New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models

The heme protein, cytochrome P450, is an oxidoreductase that plays an important role in drug metabolism. To model P450s using molecular mechanics methods and classical molecular dynamics simulations, force field parameters and atomic charges are required. Because these parameters are generally obtained by quantum chemical methods, an appropriate simplified model for the iron-porphyrin system was needed. In this study, two models with a five-coordinated Fe(III) mimicking the sextet spin state of P450s are proposed, which are optimized by semiempirical and ab initio unrestricted Hartree-Fock methods. The results produced using the simpler of the two models were similar to those of the more complex model; therefore, the more simplified model of P450 can be used without a loss of accuracy. Furthermore, several quantum chemical calculations were carried out on the simpler model to investigate which method was most suitable for iron-porphyrin systems. The results calculated by hybrid density functional theory (DFT), with the MIDI basis set for iron, reproduced the three-dimensional structures determined by X-ray diffraction and extended X-ray absorption fine-structure experiments. From these results, atomic charges and force-field parameters for molecular mechanics and molecular dynamics calculations were obtained.     

铁原子与氮分子间的相互作用——单端位构型

用杂化密度泛函B3LYP方法在6-311+G(d)基组水平上研究了Fe 原子与N2分子相互作用的单端位构型的直线形和弯曲形两种结构的平衡几何结构、电子结构、轨道布局及红外光谱等性质. 计算结果表明, 由于强的σ-σ电子对互斥作用, 基组态4s²3d⁶的Fe原子不能与N2分子发生化学作用; 当Fe 原子呈现可与N2之间发生σ-π授予反馈作用的激发组态时, Fe 与N2分子之间可形成稳定的结构; 在得到的多个电子态中, 能量最低的是直线形的1³∑^-, 比Fe(a⁵D)和N2(¹∑⁺g )能量高21.6 kJ·mol-1, 同时存在几个能量相近的电子态, 如1³∏、1³Φ; 弯曲形都是不稳定态, 可能是连接直线形和单侧双配位构型的过渡态; 单端位构型产物相对于基态的反应物均是热力学不稳定的; 单端位构型中Fe对N2的活化作用很小, N—N 键长增加不超过7 pm.     

Mapping the d-d excited-state manifolds of transition metal beta-diiminato-imido complexes. Comparison of density functional theory and CASPT2 energetics

Trigonal-planar, middle transition metal diiminato-imido complexes do not exhibit high-spin states, as might be naively expected on the basis of their low coordination numbers. Instead, the known Fe(III), Co(III), and Ni(III) complexes exhibit S = 3/2, S = 0, and S = 1/2 ground states, respectively. Kohn-Sham DFT calculations have provided a basic molecular orbital picture of these compounds as well as a qualitative rationale for the observed spin states. Reported herein are ab initio multiconfiguration second-order perturbation theory (CASPT2) calculations, which provide a relatively detailed picture of the d-d excited-state manifolds of these complexes. Thus, for a C(2v) Fe(III)(diiminato)(NPh) model complex, two near-degenerate states ((4)B(2) and (4)B(1)) compete as contenders for the ground state. Moreover, the high-spin sextet, two additional quartets and even a low-spin doublet all occur at <0.5 eV, relative to the ground state. For the Co(III) system, although CASPT2 reproduces an S = 0 ground state, as observed experimentally for a related complex, the calculations also predict two exceedingly low-energy triplet states; there are, however, no other particularly low-energy d-d excited states. In contrast to the Fe(III) and Co(III) cases, the Ni(III) complex has a clearly nondegenerate (2)B(2) ground state. The CASPT2 energetics provide benchmarks against which we can evaluate the performance of several common DFT methods. Although none of the functionals examined perform entirely satisfactorily, the B3LYP hybrid functional provides the best overall spin-state energetics.     

Flat-structural Motives in Small Alumino-Carbon Clusters C(n)Al(m) (n = 2-3, m = 2-8)

Small clusters consisting of a carbon diatom or triatom and several aluminum atoms are investigated ab initio, at an MP2 level of theory. The mainly ionic character of C-Al bonding predominantly leads to structures different from corresponding hydrocarbons (also if starting from analogous initial geometries), while still producing closed-shell ground states. It is found that in many cases stable geometries correspond to flat CAl(3) units. These include unique metal-framed dicarbon and tricarbon all-flat species with unusual planar tetra-coordination. Another frequent feature is a hyper-coordination of carbon atoms, supported by their high negative charges and critically examined via atom-in-molecule calculations. Also characterized are anionic states, electronic excitation and ionization, electron attachment and detachment, and charge distributions.     

