Broken-symmetry Density Functional Theory Research Articles

Insights into PSII's S3YZ• State: An Electronic and Magnetic Analysis.

Using BS-DFT (broken-symmetry density functional theory), the electronic and magnetic properties of the S3YZ• state of photosystem II were investigated and compared to those of the S3 state. While the O5 oxo-O6 hydroxo species presents little difference between the two states, a previously identified [O5O6]3- exhibits reduced stabilization of the O5-O6 shared spin. This species is shown to have some coupling with the YZ• center through Mn1 and O6. Similarly, a peroxo species is found to exhibit significant exchange couplings between the YZ• center and the Mn cluster through Mn1. Mechanistic changes in O-O bond formation in S3YZ• are highlighted by analysis of IBOs (intrinsic bonding orbitals) showing deviation for Mn1 and O6 centered IBOs. This change in coupling interactions throughout the complex as a result of S3YZ• formation presents implications for the determination of the mechanism spanning the end of the S3 and the start of the S4 states, affecting both electron movement and oxygen bond formation.

Magnetic and spectroscopic properties of chloride-bridged guanidinate dilanthanide complexes

The guanidinate ligand scaffold offers a unique combination of hard anionic charges, steric tunability, and electronic modulation, rendering it an ideal candidate for the molecular design of lanthanide complexes. Here, we present two dilanthanide chloride complexes [{(Me3Si)2NC(NiPr)2}2Ln(μ–Cl)]2 (Ln = Gd (1), and Tb (2)) where each metal ion is ligated to two guanidinate anions and bridged to the other metal ion by two chloride ligands. The isostructural complexes 1 and 2 were synthesized through salt metathesis reactions and characterized through single–crystal X–ray diffraction analysis, IR and UV–Vis spectroscopy, and SQUID magnetometry. The half-filled f-electron valence shell of GdIII ion allows an accurate study of magnetic coupling through fitting of the dc magnetic susceptibility data to a spin–only Hamiltonian, affording values of J = -0.0242 cm−1 and g = 2.0192. The operative superexchange coupling mechanism was confirmed through broken–symmetry density functional theory calculations, which additionally provide insight into the spectral analysis of 1.

Shape polarization in the tin isotopes near N = 60 from precision g-factor measurements on short-lived 11/2− isomers

The g factors of 11/2− isomers in semimagic 109Sn and 111Sn (isomeric lifetimes τ=2.9(3) ns and τ=14.4(7) ns, respectively) were measured by an extension of the Time Differential Perturbed Angular Distribution technique, which uses LaBr3 detectors and the hyperfine fields of a gadolinium host to achieve precise measurements in a new regime of short-lived isomers. The results, g(11/2−;109Sn)=−0.186(8) and g(11/2−;111Sn)=−0.214(4), are significantly lower in magnitude than those of the 11/2− isomers in the heavier isotopes and depart from the value expected for a near pure neutron h11/2 configuration. Broken-symmetry density functional theory calculations applied to the sequence of 11/2− states reproduce the magnitude and location of this deviation. The g(11/2−) values are affected by shape core polarization; the odd 0h11/2 neutron couples to Jπ=2+,4+,6+... configurations in the weakly-deformed effective core, causing a decrease in the g-factor magnitudes.

A Remarkably Unsymmetric Hexairon Core Embraced by Two High-Symmetry Tripodal Oligo-α-pyridylamido Ligands.

