Modeling exact exchange potential in spherically confined atoms

In this work, local exchange potentials corresponding to the Hartree–Fock (HF) electron density have been obtained using the Zhao–Morrison–Parr method for a number of closed‐shell confined atoms and ions. The exchange potentials obtained and the resulting density were compared with those given by the Becke–Johnson (BJ) model potential. It is demonstrated that introducing a scaling factor to the BJ potential allows improving the quality of the resulting density. The optimum scaling factor increases with decreasing confinement radius. The performance of Karasiev and Ludeña's SCα‐LDA method as well as of the Becke‐88 exchange potential for reproducing the HF electron densities in confined atoms has been also examined. © 2015 Wiley Periodicals, Inc.     

The performance of density functional theory for LnF (Ln=Nd,Eu, Gd,Yb) and YbH

Different density functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, experiment. The agreement between the CCSD(T) results and experiment, when available, is good. The agreement is also good between bond strengths calculated at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calculations systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calculations are generally in good agreement with the CCSD(T) results.Contribution to the Björn Roos Honorary Issue     

A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Prostaglandin H synthase catalyzes the oxygenation of arachidonic acid into the cyclic endoperoxide, prostaglandin G₂ (PGG₂), and the subsequent reduction of PGG₂ to the corresponding alcohol, prostaglandin H₂ (PGH₂), the precursor of all prostaglandins and thromboxanes. Both radical abstraction by a neighboring tyrosyl radical and combined radical/carbocationic models have been proposed to explain the cyclooxygenase part of this reaction. We have used density functional theory calculations to study the mechanism of the formation of the cyclooxygenated product PGG₂. We found an activation free energy for the initial hydrogen abstraction by the tyrosine radical of 15.6 kcal/mol, and of 14.5 kcal/mol for peroxo bridge formation, in remarkable agreement with the experimental value of 15.0 kcal/mol. Subsequent steps of the radical-based mechanism were found to happen with smaller barriers. A combined radical/carbocation mechanism proceeding through a sigmatropic hydrogen shift was ruled out, owing to its much larger activation free energy of 36.5 kcal/mol. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0476-9. Electronic Supplementary MaterialSupplementary material is available in the online version of this article at Electronic Supplementary Material: Supplementary material is available in the online version of this article at     

Theoretical investigations on the thiol–thioester exchange steps of different thioesters

As the rate-determining step in native chemical ligation reactions, the thiol–thioester exchange step is important in determining the efficiency of the ligations of peptides. In the present study, systematic theoretical calculations were carried out on the relationships between the structure of different thioesters and the free energy barriers of the thiol–thioester exchange step. According to the calculation results, the thiol–thioester exchange step is disfavored by the steric hindrance around the carbonyl center, while the electronic effect(i.e. conjugation and hyper-conjugation effects) becomes important when the steric hindrance is insignificant.     

Accuracy of geometries: influence of basis set,exchange–correlation potential,inclusion of core electrons,and relativistic corrections

The geometries of a set of small molecules were optimized using eight different exchange–correlation (xc) potentials in a few different basis sets of Slater-type orbitals, ranging from a minimal basis (I) to a triple-zeta valence basis plus double polarization functions (VII). This enables a comparison of the accuracy of the xc potentials in a certain basis set, which can be related to the accuracies of wavefunction-based methods such as Hartree–Fock and coupled cluster. Four different checks are done on the accuracy by looking at the mean error, standard deviation, mean absolute error and maximum error. It is shown that the mean absolute error decreases with increasing basis set size, and reaches a basis set limit at basis VI. With this basis set, the mean absolute errors of the xc potentials are of the order of 0.7–1.3 pm. This is comparable to the accuracy obtained with CCSD and MP2/MP3 methods, but is still larger than the accuracy of the CCSD(T) method (0.2 pm). The best performing xc potentials are found to be Becke–Perdew, PBE and PW91, which perform as well as the hybrid B3LYP potential. In the second part of this paper, we report the optimization of the geometries of five metallocenes with the same potentials and basis sets, either in a nonrelativistic or a scalar relativistic calculation using the zeroth-order regular approximation approach. For the first-row transition-metal complexes, the relativistic corrections have a negligible effect on the optimized structures, but for ruthenocene they improve the optimized Ru–ring distance by some 1.4–2.2 pm. In the largest basis set used, the absolute mean error is again of the order of 1.0 pm. As the wavefunction-based methods either give a poor performance for metallocenes (Hartree–Fock, MP2), or the size of the system makes a treatment with accurate methods such as CCSD(T) in a reasonable basis set cumbersome, the good performance of density functional theory calculations for these molecules is very promising; even more so as density functional theory is an efficient method that can be used without problems on systems of this size, or larger.     

