Binding of CO, NO, and O2 to heme by density functional and multireference ab initio calculations

Using the CASSCF/CASPT2 approach, along with several DFT methods (PBE0, B3LYP, BP86, OLYP), we have investigated the bonding of CO, NO, and O2 molecules to two model heme systems: an iron(II) porphyrin with and without an axial imidazole ligand. The experimentally available binding energies are best reproduced by the CASPT2 method and with the OLYP functional. The other functionals considered perform much worse, either severely overbinding (BP86) or underbinding (B3LYP, PBE0). Significant discrepancies between the different density functionals are observed, not only for the energetics but sometimes also for structure predictions. This confirms our viewpoint that a balanced treatment of the electronic exchange and correlation is vital to describe the weak metal-ligand bond between heme and CO, NO, or O2. The binding energies DeltaEb were split into two contributions: the so-called spin-pairing energy DeltaE sp and the "inherent" binding energy DeltaEb0, and both contributions were analyzed in terms of method and basis set effects. We have also investigated the spin density distributions resulting from the bonding of the NO molecule (a noninnocent ligand) to heme. Our analysis at the DFT and CASSCF level shows that, while various density functionals predict qualitatively very different spin distributions, the CASSCF spin populations most closely correspond to the results obtained with the pure BP86 or OLYP rather than with the hybrid functionals.     

Density functional theory study of hydrogen bonding in ionic molecular materials

Crystal structures are usually described in geometric terms. However, it is the energetics of intermolecular interactions that determine the chemical and physical properties of molecular materials.(1) In this paper, we use density functional theory (DFT) in combination with numerical basis sets to analyze the hydrogen bonding interactions in a family of novel ionic molecular materials. We find that the calculated binding energies are consistent with those of other ionic hydrogen bonded systems. We also examine electron density distributions for the systems of interest to gain insight into the nature of the hydrogen bonding interaction and investigate the effects of different aspects of the crystal field on the geometry of the hydrogen bond.     

CO在Cu/ZnO上吸附的簇模型研究

采用DFT方法和HF方法对CO在Cu／ZnO催化剂上的Zn（Ⅱ）和Cu（Ⅰ）表面位上的吸附行为进行了比较研究.结果表明：HF方法给出了较弱的M-CO（M＝Zn（Ⅱ），Cu（Ⅰ））表面吸附键描述，但无法正确预测其强弱顺序，MP2方法与DFT方法则给出与实验事实一致的描述.文章还对CO／铜基催化剂吸附体系的IR光谱进行了合理的理论预测.     

Bonding analyses, formation energies, and vibrational properties of M-R2dtc complexes (M=Ag(I), Ni(II), Cu(II), or Zn(II))

Detailed theoretical studies based on density functional theory (DFT)/B3LYP calculations of dimethyl- and diethyldithiocarbamate complexes of Ni(II), Cu(II), Zn(II), and Ag(I) are performed to characterize the metal-ligand bonding type as well as the metal-ligand bonding strength depending on the metal and the dialkyl substituent. The metal-ligand interactions in the studied complexes are investigated by means of charge decomposition analysis, energy partitioning analysis (EPA), and natural bond orbital analysis. According to the EPA calculations, the electrostatic attraction is the dominant contribution to the M-S2(R2dtc) (dtc=dithiocarbamate) bonding. The electrostatic and the orbital energies follow the order of the total binding energy, and hence both contributions are responsible for the binding energy order of M(R2dtc)2 complexes. The stability of the M(R2dtc)2 complexes is estimated by means of calculated formation reaction energies in the gas phase and solution, and it decreases in the order Ni(R2dtc)2>Cu(R2dtc)2>Zn(R2dtc)2. Larger formation reaction energies are found for M(Et2dtc)2 than for M(Me2dtc)2 complexes. The calculations predict stabilization of M(II)(R2dtc)2 complexes going from the gas phase to a polar solvent and destabilization of the bidentate AgR2dtc complex in a polar solvent. Gas-phase frequency calculations of all possible bonding types, symmetrical, asymmetrical, and uni- and bidentate, predict one band due to the nu(CS) IR absorption, and therefore the number of the bands in the 1060-920 cm(-1) region could not be used to discern the metal-ligand bonding type. Periodic DFT frequency calculations for Cu(Et2dtc)2 reveal that the splitting observed in the solid-state spectra of the complexes arises from the nonplanar MS4 fragment and intermolecular contacts but not from asymmetrical bonding. The calculations suggest that the important vibrational characteristic that can be used to discern uni- and bidentate bonding is the Raman activity of the nu(CS) band: It is very high for the unidentate dtc bonding (nu(C=S)) and low for the bidentate bonding (nuas(CS)).     

