Importance of the Basis Set for the Spin-State Energetics of Iron Complexes

Bismuthene as a novel anode material of magnesium/zinc ion batteries with high capacity and stability: a DFT calculation

In our research, we utilize density functional theory (DFT) to explore the properties of magnesium and zinc atoms adsorbed on bismuthene. Our findings indicate that the hollow site is the most favorable adsorption site for Mg and Zn atoms on bismuthene. The results indicate that Mg and Zn adsorption on the bismuthene surface results in significantly high conductivity, with notable adsorption energies of -3.38 eV for Mg and -3.91 eV for Zn. The bismuthene structure can adsorb 9 Mg and 18 Zn atoms with negative average adsorption energy. These findings suggest excellent stability of bismuthene during the adsorption of magnesium and zinc. Notably, we propose theoretical storage capacities of 2308 mA h g-1 for magnesium-ion batteries (MgIBs) and 4616 mA h g-1 for zinc-ion batteries (ZnIBs), while maintaining structural stability during the adsorption of these metal ions. The observed average open-circuit voltages for bismuthene are 0.01 V for Mg and 0.03 V for Zn, with the material retaining its metallic properties throughout the adsorption process. Furthermore, the calculated diffusion barriers for Mg and Zn are 0.1 eV and 0.21 eV, respectively. Our findings like storage capacity, diffusion energies, and low OCV surpass those of most studied two-dimensional materials, positioning bismuthene as a promising anode material for metal-ion rechargeable batteries.

Quantum Chemical and Biological Insights into Redox Activity of Metallacarborane Complexes in Cancer Cells

A relationship between the electronic properties of metal ions in metallacarboranes and their ability to modulate mitochondrial oxidase activity and membrane hyperpolarization in cancer cells was demonstrated. Quantum chemistry methods, including DFT and molecular dynamics simulations, were used to understand the oxidized and reduced forms of metallacarboranes and their intramolecular rotatory behavior. According to the low-spin assumption for metal ions, the intramolecular oscillations of cluster ligands in metallacarboranes are significantly influenced by the type of metal and correspond to the cellular uptake of these complexes in vitro. In particular, the low-spin iron compound may be a new xenogeneic booster of redox homeostasis in cancer cells resistant to cisplatin, which induces metabolic 'exhaustion' of cancer cells and their death.

Pristine and aurum-decorated tungsten ditellurides as sensing materials for VOCs detection in exhaled human breath: DFT analysis

In this research, we employed density functional theory (DFT) to evaluate the sensing capabilities of transition metal-decorated two-dimensional WTe2 TMDs nanosheets toward VOCs such as (acetone, ethanol, methanol, toluene, and formaldehyde) that are exhaled in human breath and can serve as potential biomarkers for detecting specific physiological disorders and also gases interfering in exhaled breath (CO2 and H2O) detection. Au can be physically decorated onto the surface of WTe2. We analyzed the density of states (DOS), adsorption energy, charge transfer, and sensing behavior. The pristine WTe2 monolayer, exhibiting a semiconductor characteristic with a band gap of 0.63 eV, transitions to a metallic state upon Au-decoration, due to its actively stable nature and promising negative adsorption energy value, it triggers the emergence of novel states within the DOS. Computed adsorption energies of VOCs range from -0.08 to -0.57 eV, with greater interaction distances confirming the physisorption behavior of these VOCs biomarkers on Au-WTe2. Ethanol displays greater sensitivity compared to other considered VOCs. Au-WTe2 exhibits promising potential as a viable option for detecting VOCs in breath analysis applications at room temperature, owing to its excellent adsorption capabilities and sensitivity. Overall, our results highlight aurum-decorated tungsten ditelluride's potential as an efficient nano-sensor for detecting VOCs associated with early-stage lung cancer diagnoses.

Adsorption behavior of different cresols on bismuthene: a DFT study

Phenolic compounds present in wastewater were utilized for first-principle calculations based on DFT to observe adsorption effects. Results indicate that bismuthene exhibits different adsorption characteristics for different compounds. Following the adsorption process, the aromatic ring remains in the same plane, while CH3 and OH groups move upward, causing slight changes in the molecules' overall position. The calculated results show that bisphenol A has the least atomic distance (4.00 Å) from the bismuthene surface and the highest adsorption energy value (12.8509 eV), indicating the stability and smoothness of the adsorption process. The electronic properties results reveal that phenolic compounds exhibit overlapping peaks at a distance from the Fermi level, describing the stability of the adsorption system. Additionally, the charge transfer results mirror the adsorption energy calculation results, showing that the bisphenol A adsorption system accepts a greater amount of (-0.116e) charge from the bismuthene surface, demonstrating a strong adsorption effect.

