Dynamic Gate Opening of ZIF‑8 for Bulky Molecule Adsorption as Studied by Vapor Adsorption Measurements and Computational Approach

Zeolitic imidazolate frameworks-8 (ZIF-8; [Zn­(C4H5N2)2]n) has micropores with diameters of 11.6 Å, which are three-dimensionally connected to one another by apertures. The aperture diameter increases from 3.4 to 4.0 Å when gas adsorption takes place. The observed expansion of the apertures cannot explain adsorption of large molecules such as benzene, toluene, and CCl4. In this regard, we have proposed a new adsorption mechanism where the flip motion of the linkers assists the adsorption of bulky molecules. In this study, we investigated the uptake rate of the vapor adsorption of various bulky molecules. It was found that the activation energies for adsorption were controlled by the smallest cross section of molecule with cylindrical symmetry. We examined the activation energy and the effective rate constant evaluated from the diffusivity by potential energy calculations, considering both dispersion and electrostatic forces. When the tilting angle variation of the 2-methylimidazolate ring is in the range from 18° to 19°, the potential energy profile well explained the observed activation energy and the effective rate constant for benzene diffusivity into ZIF-8. Thus, both the activation energy and the effective rate constant supported the aperture expansion accompanying the variation of the linker orientation

Stable Dispersions of PVP-Protected Au/Pt/Ag Trimetallic Nanoparticles as Highly Active Colloidal Catalysts for Aerobic Glucose Oxidation

A simple, effective method has been demonstrated to synthesize Au/Pt/Ag trimetallic nanoparticles (TNPs) with an average diameter of 1.5 nm by reduction of the corresponding ions with rapid injection of NaBH4. The prepared TNPs were characterized by UV–vis, X-ray diffraction, X-ray photoelectron spectroscopy (XPS), high-resolution transmission electron microscopy, and energy dispersion X-ray spectroscopy in high-resolution scanning transmission electron microscopy. The activity of the TNPs is several times higher than that of Au NPs with nearly the same particle size. The high catalytic activities of the Au/Pt/Ag TNPs can be ascribed to the following factors: (1) the small average size, about 1.5 nm in diameter, and (2) the formed negatively charged Au atoms due to electron donation of Ag neighboring atoms and poly(N-vinyl-2-pyrrolidone) acting as catalytically active sites for aerobic glucose oxidation. The presence of the negatively charged Au atoms was supported by XPS measurements and electron density calculation with density functional theory

Accurate Standard Hydrogen Electrode Potential and Applications to the Redox Potentials of Vitamin C and NAD/NADH

We computationally evaluated the standard hydrogen electrode (SHE) potential in aqueous phase and the Gibbs energy of a proton from the experimental p<i>K</i>_a values of alcohol molecules. From the “golden standard” CCSD­(T)/aug-cc-pVTZ level calculation, we estimated the SHE potential as 4.48 V, which is very close to the IUPAC-recommended experimental value of 4.44 V. As applications to the Gaussian-3 (G3) methods, which also reproduce the “golden standard” level calculations, we computed various p<i>K</i>_a values and redox potentials for a vitamin series. For vitamin C, we support the experimental result of +0.35 V and predict the p<i>K</i>_a value of d-ascorbic acid to be 3.7–3.9. Using a model molecule for nicotinamide adenine dinucleotide (NAD), we reproduced the redox potential and determined the order of the proton/electron addition, based on both the proton affinity and redox potential

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

Role of Perferryl–Oxo Oxidant in Alkane Hydroxylation Catalyzed by Cytochrome P450: A Hybrid Density Functional Study

We have performed hybrid density functional theory (DFT) calculations on the reactivities of low-lying doublet and quartet ferryl–oxo [Fe­(IV)O] oxidants and a doublet perferryl–oxo [Fe­(V)O] oxidant as a new key active species in cytochrome P450. Several aspects of the mechanism of hydrogen-atom abstraction from propane by the above active species of compound I models have been addressed in detail. The results, based on fully optimized structures, demonstrate that the perferryl–oxo oxidant can contribute to the reactivity of compound I owing to the presence of a highly reactive pπ atomic radical character of the oxo ligand. The perferryl–oxo species can abstract a hydrogen atom from propane with an activation barrier of only 0.6–2.5 kcal mol–1, which is substantially smaller than that for the ferryl–oxo species (13.4–17.8 kcal mol–1). The role of the doublet perferryl species in the heterolytic and homolytic O–O bond cleavage in precursor (protonated) compound 0 coupled with the subsequent C–H bond activation has also been explored by grid search of ferryl and perferryl potential surfaces using two parameters. Our calculations suggest that the perferryl–oxo oxidant is catalytically competent, if the O–O bond cleaves heterolytically. The interplay between the accessible ferryl and perferryl states of compound I with quite different reactivities could be a possible reason for elusiveness of compound I in native P450 catalysis on the one hand and various degrees of detection in shunt reactions using peroxy acids on the other hand

Theoretical Investigation of Thermal Decomposition of Peroxidized Coelenterazines with and without External Perturbations

