An extensive computational TDDFT resonance Raman study of lumiflavin is presented including 42 DFT functionals, benchmarked against the experimental Evolution Associated Spectra (EAS) of the equilibrated S1 and T1 states of FMN published earlier. Initially, off-resonance spectra were computed, yielding adequate agreement, and fine-tuning was achieved with the inclusion of specific frequency scaling factors. Since the experimental EAS were obtained under resonance for the singlet and near-resonance for the triplet state, the subsequent inclusion of resonance effects in the calculations improved the correlation for most functionals. Their evaluation according to specific criteria narrowed down the choice to HCTH, OLYP, and TPSSh. Among the included criteria were the percent error of the 0-0 transitions, the quantification of the increase/decrease in correlation due to the addition of resonance enhancements, and the reproduction of the singlet-triplet peak shifts. Owing to the extensive data set, valuable insights were gained to assist similar studies.

The ISWI family protein SMARCA5 contains the ATP-binding pocket that coordinates the catalytic Mg2+ ion and water molecules for ATP hydrolysis. In this study, we demonstrate that SMARCA5 can also possess an alternative metal-binding ability. First, we isolated SMARCA5 on the cobalt column (IMAC) to near homogeneity. Examination of the interactions of SMARCA5 with metal-chelating supports showed that, apart from Co2+, it binds to Cu2+, Zn2+ and Ni2+. The efficiency of the binding to the last-listed metal was influenced by the chelating ligand, resulting in a strong preference for Ni-NTA over the Ni-CM-Asp equivalent. To gain insight in the preferential affinity for the Ni-NTA ligand, QM calculations were performed on model systems and metal-ligand complexes with a limited protein fragment of SMARCA5 containing the double-histidine (dHis) motif. The calculations correlated the observed affinity with the relative stability of the d-block metals to tetradentate ligand coordination over tridentate, as well as their overall octahedral coordination capacity. Likewise, binding free energies derived from model imidazole complexes mirrored the observed Ni-NTA/Ni-CM-Asp preferential affinity. Finally, similar calculations on complexes with a SMARCA5 peptide fragment derived from the AlphaFold structural prediction, captured almost accurately the expected relative stability of the TM complexes, and produced a large energetic separation (~10 kcal∙mol-1) between Ni-NTA and Ni-CM-Asp in favour of the former.

Time-resolved femtosecond-stimulated Raman spectroscopy (FSRS) provides valuable information on the structural dynamics of biomolecules. However, FSRS has been applied mainly up to the nanoseconds regime and above 700 cm−1, which covers only part of the spectrum of biologically relevant time scales and Raman shifts. Here we report on a broadband (~200–2200 cm−1) dual transient visible absorption (visTA)/FSRS set-up that can accommodate time delays from a few femtoseconds to several hundreds of microseconds after illumination with an actinic pump. The extended time scale and wavenumber range allowed us to monitor the complete excited-state dynamics of the biological chromophore flavin mononucleotide (FMN), both free in solution and embedded in two variants of the bacterial light-oxygen-voltage (LOV) photoreceptor EL222. The observed lifetimes and intermediate states (singlet, triplet, and adduct) are in agreement with previous time-resolved infrared spectroscopy experiments. Importantly, we found evidence for additional dynamical events, particularly upon analysis of the low-frequency Raman region below 1000 cm−1. We show that fs-to-sub-ms visTA/FSRS with a broad wavenumber range is a useful tool to characterize short-lived conformationally excited states in flavoproteins and potentially other light-responsive proteins.

Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at 45 positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length.

Melanins are highly conjugated biopolymer pigments that provide photoprotection in a wide array of organisms, from bacteria to humans. The rate-limiting step in melanin biosynthesis, which is theortho-hydroxylation of the amino acid L-tyrosine to L-DOPA, is catalyzed by the ubiquitous enzyme tyrosinase (Ty). Ty contains a coupled binuclear copper active site that binds O2to form a μ:η2:η2-peroxide dicopper(II) intermediate (oxy-Ty), capable of performing the regioselective monooxygenation ofpara-substituted monophenols to catechols. The mechanism of this critical monooxygenation reaction remains poorly understood despite extensive efforts. In this study, we have employed a combination of spectroscopic, kinetic, and computational methods to trap and characterize the elusive catalytic ternary intermediate (Ty/O2/monophenol) under single-turnover conditions and obtain molecular-level mechanistic insights into its monooxygenation reactivity. Our experimental results, coupled with quantum-mechanics/molecular-mechanics calculations, reveal that the monophenol substrate docks in the active-site pocket of oxy-Ty fully protonated, without coordination to a copper or cleavage of the μ:η2:η2-peroxide O-O bond. Formation of this ternary intermediate involves the displacement of active-site water molecules by the substrate and replacement of their H bonds to the μ:η2:η2-peroxide by a single H bond from the substrate hydroxyl group. This H-bonding interaction in the ternary intermediate enables the unprecedented monooxygenation mechanism, where the μ-η2:η2-peroxide O-O bond is cleaved to accept the phenolic proton, followed by substrate phenolate coordination to a copper site concomitant with its aromaticortho-hydroxylation by the nonprotonated μ-oxo. This study provides insights into O2activation and reactivity by coupled binuclear copper active sites with fundamental implications in biocatalysis.