Scalar Relativistic Effects with Multiwavelets: Implementation and Benchmark

The importance of relativistic effects in quantum chemistry is widely recognized, not only for heavier elements but throughout the periodic table. At the same time, relativistic effects are strongest in the nuclear region, where the description of electrons through a linear combination of atomic orbitals becomes more challenging. Furthermore, the choice of basis sets for heavier elements is limited compared with lighter elements where precise basis sets are available. Thanks to the framework of multiresolution analysis, multiwavelets provide an appealing alternative to overcoming this challenge: they lead to robust error control and adaptive algorithms that automatically refine the basis set description until the desired precision is reached. This allows one to achieve a proper description of the nuclear region. In this work, we extended the multiwavelet-based code MRChem to the scalar zero-order regular approximation framework. We validated our implementation by comparing the total energies for a small set of elements and molecules. To confirm the validity of our implementation, we compared both against a radial numerical code for atoms and the plane-wave-based code EXCITING.

How important is the amount of exact exchange for spin-state energy ordering in DFT? Case study of molybdenum carbide cluster, Mo4C2

Since the form of the exact functional in density functional theory is unknown, we must rely on density functional approximations (DFAs). In the past, very promising results have been reported by combining semi-local DFAs with exact, i.e. Hartree-Fock, exchange. However, the spin-state energy ordering and the predictions of global minima structures are particularly sensitive to the choice of the hybrid functional and to the amount of exact exchange. This has been already qualitatively described for single conformations, reactions, and a limited number of conformations. Here, we have analyzed the mixing of exact exchange in exchange functionals for a set of several hundred isomers of the transition metal carbide, Mo4C2. The analysis of the calculated energies and charges using PBE0-type functional with varying amounts of exact exchange yields the following insights: (1) The sensitivity of spin-energy splitting is strongly correlated with the amount of exact exchange mixing. (2) Spin contamination is exacerbated when correlation is omitted from the exchange-correlation functional. (3) There is not one ideal value for the exact exchange mixing which can be used to parametrize or choose among the functionals. Calculated energies and electronic structures are influenced by exact exchange at a different magnitude within a given distribution; therefore, to extend the application range of hybrid functionals to the full periodic table the spin-energy splitting energies should be investigated.

Relativistic quantum calculations to understand the contribution of f-type atomic orbitals and chemical bonding of actinides with organic ligands

The nuclear waste problem is one of the main interests of rare earth and actinide element chemistry. Studies of actinide-containing compounds are at the frontier of the applications of current theoretical methods due to the need to consider relativistic effects and approximations to the Dirac equation in them. Here, we employ four-component relativistic quantum calculations and scalar approximations to understand the contribution of f-type atomic orbitals in the chemical bonding of actinides (Ac) to organic ligands. We studied the relativistic quantum structure of an isostructural family made of Plutonium (Pu), Americium (Am), Californium (Cf), and Berkelium (Bk) atoms with the redox-active model ligand DOPO (2,4,6,8-tetra-tert-butyl-1-oxo-1H-phenoxazin-9-olate). Crystallographic structures were available to validate our calculations for all mentioned elements except for Cf. In short, state-of-the-art relativistic calculations were performed at different levels of theory to investigate the influence of relativistic and electron correlation effects on geometrical structures and bonding energies of Ac-DOPO₃ complexes (Ac = Pu, Am, Cf, and Bk): (1) the scalar (sc) and spin-orbit (so) relativistic zeroth order regular approximation (ZORA) within the hybrid density functional theory (DFT) and (2) the four-component Dirac equation with both the Dirac-Hartree-Fock (4c-DHF) and Lévy-Leblond (LL) Hamiltonians. We show that sr- and so-ZORA-DFT could be used as efficient theoretical models to first approximate the geometry and electronic properties of actinides which are difficult to synthesize or characterize, but knowing that the higher levels of theory, like the 4c-DHF, give closer results to experiments. We also performed spin-free 4c calculations of geometric parameters for the Americium and Berkelium compounds. To the best of our knowledge, this is the first time that these kinds of large actinide compounds (the largest contains 67 atoms and 421 electrons) have been studied with highly accurate four-component methods (all-electron calculations with 6131 basis functions for the largest compound). We show that relativistic effects play a key role in the contribution of f-type atomic orbitals to the frontier orbitals of Ac-DOPO₃ complexes. The analysis of the results obtained applying different theoretical schemes to calculate bonding energies is also given.

ZORA Gaussian basis sets for Fr, Ra, and Ac

Segmented all-electron basis sets of double and triple zeta valence qualities plus polarization functions (DZP and TZP) for the elements Fr, Ra, and Ac to be used with the zeroth-order regular approximation (ZORA) were presented. These sets were constructed from the reoptimization of the contraction coefficients of the corresponding non-relativistic basis sets. In order to adequately describe electrons distant from the atomic nuclei, these sets were augmented with diffuse functions and were, respectively, designated as ADZP-ZORA and ATZP-ZORA. At the ZORA-B3LYP theory level, the relativistic sets were employed to calculate ionization energies of Fr, Ra, and Ac as well as bond lengths, dissociation energies, harmonic vibrational frequencies, and static mean dipole polarizabilities of some diatomics. Comparing with benchmark theoretical results and with experimental data available in the literature, it can be verified that our basis sets are able to produce reliable and accurate results. Evaluation of the performances of ZORA and second-order Douglas-Kroll-Hess Hamiltonians was performed.