Oligo-α-pyridylamides offer an appealing route to polyiron complexes with short Fe-Fe separations and large room-temperature magnetic moments. A derivative of tris(2-aminoethyl)amine (H6tren) containing three oligo-α-pyridylamine branches and 13 nitrogen donors (H6L) reacts with [Fe2(Mes)4] to yield an organic nanocage built up by two tripodal ligands with interdigitated branches (HMes = mesitylene). The nanocage has crystallographic D3 symmetry but hosts a remarkably unsymmetric hexairon-oxo core, with a central Fe5(μ5-O) square pyramid, two oxygen donors bridging basal sites, and an additional Fe center residing in one of the two tren-like pockets. Bond valence sum (BVS) analysis, density functional theory (DFT) calculations, and electrochemical data were then used to establish the protonation state of oxygen atoms and the formal oxidation states of the metals. For this purpose, a specialized set of BVS parameters was devised for Fe2+-N3- bonds with nitrogen donors of oligo-α-pyridylamides. This allowed us to formulate the compound as [Fe6O2(OH)(H3L)L], with nominally four FeII ions and two FeIII ions. Mössbauer spectra indicate that the compound contains two unique FeII sites, identified as a pair of closely spaced hydroxo-bridged metal ions in the central Fe5(μ5-O) pyramid, and a substantially valence-delocalized FeII2FeIII2 unit. Broken-symmetry DFT calculations predict strong ferromagnetic coupling between the two iron(II) ions, leading to a local S = 4 state that persists to room temperature and explaining the large magnetic moment measured at 300 K. The compound behaves as a single-molecule magnet, with magnetization dynamics detectable in zero static field and dominated by an Orbach-like mechanism with activation parameters Ueff/kB = 49(2) K and τ0 = 4(2) × 10-10 s.

Magneto-Structural Analysis of Hydroxido-Bridged CuII2 Complexes: Density Functional Theory and Other Treatments

A selection of dimeric Cu(II) complexes with bidentate N,N′ ligands with the general formula [Cu(L)(X)(μ-OH)]2·nH2O and [Cu(L)(μ-OH)]2X2·nH2O were magneto-structurally analyzed using the Density Functional Theory (DFT). A Broken Symmetry-Density Functional Theory (BS-DFT) study was undertaken for these complexes with relevant decomposition schemes that gave insight into the effect of the nature of the ligand and coordination environment on the DFT-predicted coupling constants (J). The impact of the spin population, which correlates well with the Cu-O-Cu bridging angles and the calculated coupling constant (J) values, was studied. The models were further refined using a complete active space self-consistent field (CASSCF) while expanding the active space from 2 orbitals 2 electrons (2,2) to 10 orbitals 18 electrons (18,10). These models were approximated using multireference methods (n-electron valence state perturbation theory and difference dedicated configuration interaction), and a better approximation of J values was found as expected. Orbitals involved in the superexchange pathway were also visualized.

A Trinuclear High-Spin Iron(III) Complex with a Geometrically Frustrated Spin Ground State Featuring Negligible Magnetic Anisotropy and Antisymmetric Exchange.

The trinuclear high-spin iron(III) complex [Fe3Cl3(saltagBr)(py)6]ClO4 {H5saltagBr = 1,2,3-tris[(5-bromo-salicylidene)amino]guanidine} was synthesized and characterized by several experimental and theoretical methods. The iron(III) complex exhibits molecular 3-fold symmetry imposed by the rigid ligand backbone and crystallizes in trigonal space group P3̅ with the complex cation lying on a crystallographic C3 axis. The high-spin states (S = 5/2) of the individual iron(III) ions were determined by Mößbauer spectroscopy and confirmed by CASSCF/CASPT2 ab initio calculations. Magnetic measurements show an antiferromagnetic exchange between the iron(III) ions leading to a geometrically spin-frustrated ground state. This was complemented by high-field magnetization experiments up to 60 T, which confirm the isotropic nature of the magnetic exchange and negligible single-ion anisotropy for the iron(III) ions. Muon-spin relaxation experiments were performed and further prove the isotropic nature of the coupled spin ground state and the presence of isolated paramagnetic molecular systems with negligible intermolecular interactions down to 20 mK. Broken-symmetry density functional theory calculations are consistent with the antiferromagnetic exchange between the iron(III) ions within the presented trinuclear high-spin iron(III) complex. Ab initio calculations further support the absence of appreciable magnetic anisotropy (D = 0.086, and E = 0.010 cm-1) and the absence of significant contributions from antisymmetric exchange, as the two Kramers doublets are virtually degenerate (ΔE = 0.005 cm-1). Therefore, this trinuclear high-spin iron(III) complex should be an ideal candidate for further investigations of spin-electric effects arising exclusively from the spin chirality of a geometrically frustrated S = 1/2 spin ground state of the molecular system.