A Quantum Chemistry Study of Inhibition Properties of Imidazole and Its Derivatives on Iron Surface Corrosion

The geometries of imidazole and its derivatives were respectively optimized by using ab initio method, and the molecular orbital energy levels and the charge densities were obtained for their optimum geometries. The frontier orbital energy levels, and the net charges of N (1) atom and the imidazole ring of those molecules were obtained with ab initio and SCC-DV-Xα methods. It was found that the inhibition properties of those compounds change with the highest occupied molecular orbital energy levels, and the net charges of N (1) atom. We took four iron atoms on the crystal plane (100) of α-iron as the surface which was used to study the adsorption towards the inhibitors. The adsorption models of the inhibitor to be adsorbed on the Fe-cluster surface were optimized with SCC-DV-Xα method. It turns out that the most favorable model is that the inhibitor molecule is adsorbed on the Fe-cluster surface in an inclined state. The calculation shows that the stabilization energies of the systems are well correlated with the inhibition efficiencies.     

Applications of effective core potentials and density functional theory to the spin states of iron porphyrin

We investigated the performance of the B3LYP density functional in combination with ab initio effective core potentials (ECPs) that are derived from either Hartree-Fock or Dirac-Fock calculations. The transferability of ab initio ECPs is assessed on the basis of comparison with all-electron density functional calculations. For iron(II) porphyrin in particular, our assessment focused on the relative energetic ordering of five low-lying spin states, 1A1G, 3A1G, 3B2G, 5A2G, and 5B1G, and their properties, including optimized structures, charge distribution, spin density, and vibrational frequencies. Our results show that core electron correlation and core-valence electron correlation do not have significant effects on the relative energetics of the spin states of iron porphyrin. Our calculations suggest that effects of replacing the core electrons with ECPs are less significant than the choice of basis functions. We conclude that ab initio ECPs such as LANL2, RCEP, and MEFIT-R may be combined with the B3LYP density functional theory to provide consistent and accurate results.     

Multi-state epoxidation of ethene by cytochrome P450: a quantum chemical study.

The epoxidation of ethene by a model for Compound I of cytochrome P450, studied by the use of density functional B3LYP calculations, involves two-state reactivity (TSR) with multiple electromer species, hence "multi-state epoxidation". The reaction is found to proceed in stepwise and effectively concerted manners. Several reactive states are involved; the reactant is an (oxo)iron(IV) porphyrin cation radical complex with two closely lying spin states (quartet and doublet), both of which react with ethene to form intermediate complexes with a covalent C-O bond and a carbon-centered radical (radical intermediates). The radical intermediates exist in two electromers that differ in the oxidation state of iron; Por(+)(*)Fe(III)OCH(2)CH(2)(*) and PorFe(IV)OCH(2)CH(2)(*) (Por = porphyrin). These radical intermediates exist in both the doublet- and quartet spin states. The quartet spin intermediates have substantial barriers for transformation to the quartet spin PorFe(III)-epoxide complex (2.3 kcal mol(-)(1) for PorFe(IV)OCH(2)CH(2)(*) and 7.2 kcal mol(-)(1) for Por(+)(*)Fe(III)OCH(2)CH(2)(*)). In contrast, the doublet spin radicals collapse to the corresponding PorFe(III)-epoxide complex with virtually no barriers. Consequently, the lifetimes of the radical intermediates are much longer on the quartet- than on the doublet spin surface. The loss of isomeric identity in the epoxide and rearrangements to other products arise therefore mostly, if not only, from the quartet process, while the doublet state epoxidation is effectively concerted (Scheme 7). Experimental trends are discussed in the light of the computed mechanistic scheme, and a comparison is made with closely related mechanistic schemes deduced from experiment.     

Structure and bonding studies of ClX-C2H4 (X = H or Br) van der Waals complexes

High-quality ab initio calculations at the MPn (n = 2, 3 or 4) levels for the π-donor complex formed by HCl and ethene, and the recently characterized ClBr-ethene complex are presented. Interaction energies were calculated with the inclusion of both basis-set superposition error and zero-point energy corrections, resulting in values of about 1 kcal mol⁻¹ for both complexes. The total charge densities for both complexes yielded molecular graphs indicative of the weak binding in these molecules, and correspondingly, calculated charges showed that the XCl moiety has an overall slightly negative charge, while the ethene moiety is slightly positive. Analysis of the Laplacian of the charge density showed that the geometry of the ClBr- C₂H₄ complex may be understood in terms of the VSEPR model as an example of an AXYE₃ molecule.     