Mechanism of Mixed-Valence Fe2.5+···Fe2.5+ Formation in Fe4S4 Clusters in the Ferredoxin Binding Motif

Most low-potential Fe₄S₄ clusters exist in the conserved binding sequence CxxCxxC (CⁿCⁿ⁺³Cⁿ⁺⁶). Fe(II) and Fe(III) at the first (Cⁿ) and third (Cⁿ⁺⁶) cysteine ligand sites form a mixed-valence Fe^2.5+···Fe^2.5+ pair in the reduced Fe(II)₃Fe(III) cluster. Here, we investigate the mechanism of how the conserved protein environment induces mixed-valence pair formation in the Fe₄S₄ clusters, F_X, F_A, and F_B in photosystem I, using a quantum mechanical/molecular mechanical approach. Exchange coupling between Fe sites is predominantly determined by the shape of the Fe₄S₄ cluster, which is stabilized by the preorganized protein electrostatic environment. The backbone NH and CO groups in the conserved CxxCxxC and adjacent helix regions orient along the Fe^Cn···Fe^C(n+6) axis, generating an electric field and stabilizing the Fe^Cn(II)Fe^C(n+6)(III) state in F_A and F_B. The overlap of the d orbitals via -S- (superexchange) is observed for the single Fe^Cn(II)···Fe^C(n+6)(III) pair, leading to the formation of the mixed-valence Fe^2.5+···Fe^2.5+ pair. In contrast, several superexchange Fe(II)···Fe(III) pairs are observed in F_X due to the highly symmetric pair of the CDGPGRGGTC sequences. This is likely the origin of F_X serving as an electron acceptor in the two electron transfer branches.

Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis

Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyond simple electron transfer, relying primarily on the redox activity of the clusters, with a remarkable diversity for different enzymes. The active-site structure and the electrostatic environment in which the cluster resides direct this redox reactivity. Oriented electric fields in enzymatic active sites can be significantly strong, and understanding the extent of their effect on iron-sulfur cluster reactivity can inform first steps toward rationally engineering their reactivity. An extensive systematic density functional theory-based screening approach using OPBE/TZP has afforded a simple electric field-effect representation. The results demonstrate that the orientation of an external electric field of strength 28.8 MV cm^-1 at the center of the cluster can have a significant effect on its relative stability in the order of 35 kJ mol^-1. This shows clear implications for the reactivity of iron-sulfur clusters in enzymes. The results also demonstrate that the orientation of the electric field can alter the most stable broken-symmetry state, which further has implications on the directionality of initiated electron-transfer reactions. These insights open the path for manipulating the enzymatic redox reactivity of iron-sulfur cluster-containing enzymes by rationally engineering oriented electric fields within the enzymes.

Borophene as a rising star in materials chemistry: synthesis, properties and applications in analytical science and energy devices

Borophene is a two-dimensional material that has shown outstanding applications in energy storage devices and analytical chemistry.

Crystal and Substituent Effects on Paramagnetic NMR Shifts in Transition-Metal Complexes

Nuclear magnetic resonance (NMR) spectroscopy of paramagnetic molecules provides detailed information about their molecular and electron-spin structure. The paramagnetic NMR spectrum is a very rich source of information about the hyperfine interaction between the atomic nuclei and the unpaired electron density. The Fermi-contact contribution to ligand hyperfine NMR shifts is particularly informative about the nature of the metal–ligand bonding and the structural arrangements of the ligands coordinated to the metal center. In this account, we provide a detailed experimental and theoretical NMR study of compounds of Cr(III) and Cu(II) coordinated with substituted acetylacetonate (acac) ligands in the solid state. For the first time, we report the experimental observation of extremely paramagnetically deshielded ¹³C NMR resonances for these compounds in the range of 900–1200 ppm. We demonstrate an excellent agreement between the experimental NMR shifts and those calculated using relativistic density-functional theory. Crystal packing is shown to significantly influence the NMR shifts in the solid state, as demonstrated by theoretical calculations of various supramolecular clusters. The resonances are assigned to individual atoms in octahedral Cr(acac)₃ and square-planar Cu(acac)₂ compounds and interpreted by different electron configurations and magnetizations at the central metal atoms resulting in different spin delocalizations and polarizations of the ligand atoms. Further, effects of substituents on the ¹³C NMR resonance of the ipso carbon atom reaching almost 700 ppm for Cr(acac)₃ compounds are interpreted based on the analysis of Fermi-contact hyperfine contributions.