Activation of dioxygen is of extreme importance due to its potential for transformation of methane to valuable products and applications in other selective oxidation reactions. Distant binuclear cationic Fe(II) centers in Fe-ferrierite were shown to split dioxygen at room temperature to form a pair of very active oxygen species (i.e., alpha-oxygens) and subsequently oxidize methane to methanol at room temperature as well. Our study reveals that the activity in splitting dioxygen represents a general property of the distant binuclear cationic Fe(II) centers stabilized in the aluminosilicate matrix. Computational models of the ferrierite, beta, A, and mordenite zeolites with various Al sitings in the rings forming the cationic sites were investigated by periodic DFT calculations including molecular dynamics simulations. The results reveal that the Fe(II) sites stabilized in various zeolite matrices can split dioxygen if the two cationic sites forming the distant binuclear Fe(II) centers (i) face each other, (ii) are parallel, and (iii) are axial, and (iv) the Fe center dot center dot center dot Fe distance lies in a narrow range from ca. 7 to ca. 8 A (ca. 7-ca. 10 A for the distance between the two rings (forming the corresponding cationic sites) in empty zeolites since this distance is equal to or larger than the Fe center dot center dot center dot Fe distances). Our study opens the possibility of developing Fe-zeolite-based systems for the dioxygen activation employed for direct oxidations using various zeolite matrices.

Splitting dioxygen to yield highly active oxygen species attracts enormous attention due to its potential in direct oxidation reactions, mainly in transformation of methane into valuable products. Distant binuclear cationic Fe(II) centers in Fe-ferrierite have recently been shown to be active in splitting dioxygen at room temperature to form very active oxygen species able to oxidize methane to methanol at room temperature as well. Computational models of the distant binuclear transition metal cationic sites (Co(II), Mn(II), and Fe(II)) stabilized in the ferrierite matrix were investigated by periodic density-functional theory calculations including molecular dynamics simulations. The results reveal that the M(II) cations capable of the M(II) -> M(IV) redox cycle with the M horizontal ellipsis M distance of ca 7.4 angstrom stabilized in two adjacent beta sites of ferrierite can split dioxygen. Our study opens the possibility of developing tunable zeolite-based systems for the activation of dioxygen employed for direct oxidations.

Photosensory receptors containing the flavin-binding light-oxygen-voltage (LOV) domain are modular proteins that fulfil a variety of biological functions ranging from gene expression to phototropism. The LOV photocycle is initiated by blue-light and involves a cascade of intermediate species, including an electronically excited triplet state, that leads to covalent bond formation between the flavin mononucleotide (FMN) chromophore and a nearby cysteine residue. Subsequent conformational changes in the polypeptide chain arise due to the remodelling of the hydrogen bond network in the cofactor binding pocket, whereby a conserved glutamine residue plays a key role in coupling FMN photochemistry with LOV photobiology. Although the dark-to-light transition of LOV photosensors has been previously addressed by spectroscopy and computational approaches, the mechanistic basis of the underlying reactions is still not well understood. Here we present a detailed computational study of three distinct LOV domains: EL222 from Erythrobacter litoralis, AsLOV2 from the second LOV domain of Avena sativa phototropin 1, and RsLOV from Rhodobacter sphaeroides LOV protein. Extended protein-chromophore models containing all known crucial residues involved in the initial steps (femtosecond-to-microsecond) of the photocycle were employed. Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path. In turn, for each evolving species, infrared difference spectra were constructed and compared to experimental EL222 and AsLOV2 transient infrared spectra, the former from original work presented here and the latter from the literature. The good agreement between theory and experiment permitted the assignment of the majority of observed bands, notably the ∼1635 cm-1 transient of the adduct state to the carbonyl of the glutamine side chain after rotation. Moreover, both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration. Additionally, the computed infrared shifts of the glutamine and interacting residues could guide experimental research addressing early events of signal transduction in LOV proteins.