Origin of Ferromagnetic Exchange Coupling in Donor–Acceptor Biradical Analogues of Charge-Separated Excited States

A new donor-acceptor biradical complex, TpCum,MeZn(SQ-VD) (TpCum,MeZn+ = zinc(II) hydro-tris(3-cumenyl-5-methylpyrazolyl)borate complex cation; SQ = orthosemiquinone; VD = oxoverdazyl), which is a ground-state analogue of a charge-separated excited state, has been synthesized and structurally characterized. The magnetic exchange interaction between the S = 1/2 SQ and the S = 1/2 VD within the SQ-VD biradical ligand is observed to be ferromagnetic, with JSQ-VD = +77 cm-1 (H = -2JSQ-VDŜSQ·ŜVD) determined from an analysis of the variable-temperature magnetic susceptibility data. The pairwise biradical exchange interaction in TpCum,MeZn(SQ-VD) can be compared with that of the related donor-acceptor biradical complex TpCum,MeZn(SQ-NN) (NN = nitronyl nitroxide, S = 1/2), where JSQ-NN ≅ +550 cm-1. This represents a dramatic reduction in the biradical exchange by a factor of ∼7, despite the isolobal nature of the VD and NN acceptor radical SOMOs. Computations assessing the magnitude of the exchange were performed using a broken-symmetry density functional theory (DFT) approach. These computations are in good agreement with those computed at the CASSCF NEVPT2 level, which also reveals an S = 1 triplet ground state as observed in the magnetic susceptibility measurements. A combination of electronic absorption spectroscopy and CASSCF computations has been used to elucidate the electronic origin of the large difference in the magnitude of the biradical exchange coupling between TpCum,MeZn(SQ-VD) and TpCum,MeZn(SQ-NN). A Valence Bond Configuration Interaction (VBCI) model was previously employed to highlight the importance of mixing an SQSOMO → NNLUMO charge transfer configuration into the electronic ground state to facilitate the stabilization of the high-spin triplet (S = 1) ground state in TpCum,MeZn(SQ-NN). Here, CASSCF computations confirm the importance of mixing the pendant radical (e.g., VD, NN) LUMO (VDLUMO and NNLUMO) with the SOMO of the SQ radical (SQSOMO) for stabilizing the triplet, in addition to spin polarization and charge transfer contributions to the exchange. An important electronic structure difference between TpCum,MeZn(SQ-VD) and TpCum,MeZn(SQ-NN), which leads to their different exchange couplings, is the reduced admixture of excited states that promote ferromagnetic exchange into the TpCum,MeZn(SQ-VD) ground state, and the intrinsically weaker mixing between the VDLUMO and the SQSOMO compared to that observed for TpCum,MeZn(SQ-NN), where this orbital mixing is significant. The results of this comparative study contribute to a greater understanding of biradical exchange interactions, which are important to our understanding of excited-state singlet-triplet energy gaps, electron delocalization, and the generation of electron spin polarization in both the ground and excited states of (bpy)Pt(CAT-radical) complexes.

Tetracoordinate Co(II) complexes with semi-coordination as stable single-ion magnets for deposition on graphene.

We present a theoretical and experimental study of two tetracoordinate Co(II)-based complexes with semi-coordination interactions, i.e., non-covalent interactions involving the central atom. We argue that such interactions enhance the thermal and structural stability of the compounds, making them appropriate for deposition on substrates, as demonstrated by their successful deposition on graphene. DC magnetometry and high-frequency electron spin resonance (HF-ESR) experiments revealed an axial magnetic anisotropy and weak intermolecular antiferromagnetic coupling in both compounds, supported by theoretical predictions from complete active space self-consistent field calculations complemented by N-electron valence state second-order perturbation theory (CASSCF-NEVPT2), and broken-symmetry density functional theory (BS-DFT). AC magnetometry demonstrated that the compounds are field-induced single-ion magnets (SIMs) at applied static magnetic fields, with slow relaxation of magnetization governed by a combination of quantum tunneling, Orbach, and direct relaxation mechanisms. The structural stability under ambient conditions and after deposition was confirmed by X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. Theoretical modeling by DFT of different configurations of these systems on graphene revealed n-type doping of graphene originating from electron transfer from the deposited molecules, confirmed by electrical transport measurements and Raman spectroscopy.