The ligand NMR shifts in paramagnetic acetylacetonato Cr(III) and Cu(II) complexes have been predicted and measured in the solid state and interpreted by relativistic DFT calculations. The effects of the metal atom, ligand, and crystal packing on the spin delocalization and polarization reflected in the Fermi-contact contribution to the hyperfine interaction are rationalized.

A computational study of intercalation of streptozotocin (STZ) into DNA base pairs

Deoxyribonucleic acid (DNA) drug intercalation is a well-known phenomenon for the treatment of cancer. Streptozotocin (STZ) is a drug agent containing toxic properties that make it good in the pancreatic cancer. The main objective of this study is the intercalation of the anticancer drug into the stacked base pair of DNA sequence with ATGC using a density functional theory (DFT) code named as ADF-Molecule. ADF code implements DFT using the Slater-type orbitals (STO) for computational analysis of atomic and molecular structures. All the calculations were carried out with the GGA and hybrid exchange correlation functional with TZ2P basis sets. It was captivatingly studied that during the intercalation process, the bonds between the DNA base pairs broken. Moreover, during the process of intercalation, the free radicals are considered responsible for disturbance in the base configurations. It was determined that the disturbances that occurred in the base pairs lead to discontinuity in the replication of that particular sequence in the DNA strand.

A DFT study on a borophene/boron nitride interface for its application as an electrode

In order to search for a new anode material for lithium-ion batteries (LIBs), a borophene/boron nitride (B/BN) interface was investigated in detail using density functional theory. Borophene is an excellent two-dimensional (2D) anode material that offers high charging capacity and a low energy barrier, but it suffers from stability issues when it is used in its free-standing form. The findings of this work indicate that the thermal and mechanical stabilities of the borophene epilayer are notably increased by preparing its interface with a boron nitride substrate. The electronic properties of the lithiated and delithiated interface exhibited metallic behavior, whereas the mechanical stiffness of the interface increased three times when compared with that of the pristine borophene. The thermal stability was calculated by molecular dynamics and indicated a six times increase in its value for the interface. The interface exhibited a specific charging capacity of 1698 mA h g^-1, which is higher than that of bare borophene and several other 2D materials. Furthermore, nudged elastic band (NEB) calculations indicated a low energy barrier to diffusion of Li in the interface. These advantages of the B/BN interface make it an excellent choice as an anode material for LIBs.

Directing self-assembly in solution towards improved cooperativity in Fe(iii) complexes with amphiphilic tridentate ligands

An amphiphilic iron(iii) complex with a tridentate Schiff-base ligand was prepared by condensation of a hexadecyloxy functionalised salycylaldehyde with a diamine followed by complexation with FeCl2 and anion methathesis with NaClO4. The complex shows spin crossover both in the solid state and solution. However in solution self-assembly and consequently aggregation of individual molecules form concentration dependent particles with sizes of 300 nm for higher concentrations, or 5 nm for lower concentrations. Aggregate formation was confirmed by NANO-flex 180° DLS Size, scan-rate dependent cyclic voltammetry and scanning electron microscopy. Molecular simulations were used to investigate the self-assembly of the complex in solution, including the role of residual water molecules. The simulations showed the self-assembly of reverse micelle-like structures when a small water cluster is inserted in solution, whereas no large aggregates formed in dehydrated environments. The perchlorate anions were found near the metal centres, stabilizing the aggregates around the water pool. Simulations of pre-assembled structures further showed the lack of stability of large aggregates in the absence of water. The larger aggregates promoted efficient communication between the iron(iii) centres and the compound displayed spin crossover in solution at around 220 K with a 10 K hysteresis window, as measured by NMR and SQUID magnetometry.

Predictable Substituent Control of CoIII/II Redox Potential and Spin Crossover in Bis(dipyridylpyrrolide)cobalt Complexes

A family of five easily prepared tridentate monoanionic 2,5-dipyridyl-3-(R¹)-4-(R²)-pyrrolide anions (dpp^R1,R2)^-, varying in the nature of the R¹ and R² substituents [R¹, R² = CN, Ph; CO₂Et, CO₂Et; CO₂Me, 4-Py; CO₂Me, Me; Me, Me], has been used to generate the analogous family of neutral [Co^II(dpp^R1,R2)₂] complexes, two of which are structurally characterized at both 100 and 298 K. Both the oxidation and spin states of these complexes can be switched in response to appropriate external stimuli. All complexes, except [Co^II(dpp^Me,Me)₂], exhibit gradual spin crossover (SCO) in the solid state, and SCO activity is observed for three complexes in CDCl₃ solution. The cobalt(II) centers in the low spin (LS) complexes are Jahn-Teller tetragonally compressed along the pyrrolide-Co-pyrrolide axis. The complexes in their high spin (HS) states are more distorted than in the LS states, as is also usually the case for SCO active iron(II) complexes. The reversible Co^III/II redox potentials are predictably tuned by choice of substituents R¹ and R², from -0.95 (Me,Me) to -0.45 (CN,Ph) V vs Fc⁺/Fc, with a linear correlation observed between E_1/2(Co^III/II) and the Swain-Lupton parameters of the pyrrolide substituents.