Proteins containing the light-oxygen-voltage (LOV) domain are photosensory receptors that mediate biological actions in response to blue light. For instance, the bacterial transcription factor EL222 regulates gene expression in a light-regulated manner and has found use in optogenetic applications. Upon excitation of the embedded flavin mononucleotide (FMN) cofactor, EL222 undergoes structural changes that ultimately drive its association with DNA. However, our knowledge of the light-adapted state(s) and the molecular mechanism underlying the transition between dark and lit states is incomplete. Typically, global protein secondary structure changes and local changes around the FMN chromophore have been detected by Fourier transform infrared (FTIR) spectroscopy (amide I band) and UV-Vis spectroscopy, respectively. To complement these studies, we chose the nitrile stretching vibration as a site-specific infrared reporter of protein microenvironment. EL222 mutants carrying the non-canonical amino acid p-cyanophenylalanine (CNF) were prepared by genetic code expansion technology. We recorded steady-state FTIR difference spectra between irradiated and non-irradiated samples at forty residue positions. Selected EL222 variants were further investigated by time-resolved methods in order to follow the propagation of conformational changes at the FMN, protein backbone (amide I), and protein side-chain (CNF) sites. The varying responses of the CNF tag, which depend on its location, highlights its specificity and sensitivity to evolving amino acid surroundings along the photocycle. Our results emphasize the synergistic combination of protein engineering tools with infrared spectroscopy for delivering site-specific information on light-triggered protein dynamics. Moreover, we show the importance of measuring multiple local and global probes to reveal, with the utmost detail, kinetic pathways in light-sensing proteins.

Flavin mononucleotide (FMN) belongs to the large family of flavins, ubiquitous yellow-coloured biological chromophores that contain an isoalloxazine ring system. As a cofactor in flavoproteins, it is found in various enzymes and photosensory receptors, like those featuring the light-oxygen-voltage (LOV) domain. The photocycle of FMN is triggered by blue light and proceeds via a cascade of intermediate states. In this work, we have studied isolated FMN in an aqueous solution in order to elucidate the intrinsic electronic and vibrational changes of the chromophore upon excitation. The ultrafast transitions of excited FMN were monitored through the joint use of femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy encompassing a time window between 0 ps and 6 ns with 50 fs time resolution. Global analysis of the obtained transient visible absorption and transient Raman spectra in combination with extensive quantum chemistry calculations identified unambiguously the singlet and triplet FMN populations and addressed solvent dynamics effects. The good agreement between the experimental and theoretical spectra facilitated the assignment of electronic transitions and vibrations. Our results represent the first steps towards more complex experiments aimed at tracking structural changes of FMN embedded in light-inducible proteins upon photoexcitation.

Activation of dioxygen attracts enormous attention due to its potential for utilization of methane and applications in other selective oxidation reactions. We report a cleavage of dioxygen at room temperature over distant binuclear Fe(II) species stabilized in an aluminosilicate matrix. A pair of formed distant α-oxygen species [i.e., (Fe(IV)═O)2+] exhibits unique oxidation properties reflected in an outstanding activity in the oxidation of methane to methanol at room temperature. Designing a man-made system that mimicks the enzyme functionality in the dioxygen activation using both a different mechanism and structure of the active site represents a breakthrough in catalysis. Our system has an enormous practical importance as a potential industrial catalyst for methane utilization because (i) the Fe(II)/Fe(IV) cycle is reversible, (ii) the active Fe centers are stable under the reaction conditions, and (iii) methanol can be released to gas phase without the necessity of water or water-organic medium extraction.

Highly active oxygen capable to selectively oxidize methane to methanol at low temperature can be prepared in transition-metal cation exchanged zeolites. Here we show that the α -oxygen stabilized by the negative charges of two framework aluminum atoms can be prepared by the dissociation of nitrous oxide over distant binuclear cation structures (M(II)…M(II), M = cobalt, nickel, and iron) accommodated in two adjacent 6-rings forming cationic sites in the ferrierite zeolite. This α -oxygen species is analogous to that known only for iron exchanged zeolites. In contrast to divalent iron cations, only binuclear divalent cobalt cationic structures and not isolated divalent cobalt cations are active. Created methoxy moieties are easily protonated to yield methanol, formaldehyde, and formic acid which are desorbed to the gas phase without the aid of water vapor while previous studies showed that highly stable methoxy groups were formed on isolated iron cations in iron exchanged ZSM-5 zeolites.

Attractive metallophilic (aurophilic, argentophilic, cuprophilic, etc.) interactions play an important role in arrangement and stabilization of oligonuclear metal ion complexes. We report a combined experimental and theoretical assessment of aurophilic interactions in closed-shell gold(I) dimers. The experimental binding energies were obtained for charged [(LH)AuCl]+...[(L')AuCl] dimers (L is either a phosphine or an N-heterocyclic carbene ligand) in the gas phase. These energies served for benchmarking of correlated quantum chemical calculations (CCSD(T)-calibrated SCS-MP2/CBS method) that were then applied to neutral [(L)AuCl]...[(L')AuCl] dimers. The overall attractive interactions between monomeric units are in the order of 100-165 kJ mol-1 in the charged dimers and of 70-105 kJ mol-1 in the corresponding neutral dimers. In the neutral dimers, pure aurophilic interactions account for 25-30 kJ mol-1, the dipole-dipole interactions for 30-45 kJ mol-1, and the L···L' "inter-ligand" dispersion interactions for 5-25 kJ mol-1. Energy of the aurophilic interactions is thus comparable or even larger than that of strong hydrogen bonds.