Thermal decomposition of peroxidized coelenterazines with and without external perturbations has been studied theoretically using the hybrid density functional theory (B3LYP) and the Coulomb-attenuating method (CAM). Possible roles of a hydrogen-bonding interface constituted by amino acid residues in the coelenterazine-biding site of aequorin are addressed by using simple model clusters with a polarizable continuum model to grasp some important aspects that may affect the electronic mechanism operating within the photoprotein. Calculations have revealed that the electronic property and stability of the peroxide are greatly affected by its protonation state and/or environmental effects, such as a polarizing medium and specific (localized) short-range electrostatic interactions, which may be critical for the bioluminescence activity. Theory highlights two mechanisms by which the neutral species can be activated, which otherwise decomposes by a homolytic O−O dissociation with a high barrier. In the first mechanism, the Tyr82-His16-Trp86 triad motif facilitates the deprotonation process of the phenolic OH group at the C6 position of the coelenterazine and thereby makes it a sufficiently good electron donor to activate the O−O bond. In the second mechanism, intramolecular charge transfer is accomplished within the neutral peroxide by a proton delivery mediated via another triad motif, Tyr184-His169-Trp173, without the activation of the substrate itself. The combination of the first and second mechanisms leads to complete electron transfer for the formation of a radical pair as a local intermediate stabilized by the nearby triad motifs

Unique Structural and Electronic Features of Perferryl–Oxo Oxidant in Cytochrome P450

We have performed hybrid density functional theory (DFT) calculations on the geometric and electronic structures of low-lying doublet and quartet ferryl–oxo [Fe(IV)O] oxidants and a doublet perferryl–oxo [Fe(V)O] oxidant in Cytochrome P450. Fully optimized structures of compound I models have been determined, and the proper symmetry of wave functions has been restored by the spin-projection technique. The results show that the perferryl–oxo species is relatively low lying, as compared with the excited state of the ferryl–oxo species, if the iron–oxo bond is properly described as the mixing of several appropriate excited electronic configurations to minimize electron repulsion. This means that the perferryl–oxo species is virtually in a mixed-valent resonance state, ↑Fe(V)O ↔ ↑Fe(IV)•↑–↓•O, containing a highly reactive pπ atomic oxygen radical. The anionic thiolate ligand acts as a Lewis σ base and functions to achieve the stability of the perferryl–oxo complex and to activate the oxo ligand trans to it by asymmetric bond distortion along the O–Fe–S axis by lengthening the Fe–O bond and shortening the Fe–S bond, prior to the hydrogen-atom abstraction from the substrate

Mechanistic Insights in Charge-Transfer-Induced Luminescence of 1,2-Dioxetanones with a Substituent of Low Oxidation Potential

We have investigated the decomposition pathway of dioxetanones 1c with a phenoxide anion group by the B3LYP/6-31+G(d) method together with the second-order multireference Møller−Plesset perturbation (MRMP) theory and propose charge-transfer-induced luminescence (CTIL) with polarization-induced branching excitation processes. In the gas phase, the thermal decomposition of 1c occurs by an asynchronous two-stage pathway without a discrete intermediate; that is, the initial O−O bond breaking to generate a charge-transfer (CT) diradical species is immediately followed by the subsequent C−C bond breaking with simultaneous back CT, which is responsible for the surface crossing at the avoided crossing. The activation energy is dramatically reduced from 19.4 to 3.8 kcal mol-1 by the deprotonation of phenol meta-1d to its anion meta-1c, showing an important role of the endothermic CT. The odd/even selection rule for the chemiluminescence efficiency can be explained by the orbital interaction for the back CT between the carbonyl π* orbital and either a HOMO or a LUMO of the generated light emitters. To examine the accessibility of the chemically initiated electron exchange luminescence (CIEEL) route, we considered the solvent effects on the free-energy change of meta-1c by using continuum solvent models. The bending vibration mode of the CO2 fragment is specifically considered. Borderline features emerges from the solution-phase CT reaction of meta-1c, which depends on the solvent polarity:  one is a nonadiabatic or adiabatic back CT process (polarization-induced concerted CTIL), and the other is a radical dissociation, i.e., complete one-electron-transfer process (CIEEL)

Free energy reaction root mapping of alanine tripeptide in water

We have investigated the free energy surface of alanine tripeptide in water. To elucidate the secondary structure of the amide chain, information on the free energy surface with explicit water at room temperature, and the multidimensional reaction coordinates are required. We studied the minimum free energy paths (MFEPs) connecting reactants, transition structures (TS) and products. To solve this problem, we used the free energy reaction root mapping (FERRMap) method. This is an automated search method to find MFEPs by using umbrella integration and the scaled hypersphere search method. We calculated the four-dimensional free energy surface for alanine tripeptide in water using FERRMap and found 61 equilibrium structures (EQ) connected by 133 TS points. After elucidating the MFEP network, we analysed the structures of the EQ points and the MFEPs connecting beta-sheet structures and beta-turn structures or left-handed helix structures.</p