Density functional theory studies on the conversion of hydroxyheme to iron-verdoheme in the presence of dioxygen

Detailed insight into the second step of heme degradation by heme oxygenase, oxophlorin to verdoheme and biliverdin, is presented. Density functional theory methods are reported for the conversion of oxophlorin to verdoheme. Since it is currently unclear whether dioxygen binding to iron oxophlorin is followed by a reduction or not, in this work we have focused on the difference in reactivity between [(Im)(O₂˙)Fe^III(PO˙)] (PO˙ is the oxophlorin dianion radical) and [(Im)(O₂˙)Fe^III(PO)]^- (PO is the oxophlorin trianion). Thus, we have shown that in [(Im)(O₂˙)Fe^III(PO˙)] and [(Im)(O₂˙)Fe^III(PO)]^-, the mechanisms are stepwise with an initial C-O bond activation to form a ring-structure where the oxophlorin is distorted from planarity. This is followed by homolytic dioxygen bond breaking that directly leads to iron-oxo verdoheme products. The [(Im)(O₂˙)Fe^III(PO˙)] mechanism proceeds via two-state-reactivity patterns on the adjacent doublet and quartet spin state surfaces, whereas the [(Im)(O₂˙)Fe^III(PO)]^- route shows single-state-reactivity on a triplet spin state surface. In both, the rate determining step is the C-O bond activation, with substantially lower barriers on the [(Im)(O₂˙)Fe^III(PO˙)] surface of 12.15 kcal mol^-1 in the gas phase compared to 22.55 kcal mol^-1 for the intermediate-spin of [(Im)(O₂˙)Fe^III(PO)]^-. The complete active space self-consistent-field wave functions with second-order multi-reference perturbation theory were also studied. Finally, the effects of the solvent and the medium on the reaction barriers were tested and shown to be considerable.

Interplay of Through-Bond Hyperfine and Substituent Effects on the NMR Chemical Shifts in Ru(III) Complexes

The links between the molecular structure and nuclear magnetic resonance (NMR) parameters of paramagnetic transition-metal complexes are still relatively unexplored. This applies particularly to the contact term of the hyperfine contribution to the NMR chemical shift. We report combining experimental NMR with relativistic density functional theory (DFT) to study a series of Ru(III) complexes with 2-substituted β-diketones. A series of complexes with systematically varied substituents was synthesized and analyzed using ¹H and ¹³C NMR spectroscopy. The NMR spectra recorded at several temperatures were used to construct Curie plots and estimate the temperature-independent (orbital) and temperature-dependent (hyperfine) contributions to the NMR shift. Relativistic DFT calculations of electron paramagnetic resonance and NMR parameters were performed to interpret the experimental observations. The effects of individual factors such as basis set, density functional, exact-exchange admixture, and relativity are analyzed and discussed. Based on the calibration study in this work, the fully relativistic Dirac-Kohn-Sham (DKS) method, the GIAO approach (orbital shift), the PBE0 functional with the triple-ζ valence basis sets, and the polarizable continuum model for describing solvent effects were selected to calculate the NMR parameters. The hyperfine contribution to the total paramagnetic NMR (pNMR) chemical shift is shown to be governed by the Fermi-contact (FC) term, and the substituent effect (H vs Br) on the through-bond FC shifts is analyzed, interpreted, and discussed in terms of spin-density distribution, atomic spin populations, and molecular-orbital theory. In contrast to the closed-shell systems of Rh(III), the presence of a single unpaired electron in the open-shell Ru(III) analogs significantly alters the NMR resonances of the ligand atoms distant from the metal center in synergy with the substituent effect.

Formally Copper(III)-Alkylperoxo Complexes as Models of Possible Intermediates in Monooxygenase Enzymes

Reaction of [NBu₄][LCu^IIOH] with excess ROOH (R = cumyl or tBu) yielded [NBu₄][LCu^IIOOR], the reversible one-electron oxidation of which generated novel species with [CuOOR]²⁺ cores (formally Cu^IIIOOR), identified by spectroscopy and theory for the case R = cumyl. This species reacts with weak O-H bonds in TEMPO-H and 4-dimethylaminophenol (^NMe2PhOH), the latter yielding LCu(OPh^NMe2), which was also prepared independently. With the identification of [CuOOR]²⁺ complexes, the first precedent for this core in enzymes is provided, with implications for copper monooxygenase mechanisms.

Assessment of electronic structure methods for the determination of the ground spin states of Fe(ii), Fe(iii) and Fe(iv) complexes

We studied spin states of Fe²⁺ ion, gaseous FeO, and 14 Fe(ii), Fe(iii) and Fe(iv) complexes using density functional theory.

