) are a broad class of compounds structurally derived from phloroglucinol and characterised by the presence of a CRO group. They are interesting for their biological activities and their potentialities as lead compounds in drug development. The current review considers a series of works which, altogether, sum up to a systematic computational study of ACPLs in vacuo and in three solvents – chloroform, acetonitrile and water. An initial set of studies, focusing on ACPLs as a class and utilising an adequately representative selection of molecules, identified patterns in the conformational preferences and molecular properties of ACPLs, which appear valid for the whole class or for specific subclasses such as monomeric ACPLs, dimeric ACPLs, ACPLs with substituents containing C=C double bonds, etc. The validity of the identified patterns was further verified through the study of additional and significantly different ACPL molecules, as well as other molecular structures containing ACPL units. Furthermore, the computational study of ACPLs proved interesting for the insights into the factors stabilising their conformers, first of all intramolecular hydrogen bonding, which plays dominant roles in determining conformational preferences and energetics. The current review outlines the objectives, approaches and main results of these studies. The obtained information may be relevant for further studies aimed at a better understanding of the molecular bases of the biological activities of ACPLs.

How does Mo-dependent perchlorate reductase work in the decomposition of oxyanions?

The mechanisms of Mo-dependent perchlorate reductase (PcrAB)-catalyzed decomposition of perchlorate, bromate, iodate, and nitrate were revealed by density functional calculations.

Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory

We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag+-mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag+-mediated DNA species.

Biocatalytic Routes to Lactone Monomers for Polymer Production

Monoterpenoids offer potential as biocatalytically derived monomer feedstocks for high-performance renewable polymers. We describe a biocatalytic route to lactone monomers menthide and dihydrocarvide employing Baeyer-Villiger monooxygenases (BVMOs) from Pseudomonas sp. HI-70 (CPDMO) and Rhodococcus sp. Phi1 (CHMOPhi1) as an alternative to organic synthesis. The regioselectivity of dihydrocarvide isomer formation was controlled by site-directed mutagenesis of three key active site residues in CHMOPhi1. A combination of crystal structure determination, molecular dynamics simulations, and mechanistic modeling using density functional theory on a range of models provides insight into the origins of the discrimination of the wild type and a variant CHMOPhi1 for producing different regioisomers of the lactone product. Ring-opening polymerizations of the resultant lactones using mild metal-organic catalysts demonstrate their utility in polymer production. This semisynthetic approach utilizing a biocatalytic step, non-petroleum feedstocks, and mild polymerization catalysts allows access to known and also to previously unreported and potentially novel lactone monomers and polymers.

σ-Holes and σ-lumps direct the Lewis basic and acidic interactions of noble metal nanoparticles: introducing regium bonds

Using local DFT-based probes for electrostatic as well as charge transfer/polarization interactions, we are able to characterize Lewis basic and acidic sites on copper, silver and gold nanoparticles.

Complexes of arzanol with a Cu2+ ion: a DFT study

Arzanol (C₂₂H₂₆O₇) is a naturally occurring acylphloroglucinol largely responsible for the anti-inflammatory, anti-oxidant, antibiotic and antiviral activities of Helichrysum italicum. Like all acylphloroglucinols, the molecule contains a carboxylic substituent (-COR group); for arzanol, this is a -COCH₃ group. The molecule is further characterized by the presence of an α-pyrone ring bonded in meta to -COR through a methylene bridge, and of a prenyl chain bonded to the other meta position. The molecule can form up to three intramolecular hydrogen bonds (IHB) simultaneously, and their presence and patterns are the major stabilizing factors. This work considers complexes of representative conformers of arzanol with a Cu²⁺ ion, taking into account the different possibilities for the binding of the Cu²⁺ ion to the electron-density rich sites of the molecule and including simultaneous coordination to two geometrically suitable sites. Calculations were performed at the DFT/B3LYP level, using the 6-31+G(d,p) basis set for the C, O and H atoms and the LANL2DZ pseudopotential for the Cu²⁺ ion. Interaction energies show preference for simultaneous binding of Cu²⁺ to two sites. Simultaneous binding to the O of a phenol OH neighboring the prenyl chain and to the π bond of the prenyl chain appears to be the most favorable option, followed by simultaneous binding to the sp² O of the α-pyrone ring and the O of the phenol OH ortho to -COR on the side of the α-pyrone ring. The charge of the Cu²⁺ ion is reduced to +1 or slightly less in the complexes, which is consistent with the molecules' antioxidant (reducing) ability. Graphical abstract The copper ion prefers to attach to two sites of the arzanol molecule simultaneously. The arzanol molecule reduces the charge of the copper ion from +2 to +1 by transferring an electron to it; it becomes a radical molecular cation. The distribution of the unpaired electron in the molecule (as highlighted by the spin density maps) depends on the site/s to which the Cu²⁺ ion binds and on the molecule's conformer.

