Computational Study of Catalytic Reaction of Quercetin 2,4-Dioxygenase

We present a quantum mechanics/molecular mechanics (QM/MM) and QM-only study on the oxidative ring-cleaving reaction of quercetin catalyzed by quercetin 2,4-dioxygenase (2,4-QD). 2,4-QD has a mononuclear type 2 copper center and incorporates two oxygen atoms at C2 and C4 positions of the substrate. It has not been clear whether dioxygen reacts with a copper ion or a substrate radical as the first step. We have found that dioxygen is more likely to bind to a Cu²⁺ ion, involving the dissociation of the substrate from the copper ion. Then a Cu²⁺-alkylperoxo complex can be generated. Comparison of geometry and stability between QM-only and QM/MM results strongly indicates that steric effects of the protein environment contribute to maintain the orientation of the substrate dissociated from the copper center. The present QM/MM results also highlight that a prior rearrangement of the Cu²⁺-alkylperoxo complex and a subsequent hydrogen bond switching assisted by the movement of Glu73 can facilitate formation of an endoperoxide intermediate selectively

A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion: General Theory and Applications

We propose an accurate scheme to evaluate the redox potential of a wide variety of transition metal complexes by adding a charge-dependent correction term for a counterion around the charged complexes, which is based on Generalized Born theory, to the solvation energy. The mean absolute error (MAE) toward experimental redox potentials of charged complexes is considerably reduced from 0.81 V (maximum error 1.22 V) to 0.22 V (maximum error 0.50 V). We found a remarkable exchange-correlation functional dependence on the results rather than the basis set ones. The combination of Wachters+f (for metal) and 6-31++G­(d,p) (for other atoms) with the B3LYP functional gives the least MAE 0.15 V for the test complexes. This scheme is applicable to other solvents, and heavier transition metal complexes such as M₁(CO)₅(pycn) (M₁ = Cr, Mo, W), M₂(mnt)₂ (M₂ = Ni, Pd, Pt), and M₃(bpy)₃ (M₃ = Fe, Ru, Os) with the same quality

Novel Formation of Ag/Au Bimetallic Nanoparticles by Physical Mixture of Monometallic Nanoparticles in Dispersions and Their Application to Catalysts for Aerobic Glucose Oxidation

Ag/Au bimetallic nanoparticles (BNPs) with a size less than 2 nm were prepared by physical mixture of colloidal dispersions of Ag and Au nanoparticles (NPs). This provides an example of fabrication of BNPs with self-organization by the reaction between metal NPs. Although Ag/Au BNPs having different structures and compositions are one of the most widely studied bimetallic systems in the literature due to their wide range of uses such as in catalysis, electronics, plasmonics, optical sensing, and surface-enhanced Raman scattering, we first prepared such BNPs by physical mixture and characterized them by UV–vis spectroscopy, SERS, XPS, TEM, and EDS in HR-STEM. The present fabrication method has the advantage of avoiding the unfavorable formation of AgCl precipitates in the reaction process which are always produced when Ag⁺ ions are used as a starting material in combination with a HAuCl₄ precursor. These Ag/Au BNPs showed high catalytic activities for aerobic glucose oxidation, and the highest activity of 11 510 mol of glucose·h^–1·mol of metal^–1 was observed for the BNPs with a Ag/Au atomic ratio of 1/4; the activity value is about 2 times higher than that of Au NPs with nearly the same particle size. XPS and DFT calculation results show that the negatively charged Au atoms due to the electron charge transfer effects from neighboring Ag atoms and poly­(<i>N</i>-vinyl-2-pyrrolidone) act as catalytically active sites and play an important role in the aerobic glucose oxidation

Full-valence density matrix renormalisation group calculations on meta-benzyne based on unrestricted natural orbitals. Revisit of seamless continuation from broken-symmetry to symmetry-adapted models for diradicals

