Electronic Structure Investigation and Parametrization of Biologically Relevant Iron–Sulfur Clusters

The application of classical molecular dynamics simulations to the study of metalloenzymes has been hampered by the lack of suitable molecular mechanics force field parameters to treat the metal centers within standard biomolecular simulation packages. These parameters cannot be generalized, nor be easily automated, and hence should be obtained for each system separately. Here we present density functional theory calculations on [Fe₂S₂(SCH₃)₄]^2+/+, [Fe₃S₄(SCH₃)₃]^+/0 and [Fe₄S₄(SCH₃)₄]^2+/+ and the derivation of parameters that are compatible with the AMBER force field. Molecular dynamics simulations performed using these parameters on respiratory Complex II of the electron transport chain showed that the reduced clusters are more stabilized by the protein environment, which leads to smaller changes in bond lengths and angles upon reduction. This effect is larger in the smaller iron–sulfur cluster, [Fe₂S₂(SCH₃)₄]^2+/+

Tuning the Reactivity of Terminal Nickel(III)–Oxygen Adducts for C–H Bond Activation

Two metastable Ni^III complexes, [Ni^III(OAc)­(L)] and [Ni^III(ONO₂)­(L)] (L = <i>N</i>,<i>N</i>′-(2,6-dimethylphenyl)-2,6-pyridinedicarboxamidate, OAc = acetate), were prepared, adding to the previously prepared [Ni^III(OCO₂H)­(L)], with the purpose of probing the properties of terminal late-transition metal oxidants. These high-valent oxidants were prepared by the one-electron oxidation of their Ni^II precursors ([Ni^II(OAc)­(L)]⁻ and [Ni^II(ONO₂)­(L)]⁻) with tris­(4-bromophenyl)­ammoniumyl hexachloroantimonate. Fascinatingly, the reaction between any [Ni^II(X)­(L)]⁻ and NaOCl/acetic acid (AcOH) <i>or</i> cerium ammonium nitrate ((NH₄)₂[Ce^IV(NO₃)₆], CAN), yielded [Ni^III(OAc)­(L)] and [Ni^III(ONO₂)­(L)], respectively. An array of spectroscopic characterizations (electronic absorption, electron paramagnetic resonance, X-ray absorption spectroscopies), electrochemical methods, and computational predictions (density functional theory) have been used to determine the structural, electronic, and magnetic properties of these highly reactive metastable oxidants. The Ni^III-oxidants proved competent in the oxidation of phenols (weak O–H bonds) and a series of hydrocarbon substrates (some with strong C–H bonds). Kinetic investigation of the reactions with di-<i>tert</i>-butylphenols showed a 15-fold enhanced reaction rate for [Ni^III(ONO₂)­(L)] compared to [Ni^III(OCO₂H)­(L)] and [Ni^III(OAc)­(L)], demonstrating the effect of electron-deficiency of the O-ligand on oxidizing power. The oxidation of a series of hydrocarbons by [Ni^III(OAc)­(L)] was further examined. A linear correlation between the rate constant and the bond dissociation energy of the C–H bonds in the substrates was indicative of a hydrogen atom transfer mechanism. The reaction rate with dihydroanthracene (<i>k</i>₂ = 8.1 M^–1 s^–1) compared favorably with the most reactive high-valent metal-oxidants, and showcases the exceptional reactivity of late transition metal–oxygen adducts

Unraveling the Origin of the Relative Stabilities of Group 14 M₂N₂²⁺ (M, N = C, Si, Ge, Sn, and Pb) Isomer Clusters

