Magnetically Recyclable Fe3O4@TMU-32 Metal-Organic Framework Photocatalyst for Tetracycline Degradation Under Visible Light.

Metal-organic frameworks (MOFs) are a new class of porous crystalline materials being used as photocatalysts for efficient pollutant removal and environmental remediation. In this study, the TMU-32 MOF was synthesized as an effective photocatalyst for the photodegradation of tetracycline (TC) with 96% efficiency in 60 min under visible light. The high photocatalytic activity of the TMU-32 MOF is mainly due to its large specific surface area, which is beneficial for promoting both the adsorption of TC and the separation of the photoinduced charges. Moreover, its desired crystallinity makes it a semiconductor with an appropriate band gap energy. Next, a composite of the TMU-32 MOF with Fe3O4 nanoparticles (as Fe3O4@TMU-32) was prepared as a magnetically recyclable photocatalyst. The results showed that the photocatalytic activity of the Fe3O4@TMU-32 nanocomposite is slightly lower (68% degradation of TC within 60 min) than that of TMU-32 toward TC degradation since Fe3O4 nanoparticles are not acting as a photocatalyst and are used only to make the host photocatalyst (here, TMU-32) magnetically separable. The effects of the photocatalyst concentration and recyclability on the photodegradation of TC were studied under similar conditions. We found that the Fe3O4@TMU-32 composite is easily recycled without a significant loss of photocatalytic activity after being used several times, indicating the stability of the photocatalyst. Finally, a density functional theory study was also conducted to investigate the structural and electronic properties such as the band gap energy and density of states of the TMU-32 MOF and the Fe3O4@TMU-32 composite. Our computational results are in good agreement with the experimental ones. A photocatalytic degradation mechanism was finally proposed under visible-light photoirradiation.

Towards developing efficient metalloporphyrin-based hybrid photocatalysts for CO2 reduction; an ab initio study.

A series of thiophene-based donor-acceptor-donor (D-A-D) oligomer substituted metalloporphyrins (MPors) with different 3d central metal-ions (M = Co, Ni, Cu, and Zn) were systematically investigated to screen efficient hybrid photocatalysts for CO2 reduction based on density functional theory (DFT) and time-dependent DFT simulations. Compared with base MPors, the newly designed hybrid photocatalysts have a lower bandgap energy, stronger and broader absorption spectra, and enhanced intermolecular charge transfer, exciton lifetime, and light-harvesting efficiency. Then, the introduction of D-A-D electron donor (ED) groups into the meso-positions of MPors is a promising method for the construction of efficient photocatalysts. According to the calculated adsorption distance, adsorption energy, Hirshfeld charge and electrostatic potential analysis, it was revealed that CO2 physically adsorbed on the designed photocatalyst surface. In addition, among the studied model systems the ZnPor(ED)4 catalyst with four D-A-D electron donors exhibits the best photocatalytic performance due to its broadest absorption spectra with λmax = 500.12 nm and the highest adsorption energy of about 26 kJ mol-1. Finally, the sensing ability of the ZnPor(ED)4-based multi-terminal molecular junction for CO2 gas detection is determined using Green's functions. The transmission plots of this molecular junction are barely changed due to the physical adsorption of CO2 on the molecular surface, leading to the low sensitivity of the device. We believe that such a theoretical design can provide a general approach for further experimental and computational studies of photocatalysts used in the CO2 reduction process.

To What Extent are "Atoms in Molecules" Structures of Hydrocarbons Reproducible from the Promolecule Electron Densities?

The "atoms in molecules" structures of 225 unsubstituted hydrocarbons are derived from both the optimized and the promolecule electron densities. A comparative analysis demonstrates that the molecular graphs derived from these two types of electron densities at the same geometry are equivalent for almost 90 % of the hydrocarbons containing the same number and types of critical points. For the remaining 10 % of molecules, it is demonstrated that by inducing small perturbations, through the variation of the used basis set or slight changes in the used geometry, the emerging molecular graphs from both densities are also equivalent. Interestingly, the (3, -1) critical point between two "non-bonded" hydrogen atoms, which triggered "H-H bonding" controversy is also observed in the promolecule densities of certain hydrocarbons. Evidently, the topology of the electron density is not dictated by chemical bonds or strong interactions and deformations induced by the interactions of atoms in molecules have a quite marginal role, virtually null, in shaping the general traits of the topology of molecular electron densities of the studied hydrocarbons, whereas the key factor is the underlying atomic densities.