<p>In this work, we show that the natural orbitals of unrestricted hybrid density functional theory (UHDFT) can be used as the active space orbitals to perform multireference (MR) calculations, for example, the density matrix renormalisation group (DMRG) and Mukherjee-type (Mk) MR coupled-cluster (CC) method. By including a sufficiently large number of these natural orbitals, full-valence (FV) active space can be identified without recourse of the expensive self-consistent procedures for DMRG-SCF. Several useful chemical indices are derived based on the occupation numbers of the natural orbitals for seamless continuation from broken-symmetry (BS) to symmetry-adapted (SA) methods. These procedures are used on 1,3-didehydrobenzene (meta-benzyne) to calculate its singlet (S)-triplet (T) gap. We compare our results to available experiments and computational results obtained by several other groups. We see our procedures as a seamless bridge between single-reference BS methods, such as UHDFT, and the SA MR methods, such as FV DMRG and MkMRCC.</p

π‑Conjugated Trinuclear Group‑9 Metalladithiolenes with a Triphenylene Backbone

Previously, we synthesized π-conjugated trinuclear metalladithiolene complexes based on benzenehexathiol (<i>J. Chem. Soc., Dalton Trans.</i> <b>1998</b>, 2651; <i>Dalton Trans.</i> <b>2009</b>, 1939; <i>Inorg. Chem.</i> <b>2011</b>, <i>50</i>, 6856). Here we report trinuclear complexes with a triphenylene backbone. A reaction with triphenylenehexathiol and group 9 metal precursors in the presence of triethylamine gives rise to trinuclear complexes <b>9</b>–<b>11</b>. The planar structure of <b>11</b> is determined using single crystal X-ray diffraction analysis. The ligand-to-metal charge transfer bands of <b>9</b>–<b>11</b> move to longer wavelengths compared with those of mononuclear <b>12</b>–<b>14</b>. Electrochemical measurements disclose that the one-electron and two-electron reduced mixed-valent states are stabilized thermodynamically. UV–vis–NIR spectroscopy for the reduced species of <b>9</b> identifies intervalence charge transfer bands for <b>9</b>^– and <b>9</b>^2–, substantiating the existence of electronic communication among the three metal nuclei. These observations prove that the triphenylene backbone transmits π-conjugation among the three metalladithiolene units

UNO DMRG CASCI calculations of effective exchange integrals for <i>m</i>-phenylene-bis-methylene spin clusters

<p>Theoretical examinations of the ferromagnetic coupling in the <i>m</i>-phenylene-bis-methylene molecule and its oligomer were carried out. These systems are good candidates for exchange-coupled systems to investigate strong electronic correlations. We studied effective exchange integrals (<i>J</i>), which indicated magnetic coupling between interacting spins in these species. First, theoretical calculations based on a broken-symmetry single-reference procedure, i.e. the UHF, UMP2, UMP4, UCCSD(T) and UB3LYP methods, were carried out with a GAUSSIAN program code under an SR wave function. From these results, the <i>J</i> value by the UHF method was largely positive because of the strong ferromagnetic spin polarisation effect. The <i>J</i> value by the UCCSD(T) and UB3LYP methods improved an overestimation problem by correcting the dynamical electronic correlation. Next, magnetic coupling among these spins was studied using the CAS-based method of the symmetry-adapted multireference methods procedure. Thus, the UNO DMRG CASCI (UNO, unrestricted natural orbital; DMRG, density matrix renormalised group; CASCI, complete active space configuration interaction) method was mainly employed with a combination of ORCA and BLOCK program codes. DMRG CASCI calculations in valence electron counting, which included all orbitals to full valence CI, provided the most reliable result, and support the UB3LYP method for extended systems.</p

X‑ray Magnetic Circular Dichroism Investigation of the Electron Transfer Phenomena Responsible for Magnetic Switching in a Cyanide-Bridged [CoFe] Chain