Joint Studies of Spin Frustration Induced by Doping Small ZnSe Nanoparticles with Fe Atoms

AbstractAs a 1.8 nm ZnSe nanocrystal is progressively doped with 1%, 5%, and 10% Fe, it shows a progressive change in its magnetic properties from a superparamagnetic FM‐dominated exchange type to an onset of AFM exchange with evidence of spin frustration. Magnetization measurements allow to obtain exchange coupling constants that are compared to the results of a Broken‐Symmetry Density Functional Theory (BS‐DFT) model of a doped (ZnSe)34 cluster. DFT shows a capability to reproduce the experimental pattern of the increasing influence of AFM exchange as doping concentration increases. The material phase segregates at the edges where strained rhombic surface sites are the preferred doping sites of iron. Large concentrations of iron leads to the formation of Fe clusters and complex exchange patterns that result in spin frustration in some iron trimers but none in the others. The spin frustration of these complex systems by assuming mirror symmetry of the sites when fitting by using BS‐DFT formalism is classified and analyzed. While some individual J constants obtained have significant errors, the averaged exchange constants are generally in good agreement with our experimental data.

Magnetic and Electronic Structural Properties of the S3 State of Nature's Water Oxidizing Complex: A Combined Study in ELDOR-Detected Nuclear Magnetic Resonance Spectral Simulation and Broken-Symmetry Density Functional Theory.

ELDOR-detected nuclear magnetic resonance (EDNMR) spectral simulations combined with broken-symmetry density functional theory (BS-DFT) calculations are used to obtain and to assign the 55Mn hyperfine coupling constants (hfcs) for modified forms of the water oxidizing complex in the penultimate S3 state of the water oxidation cycle. The study shows that an open cubane form of the core Mn4CaO6 cluster explains the magnetic properties of the dominant S = 3 species in all cases studied experimentally with no need to invoke a closed cubane intermediate possessing a distorted pentacoordinate Mn4 ion as recently suggested. EDNMR simulations found that both the experimental bandwidth and multinuclear transitions may alter relative EDNMR peak intensities, potentially leading to incorrect assignment of hfcs. The implications of these findings for the water oxidation mechanism are discussed.

Pulsed Multifrequency Electron Paramagnetic Resonance Spectroscopy Reveals Key Branch Points for One- vs Two-Electron Reactivity in Mn/Fe Proteins.

Traditionally, the ferritin-like superfamily of proteins was thought to exclusively use a diiron active site in catalyzing a diverse array of oxygen-dependent reactions. In recent years, novel redox-active cofactors featuring heterobimetallic Mn/Fe active sites have been discovered in both the radical-generating R2 subunit of class Ic (R2c) ribonucleotide reductases (RNRs) and the related R2-like ligand-binding oxidases (R2lox). However, the protein-specific factors that differentiate the radical reactivity of R2c from the C-H activation reactions of R2lox remain unknown. In this work, multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy and ligand hyperfine techniques in conjunction with broken-symmetry density functional theory calculations are used to characterize the molecular and electronic structures of two EPR-active intermediates trapped during aerobic assembly of the R2lox Mn/Fe cofactor. A MnIII(μ-O)(μ-OH)FeIII species is identified as the first EPR-active species and represents a common state between the two classes of redox-active Mn/Fe proteins. The species downstream from the MnIII(μ-O)(μ-OH)FeIII state exhibits unique EPR properties, including unprecedented spectral breadth and isotope-dependent g-tensors, which are attributed to a weakly coupled, hydrogen-bonded MnIII(μ-OH)FeIII species. This final intermediate precedes formation of the MnIII/FeIII resting state and is suggested to be relevant to understanding the endogenous reactivity of R2lox.

Broken-Symmetry Density Functional Theory Analysis of the Ω Intermediate in Radical S-Adenosyl-l-methionine Enzymes: Evidence for a Near-Attack Conformer over an Organometallic Species.