Ab initio and density functional studies on the structure and vibrational spectra of 2-hydroxy-1,4-naphthoquinone-1-oxime derivatives

Structure and vibrational frequencies of lawsoneoxime and its C₃-substituted (R=CH₃, NH₂, Cl, NO₂) derivatives in keto and nitrosophenol forms have been obtained employing the Hartree–Fock and density functional methods. Charge distributions in different conformers have been studied using the molecular electrostatic potential topography as a tool. For all these derivatives except for nitrolawsoneoxime the amphi conformer in the keto form is predicted to be of lowest energy, which can partly be attributed to hydrogen bonding through the oximino nitrogen. In the nitro derivative, however, the preference to form a six membered ring owing to O–H–O hydrogen-bonded interactions makes the anti conformer (keto) the stablest. Further one of the nitrosophenol conformers of nitrolawsoneoxime turns out to be very close in energy (0.21 kJ mol^–1 higher) to this anti conformer. The consequences of hydrogen bonding on charge distribution and vibrational spectra are discussed.     

Correlation factor approach to the correlation energy functional

A global survey of the correlation factor energy functionals and its application to atomic and molecular properties is made. Its performances are compared with those of the density functional theory (DFT) correlation energy functionals, and some interesting conclusions from previous publications are reinforced here; namely, after removing the one-Slater-determinant hypothesis from the Kohn–Sham method, all DFT correlation functionals are able to provide reasonable results in any circumstance, with an additional restriction, for systems having a quasi-degenerate wave function, the DFT correlation functionals must depend explicitly on the on-top density. Acknowledgement.This work has been done under the support of the Spain DGICYT, project n⁰ BQU2001-0883.     

A density functional theory study of a concerted mechanism for proton exchange between amino acid side chains and water

 A concerted mechanism for proton exchange between water and the amino acid side chains of cysteine, serine, arginine and glutamic acid has been investigated with hybrid density functional theory. The models used include, besides the amino acid side chain, a number of water molecules ranging from one to five in some cases. The modeling of the amino acids without their backbones is shown to be an excellent approximation. Long-range polarization effects were incorporated through a dielectric cavity method allowing a better comparison to existing measurements for free amino acids in water. The barriers converge rather fast with the number of water molecules for all the present amino acids and the converged values are in reasonable agreement with experiments with discrepancies in the range 2–6 kcal/mol. The dielectric effects were found to be small for all systems except cysteine, where there is a lowering of the barrier by 3–5 kcal/mol. The transition states for these concerted pathways form rings in which the separated charges can be stabilized. Received: 25 October 1999 / Accepted: 5 April 2000 / Published online: 21 June 2000     

Cu-ZnO催化剂上水活化的第一性原理研究

采用密度泛函理论计算研究了水在Cu-ZnO催化剂表面上不同位点的解离过程. 结果发现, 水在纯Cu密堆积面和台阶面解离能垒都较高; 而在负载的ZnO薄膜上, 由于水解离过程能垒较低并且反应约为热中性, 水将会在表面上部分解离并达到动力学平衡. Cu-ZnO界面被确定为水解离的活性中心. 水解离后产生的H原子和羟基均可以较大吸附能吸附在界面处, 并且界面处的类似台阶结构大大降低了解离能垒, 从而使得水的解离可自发进行. 另外, H原子和羟基在ZnO薄膜表面可以较低的能垒扩散, 因此水解离活性位点可以持续催化后续解离过程. 该结果深化了对水在Cu-ZnO催化剂表面活化过程的认识.     

Theoretical studies on the role of bridging group of CGC type ligands for the Ziegler–Natta catalysis

The potential energy surfaces of the initial reactions of ethylene polymerization with the Ziegler–Natta catalysis related to the constrained geometric catalysts (CGCs) were studied by the B3LYP density functional method. Three metals (Ti, Zr, and Hf) in the Ziegler–Natta catalysis and eight bridging groups (BH, CH₂, NH, O, AlH, SiH₂, PH, and S) between cyclopentadienyl (Cp) and NH ligands were treated. The reaction occurs through two steps as that of Kaminsky type: the first step produces the complex without a barrier and the second is the insertion of ethylene into the metal–carbon bond through the transition state. The complex formation energy for each metal system correlates linearly to the electronegativity of the bridging atom for each row atom of the periodic table except for those of the BH-bridging systems. The energies of the reactions for the BH-bridging systems could be explained with the through-bond model as the reactions of ansa-metallocenes and the π back-donation of BN double bond.     