The cyanide-bridged [CoFe] one-dimensional chain, [Co^II((<i>R</i>)-pabn)]­[Fe^III(Tp)­(CN)₃]­(BF₄)·MeOH·2H₂O, where (<i>R</i>)-pabn = (<i>R</i>)-<i>N</i>2,<i>N</i>(2′)-bis­(pyridin-2-ylmethyl)-1,1′-binaphthyl-2,2′-diamine and Tp = hydrotris­(pyrazolyl)­borate, exhibits magnetic and electric bistabilities originating from an electron transfer coupled spin transition between Fe–CN–Co pairs. The use of L-edge X-ray absorption spectroscopy (XAS) in combination with L-edge X-ray magnetic circular dichroism (XMCD) is explored for the investigation of the electronic structure and magnetization of Co and Fe ions separately, in both diamagnetic and paramagnetic states. It has been established from susceptibility results that the switching between diamagnetic and paramagnetic phases emanates from electron transfer between low spin Fe­(II) and Co­(III), resulting in low spin Fe­(III) (<i>S</i> = 1/2) and high spin Co­(II) (<i>S</i> = 3/2). The XAS and XMCD results are consistent with the bulk susceptibility measurements, where greater detail regarding the charge transfer process is determined. The Fe–CN–Co electron transfer pathway is highlighted by a strongly XMCD dependent transition to a cyanide back bonding orbital, giving evidence for strong hybridization with Fe­(III) t_2g orbitals. In addition to thermally induced and photoinduced switching, [CoFe] is found to exhibit a switching by grinding induced dehydration. Analysis of XAS shows that on grinding diamagnetic [CoFe], 75% of metal ions lock into the magnetic Co­(II)­Fe­(III) phase. Density functional theory calculations based on the [CoFe] crystal structure in the magnetic and nonmagnetic phases aid the spectroscopic results and provide a complementary insight into the electronic configuration of the [CoFe] 3d shells, quantifying the change in ligand field around Co and Fe centers on charge transfer

Bistable Multifunctionality and Switchable Strong Ferromagnetic-to-Antiferromagnetic Coupling in a One-Dimensional Rhodium(I)–Semiquinonato Complex

We present a comprehensive study of the synthesis, heat capacity, crystal structures, UV–vis−NIR and mid-IR spectra, DFT calculations, and magnetic and electrical properties of a one-dimensional (1D) rhodium­(I)–semiquinonato complex, [Rh­(3,6-DBSQ-4,5-(MeO)₂)­(CO)₂]_∞ (<b>3</b>), where 3,6-DBSQ-4,5-(MeO)₂^•– represents 3,6-di-<i>tert</i>-butyl-4,5-dimethoxy-1,2-benzosemiquinonato radical anion. The compound <b>3</b> comprises neutral 1D chains of complex molecules stacked in a staggered arrangement with short Rh–Rh distances of 3.0796(4) and 3.1045(4) Å at 226 K and exhibits unprecedented bistable multifunctionality with respect to its magnetic and conductive properties in the temperature range of 228–207 K. The observed bistability results from the thermal hysteresis across a first-order phase transition, and the transition accompanies the exchange of the interchain C–H···O hydrogen-bond partners between the semiquinonato ligands. The strong overlaps of the complex molecules lead to unusually strong ferromagnetic interactions in the low-temperature (LT) phase. Furthermore, the magnetic interactions in the 1D chain drastically change from strongly ferromagnetic in the LT phase to antiferromagnetic in the room-temperature (RT) phase with hysteresis. In addition, the compound <b>3</b> exhibits long-range antiferromagnetic ordering between the ferromagnetic chains and spontaneous magnetization because of spin canting (canted antiferromagnetism) at a transition temperature <i>T</i>_N of 14.2 K. The electrical conductivity of <b>3</b> at 300 K is 4.8 × 10^–4 S cm^–1, which is relatively high despite Rh not being in a mixed-valence state. The temperature dependence of electrical resistivity also exhibits a clear hysteresis across the first-order phase transition. Furthermore, the ferromagnetic LT phase can be easily stabilized up to RT by the application of a relatively weak applied pressure of 1.4 kbar, which reflects the bistable characteristics and demonstrates the simultaneous control of multifunctionality through external perturbation