Spinning around in Transition-Metal Chemistry

The great diversity and richness of transition metal chemistry, such as the features of an open d-shell, opened a way to numerous areas of scientific research and technological applications. Depending on the nature of the metal and its environment, there are often several energetically accessible spin states, and the progress in accurate theoretical treatment of this complicated phenomenon is presented in this Account. The spin state energetics of a transition metal complex can be predicted theoretically on the basis of density functional theory (DFT) or wave function based methodology, where DFT has advantages since it can be applied routinely to medium-to-large-sized molecules and spin-state consistent density functionals are now available. Additional factors such as the effect of the basis set, thermochemical contributions, solvation, relativity, and dispersion, have been investigated by many researchers, but challenges in unambiguous assignment of spin states still remain. The first DFT studies showed intrinsic spin-state preferences of hybrid functionals for high spin and early generalized gradient approximation functionals for low spin. Progress in the development of density functional approximations (DFAs) then led to a class of specially designed DFAs, such as OPBE, SSB-D, and S12g, and brought a very intriguing and fascinating observation that the spin states of transition metals and the S_N2 barriers of organic molecules are somehow intimately linked. Among the many noteworthy results that emerged from the search for the appropriate description of the complicated spin state preferences in transition metals, we mainly focused on the examination of the connection between the spin state and the structures or coordination modes of the transition metal complexes. Changes in spin states normally lead only to changes in the metal-ligand bond lengths, but to the best of our knowledge, the dapsox ligand showed the first example of a transition-metal complex where a change in spin state leads also to changes in the coordination, switching between pentagonal-bipyramidal and capped-octahedron. Moreover, we have summarized the results of the thorough study that corrected the experimental assignment of the nature of the recently synthesized Sc³⁺ adduct of [Fe^IV(O)(TMC)]²⁺ (TMC = 1,4,8,11-tetramethylcyclam) and firmly established that the Sc³⁺-capped iron-oxygen complex corresponds to high-spin Fe^III. Last, but not least, we have provided deeper insight and rationalization of the observation that unlike in metalloenzymes, where the Fe^IV-oxo is usually observed with high spin, biomimetic Fe^IV-oxo complexes typically have a intermediate spin state. Energy decomposition analyses on the trigonal-bypiramidal (TBP) and octahedral model systems with ammonia ligands have revealed that the interaction energy of the prepared metal ion in the intermediate spin state is much smaller for the TBP structure. This sheds light on the origin of the intermediate spin state of the biomimetic TBP Fe^IV-oxo complexes.

Substrate Sulfoxidation by an Iron(IV)-Oxo Complex: Benchmarking Computationally Calculated Barrier Heights to Experiment

High-valent metal-oxo oxidants are common reactive species in synthetic catalysts as well as heme and nonheme iron enzymes. In general, they efficiently react with substrates through oxygen atom transfer, and for a number of cases, experimental rate constants have been determined. However, because these rate constants are generally measured in a polar solution, it has been found difficult to find computational methodologies to reproduce experimental trends and reactivities. In this work, we present a detailed computational study into para-substituted thioanisole sulfoxidation by a nonheme iron(IV)-oxo complex. A range of density functional theory methods and basis sets has been tested for their suitability to describe the reaction mechanism and compared with experimentally obtained free energies of activation. It is found that the enthalpy of activation is reproduced well, but all methods overestimate the entropy of activation by about 50%, for which we recommend a correction factor. The effect of solvent and dispersion on the barrier heights is explored both at the single-point level and also through inclusion in geometry optimizations, and particularly, solvent is seen as highly beneficial to reproduce experimental free energies of activation. Interestingly, in general, experimental trends and Hammett plots are reproduced well with almost all methods and procedures, and only a systematic error seems to apply for these chemical systems. Very good agreement between experiment and theory is found for a number of different methods, including B3LYP and PBE0, and procedures that are highlighted in the paper.

Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center

Dioxygenase (dOx) utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys₂[2Fe-2S]His₂ and a non-heme reactive oxygen center (ROC). Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx). Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys). In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC) and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA) that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available). The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor) complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated structures. The results are consistent with a proton coupled electron transfer mechanism.

On the physical origins of interaction-induced vibrational (hyper)polarizabilities

This paper presents the results of a pioneering exploration of the physical origins of vibrational contributions to the interaction-induced electric properties of molecular complexes. In order to analyze the excess nuclear relaxation (hyper)polarizabilities, a new scheme was proposed which relies on the computationally efficient Bishop-Hasan-Kirtman method for determining the nuclear relaxation contributions to electric properties. The extension presented herein is general and can be used with any interaction-energy partitioning method. As an example, in this study we employed the variational-perturbational interaction-energy decomposition scheme (at the MP2/aug-cc-pVQZ level) and the extended transition state method by employing three exchange-correlation functionals (BLYP, LC-BLYP, and LC-BLYP-dDsC) to study the excess properties of the HCN dimer. It was observed that the first-order electrostatic contribution to the excess nuclear relaxation polarizability cancels with the negative exchange repulsion term out to a large extent, resulting in a positive value of Δα(nr) due to the contributions from the delocalization and the dispersion terms. In the case of the excess nuclear relaxation first hyperpolarizability, the pattern of interaction contributions is very similar to that for Δα(nr), both in terms of their sign as well as relative magnitude. Finally, our results show that the LC-BLYP and LC-BLYP-dDsC functionals, which yield smaller values of the orbital relaxation term than BLYP, are more successful in predicting excess properties.