A theoretical and computational study of the anion, neutral, and cation Cu(H(2)O) complexes

An ab initio investigation of the potential energy surfaces and vibrational energies and wave functions of the anion, neutral, and cation Cu(H(2)O) complexes is presented. The equilibrium geometries and harmonic frequencies of the three charge states of Cu(H(2)O) are calculated at the MP2 level of theory. CCSD(T) calculations predict a vertical electron detachment energy for the anion complex of 1.65 eV and a vertical ionization potential for the neutral complex of 6.27 eV. Potential energy surfaces are calculated for the three charge states of the copper-water complexes. These potential energy surfaces are used in variational calculations of the vibrational wave functions and energies and from these, the dissociation energies D(0) of the anion, neutral, and cation charge states of Cu(H(2)O) are predicted to be 0.39, 0.16, and 1.74 eV, respectively. In addition, the vertical excitation energies, that correspond to the 4 (2)P<--4 (2)S transition of the copper atom, and ionization potentials of the neutral Cu(H(2)O) are calculated over a range of Cu(H(2)O) configurations. In hydrogen-bonded, Cu-HOH configurations, the vertical excitation and ionization energies are blueshifted with respect to the corresponding values for atomic copper, and in Cu-OH(2) configurations where the copper atom is located near the oxygen end of water, both quantities are redshifted.     

Electronic ground states of iron porphyrin and of the first species in the catalytic reaction cycle of cytochrome P450s

Electronic structures of iron(II) and iron(III) porphyrins are studied with density functional theory (DFT) using the GGA exchange functional OPTX in combination with the correlation functional PBE (OPBE) and with the correlation functional Perdew (OPerdew) together with a triple zeta-type basis set. These functionals, known for accurately predicting the spin ground state of iron complexes, are evaluated against other functionals for their performance in calculating relative energies for the various electronic states of both the iron porphyrins. The calculated energy orderings are triplet < quintet < singlet for the iron(II) porphyrin and quartet < sextet < doublet for the iron(III) porphyrin cation. Complexation by a thiolate ion (SH-) changes the preferred ground state for both species to high spin. This thiolate complex is used as a mimic for the cytochrome P450s active site to model the first step of the catalytic cycle of this enzyme. This first step is believed to concern the removal of an axial oxygen donating ligand from the hexacoordinated aqua-thiolate-porphyrin-iron(III) resting state. The DFT results suggest that this is not a free water molecule, because of its repulsive nature, but that it has instead hydroxy anion character. These calculations are in line with the experimentally observed change in the spin state from low to high spin upon this removal of the axial hydroxo ligand by binding of the substrate in the heme pocket of cytochrome P450.     

Molecular simulation of guanidinium-based ionic liquids

A new systematic all-atom force field was developed for cyclic guanidinium-based ionic liquids (ILs) based on the AMBER force field. Optimized molecular geometries and equilibrium bond lengths and angles were obtained by ab initio calculations, and charges were allocated to each atom center by fitting the ab initio electrostatic potential. Molecular dynamics simulations were performed for eleven kinds of ILs that are comprised of NO3(-) anions and cyclic guanidinium-based cations. Validation was carried out by comparing our simulated densities with experimental and calculated data from the literature. Transport properties such as self-diffusion coefficients, viscosities, and conductivities were calculated by molecular dynamic simulation, and their dependence on the length of the alkyl chains of cyclic guanidinium-based cations are discussed. Radial distribution functions and spatial distribution functions were investigated to depict the microscopic structures of the ILs, and the relationship between their properties and microstructures is also discussed.     

On the structure and spin states of Fe(III)-EDDHA complexes

DFT methods are suitable for predicting both the geometries and spin states of EDDHA-Fe(III) complexes. Thus, extensive DFT computational studies have shown that the racemic-Fe(III) EDDHA complex is more stable than the meso isomer, regardless of the spin state of the central iron atom. A comparison of the energy values obtained for the complexes under study has also shown that high-spin (S = 5/2) complexes are more stable than low-spin (S = 1/2) ones. These computational results matched the experimental results of the magnetic susceptibility values of both isomers. In both cases, their behavior has been fitted as being due to isolated high-spin Fe(III) in a distorted octahedral environment. The study of the correlation diagram also confirms the high-spin iron in complex 2b. The geometry optimization of these complexes performed with the standard 3-21G* basis set for hydrogen, carbon, oxygen, and nitrogen and the Hay-Wadt small-core effective core potential (ECP) including a double-xi valence basis set for iron, followed by single-point energy refinement with the 6-31G* basis set, is suitable for predicting both the geometries and the spin-states of EDDHA-Fe(III) complexes. The presence of a high-spin iron in Fe(III)-EDDHA complexes could be the key to understanding their lack of reactivity in electron-transfer processes, either chemically or electrochemically induced, and their resistance to photodegradation.     