Self-consistent hybrid functionals for solids: a fully-automated implementation

A fully-automated algorithm for the determination of the system-specific optimal fraction of exact exchange in self-consistent hybrid functionals of the density-functional-theory is illustrated, as implemented into the public Crystal program. The exchange fraction of this new class of functionals is self-consistently updated proportionally to the inverse of the dielectric response of the system within an iterative procedure (Skone et al 2014 Phys. Rev. B 89, 195112). Each iteration of the present scheme, in turn, implies convergence of a self-consistent-field (SCF) and a coupled-perturbed-Hartree-Fock/Kohn-Sham (CPHF/KS) procedure. The present implementation, beside improving the user-friendliness of self-consistent hybrids, exploits the unperturbed and electric-field perturbed density matrices from previous iterations as guesses for subsequent SCF and CPHF/KS iterations, which is documented to reduce the overall computational cost of the whole process by a factor of 2.

Nonclassical Single-State Reactivity of an Oxo-Iron(IV) Complex Confined to Triplet Pathways

C-H bond activation mediated by oxo-iron (IV) species represents the key step of many heme and nonheme O₂-activating enzymes. Of crucial interest is the effect of spin state of the Fe^IV(O) unit. Here we report the C-H activation kinetics and corresponding theoretical investigations of an exclusive tetracarbene ligated oxo-iron(IV) complex, [L^NHCFe^IV(O)(MeCN)]²⁺ (1). Kinetic traces using substrates with bond dissociation energies (BDEs) up to 80 kcal mol^-1 show pseudo-first-order behavior and large but temperature-dependent kinetic isotope effects (KIE 32 at -40 °C). When compared with a topologically related oxo-iron(IV) complex bearing an equatorial N-donor ligand, [L^TMCFe^IV(O) (MeCN)]²⁺ (A), the tetracarbene complex 1 is significantly more reactive with second order rate constants k'₂ that are 2-3 orders of magnitude higher. UV-vis experiments in tandem with cryospray mass spectrometry evidence that the reaction occurs via formation of a hydroxo-iron(III) complex (4) after the initial H atom transfer (HAT). An extensive computational study using a wave function based multireference approach, viz. complete active space self-consistent field (CASSCF) followed by N-electron valence perturbation theory up to second order (NEVPT2), provided insight into the HAT trajectories of 1 and A. Calculated free energy barriers for 1 reasonably agree with experimental values. Because the strongly donating equatorial tetracarbene pushes the Fe-d_x²-y² orbital above d_z², 1 features a dramatically large quintet-triplet gap of ∼18 kcal/mol compared to ∼2-3 kcal/mol computed for A. Consequently, the HAT process performed by 1 occurs on the triplet surface only, in contrast to complex A reported to feature two-state-reactivity with contributions from both triplet and quintet states. Despite this, the reactive Fe^IV(O) units in 1 and A undergo the same electronic-structure changes during HAT. Thus, the unique complex 1 represents a pure "triplet-only" ferryl model.

Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes

The 1994 structure of a transition-state analogue with AlF₄^- and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO₃^- ) groups. The number of enzyme structures in the PDB containing metal fluorides (MF_x ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF₃^- that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF₄^- , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF₃^- and putative AlF₃⁰ moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.