Tracing the Fingerprint of Chemical Bonds within the Electron Densities of Hydrocarbons: A Comparative Analysis of the Optimized and the Promolecule Densities.

The equivalence of the molecular graphs emerging from the comparative analysis of the optimized and the promolecule electron densities in two hundred and twenty five unsubstituted hydrocarbons was recently demonstrated [Keyvani et al. Chem. Eur. J. 2016, 22, 5003]. Thus, the molecular graph of an optimized molecular electron density is not shaped by the formation of the C-H and C-C bonds. In the present study, to trace the fingerprint of the C-H and C-C bonds in the electron densities of the same set of hydrocarbons, the amount of electron density and its Laplacian at the (3, -1) critical points associated with these bonds are derived from both optimized and promolecule densities, and compared in a newly proposed comparative analysis. The analysis not only conforms to the qualitative picture of the electron density build up between two atoms upon formation of a bond in between, but also quantifies the resulting accumulation of the electron density at the (3, -1) critical points. The comparative analysis also reveals a unified mode of density accumulation in the case of 2318 studied C-H bonds, but various modes of density accumulation are observed in the case of 1509 studied C-C bonds and they are classified into four groups. The four emerging groups do not always conform to the traditional classification based on the bond orders. Furthermore, four C-C bonds described as exotic bonds in previous studies, for example the inverted C-C bond in 1,1,1-propellane, are naturally distinguished from the analysis.

Chameleonic nature of hydroxyheme in heme oxygenase and its reactivity: a density functional theory study.

Iron hydroxyheme is an intermediate in heme degradation that binds to HO-1 in a five-coordinated fashion wherein the fifth ligand is His25. The structure and reactivity of hydroxyheme have been investigated using the B3LYP*, OPBE, and CASSCF methods with the 6-31+G* and 6-311+G** basis sets. Hydroxyheme [(Im)Fe(II)(POH)] (POH is the hydroxyporphyrin) is readily oxidized to oxophlorin [(Im)Fe(III)(PO)] (PO is the oxophlorin trianion) in the protein heme oxygenase. A computational study in the gas phase has shown that (6)[(Im)Fe(II)(POH)] loses one electron from its a2u orbital in the presence of O2 and produces [(Im)Fe(II)(PO(•))]a2u(PO(•) is the oxophlorin dianion radical) in the sextet ground state with a ferrous keto π-neutral radical structure and dxy(2)a2u(1)dyz(1)dxz(1)σ*z2(1)d(x(2)-y(2))(1) electronic configuration. There is a closely lying exited state accompanying this ferrous keto π-neutral radical that has a high-spin ferric keto anion form of (6)[(Im)Fe(III)(PO)]xy with a2u(2)dxy(1)dyz(1)dxz(1)σ*z2(1)d(x(2)-y(2))(1) electronic configuration. In the protein environment with a dipole moment larger than 5.7, the ground state is reversed and (6)[(Im)Fe(III)(PO)]xy is at least 1.47 kcal/mol lower than the ferrous π-neutral radical of (6)[(Im)Fe(II) (PO(•))]a2u. The interaction of H2O, O2, and CO with iron oxophlorin will shift the electronic structure toward the formation of a keto π-neutral radical resonance form in the following order: CO > O2 > H2O.

Interaction modes and absolute affinities of α-amino acids for Mn2+: a comprehensive picture.

Manganese is involved as a cofactor in the activation of numerous enzymes as well as the oxygen-evolving complex of photosystem II. Full understanding of the role played by the Mn(2+) ion requires detailed knowledge of the interaction modes and energies of manganese with its various environments, a knowledge that is far from complete. To bring detailed insight into the local interactions of Mn in metallopeptides and proteins, theoretical studies employing first-principles quantum mechanical calculations are carried out on [Mn-amino acid](2+) complexes involving all 20 natural α-amino acids (AAs). Detailed investigation of [Mn-serine](2+), [Mn-cysteine](2+), [Mn-phenylalanine](2+), [Mn-tyrosine](2+), and [Mn-tryptophan](2+) indicates that with an electron-rich side chain, the most stable species involves interaction of Mn(2+) with carbonyl oxygen, amino nitrogen, and an electron-rich section of the side chain of the AA in its canonical form. This is in sharp contrast with aliphatic side chains for which a salt bridge is formed. For aromatic AAs, complexation to manganese leads to partial oxidation as well as aromaticity reduction. Despite multisite binding, AAs do not generate strong enough ligand fields to switch the metal to a low- or even intermediate-spin ground state. The affinities of Mn(2+) for all AAs are reported at the B3LYP and CCSD(T) levels of theory, thereby providing the first complete series of affinities for a divalent metal ion. The trends are compared with those of other cations for which affinities of all AAs have been previously obtained.