The intermolecular interaction in the charge-transfer complexes between amines and halogens: A theoretical characterization of the trends in halogen bonding

The trends in the properties of prereactive or charge-transfer complexes formed between the simple amines NH₃, CH₃NH₂, (CH₃)₂NH, and (CH₃)₃N and the halogens F₂, ClF, Cl₂, BrF, BrCl, and Br₂ were investigated by the ab initio restricted Hartree–Fock approach, the Møller–Plesset second-order method, and with several density functional theory variants using extended polarized basis sets. The most important structural parameters, the stabilization energies, the dipole moments, and other quantities characterizing the intermolecular halogen bond in these complexes are monitored, discussed, and compared. A wide range of interaction strengths is spanned in these series. Successive methyl substitution of the amine as well as increasing polarities and polarizabilities of the halogen molecules both systematically enhance the signature of charge-transfer interaction. These trends in halogen bonds of varying strength, in many aspects, parallel the features of hydrogen bonding.     

过渡金属表面上水生成经典Horiuti-Polanyi机理与非Horiuti-Polanyi机理选择的总体趋势（英文）

在非均相催化加氢反应中,氢气(H₂)一直被公认为是通过两步基元步骤参加还原反应的,包括第一步的分子解离和之后的反应物与原子氢键合,即所谓的Horiuti-Polanyi(HP)机理.直到我们研究组在Ag或Au催化丙烯醛加氢还原反应理论研究中发现非HP机理加氢路径存在时,新的机理才被提出,并引起广大研究者的浓厚兴趣.考虑到表面羟基(OH)和氧(O)在非均相催化体系中广泛存在,如常见的过渡金属催化的费托合成、甲烷重整、水汽转化及氨氧化等反应,基于第一性原理的密度泛函理论计算方法,我们对OH/O在一系列过渡金属催化作用下还原生成水的微观机理进行了系统全面的探究.研究发现,不同金属对应于不同的催化氢化反应活性,以及不同的催化反应机理.在某些金属上H₂以分子形式进攻反应物种的非HP机理有利,而在其它金属上经典的H₂解离后参与氢化还原反应的HP机理更容易发生.详细分析显示, H₂的解离活性决定了反应机理的种类:在对H₂解离具有催化活性的金属(如Pt、Ni)表面,不论是(211)台阶面还是(...     

Computer modeling of semiconductor nanotubes for water splitting

One-dimensional nanostructures such as nanorods and nanotubes (NTs) are regarded as promising materials for photoelectrochemical water splitting. Modeling the electronic properties of oxidic NTs with diameters in the range of 3–30 nm in contact with liquid water is challenging owing to the fact that the systems are too large for direct ab initio molecular dynamics simulations. Here we summarize recent efforts to develop strained two-dimensional model systems for pristine and doped titania NTs. We have studied their structural, optical and photoelectrochemical properties by a number of different techniques attributable to quantum mechanical density functional theory.     

Computational examination on monomeric,dimeric, trimeric structural and vibrational interactions,AIM, Hirshfeld,IGM and oxygenated solvent effect on optical properties for pyridine N-oxide

This work reports DFT (Density functional theory) and topological examination by means of AIM (Atom in molecule) theory, Laplacian electron density (ED), Electron –Localization function (ELF) and Hirshfeld surface were executed monomer, dimer and trimer structure of PNO molecule. These structures were optimized and Structural parameters like bond – length and Angles are compared by using B3LYP/6-311G++(d,p) basis set. Computed vibrational – frequencies and corresponding PED (Potential energy – Distribution) were also compared. Polarizability, Dipole moment and the electronic properties were calculated for all three cases of PNO molecule. Hirshfeld surface investigation has been executed to achieve the C–H?O/N–O?H type of hydrogen -bond intermolecular interactions. Moreover, Reactive site, inter/intra interactions are calculated, the optical behaviors for monomer structure of PNO were investigate by using UV–Vis spectroscopy in oxygenated solvents.     