Tracking the Structural and Electronic Configurations of a Cobalt Proton Reduction Catalyst in Water

X-ray transient absorption spectroscopy (X-TAS) has been used to study the light-induced hydrogen evolution reaction catalyzed by a tetradentate macrocyclic cobalt complex with the formula [LCo(III)Cl2](+) (L = macrocyclic ligand), [Ru(bpy)3](2+) photosensitizer, and an equimolar mixture of sodium ascorbate/ascorbic acid electron donor in pure water. X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analysis of a binary mixture of the octahedral Co(III) precatalyst and [Ru(bpy)3](2+) after illumination revealed in situ formation of a Co(II) intermediate with significantly distorted geometry and electron-transfer kinetics of 51 ns. On the other hand, X-TAS experiments of the complete photocatalytic system in the presence of the electron donor showed the formation of a square planar Co(I) intermediate species within a few nanoseconds, followed by its decay in the microsecond time scale. The Co(I) structural assignment is supported by calculations based on density functional theory (DFT). At longer reaction times, we observe the formation of the initial Co(III) species concomitant to the decay of Co(I), thus closing the catalytic cycle. The experimental X-ray absorption spectra of the molecular species formed along the catalytic cycle are modeled using a combination of molecular orbital DFT calculations (DFT-MO) and finite difference method (FDM). These findings allowed us to assign the full mechanistic pathway, followed by the catalyst as well as to determine the rate-limiting step of the process, which consists in the protonation of the Co(I) species. This study provides a complete kinetics scheme for the hydrogen evolution reaction by a cobalt catalyst, revealing unique information for the development of better catalysts for the reductive side of hydrogen fuel cells.

Implementation of the SM12 Solvation Model into ADF and Comparison with COSMO

In this article, an implementation of the newest iteration of the Minnesota solvation model, SM12, into the Amsterdam density functional (ADF) computational package is presented. ADF makes exclusive use of Slater-type orbitals (STO), which correctly represent the true atomic orbitals for atoms, whereas SM12 and the underlying charge model 5 (CM5) have previously only been tested on Gaussian-type orbitals (GTO). This new implementation is used to prove the basis set independence of both CM5 and SM12. A detailed comparison of the SM12 and COSMO solvation models, as implemented in ADF, is also presented. We show that this new implementation of SM12 has a mean unsigned error (MUE) of 0.68 kcal/mol for 272 molecules in water solvent, 4.10 kcal/mol MUE for 112 charged ions in water, and 0.92 kcal/mol MUE for 197 solvent calculations of various molecules. SM12 outperforms COSMO for all neutral molecules and performs as well as COSMO for cationic molecules, only falling short when anionic molecules are taken into consideration, likely due to CM5's use of Hirshfeld charges and their poor description of anionic molecules, though CM5 seems to improve upon this discrepancy.

Conformational Stability and Spin States of Cobalt(II) Acetylacetonate: CASPT2 and DFT Study

Electronic structure and conformation of bis(acetylacetonate) cobalt(II), Co(acac)2, a prototypical mediator in controlled radical polymerization of olefins, is reinvestigated. The ab initio multiconfigurational CASSCF/CASPT2 method is used to resolve the doubts stemming from density functional theory results. We assign the quartet ground state for a single molecule and point at tetrahedral conformation as the preferred one. Several density functionals are tested against the ab initio calculations, and their performance is assessed. The strength of intermolecular interactions in the crystal structure composed of square-planar Co(acac)2 molecules ( Burgess , J. ; et al. Acta Crystallogr. 2000 , C56 , 649 - 650 ) is estimated to be sufficient for their planarization (suggested by Matyjaszewski , K. ; et al. Chem.-Eur. J. 2007 , 13 , 2480 - 2492 ).