三聚氰胺金属(II)配合物的结构、紫外-可见光谱和反应活性

三聚氰胺是婴幼儿“肾结石事件”的重要前体. 本文选取几个典型的二价金属离子与三聚氰胺(L)形成的三聚氰胺金属配合物ML2(OH)2(M=Ca, Mg, Zn, Cu, Ni, Fe), 使用密度泛函理论(DFT)、含时DFT和概念DFT等工具, 系统地计算和比较了ML2(OH)2的结构、紫外-可见光谱和反应性质的异同. 模拟结果揭示了ML2(OH)2的结构、光谱及其反应性质是一类不同于其前体L, 形成ML2(OH)2配合物后, 将有较高的亲电指数和较低的化学硬度以及呈现红外吸收峰红移; 在这些典型的二价金属配合物中, 金属M离子电荷与配体O和N原子之间的电荷、以及与金属M离子和配体原子之间的二级微扰相互作用能, 配合物最低空轨道能级与其亲电反应指数、最低空轨道能级与化学硬度指数等方面, 存在着一系列定量的相关关系, 相关系数(R2)达0.889-0.997; 前线分子轨道模拟结果表明, ML2(OH)2体系反应活性的差异源于金属离子对前线轨道贡献有所不同, FeL2(OH)2、CuL2(OH)2、NiL2(OH)2等过渡金属离子的配合物中, 金属离子贡献较多, 共价性成分较多. 这些结果将为进一步理解人体内三聚氰胺致结石的成因提供有益的启示.     

Similarities and differences in the structure of 3<Emphasis Type="Italic">d</Emphasis>-metal monocarbides and monoxides

The structure and properties of the monocarbides ScC, TiC, VC, CrC, MnC, FeC, CoC, NiC, CuC, ZnC and their negatively and positively charged ions together with 3 d-metal monoxide cations are calculated by density functional theory (DFT) and hybrid DFT methods. In addition to the spectroscopic constants, the computed properties include the electron affinities, ionization energies, and dissociation energies. These results along with our previous results for the neutral and negatively charged 3 d-metal monoxides allow a detailed comparison of similarity and differences in the bonding of the metal oxides and carbides. These results are compared with results obtained using other theoretical approaches and with experiment. Chemical bonding, analyzed using the natural bond orbital scheme, was found to be rather different in the 3 d-metal monocarbides and monoxides.     

Structural and electronic properties of reduced transition metal oxide clusters, M4O10 and M4O10- (M = Cr, W), from photoelectron spectroscopy and quantum chemical calculations