A theoretical study on the enthalpies of homolytic and heterolytic N-H bond cleavage in substituted melatonins in the gas-phase and aqueous solution.

In this paper, the study of melatonin and 60 meta- and ortho-substituted melatonins is presented. The reaction enthalpies related to the hydrogen atom transfer (HAT), single electron transfer - proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET) have been calculated using DFT/B3LYP method in gas-phase and water. Results show that electron-withdrawing substituents increase the bond dissociation enthalpy (BDE), ionization potential (IP) and electron transfer enthalpy (ETE), while electron-donating ones cause a rise in the proton dissociation enthalpy (PDE) and proton affinity (PA). In ortho position, substituents show larger effect on reaction enthalpies than in meta position. In comparison to gas-phase, water attenuates the substituent effect on all reaction enthalpies. Results show that IP and BDE values can be successfully correlated with the indolic N-H bond length after electron abstraction, R(N-H(+*)), and the partial charge on the indolyl radical nitrogen atom, q(N). Furthermore, calculated IP and PA values for meta and ortho substituted melatonins show linear dependence on the energy of the highest occupied molecular orbital (E(HOMO)) of studied molecules in the two environments. SPLET represents the thermodynamically preferred mechanism in water.

Density functional theory (B3LYP) study of substituent effects on O-H bond dissociation enthalpies of trans-resveratrol derivatives and the role of intramolecular hydrogen bonds.

In this paper, 23 substituents with various electron-donating and electron-withdrawing characters were placed in available positions of trans-resveratrol in order to study their effect on the three O-H bond dissociation enthalpies (BDEs) via density functional theory (DFT) with Becke three-parameter exchange and Lee-Yang-Parr correlation (B3LYP). It has been found that the mutual positions of substituents and OH groups affect investigated BDEs substantially. Formation of strong intramolecular hydrogen bonds and suitable spin density distributions in several radicals result in low BDEs. Calculated BDEs have been correlated with Hammett constants, selected geometry parameters, and charge on phenoxy radical oxygen q(O). Found dependences are satisfactorily linear.

Structure and redox behavior of iron oxophlorin and role of electron transfer in the heme degradation process.

Iron-oxophlorin is an intermediate in heme degradation, and the metal oxidation number can alter spin, electron distribution, and the reactivity of the metal and the oxophlorin ring. The role of electron transfer in the structure and reactivity of [(Py)(2)Fe(III)(PO)] (PO is the oxophlorin trianion) in different redox states has been investigated using the B3LYP and OPBE methods with the 6-31+G* and 6-311+G** basis sets. A computation study has shown that [(py)(2) Fe(III)(PO)] loses one electron from its a(2u) orbital. Thus the oxidized species, [(Py)(2)Fe(III)(PO(•))](+) (where PO(•) is the oxophlorin dianion radical), has an open-shell-singlet ground state with a d(xy)(2) d(xz)(2) a(2u)(1) d(yz)(1) electronic configuration with closely lying triplet and quintet states which are populated at ambient temperature. The aforementioned complex is highly reactive toward O(2). The reduced species [(Py)(2)Fe(II)(POH)] (where POH is the hydroxyheme) has the closed-shell-singlet ground state (π(xz) π(yz))(4) a(2u)(2) d(xy)(2) electronic configuration in which pyridines have a more π-accepting character and, thus, are tightly bound to iron. This reduced form is considerably less reactive toward O(2). The axial ligands effects (Im, t-BuNC) have also been studied in redox reactions of iron oxophlorin complexes. Complex [(Im)(2)Fe(III)(PO)] shows facile oxidation to form a cation radical and a reduction to form hydroxy while the [(t-BuNC)(2)Fe(II)(PO(•))] has high positive oxidation potential.