Theoretical study of the intermolecular hydrogen bond interaction for furan-HCl and furan-CHCl_3 complexes

The importance of intermolecular interactions in biology and material science has prompted chemists to explore the nature of the variety of such interactions. The strongest of these interac-tions are the hydrogen bonds, which play an important role in determining the molecular confor-mation, crystal packing, and the structure of biological systems such as nucleic acids. Extensive experimental and theoretical efforts[1—5] have been devoted to the studies of this type of interac-tions, such as …     

Electronic properties of the low‐lying spin states of dimethylnitrosamine coordinated to Fe(III) heme models: An ab initio study

The unusual O‐coordination mode of nitrosamines to Fe(III) heme models has been observed in the bis(dimethylnitrosamine)(meso‐tetraphenylporphyrinate)iron(III) cation. For the first time, this latter as well as the simpler bis(dimethylnitrosamine)(porphinate)iron(III) heme model cations have been studied through ab initio methods. The sextet, quartet, and doublet spin states of both cations have been studied through single‐point calculations based on the experimental (X‐ray) geometry. Their energies, charges, and spin densities have been analyzed. The obtained results (at the UHF/cc‐pVDZ and ROHF/cc‐pVDZ levels) indicate that the peripheral benzene rings are of secondary importance for the coordination of dimethylnitrosamine to the Fe(III) porphyrin core. The obtained energy ordering is sextet < quartet < doublet, at all computational levels. The UHF, ROHF, and UMP2 results indicate an excess of alpha spin density around the Fe atom, a low covalency for the Fe? O bond and a substantial charge transfer to the Fe atom. Our best estimates [obtained at ROMP2 level with the mixed cc‐pVDZ/cc‐pVTZ‐DK(Fe) basis set] for the energy differences (in eV) between the three spin states considered are 0.929 for the sextet‐quartet gap and 0.812 for the quartet‐doublet gap, which indicate that the spin crossover (at room temperature) is very unlikely. These results represent the substantial decrease in the uncorrelated values. The implications of spin contaminations at the UHF and UMP2 levels for subsequent geometry optimizations to be performed in the smaller cation have also been discussed. © 2013 Wiley Periodicals, Inc.     

三硝基苯-对位取代苯酚负离子荷移复合物从头算研究

运用G94W量子化学程序,在HF/3-21G基组水平上对三硝基苯-对位取代苯酚(取代基:CH~3O-,CH~3-,Cl-)负离子的电荷转移复合物进行从头计算。把电荷转移复合物看成一个超分子,研究该系列复合物的稳定性、电荷转移及几何构型等规律。计算结果表明,苯酚负离子供电中心O沿一倾角指向三硝基苯中的任意相邻两个硝基之间的C位置上,复合物的稳定性按对位取代苯酚取代基CH~3O-,CH~3-,Cl-的次序减小,与实验规律相一致。计算结果还表明,形成该系列复合物具有明显的电荷转移,其稳定性与电荷转移量有关等。     

The structure of geminal imidazolium bis(trifluoromethylsulfonyl)amide ionic liquids: a theoretical study of the gas phase ionic complexes

In this work we report molecular mechanics and ab initio calculations on the geminal di-imidazolium bis(trifluoromethylsulfonyl)amide ionic liquid in the gas phase. We report the likely energetically preferred geometries of the ionic complex and its main features in terms of charge distribution, electronic density, structure, and energetics. We find that the gas phase structure of the ionic complex is quite compact and that the alkyl chain connecting the two imidazolium charged rings is strongly bent in order to maximize their electrostatic interactions with the two anions.     

Highly Reactive Nonheme Iron(III) Iodosylarene Complexes in Alkane Hydroxylation and Sulfoxidation Reactions

High‐spin iron(III) iodosylarene complexes bearing an N‐methylated cyclam ligand are synthesized and characterized using various spectroscopic methods. The nonheme high‐spin iron(III) iodosylarene intermediates are highly reactive oxidants capable of activating strong C? H bonds of alkanes; the reactivity of the iron(III) iodosylarene intermediates is much greater than that of the corresponding iron(IV) oxo complex. The electrophilic character of the iron(III) iodosylarene complexes is demonstrated in sulfoxidation reactions.     

Approximate additivity of anion-pi interactions: an ab initio study on anion-pi, anion-pi(2) and anion-pi(3) complexes

We have studied the additivity of the anion-pi interaction using high level ab initio calculations. We have optimized chloride and bromide complexes with one, two and three aromatic units (such as trifluoro-s-triazine and s-triazine). We have analyzed the interaction using the atoms in molecules theory and studied the charge transfer using several methods for deriving atomic charges. The results revealed additivities of both the geometries and the binding energies. We have also proposed a neutral receptor for chloride based on multiple anion-pi interactions. Finally, we have simulated solvent effects within the self-consistent reaction field model.