Anion photoelectron spectroscopy and quantum chemical calculations at the density functional theory (DFT), coupled cluster theory (CCSD(T)), and complete active space self-consistent field (CASSCF) theory levels are employed to study the reduced transition metal oxide clusters M(4)O(10)(-) (M = Cr, W) and their neutrals. Photoelectron spectra are obtained at 193 and 157 nm photon energies, revealing very different electronic structures for the Cr versus W oxide clusters. The electron affinity and HOMO-LUMO gap are measured to be 3.68 ± 0.05 and 0.7 eV, respectively, for the Cr(4)O(10) neutral cluster, as compared to 4.41 ± 0.04 and 1.3 eV for W(4)O(10). A comprehensive search is performed to determine the ground-state structures for M(4)O(10) and M(4)O(10)(-), in terms of geometry and electronic states by carefully examining the calculated relative energies at the DFT, CCSD(T), and CASSCF levels. The ground states of Cr(4)O(10) and Cr(4)O(10)(-) have tetrahedral structures similar to that of P(4)O(10) with the anion having a lower symmetry due to a Jahn-Teller distortion. The ground states of W(4)O(10) and W(4)O(10)(-) have butterfly shape structures, featuring two fused five-member rings with a metal-metal multiple bond between the central metal atoms. The much stronger WW bonding than the CrCr bonding is found to be the primary cause for the different ground state structures of the reduced Cr(4)O(10)(0/-) versus W(4)O(10)(0/-) oxide clusters. The photoelectron spectra are assigned by comparing the experimental and theoretical adiabatic and vertical electron detachment energies, further confirming the determination of the ground electronic states of M(4)O(10) and M(4)O(10)(-). The time-dependent DFT method is used to calculate the excitation energies of M(4)O(10). The TD-DFT results in combination with the self-consistently calculated vertical detachment energies for some of the excited states at the DFT and CCSD(T) levels are used to assign the higher energy bands. Accurate clustering energies and heats of formation of M(4)O(10) are calculated and used to calculate accurate reaction energies for the reduction of M(4)O(12) to M(4)O(10) by CH(3)OH, as well as for the oxidation of M(4)O(10) to M(4)O(12) by O(2). The performance of the DFT method with the B3LYP and BP86 functionals in the calculations of the relative energies, electron detachment energies, and excitation energies are evaluated, and the BP86 functional is found to give superior results for most of these energetic properties.     

Experimental and theoretical electron density study of estrone

The electron density and the electrostatic potential (ESP) distributions of estrone have been determined using X-ray diffraction analysis and compared with theoretical calculations in the solid and gas phases. X-ray diffraction measurements are performed with a Rigaku Rapid rotating anode diffractometer at 20 K. The electron density in the estrone crystal has been described with the multipole model, which allowed extensive topological analysis and calculation of the ESP. From DFT calculations in the solid state a theoretical X-ray diffraction data set has been produced and treated in the same way as the experimental data. Two sets of single molecule DFT calculations were performed: (a) An electron density distribution was obtained via a single-point calculation with a large basis set at the experimental geometry and subsequently analyzed according to the quantum theory of atoms in molecules (AIM) to obtain the bond and most atomic properties, and (b) another electron density distribution was obtained with a smaller basis set, but at a geometry optimized using the same basis set for the analysis of atomic energies. An interesting locally stabilizing hydrogen-hydrogen bond path linking H(1) and H(11B) is found which represents the first characterization of such bonding in a steroid molecule. AIM delocalization indices were shown to be well correlated to the experimental electron density at the bond critical points through an exponential relationship. The aromaticity of ring A, chemical bonding, the O(1)...O(2) distance necessary for estrogenic activity, and the electrostatic potential features are also discussed.     

Probing the electronic structure,chemical bonding,and excitation spectra of [CuE]+/0/− (E = 14 group element) diatomics employing DFT and ab initio methods

The electronic structure, chemical bonding, and excitation spectra of neutral, cationic, and anionic diatomic molecules of Cu and 14 group elements formulated as [CuE]^+/0/? (E = C, Si, Ge, Sn, Pb) were investigated by density functional theory (DFT) and time‐dependent (TD)‐DFT methods. The electronic and bonding properties of the diatomics analyzed by natural bond orbital (NBO) analysis approch revealed a clear picture of the chemical bonding in these species. The spatial organization of the bonding between Cu and E atoms in the [CuE]^+/0/? (E = Si, Ge, Sn, Pb) molecules can easily be recognized by the cut‐plane electron localization function representations. Particular emphasis was given on the absorption spectra of the [CuE]^+/0/? which were simulated using the results of TD‐DFT calculations employing the hybrid Coulomb‐attenuating CAM‐B3LYP functional. The absorption bands have thoroughly been analyzed and assignments of the contributing principal electronic transitions associated to individual excitations have been made. © 2012 Wiley Periodicals, Inc.     