Effect of axial ligand on the electronic configuration, spin states, and reactivity of iron oxophlorin.

Iron-oxophlorin is an intermediate in heme degradation, and the nature of the axial ligand can alter the spin, electron distribution, and reactivity of the metal and the oxophlorin ring. The structure and reactivity of iron-oxophlorin in the presence of imidazole, pyridine, and t-butyl isocyanide as axial ligands was investigated using the B3LYP and OPBE methods with the 6-31+G* and 6-311+G** basis sets. OPBE/6-311+G** has shown that the doublet state of [(Py)(2)Fe(III)(PO)] (where pyridines are in perpendicular planes and PO is the oxophlorin trianion) is 3.45 and 5.27 kcal/mol more stable than the quartet and sextet states, respectively. The ground-state electronic configuration of the aforementioned complex is π(xz)(2) π(yz)(2) a(2u)(2) d(xy)(1) at low temperatures and changes to π(xz)(2) π(yz)(2) d(xy)(2) a(2u)(1) at high temperatures. This latter electronic configuration is consistently seen for the [(t-BuNC)(2)Fe(II)(PO(•))] complex (where PO(•) is the oxophlorin dianion radical). The complex [(Im)(2)Fe(III)(PO)] adopted the d(xy)(2) (π(xz) π(yz))(3) ground state and has low-lying quartet excited state which is readily populated when the temperature is increased.

Comparative DFT study to determine if α-oxoaldehydes are precursors for pentosidine formation.

We report a comprehensive density functional theory (DFT) study of the mechanism of pentosidine formation. This work is a continuation of our earlier studies in which we proposed pathways for formation of glucosepane (J. Mol. Model. 2011, pp 1-15, DOI 10.1007/s00894-011-1161-x), GODIC (glyoxal-derived imidazolium cross-link), and MODIC (methyl glyoxal-derived imidazolium cross-link; J. Phys. Chem. 2011, 115, pp 13542-13555). Here we show that formation of pentosidine via reaction of α-oxoaldehydes with lysine and arginine in aqueous solution is possible thermodynamically and kinetically, in good agreement with the available experimental evidence. Five pathways, A-E, were characterized, as in our previous GODIC and MODIC work. In pathways A and B, a Schiff base is first formed from lysine and methyl glyoxal (MGO), and this is followed by addition of arginine and glyoxal (GO). By contrast, in pathways C, D, and E, addition of arginine to MGO occurs first, resulting in the formation of imidazolone, which then reacts with lysine and GO to give pentosidine. Our calculations show that the reaction process is highly exergonic and that the three pathways A, C, and E are competitive. These results serve to underline the potentially important role that α-oxoaldehydes play as precursors in pentosidine formation in the complex field of glycation.

Cross-linking mechanisms of arginine and lysine with α,ß-dicarbonyl compounds in aqueous solution.

Cross-linking in proteins by α,ß-dicarbonyl compounds is one of the most damaging consequences of reactive carbonyl species in vivo and in foodstuffs. In this article we investigate computationally the cross-linking of glyoxal and methylglyoxal with lysine and arginine residues using density functional theory and the wB97XD dispersion-corrected functional. Five pathways, A-E, have been characterized. In pathways A and B, the reaction proceeds via formation of the Schiff base, aldimine, followed by addition of arginine. In contrast, in pathways C-E, direct addition of arginine to the dicarbonyl compounds occurs first, leading to a dihydroxyimidazolidine intermediate, which then reacts with lysine after dehydration and proton transfer reactions. The results reveal that pathways A, C, and E are competitive whereas reactions via pathways B and D are much less favorable. Inclusion of up to five explicit water molecules in the proton transfer and dehydration steps is found to lower the energy barriers in the feasible pathways by about 5-20 kcal/mol. Comparison of the mechanisms of methylglyoxal-derived imidazolium cross-linking (MODIC) and glyoxal-derived imidazolium cross-linking (GODIC) shows that the activation barriers are lower for GODIC than MODIC, in agreement with experimental observations.

The effect of external electric field and metal impurities on the interaction of HF and boraphene: a computational study.