Radical S-adenosyl-l-methionine (SAM) enzymes are found in all domains of life and catalyze a wide range of biochemical reactions. Recently, an organometallic intermediate, Ω, has been experimentally implicated in the 5'-deoxyadenosyl radical generation mechanism of the radical SAM superfamily. In this work, we employ broken-symmetry density functional theory to evaluate several structural models of Ω. The results show that the calculated hyperfine coupling constants (HFCCs) for the proposed organometallic structure of Ω are inconsistent with the experiment. In contrast, a near-attack conformer of SAM bound to the catalytic [4Fe-4S] cluster, in which the distance between the unique iron and SAM sulfur is ∼3 Å, yields HFCCs that are all within 1 MHz of the experimental values. These results clarify the structure of the ubiquitous Ω intermediate and suggest a paradigm shift reversal regarding the mechanism of SAM cleavage by members of the radical SAM superfamily.

Analysis of the Geometric and Electronic Structure of Spin-Coupled Iron-Sulfur Dimers with Broken-Symmetry DFT: Implications for FeMoco.

The open-shell electronic structure of iron–sulfur clusters presents considerable challenges to quantum chemistry, with the complex iron–molybdenum cofactor (FeMoco) of nitrogenase representing perhaps the ultimate challenge for either wavefunction or density functional theory. While broken-symmetry density functional theory has seen some success in describing the electronic structure of such cofactors, there is a large exchange–correlation functional dependence in calculations that is not fully understood. In this work, we present a geometric benchmarking test set, FeMoD11, of synthetic spin-coupled Fe–Fe and Mo–Fe dimers, with relevance to the molecular and electronic structure of the Mo-nitrogenase FeMo cofactor. The reference data consists of high-resolution crystal structures of metal dimer compounds in different oxidation states. Multiple density functionals are tested on their ability to reproduce the local geometry, specifically the Fe–Fe/Mo–Fe distance, for both antiferromagnetically coupled and ferromagnetically coupled dimers via the broken-symmetry approach. The metal–metal distance is revealed not only to be highly sensitive to the amount of exact exchange in the functional but also to the specific exchange and correlation functionals. For the antiferromagnetically coupled dimers, the calculated metal–metal distance correlates well with the covalency of the bridging metal–ligand bonds, as revealed via the corresponding orbital analysis, Hirshfeld S/Fe charges, and Fe–S Mayer bond order. Superexchange via bridging ligands is expected to be the dominant interaction in these dimers, and our results suggest that functionals that predict accurate Fe–Fe and Mo–Fe distances describe the overall metal–ligand covalency more accurately and in turn the superexchange of these systems. The best performing density functionals of the 16 tested for the FeMoD11 test set are revealed to be either the nonhybrid functionals r2SCAN and B97-D3 or hybrid functionals with 10–15% exact exchange: TPSSh and B3LYP*. These same four functionals are furthermore found to reproduce the high-resolution X-ray structure of FeMoco well according to quantum mechanics/molecular mechanics (QM/MM) calculations. Almost all nonhybrid functionals systematically underestimate Fe–Fe and Mo–Fe distances (with r2SCAN and B97-D3 being the sole exceptions), while hybrid functionals with >15% exact exchange (including range-separated hybrid functionals) overestimate them. The results overall suggest r2SCAN, B97-D3, TPSSh, and B3LYP* as accurate density functionals for describing the electronic structure of iron–sulfur clusters in general, including the complex FeMoco cluster of nitrogenase.

Theoretical Investigation on Electron Transport Capabilities of Helically Twisted Molecules Based on Decay Constants of Exchange Interaction

Abstract The electron transport capabilities of helically twisted molecules were theoretically evaluated based on the decay constant of the exchange interaction (βJ) between terminal nitronyl nitroxide radicals using broken-symmetry unrestricted density functional theory (UDFT) calculations. A small βJ value (βJ = 0.16 Å−1) was estimated for a homogeneously π-extended helicene consisting of a helically fused oligo-phenanthrenes, which is less than half that of the original carbohelicene (βJ = 0.39 Å−1) and comparable to that of rylene (βJ = 0.13 Å−1). The excellent electron transport capability suggested by the small βJ of the π-extended helicene can be attributed to the olefinic electronic nature found inside the helical framework.