IB 族金属-乙烯配合物[N{(Me)C(Ph)N}2]M-C2H4 (M=Cu,Ag, Au)的电子结构

采用从头算Hartree-Fock(HF),M??ller-Plesset微扰(MP2),二级近似耦合簇(CC2)和密度泛函理论(DFT)方法,对IB族金属-乙烯配合物LM-C2H4(L=[N{(Me)C(Ph)N}2];M=Cu,Ag,Au)的几何结构、电子结构以及LM与C2H4之间的结合能进行了理论研究.MP2、CC2和密度泛函方法对C2H4配位前后C=C键长的变化情况都给出了正确的描述.电子结构分析显示LM与C2H4之间主要以C2H4→LM"σ-给予"和LM→C2H4"π-反馈"方式协同成键,这种成键方式使C2H4配体π轨道上的电子密度下降,π*轨道上的电子密度增加,并使得C=C键长增加、键能下降,从而达到活化C=C键的目的.自然电荷布居和能量分解分析显示LM-C2H4中的"σ-给予"作用弱于"π-反馈"作用,若使用"σ-给予"作用强于"π-反馈"作用的M+-C2H4体系作为LM-C2H4的简化模型进行理论研究是不合适的.LM-C2H4中金属原子M的改变对C=C键长、C2H4电荷布居以及LM与C2H4之间的结合能等性质影响显著.LAu与LCu、LAg相比其接受和反馈电子的能力最强,使C2H4配体π轨道电子密度减少的程度和π*轨道电子密度增加的程度也最大,因此LAu对C2H4中C=C键的活化效果最好.螯合配体取代基供、吸电能力的改变对上述性质的影响则非常有限.     

Energetics driving the short-range order in CuxPd1-x/Ru(0001) monolayer surface alloys

The energetics determining the distinct short-range order in two-dimensional (2D) monolayer Cu(x)Pd(1-x) surface alloys on a Ru(0001) substrate were investigated by Monte Carlo simulations and density functional theory calculations. Using a 2D lattice gas Hamiltonian based on effective pair interaction (EPI) parameters, the EPIs were derived for different Cu concentrations with Monte Carlo (MC) simulations by comparing with the atomic distributions obtained from atomic resolution STM images and the related Warren-Cowley short-range order parameters (Hoster et al., Phys. Rev. B, 2006, 73 165413). The ground state structures and mixing energies at 0 K derived from these EPIs agree well with mixing energies determined from DFT calculations of different ordered surface alloys. Additional MC simulations yield rather low transition temperatures which explain the absence of ordered 2D phases in the experiments. The consequences of our findings for the use of alloy surfaces and surface alloys as model systems for adsorption and catalytic reaction studies are discussed.     

Copper cation interactions with biologically essential types of ligands: a computational DFT study

This work presents a systematic theoretical study on Cu(I) and Cu(II) cations in variable hydrogen sulfide-aqua-ammine ligand fields. These ligands model the biologically most common environment for Cu ions. Molecular structures of the complexes were optimized at the density functional theory (DFT) level. Subsequent thorough energy analyses revealed the following trends: (i) The ammine complexes are the most stable, followed by those containing the aqua and hydrogen sulfide ligands, which are characterized by similar stabilization energies. (ii) The most preferred Cu(I) coordination number is 2 in ammine or aqua ligand fields. A qualitatively different binding picture was obtained for complexes with H(2)S ligands where the 4-coordination is favored. (iii) The 4- and 5-coordinated structures belong to the most stable complexes for Cu(II), regardless of the ligand types. Vertical and adiabatic ionization potentials of Cu(I) complexes were calculated. Charge distribution (using the natural population analysis (NPA) method) and molecular orbital analyses were performed to elucidate the nature of bonding in the examined systems. The results provide in-depth insight into the Cu-binding properties and can be, among others, used for the calibration of bioinorganic force fields.     

Theoretical study of the dimerization of rhodanine in various tautomeric forms

The density functional theory (DFT) was used to calculate the relative stability of rhodanine dimers and the energy of intermolecular interaction in them. Analysis of the electron density showed hydrogen bonding in the dimers. The energies of individual hydrogen bonds were determined for the symmetrical dimers. The polarizable continuum model was used to calculate the solvation (hydration) energies of the structures studied. The effect of dimerization on the position of infrared absorption bands was demonstrated.     