Using density functional theory, the effects of P, Al, and Ga atoms doping on electronic structure of boraphene (B36) were investigated. The results show the highest change in electronic structure of doped-B36 systems belongs to Al-B36 structures wherein the gap energy of the system is decreased by 17.92%. DOS diagrams and absorption spectra of doped B36 are compared to pristine and discussed. The capability of pristine and modified B36 in the field of detection/adsorption of HF molecule has been evaluated. The calculated values of adsorption energies of 0.13, 0.63, 0.24, and 0.16 eV for adsorption of HF on pristine, Al-, Ga-, and P-B36 and related DOS diagrams reveal that these systems are not superior host materials for detection/adsorption applications. It was found that the external electric field could increase the interaction between HF and B36 systems leading to suggesting Al-B36 as proper candidate for HF removal applications.

Separation of CH4, H2S, N2 and CO2 gases using four types of nanoporous graphene cluster model: a quantum chemical investigation.

Nanoporous graphene is being regarded as a promising candidate for reliable gas separation and purification applications. In the present research, the permeation barrier, selectivity and all thermodynamic functions for passing of four different molecules including CH4, H2S, N2 and CO2 gases on four types of porous graphene which is doped by two, three and six nitrogen atoms using quantum mechanical modelling, based on the density functional theory, B97D, and cc-pVTZ basis set have been evaluated. We find that the permeation barrier of all studied gases especially carbon dioxide decreased by considering the functionalized porous graphene by two, three and six nitrogens-doped, respectively. The results of our study propose using a porous graphene sheet as highly efficient and highly selective membranes for gas separations.

A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations.

Heme degradation by heme oxygenase enzymes is important for maintaining iron homeostasis and prevention of oxidative stress. Previous studies have reported that heme degradation proceeds through three consecutive steps of O2 activation: the regiospecific self-hydroxylation of heme, the conversion of hydroxyheme to verdoheme and CO, and the cleavage of the verdoheme macrocycle to release biliverdin and free ferrous iron. Our results indicate that in the second step of heme degradation, not only verdoheme is generated but ring opening and biliverdin production also occur. We have performed QM-cluster and QM/MM calculations, which show that calculations with H2O as the axial ligand of Fe give the lowest barrier. In the QM-cluster calculation, the reaction is exothermic by -85 kcal mol-1 and the rate-limiting barrier is 5 kcal mol-1, whereas the corresponding QM/MM calculations give a slightly lower barrier of 3 kcal mol-1, owing to strong hydrogen bonds and the protein environment.

A theoretical elucidation of bilirubin interaction with HSA's lysines: first electrostatic binding site in IIA subdomain.

The electrostatic interaction of amino acid lysines 190, 195 and 199 of human serum albumin (HSA) with bilirubin have been investigated using molecular dynamic simulations, QM and QM/MM minimization methods. In this study two methodological approaches have been employed. In the first approach X-ray structure and the structure obtained from the molecular dynamic simulation of subdomain IIA of HSA in vacuum have been utilized. Interactions have been evaluated with the segment 186-200 of the cited subdomain. Calculations on the X-ray structure of above segment indicate an effective interaction of the lysine 195 with bilirubin, although that of the lysine 190 is also found considerable in this structure. Performing simulation in vacuum, it has been revealed that except for the lysine 195, the other two lysine residues (190 and 199) could not be considered as centers of interaction. Such finding, which is in accord with experimental data, lends support to the procedure employed in this study. NBO analyses suggest that tasks to achieve a structure indicating bilirubin interaction with the lysine 195 from the 186-200 segment extracted from X-ray structure, results in a structure that lacks any electrostatic interaction. In fact, it has been found that the stability of the latter species can be attributed to the H-bonding interaction of the glutamate 188 with both bilirubin and the lysine 195. Further NBO analysis on the structure of the same species, while achieved after molecular dynamic simulation on subdomain IIA in vacuum has revealed that a favorable electrostatic interaction between the lysine 195 and bilirubin has occurred. Besides, H-bonding interaction of the glutamate 188 with bilirubin has been evident in the same species. For the second approach, presence of water molecules and ions has been considered to simulate condensed medium. Applying docking, conformational sampling, and QM/MM minimization steps in sequence, a structure has been achieved which presents a specific interaction between epsilon-NH3(+) group of the lysine 195 residue and the lactam oxygen atom of bilirubin. NBO analyses suggest that above electrostatic interaction is combined with hydrogen bonding interaction between same two groups. Moreover, a hydrogen bond between oxygen atom of bilirubin's acetate group and alpha-NH group of lysine 195 has been observed. Molecular orbital calculations have been presented which support the NBO analyses.