We analyze the molecular structure, relative stability, and aromaticity of the lowest-lying isomers of group 14 M₂N₂²⁺ (M and N = C, Si, and Ge) clusters. We use the gradient embedded genetic algorithm to make an exhaustive search for all possible isomers. Group 14 M₂N₂²⁺ clusters are isoelectronic with the previously studied group 13 M₂N₂^2– (M and N = B, Al, and Ga) clusters that includes Al₄^2–, the archetypal all-metal aromatic molecule. In the two groups of clusters, the cyclic isomers present both σ- and π-aromaticity. However, at variance with group 13 M₂N₂^2– clusters, the linear isomer of group 14 M₂N₂²⁺ is the most stable for two of the clusters (C₂Si₂²⁺ and C₂Ge₂²⁺) , and it is isoenergetic with the cyclic <i>D</i>_4<i>h</i> isomer in the case of C₄²⁺. Energy decomposition analyses of the lowest-lying isomers and the calculated magnetic- and electronic-based aromaticity criteria of the cyclic isomers help to understand the nature of the bonding and the origin of the stability of the global minima. Finally, for completeness, we have also analyzed the structure and stability of the heavier Sn and Pb group 14 M₂N₂²⁺ analogues

Reaction Mechanisms for the Formation of Mono- And Dipropylene Glycol from the Propylene Oxide Hydrolysis over ZSM‑5 Zeolite

Stepwise and concerted mechanisms for the formation of mono- and dipropylene glycol over ZSM-5 zeolite were investigated. For the calculations, a T128 cluster model of zeolite was used with a QM/QM scheme to investigate the reaction mechanism. The active inner part of zeolite was represented by a T8 model and was treated at the DFT (BP86) level, including D3 Grimme dispersion, and the outer part of the zeolite was treated at the DFTB level. The solvent effects were taken into account by including explicitly water molecules in the cavity of the zeolite. The Gibbs energies were calculated for both mechanisms at 70 °C. In the case of the stepwise mechanism for the monopropylene glycol formation, the rate-limiting step is the opening of the epoxide ring. The activation energy for this process is 35.5 kcal mol^–1, while in the case of the concerted mechanism the rate-limiting step is the simultaneous ring opening of the epoxide and the attack by a water molecule. This process has an activation energy of 27.4 kcal mol^–1. In the case of the stepwise mechanism of the dipropylene glycol formation, the activation energy for the rate-limiting step is the same as for the monopropylene glycol formation, and in the case of the concerted mechanism, the activation energy for the rate-limiting step is 30.8 kcal mol^–1. In both cases (mono- and dipropylene glycol formation), the concerted mechanism should be dominant over the stepwise one. The barrier for monopropylene glycol formation is lower than that for dipropylene glycol formation. Consequently, our results show that the formation of the monopropylene glycol is faster, although the formation of dipropylene glycol as a byproduct cannot be avoided using this zeolite

Role of Spin State and Ligand Charge in Coordination Patterns in Complexes of 2,6-Diacetylpyridinebis(semioxamazide) with 3d-Block Metal Ions: A Density Functional Theory Study

We report here a systematic computational study on the effect of the spin state and ligand charge on coordination preferences for a number of 3d-block metal complexes with the 2,6-diacetylpyridinebis­(semioxamazide) ligand and its mono- and dianionic analogues. Our calculations show excellent agreement for the geometries compared with the available X-ray structures and clarify some intriguing experimental observations. The absence of a nickel complex in seven-coordination is confirmed here, which is easily explained by inspection of the molecular orbitals that involve the central metal ion. Moreover, we find here that changes in the spin state lead to completely different coordination modes, in contrast to the usual situation that different spin states mainly result in changes in the metal–ligand bond lengths. Both effects result from different occupations of a combination of π- and σ-antibonding and nonbonding orbitals

The Frozen Cage Model: A Computationally Low-Cost Tool for Predicting the Exohedral Regioselectivity of Cycloaddition Reactions Involving Endohedral Metallofullerenes