Thiolated arsenicals in arsenic metabolism: Occurrence, formation, and biological implications

Arsenic (As) is a notoriously toxic pollutant of health concern worldwide with potential risk of cancer induction, but meanwhile it is used as medicines for the treatment of different conditions including hematological cancers. Arsenic can undergo extensive metabolism in biological systems, and both toxicological and therapeutic effects of arsenic compounds are closely related to their metabolism. Recent studies have identified methylated thioarsenicals as a new class of arsenic metabolites in biological systems after exposure of inorganic and organic arsenicals, including arsenite, dimethylarsinic acid (DMA^V), dimethylarsinous glutathione (DMA^IIIGS), and arsenosugars. The increasing detection of thiolated arsenicals, including monomethylmonothioarsonic acid (MMMTA^V), dimethylmonothioarsinic acid (DMMTA^V) and its glutathione conjugate (DMMTA^VGS), and dimethyldithioarsinic acid (DMDTA^V) suggests that thioarsenicals may be important metabolites and play important roles in arsenic toxicity and therapeutic effects. Here we summarized the reported occurrence of thioarsenicals in biological systems, the possible formation pathways of thioarsenicals, and their toxicity, and discussed the biological implications of thioarsenicals on arsenic metabolism, toxicity, and therapeutic effects.

The Decarboxylation of α,β-Unsaturated Acid Catalyzed by Prenylated FMN-Dependent Ferulic Acid Decarboxylase and the Enzyme Inhibition

Ferulic acid decarboxylase (Fdc1) is able to catalyze the decarboxylation of α,β-unsaturated acids using a novel cofactor, prenylated flavin mononucleotide (PrFMN). Using density functional theory calculations, we here have investigated the Fdc1 reaction mechanism with the substrate of α-methylcinnamic acid. It is demonstrated that Fdc1 employs a 1,3-dipolar cycloaddition mechanism involving four concerted steps, where the Glu282 acts as a crucial proton donor to protonate the α carbon (C_α). The last step, the decomposition of a pyrrolidine species, is rate-limiting with an overall barrier of 18.9 kcal mol^-1. Furthermore, when α-hydroxycinnamic acid is used, the Glu282 is found to have another face to transport the hydroxyl proton to the C_β atom to promote the tautomerization from enol intermediate to ketone species leading to the inhibition of the Fdc1 enzyme. The PrFMN roles are also discussed in detail.

Spectroscopic Evidence for the Two C-H-Cleaving Intermediates of Aspergillus nidulans Isopenicillin N Synthase

The enzyme isopenicillin N synthase (IPNS) installs the β-lactam and thiazolidine rings of the penicillin core into the linear tripeptide l-δ-aminoadipoyl-l-Cys-d-Val (ACV) on the pathways to a number of important antibacterial drugs. A classic set of enzymological and crystallographic studies by Baldwin and co-workers established that this overall four-electron oxidation occurs by a sequence of two oxidative cyclizations, with the β-lactam ring being installed first and the thiazolidine ring second. Each phase requires cleavage of an aliphatic C-H bond of the substrate: the pro-S-CCys,β-H bond for closure of the β-lactam ring, and the CVal,β-H bond for installation of the thiazolidine ring. IPNS uses a mononuclear non-heme-iron(II) cofactor and dioxygen as cosubstrate to cleave these C-H bonds and direct the ring closures. Despite the intense scrutiny to which the enzyme has been subjected, the identities of the oxidized iron intermediates that cleave the C-H bonds have been addressed only computationally; no experimental insight into their geometric or electronic structures has been reported. In this work, we have employed a combination of transient-state-kinetic and spectroscopic methods, together with the specifically deuterium-labeled substrates, A[d2-C]V and AC[d8-V], to identify both C-H-cleaving intermediates. The results show that they are high-spin Fe(III)-superoxo and high-spin Fe(IV)-oxo complexes, respectively, in agreement with published mechanistic proposals derived computationally from Baldwin's founding work.