Synergistic Experimental and Theoretical Studies of Luminescent-Magnetic Ln2Zn6 Clusters.

The present work is part of our ongoing quest for developing functional inorganic complexes using unorthodox pyridyl-pyrazolyl-based ligands. Accordingly, we report herein the synthesis, characterization, and luminescence and magnetic properties of four 3d-4f mixed-metal complexes with a general core of Ln2Zn6 (Ln = Dy, Gd, Tb, and Eu). In stark contrast to the popular wisdom of using a compartmental ligand with separate islands of hard and soft coordinating sites for selective coordination, we have vindicated our approach of using a ligand with overcrowded N-coordinating sites that show equal efficiency with both 4f and 3d metals toward multinuclear cage-cluster formation. The encouraging red and green photolumiscent features of noncytotoxic Eu2Zn6 and Tb2Zn6 complexes along with their existence in nanoscale dimension have been exploited with live-cell confocal microscopy imaging of human breast adenocarcinoma (MCF7) cells. The magnetic features of the Dy2Zn6 complex confirm the single-molecule-magnet behavior with befitting frequency- and temperature-dependent out-of-phase signals along with an Ueff value of ∼5 K and a relaxation time of 8.52 × 10-6 s. The Gd2Zn6 complex, on the other hand, shows cryogenic magnetic refrigeration with an entropy change of 11.25 J kg-1 K-1 at a magnetic field of 7 T and at 2 K. Another important aspect of this work reflects the excellent agreement between the experimental results and theoretical calculations. The theoretical studies carried out using the broken-symmetry density functional theory, ORCA suite of programs, and MOLCAS calculations using the complete-active-space self-consistent-field method show an excellent synergism with the experimentally measured magnetic and spectroscopic data.

Strong magnetic exchange coupling in a radical-bridged trinuclear nickel complex.

Reaction of 2,3,6,7,10,11-hexaaminotriphenylene hexahydrochloride (HATP·6HCl) and (TpPhNi)Cl (TpPh = tris(3,5-diphenyl-1-pyrazolyl)borate) produces the radical-bridged trinickel complex [(TpPhNi)3(HITP)] (HITP3-˙ = 2,3,6,7,10,11-hexaiminotriphenylene). Magnetic measurements and broken-symmetry density functional theory calculations reveal strong exchange coupling persisting at room temperature between HITP3-˙ and two of the three Ni2+ centers, a rare example of strong radical-mediated magnetic coupling in multimetallic complexes. These results demonstrate the potential of radical-bearing tritopic HITP ligands as building blocks for extended molecule-based magnetic materials.

Solvent mediated synthesis of homoleptic tri and tetranuclear nickel complex derived from [Ni2(µ-SeC5H4N)2(dppe)2]2+ and theoretical studies

In the present report, the reactivity of the binuclear complex [Ni2(µ-SeC5H4N)2(dppe)2]2+ towards dichloromethane and methanol has been studied. The complex [Ni2(µ-SeC5H4N)2(dppe)2]2+ in the presence of chlorinated solvent resulted in selenido bridged trinuclear complex of composition [Ni3(µ-Se)2(dppe)2]2+ (1) whereas in the presence of methanol hydrolyzed product having cubane core [Ni4{(C5H4N)2Se}4(μ3OH)4(C6H5COO)(HCOO)]2+ (2) was isolated. Both the complexes were characterized by elemental analysis, IR, 1H, and 31P{1H} NMR spectroscopy. An attempt has also been made to investigate their thermal studies. The molecular structure of both the complex [Ni3(µ-Se)2(dppe)2]2+ (1) and [Ni4{(C5H4N)2Se}4(μ3OH)4(C6H5COO)(HCOO)]2+ (2) were established by single-crystal X-ray diffraction analysis. Broken-symmetry density functional theory (BS-DFT) calculations were carried out on complex 2 to investigate the electronic structure and nature of magnetic exchange interaction. BS-DFT reveals the existence of three different J values i.e. -8.9 cm−1, +18.7 cm−1 and +1.8 cm−1 between different Ni(II) pairs. A strong ferromagnetic interaction was observed between formate/phenylacetate bridged Ni(II) centers. An antiferromagnetic interaction between the ferromagnetically coupled formate and phenylacetate bridged Ni(II) dimers result in isolation of S = 0 spin ground state for complex 2. Molecular orbital, spin-density analyses were performed on the X-ray and optimized geometries to probe the electronic structure of complex 2.