Properties and reactivities of nonheme iron(IV)-oxo versus iron(V)-oxo: long-range electron transfer versus hydrogen atom abstraction

Recent work of Nam and co-workers [J. Yoon, S. A. Wilson, Y. K. Jang, M. S. Seo, K. Nehru, B. Hedman, K. O. Hodgson, E. Bill, E. I. Solomon and W. Nam, Angew. Chem., Int. Ed., 2009, 48, 1257] on a biomimetic iron complex implicated a mixture of iron(IV)-oxo and iron(V)-oxo intermediates but the latter could not be spectroscopically characterized, hence its involvement was postulated. To gain insight into the relative activity of these iron(IV)-oxo versus iron(V)-oxo intermediates, we have performed an extensive density functional theory (DFT) study on the chemical properties of the chemical system of Nam et al., namely [Fe(O)(BQEN)(NCCH3)](2+/3+) with BQEN = N,N'-dimethyl-N,N'-bis(8-quinolyl)ethane-1,2-diamine and their reactivity in hydrogen atom abstraction from ethylbenzene. We show that the perceived iron(V)-oxo species actually is an iron(IV)-oxo ligand cation radical, similar to cytochrome P450 compound I. Moreover, this intermediate has an extremely large electron affinity and therefore can abstract electrons from substrates readily. In our particular system, this means that prior to the hydrogen atom abstraction, an electron is abstracted to form an iron(IV)-oxo species, which subsequently abstracts a hydrogen atom from the substrate. Thus, our calculations show for the first time how some nonheme iron complexes react by long-range electron transfer and others directly via hydrogen atom abstraction. We have rationalized our results with detailed thermochemical cycles that explain the observed reactivity patterns.

Predicting the spin state of paramagnetic iron complexes by DFT calculation of proton NMR spectra

Many transition-metal complexes easily change their spin state S in response to external perturbations (spin crossover). Determining such states and their dynamics can play a central role in the understanding of useful properties such as molecular magnetism or catalytic behavior, but is often far from straightforward. In this work we demonstrate that, at a moderate computational cost, density functional calculations can predict the correct ground spin state of Fe(ii) and Fe(iii) complexes and can then be used to determine the (1)H NMR spectra of all spin states. Since the spectral features are remarkably different according to the spin state, calculated (1)H NMR resonances can be used to infer the correct spin state, along with supporting the structure elucidation of numerous paramagnetic complexes.

Structural and electronic properties of the Pt(n)-PAH complex (n = 1, 2) from density functional calculations

A detailed density functional study of the Pt atom and the Pt dimer adsorption on a polyaromatic hydrocarbon (PAH) is presented. The preferred adsorption site for a Pt atom is confirmed to be the bridge site. Upon adsorption of a single Pt atom, however, it is found here that the electronic ground state changes from the triplet state (5d(9)6s(1) configuration) to the closed-shell singlet state (5d(10)6s(0) configuration), which consequently will affect the catalytic activity of Pt when single Pt atoms bind to a carbon surface. The preferred adsorption site for the Pt dimer in the upright configuration is the hollow site. In contrast to the adsorption of a single Pt atom, the formation of a Pt-C bond in the adsorption of a Pt dimer is not accompanied by a change in the spin state, so the most stable electronic state is still the triplet state. While the atomic charge on the Pt atoms and dimers (in parallel configuration) in the Ptn-PAH complex is positive, a negative charge is found on the upper Pt atom for the upright configuration, indicating that single layers of Pt atoms will have a different catalytic activity as compared to Pt clusters on a carbon surface. Comparing the Pt-C bond length and the charge transfer on different sites, the magnitude of the charge transfer decreases with bond elongation, indicating that the catalytic activity of the Pt atom and dimer can be changed by modifying its chemical surroundings. The adsorption energy for the Pt dimer on a PAH surface is larger than that for two individual Pt atoms on the surface indicating that aggregation of Pt atoms on the PAH surface is favorable.

Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition

With current therapies becoming less efficacious due to increased drug resistance, new inhibitors of both bacterial and malarial targets are desperately needed. The recently discovered methylerythritol phosphate (MEP) pathway for isoprenoid synthesis provides novel targets for the development of such drugs. Particular attention has focused on the IspH protein, the final enzyme in the MEP pathway, which uses its [4Fe-4S] cluster to catalyze the formation of the isoprenoid precursors IPP and DMAPP from HMBPP. IspH catalysis is achieved via a 2e-/2H+ reductive dehydroxylation of HMBPP; the mechanism by which catalysis is achieved, however, is highly controversial. The work presented herein provides the first step in assessing different routes to catalysis by using computational methods. By performing broken-symmetry density functional theory (BS-DFT) calculations that employ both the conductor-like screening solvation model (DFT/COSMO) and a finite-difference Poisson-Boltzmann self-consistent reaction field methodology (DFT/SCRF), we evaluate geometries, energies, and Mössbauer signatures of the different protonation states that may exist in the oxidized state of the IspH catalytic cycle. From DFT/SCRF computations performed on the oxidized state, we find a state where the substrate, HMBPP, coordinates the apical iron in the [4Fe-4S] cluster as an alcohol group (ROH) to be one of two, isoenergetic, lowest-energy states. In this state, the HMBPP pyrophosphate moiety and an adjacent glutamate residue (E126) are both fully deprotonated, making the active site highly anionic. Our findings that this low-energy state also matches the experimental geometry of the active site and that its computed isomer shifts agree with experiment validate the use of the DFT/SCRF method to assess relative energies along the IspH reaction pathway. Additional studies of IspH catalytic intermediates are currently being pursued.