Theoretical investigations of the hydrolysis pathway of verdoheme to biliverdin.

Conversion of iron(II) verdoheme to iron biliverdin in the presence of OH(-) was investigated using B3LYP method. Both 3-21G and 6-31G* basis sets were employed for geometry optimization calculation as well as energy stabilization estimation. Calculation at 6-31G* level was found necessary for a correct spin state estimation of the iron complexes. Two possible pathways for the conversion of iron verdoheme to iron biliverdin were considered. In one path the iron was six-coordinate while in the other it was considered to be five-coordinate. In the six-coordinated pathway, the ground state of bis imidazole iron verdoheme is singlet while that for open chain iron biliverdin it is triplet state with 4.86 kcal/mol more stable than the singlet state. The potential energy surface suggests that a spin inversion take place during the course of reaction after TS. The ring opening process in the six-coordinated pathway is in overall -2.26 kcal/mol exothermic with a kinetic barrier of 9.76 kcal/mol. In the five-coordinated pathway the reactant and product are in the ground triplet state. In this path, hydroxyl ion attacks the iron center to produce a complex, which is only 1.59 kcal/mol more stable than when OH(-) directly attacks the macrocycle. The activation barrier for the conversion of iron hydroxy species to the iron biliverdin complex by a rebound mechanism is estimated to be 32.68 kcal/mol. Large barrier for rebound mechanism, small barrier of 4.18 kcal/mol for ring opening process of the hydroxylated macrocycle, and relatively same stabilities for complexes resulted by the attack of nucleophile to the iron and macrocycle indicate that five-coordinated pathway with direct attack of nucleophile to the 5-oxo position of macrocycle might be the path for the conversion of verdoheme to biliverdin.

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˙)FeIII(PO˙)] (PO˙ is the oxophlorin dianion radical) and [(Im)(O2˙)FeIII(PO)]- (PO is the oxophlorin trianion). Thus, we have shown that in [(Im)(O2˙)FeIII(PO˙)] and [(Im)(O2˙)FeIII(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˙)FeIII(PO˙)] mechanism proceeds via two-state-reactivity patterns on the adjacent doublet and quartet spin state surfaces, whereas the [(Im)(O2˙)FeIII(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˙)FeIII(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˙)FeIII(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.

QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase.

Heme oxygenase is an enzyme that degrades heme, thereby recycling iron in most organisms, including humans. Pervious density functional theory (DFT) calculations have suggested that iron(III) hydroxyheme, an intermediate generated in the first step of heme degradation by heme oxygenase, is converted to iron(III) superoxo oxophlorin in the presence of dioxygen. In this article, we have studied the detailed mechanism of conversion of iron(III) superoxo oxophlorin to verdoheme by using combined quantum mechanics and molecular mechanics (QM/MM) calculations. The calculations employed the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. The reaction was found to be exothermic by -35 kcal/mol, with a rate-determining barrier of 19 kcal/mol in the doublet state. The protein environment and especially water in the enzyme pocket significantly affects the reaction by decreasing the reaction activation energies and changing the structures by providing strategic hydrogen bonds.

Computational study for the circular redox reaction of N2O with CO catalyzed by fullerometallic cations C60Fe+ and C70Fe.

We applied density functional calculations to study the circular redox reaction mechanism of N2O with CO catalyzed by fullerometallic cations C60Fe+ and C70Fe+. The on-top sites of six-membered rings (η6) of fullerene cages are the most preferred binding sites for Fe+ cation, and the hexagon to pentagon migration of Fe+ is unlikely under ambient thermodynamic conditions. The initial ion/molecule reaction, N2O rearrangement and N2 abstraction on the considered fullerometallic cations are easier than those on the bare Fe+ cation in the gas phase. Generally, our results indicate that fullerometallic ions, C60Fe+ and C70Fe+, are more favorable substrates for redox reaction of N2O with CO in comparison to the other previously studied carbon nanostructures such as graphene and nanotubes.