We report a gas-phase UV photodissociation study investigating non-covalent interactions between neutral hydrophobic pentapeptides and peptide ions incorporating a diazirine-tagged photoleucine residue. Phenylalanine (Phe) and proline (Pro) were chosen as the conformation-affecting residues that were incorporated into a small library of neutral pentapeptides. Gas-phase ion-molecule complexes of these peptides with photo-labeled pentapeptides were subjected to photodissociation. Selective photocleavage of the diazirine ring at 355 nm formed short-lived carbene intermediates that underwent cross-linking by insertion into H–X bonds of the target peptide. The cross-link positions were established from collision-induced dissociation tandem mass spectra (CID-MS3) providing sequence information on the covalent adducts. Effects of the amino acid residue (Pro or Phe) and its position in the target peptide sequence were evaluated. For proline-containing peptides, interactions resulting in covalent cross-links in these complexes became more prominent as proline was moved towards the C-terminus of the target peptide sequence. The photocross-linking yields of phenylalanine-containing peptides depended on the position of both phenylalanine and photoleucine. Density functional theory calculations were used to assign structures of low-energy conformers of the (GLPMG + GLL*LK + H)+ complex. Born-Oppenheimer molecular dynamics trajectory calculations were used to capture the thermal motion in the complexes within 100 ps and determine close contacts between the incipient carbene and the H–X bonds in the target peptide. This provided atomic-level resolution of potential cross-links that aided spectra interpretation and was in agreement with experimental data.

Peptide cation-radicals containing the threonine residue undergo radical-induced dissociations upon collisional activation and photon absorption in the 210-400 nm range. Peptide cation-radicals containing a radical defect at the N-terminal residue, [•Ala-Thr-Ala-Arg+H]+, were generated by electron transfer dissociation (ETD) of peptide dications and characterized by UV-vis photodissociation action spectroscopy combined with time-dependent density functional theory (TD-DFT) calculations of absorption spectra, including thermal vibronic band broadening. The action spectrum of [•Ala-Thr-Ala-Arg+H]+ ions was indicative of the canonical structure of an N-terminally deaminated radical whereas isomeric structures differing in the position of the radical defect and amide bond geometry were excluded. This indicated that exothermic electron transfer to threonine peptide ions did not induce radical isomerizations in the fragment cation-radicals. Several isomeric structures, ion-molecule complexes, and transition states for isomerizations and dissociations were generated and analyzed by DFT and Møller-Plesset perturbational ab initio calculations to aid interpretation of the major dissociations by loss of water, hydroxyl radical, C3H6NO•, C3H7NO, and backbone cleavages. Born-Oppenheimer molecular dynamics (BOMD) in combination with DFT gradient geometry optimizations and intrinsic reaction coordinate analysis were used to search for low-energy cation-radical conformers and transition states. BOMD was also employed to analyze the reaction trajectory for loss of water from ion-molecule complexes.

Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L*nLm)K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X−H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific 13C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)+ ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H]+ ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide–peptide ion interactions in the gas phase.

In this minireview, we provide an account of the current state-of-the-art developments in the area of mono- and binuclear non-heme enzymes (NHFe and NHFe2) and the smaller NHFe(2) synthetic models, mostly from a theoretical and computational perspective. The sheer complexity, and at the same time the beauty, of the NHFe(2) world represents a challenge for experimental as well as theoretical methods. We emphasize that the concerted progress on both theoretical and experimental side is a conditio sine qua non for future understanding, exploration and utilization of the NHFe(2) systems. After briefly discussing the current challenges and advances in the computational methodology, we review the recent spectroscopic and computational studies of NHFe(2) enzymatic and inorganic systems and highlight the correlations between various experimental data (spectroscopic, kinetic, thermodynamic, electrochemical) and computations. Throughout, we attempt to keep in mind the most fascinating and attractive phenomenon in the NHFe(2) chemistry, which is the fact that despite the strong oxidative power of many reactive intermediates, the NHFe(2) enzymes perform catalysis with high selectivity. We conclude with our personal viewpoint and hope that further developments in quantum chemistry and especially in the field of multireference wave function methods are needed to have a solid theoretical basis for the NHFe(2) studies, mostly by providing benchmarking and calibration of the computationally efficient and easy-to-use DFT methods.