Functionalization of endohedral metallofullerenes (EMFs) is an active line of research that is important for obtaining nanomaterials with unique properties that might be used in a variety of fields, ranging from molecular electronics to biomedical applications. Such functionalization is commonly achieved by means of cycloaddition reactions. The scarcity of both experimental and theoretical studies analyzing the exohedral regioselectivity of cycloaddition reactions involving EMFs translates into a poor understanding of the EMF reactivity. From a theoretical point of view, the main obstacle is the high computational cost associated with this kind of studies. To alleviate the situation, we propose an approach named the frozen cage model (FCM) based on single point energy calculations at the optimized geometries of the empty cage products. The FCM represents a fast and computationally inexpensive way to perform accurate qualitative predictions of the exohedral regioselectivity of cycloaddition reactions in EMFs. Analysis of the Dimroth approximation, the activation strain or distortion/interaction model, and the noncluster energies in the Diels–Alder cycloaddition of <i>s-cis</i>-1,3-butadiene to X@<i>D</i>_3<i>h</i>-C₇₈ (X = Ti₂C₂, Sc₃N, and Y₃N) EMFs provides a justification of the method

Combined Experimental and Theoretical Investigation of Ligand and Anion Controlled Complex Formation with Unprecedented Structural Features and Photoluminescence Properties of Zinc(II) Complexes

By using two potential tridentate ligands, HL¹ [4-chloro-2-[(2-morpholin-4-yl-ethylimino)-methyl]-phenol] and HL² [4-chloro-2-[(3-morpholin-4-yl-propylimino)-methyl]-phenol], which differ by one methylene group in the alkyl chain, four new Zn^II complexes, namely, [Zn­(L²H)₂]­(ClO₄)₂ (<b>1</b>), [Zn­(L¹)­(H₂O)₂]­[Zn­(L¹)­(SCN)₂] (<b>2</b>), [Zn­(L¹)­(dca)]_<i>n</i> (<b>3</b>), and [Zn₂(L¹)₂(N₃)₂(H₂O)₂] (<b>4</b>) [where dca = dicyanamide anion] were synthesized and structurally characterized. The results indicate that the slight structural difference between the ligands, HL¹ and HL², because of the one methylene group connecting the nitrogen atoms provokes a chemical behavior completely different from what was expected. Any attempt to isolate the Zn­(L²) complexes with thiocyanato, dicyanamido, and azide was unsuccessful, and perchlorate complex <b>1</b> was always obtained. In contrast, with HL¹ we obtained structural diversity on varying the anions, but we failed to isolate the analogous perchlorate complex of HL¹. Single-crystal X-ray analyses revealed that the morpholine nitrogen of ligand L² is protonated and thus does not take part in coordination with Zn^II in complex <b>1</b>. On the other hand, the morpholine nitrogen of L¹ is coordinated to Zn^II in <b>2</b>–<b>4</b>. Of these, <b>2</b> and <b>4</b> are rare examples of a cocrystallized cationic/anionic complex and of a dinuclear complex bridged by a single azide, respectively. Some of these unexpected findings and some interesting noncovalent interactions leading to the formation of dimeric entities in solid-state compound <b>4</b> were rationalized by a DFT approach. Photoluminescence properties of the complexes as well as the ligands were investigated in solution at ambient temperature and at 77 K. The very fast photoinduced electron transfer (PET) from the nitrogen lone pair to the conjugated phenolic moiety is responsible for very low quantum yield (Φ) exhibited by the ligands, whereas complexation prevents PET, thus enhancing the Φ in the complexes. The origin of the electronic and photoluminescence properties of the ligands and complexes was assessed in light of theoretical calculations

Reactivity of an Fe^IV-Oxo Complex with Protons and Oxidants

High-valent Fe-OH species are often invoked as key intermediates but have only been observed in Compound II of cytochrome P450s. To further address the properties of non-heme Fe^IV-OH complexes, we demonstrate the reversible protonation of a synthetic Fe^IV-oxo species containing a tris-urea tripodal ligand. The same protonated Fe^IV-oxo species can be prepared via oxidation, suggesting that a putative Fe^V-oxo species was initially generated. Computational, Mössbauer, XAS, and NRVS studies indicate that protonation of the Fe^IV-oxo complex most likely occurs on the tripodal ligand, which undergoes a structural change that results in the formation of a new intramolecular H-bond with the oxido ligand that aids in stabilizing the protonated adduct. We suggest that similar protonated high-valent Fe-oxo species may occur in the active sites of proteins. This finding further argues for caution when assigning unverified high-valent Fe-OH species to mechanisms