Benchmark study of popular density functionals for calculating binding energies of three-center two-electron bonds

Density functional theory (DFT) can be used to study the three-center two-electron (3c2e) bonding mode, which is universal in catalysts containing alkaline-earth (Ae) and boron-group (Bg) elements. However, because of the delocalization pattern of the 3c2e bond, the wavefunction cannot be accurately described by DFT methods. The calculated energies of Ae and Bg catalysts therefore fluctuate greatly when different functionals are used, largely because of inconsistent DFT-calculated binding energies of 3c2e bonds. Nevertheless, with the development of supercomputers and theoretical calculation software, the DFT method is becoming increasingly popular for studying Ae and Bg catalysts. In this study, we compared the performances of 21 functionals with the high-level composite G3B3 method in calculations for the binding energies of 3c2e bonds. Several frequently used post-Hartree–Fock methods were also tested. The calculation results indicate that the M06-2X, MN12-L, and MN15 functionals give consistent and reliable binding energies for common 3c2e bonds. © 2018 Wiley Periodicals, Inc.     

Estimations of energy of noncovalent bonding from integrals over interatomic zero‐flux surfaces: Correlation trends and beyond

Bonding energies of 50 associates composed by neutral molecules (atoms) and bounded by various weak noncovalent interactions are calculated within the DFT framework using the PBE0/aug‐cc‐pVTZ combination. The electronic virial and electron density values at bond critical points together with their integrals over interatomic surfaces are tested to check their ability to estimate bonding energies. Two correlations schemes dealing with integrals over interatomic surface are suggested to estimate bonding energy of any noncovalent interaction. The physical meaning of explored and several known correlations is discussed. Methods to estimate interatomic surface integrals of electronic virial and electron density are proposed. © 2018 Wiley Periodicals, Inc.     

Site-selective Cu deposition on Pt dendrimer-encapsulated nanoparticles: correlation of theory and experiment

The voltammetry of Cu underpotential deposition (UPD) onto Pt dendrimer-encapsulated nanoparticles (DENs) containing an average of 147 Pt atoms (Pt(147)) is correlated to density functional theory (DFT) calculations. Specifically, the voltammetric peak positions are in good agreement with the calculated energies for Cu deposition and stripping on the Pt(100) and Pt(111) facets of the DENs. Partial Cu shells on Pt(147) are more stable on the Pt(100) facets, compared to the Pt(111) facets, and therefore, Cu UPD occurs on the 4-fold hollow sites of Pt(100) first. Finally, the structures of Pt DENs having full and partial monolayers of Cu were characterized in situ by X-ray absorption spectroscopy (XAS). The results of XAS studies are also in good agreement with the DFT-optimized models.     

True nanocable assemblies with insulating BN nanotube sheaths and conducting Cu nanowire cores

Nanocable models comprised of BN nanotubes filled with close-packed Cu nanowires were investigated by gradient-corrected density functional theory (DFT) computations. The optimal distance between the sidewall of BN nanotubes and the atoms in a copper nanowire is about 0.35 nm, with a weak insertion energy (ca. -0.04 eV per Cu atom). Hence, such nanocables are assembled by weaker van der Waals (vdW) forces, rather than by chemical bonding interactions. The electronic band structures of the BN/Cu hybrid systems are superposition of those of the separate components, the BN nanotubes, and the Cu nanowires. Since charge density analyses show that the conduction electrons are distributed only on the copper atoms, charge transport will occur only in these inner nanowires, which are effectively insulated by the outer BN nanotubes. On the basis of these computational results, BN/Cu hybrid structures should be ideal nanocables.     

Direct and indirect causes of Fermi level pinning at the SiO/GaAs interface

The correlation between atomic bonding sites and the electronic structure of SiO on GaAs(001)-c(2x8)/(2x4) was investigated using scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and density functional theory (DFT). At low coverage, STM images reveal that SiO molecules bond Si end down; this is consistent with Si being undercoordinated and O being fully coordinated in molecular SiO. At approximately 5% ML (monolayer) coverage, multiple bonding geometries were observed. To confirm the site assignments from STM images, DFT calculations were used to estimate the total adsorption energies of the different bonding geometries as a function of SiO coverage. STS measurements indicated that SiO pins the Fermi level midgap at approximately 5% ML coverage. DFT calculations reveal that the direct causes of Fermi level pinning at the SiO GaAs(001)-(2x4) interface are a result of either local charge buildups or the generation of partially filled dangling bonds on Si atoms.