水分子和二氧化铈(111)表面相互作用的DFT+U研究

采用引入Hubbard参数U修正的密度泛函理论(DFT+U)方法, 对水分子在二氧化铈(111)表面的吸附作用进行了研究. 计算结果表明: 在氧化的二氧化铈(111)表面, 水分子以单氢键构型吸附在二氧化铈表面, 但是不能自发解离; 在还原的二氧化铈(111)表面, 水分子或化学吸附在衬底上, 或自发解离成表面羟基结构. 与氢气在氧化的二氧化铈(111)表面上物理吸附体系的总能相比, 羟基化表面构型是能量更低的构型, 所以羟基解离形成氢气, 从而使表面被氧化的过程需要有外部条件, 反应不能自发进行. 因此, 水分子在还原的二氧化铈(111)表面有两个可能的状态, 即无氢键结构的化学吸附和表面羟基结构的解离吸附. 在一定的外部条件下, 表面羟基结构进一步解离形成氢气, 并使还原的二氧化铈(111)表面得以氧化.     

DFT study on second-order nonlinear optical properties of the derivatives of 7-vertex cobalt–carborane metallocenyl

Density functional theory (DFT) B3LYP method was employed to calculate electron properties and the second-order nonlinear optical (NLO) responses of the derivatives which were formed by (C₅H₅)Co(C₂B₄H₆) and CHCHC₆H₄NO₂, CHCHC₆H₄NH₂. The results show: when H atom of (C₅H₅)Co(C₂B₄H₆) is substituted by CHCHC₆H₄NO₂, the β_tot values of isomers are all slightly smaller than that of ferrocene (Fc) derivative (FcCHCHC₆H₄NO₂). However, when H atom of (C₅H₅)Co(C₂B₄H₆) is substituted by CHCHC₆H₄NH₂, the β_tot values of isomers are close to that of ferrocene (Fc) derivative (FcCHCHC₆H₄NH₂). It indicates that (C₅H₅)Co(C₂B₄H₆) can be either a donator or an acceptor.     

Additivity and transferability of exchange energy

Exchange energy of molecules at equilibrium geometries is shown to be highly independent of the basis set and nearly equal to the sum of the exchange energies of isolated atoms. Furthermore, molecular exchange can be predicted along a chemical series with high accuracy in terms of empirical exchange contributions associated to the constituent atoms, whose values, obtained by fitting, are similar to those of the isolated atoms. It is concluded that molecular exchange is essentially a sum of atomic contributions whose differences from those of the isolated atoms are small and characteristic of the neighboring atoms. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Implications of Nitrogen Doping on Geometrical and Electronic Structure of the Fullerene Dimers

Because of its unsaturated bonds, C₆₀ is susceptible to polymerize into dimers. The implications of nitrogen doping on the geometrical and electronic structure of C₆₀ dimers have been ambiguous for years. A quarter‐century after the discovery of azafullerene dimer (C₅₉N)₂, we reported its single crystallographic structure in 2019. Herein, the unambiguous crystal structure information of (C₅₉N)₂ is elucidated specifically, revealing that the inter‐cage C—C single bond length of (C₅₉N)₂ is comparable with that of an ordinary C(sp³)‐C(sp³) single bond, and that the most stable conformer of (C₅₉N)₂ is gauche‐conformer with a dihedral angle of 66°. To amend the structural deviations, geometrical structure of (C₅₉N)₂ is optimized by a B3LYP‐D3BJ function, which is proved to be more consistent with its single crystal structure than those by the commonly used B3LYP function. Moreover, the calculation method is also suitable for other representative fullerene dimers, such as (C₆₀)₂ and its divalent anion. Additionally, the dissociation of (C₅₉N)₂ at 473 K under mass spectrometric conditions suggests the inter‐cage C—C bond is relatively weaker than an ordinary C—C single bond, which can be explained by the interaction energies of inter‐cages.     

Structure,epr parameters,and reactivity of organic free radicals from a density functional approach

Summary A recently introduced density functional incorporating gradient corrections and some Hartree-Fock exchange has been used to study the structures, properties, and reactivity of representative organic free radicals. A general theoretical model has been introduced, in which standardized grid, functional, and orbital basis set are used to compute geometrical parameters, vibrational frequencies, and one-electron properties. The results are compared with available experimental data from diatomic to polyatomic radicals. All the geometric and electronic parameters compare favourably with available experimental data and with the results of refined post Hartree-Fock computations. Also the thermodynamics and kinetics of a representative unimolecular reaction (isomerization of formaldehyde radical cation) are well reproduced. These findings together with the very favourable scaling of the computations with the number of electrons suggest that the density functional approach is a promising theoretical tool for the study of relationships between structure and properties of large free radicals.