The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes

HIGHLIGHTS Computational techniques provide accurate descriptions of the structure and dynamics of biological systems, contributing to their understanding at an atomic level.Classical MD simulations are a precious computational tool for the processes where no chemical reactions take place.QM calculations provide valuable information about the enzyme activity, being able to distinguish among several mechanistic pathways, provided a carefully selected cluster model of the enzyme is considered.Multiscale QM/MM simulation is the method of choice for the computational treatment of enzyme reactions offering quantitative agreement with experimentally determined reaction parameters.Molecular simulation provide insight into the mechanism of both the catalytic activity and inhibition of monoamine oxidases, thus aiding in the rational design of their inhibitors that are all employed and antidepressants and antiparkinsonian drugs. Aging society and therewith associated neurodegenerative and neuropsychiatric diseases, including depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease, urgently require novel drug candidates. Targets include monoamine oxidases A and B (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and various receptors and transporters. For rational drug design it is particularly important to combine experimental synthetic, kinetic, toxicological, and pharmacological information with structural and computational work. This paper describes the application of various modern computational biochemistry methods in order to improve the understanding of a relationship between the structure and function of large biological systems including ion channels, transporters, receptors, and metabolic enzymes. The methods covered stem from classical molecular dynamics simulations to understand the physical basis and the time evolution of the structures, to combined QM, and QM/MM approaches to probe the chemical mechanisms of enzymatic activities and their inhibition. As an illustrative example, the later will focus on the monoamine oxidase family of enzymes, which catalyze the degradation of amine neurotransmitters in various parts of the brain, the imbalance of which is associated with the development and progression of a range of neurodegenerative disorders. Inhibitors that act mainly on MAO A are used in the treatment of depression, due to their ability to raise serotonin concentrations, while MAO B inhibitors decrease dopamine degradation and improve motor control in patients with Parkinson disease. Our results give strong support that both MAO isoforms, A and B, operate through the hydride transfer mechanism. Relevance of MAO catalyzed reactions and MAO inhibition in the context of neurodegeneration will be discussed.

Spectroscopic and Theoretical Study of Spin-Dependent Electron Transfer in an Iron(III) Superoxo Complex

It was shown previously (J. Am. Chem. Soc. 2014, 136, 10846) that bubbling of O2 into a solution of Fe(II)(BDPP) (H2BDPP = 2,6-bis[[(S)-2-(diphenylhydroxymethyl)-1-pyrrolidinyl]methyl]pyridine) in tetrahydrofuran at -80 °C generates a high-spin (SFe = (5)/2) iron(III) superoxo adduct, 1. Mössbauer studies revealed that 1 is an exchange-coupled system, [Formula: see text], where SR = (1)/2 is the spin of the superoxo radical, of which the spectra were not well enough resolved to determine whether the coupling was ferromagnetic (S = 3 ground state) or antiferromagnetic (S = 2). The glass-forming 2-methyltetrahydrofuran solvent yields highly resolved Mössbauer spectra from which the following data have been extracted: (i) the ground state of 1 has S = 3 (J < 0); (ii) |J| > 15 cm(-1); (iii) the zero-field-splitting parameters are D = -1.1 cm(-1) and E/D = 0.02; (iv) the major component of the electric-field-gradient tensor is tilted ≈7° relative to the easy axis of magnetization determined by the MS = ±3 and ±2 doublets. The excited-state MS = ±2 doublet yields a narrow parallel-mode electron paramagnetic resonance signal at g = 8.03, which was used to probe the magnetic hyperfine splitting of (17)O-enriched O2. A theoretical model that considers spin-dependent electron transfer for the cases where the doubly occupied π* orbital of the superoxo ligand is either "in" or "out" of the plane defined by the bent Fe-OO moiety correctly predicts that 1 has an S = 3 ground state, in contrast to the density functional theory calculations for 1, which give a ground state with both the wrong spin and orbital configuration. This failure has been traced to a basis set superposition error in the interactions between the superoxo moiety and the adjacent five-membered rings of the BDPP ligand and signals a fundamental problem in the quantum chemistry of O2 activation.

Recent application of calculations of metal complexes based on density functional theory

Recent application of density functional theory (DFT) for metal complexes is reviewed to show the achievements of DFT and the challenges for it, as well as the methods for selecting proper functionals.