Quantum Chemical Study of a Radical Relay Mechanism for the HydG-Catalyzed Synthesis of a Fe(II)(CO)2(CN)cysteine Precursor to the H-Cluster of [FeFe] Hydrogenase.

The [FeFe] hydrogenase catalyzes the redox interconversion of protons and H2 with a Fe-S "H-cluster" employing CO, CN, and azadithiolate ligands to two Fe centers. The biosynthesis of the H-cluster is a highly interesting reaction carried out by a set of Fe-S maturase enzymes called HydE, HydF, and HydG. HydG, a member of the radical S-adenosylmethionine (rSAM) family, converts tyrosine, cysteine, and Fe(II) into an organometallic Fe(II)(CO)2(CN)cysteine "synthon", which serves as the substrate for HydE. Although key aspects of the HydG mechanism have been experimentally determined via isotope-sensitive spectroscopic methods, other important mechanistic questions have eluded experimental determination. Here, we use computational quantum chemistry to refine the mechanism of the HydG catalytic reaction. We utilize quantum mechanics/molecular mechanics simulations to investigate the reactions at the canonical Fe-S cluster, where a radical cleavage of the tyrosine substrate takes place and proceeds through a relay of radical intermediates to form HCN and a COO•- radical anion. We then carry out a broken-symmetry density functional theory study of the reactions at the unusual five-iron auxiliary Fe-S cluster, where two equivalents of CN- and COOH• coordinate to the fifth "dangler iron" in a series of substitution and redox reactions that yield the synthon as the final product for further processing by HydE.

S3 State Models of Nature's Water Oxidizing Complex: Analysis of Bonding and Magnetic Exchange Pathways, Assessment of Experimental Electron Paramagnetic Resonance Data, and Implications for the Water Oxidation Mechanism.

Broken symmetry density functional theory (BS-DFT) calculations on large models of Nature's water oxidizing complex (WOC) are used to investigate the electronic structure and associated magnetic interactions of this key intermediate state. The electronic origins of the ferromagnetic and antiferromagnetic couplings between neighboring Mn ions are investigated and illustrated by using corresponding orbital transformations. Protonation of the O4 and/or O6 atoms leads to large variation in the distribution of spin around the complex with associated changes in its magnetic resonance properties. Models for Sr2+ exchange and methanol addition indicate minor perturbations reflected in slightly altered spin projection coefficients for the Mn1 and Mn2 ions. These are shown to account for the observed changes observed experimentally via electron paramagnetic resonance methods and suggest a reinterpretation of the experimental findings. By comparison with experimental determinations, we show that the spin projections and resulting calculated 55Mn hyperfine couplings support the open cubane form of an oxo (O5)-hydroxo (O6) cluster in all cases with no need to invoke a closed cubane intermediate. The implications of these findings for the water oxidation mechanism are discussed.

X−[Pd(dmit)2]2 as a quasi-one-dimensional scalene Heisenberg model

From first principles, we calculate the Heisenberg interactions between neighboring dimers in several compounds within the Et$_{n}$Me$_{4-n}X$[Pd(dmit)$_2$]$_2$ (Et = ethyl, Me = methyl, dmit = 2-thioxo-1,3-dithiole-4,5-dithiolate) family using an atomistic approach; with broken-symmetry density functional theory. In all materials, we find a scalene triangular model where the strongest exchange coupling along one crystallographic axis is up to three times larger than the others and that frustration further enhances this quasi-one-dimensionality. We calculate the N\'eel ordering temperature via the chain random phase approximation (CRPA). We show that the difference in the frustrated interchain couplings is equivalent to a single bipartite interchain coupling, favoring long-range magnetic order. We find that the N\'eel ordering temperatures are in good agreement with the experimentally measured values for most compounds.