Structure and ionization energies of some analogues of iron-only hydrogenases studied by density functional theory methods

Density functional theory calculations using both the B3LYP and BP86 functional in conjunction with a medium and large size basis set have been used to predict the structures and ionization energies of 12 models of iron-only hydrogenases. Although the structural predictions do not allow a clear discrimination between the different computational models, these models do yield significantly different adiabatic and vertical ionization energies. The closest agreement with experiment is given by the BP86 functional and the large all-electron basis. At this level of theory the adiabatic ionization energies are very close to experiment, but the vertical values are uniformly too small, leading to an underestimation of the reorganization energies. The calculations also suggest that measured ionization energies may help in identifying both the bridge-head group and whether CO bridging takes place upon ionization.     

Electronic structures of 4d transition metal monoxides by density functional theory

Bond distances, dissociation energies, ionization potentials and electron affinities of 4d transition metal monoxides from YO to CdO and their positive and negative ions were studied by use of density functional methods B3LYP, BLYP, B3PW91, BPW91, B3P86, BP86, SVWN, MPW1PW91 and PBE1PBE. It was found that calculated properties are highly dependent on the functionals employed, especially for dissociation energy. For most neutral species, pure density functionals BLYP, BPW91 and BP86 have good performance in predicting dissociation energy than hybrid density functionals B3LYP, B3PW91 and B3P86. In addition, BLYP gives the largest bond distance compared with other density functional methods, while SVWN gives shortest bond distance, largest dissociation energy and electron affinity. For the ground state, the spin multiplicity of the charged species can be obtained by ± 1 of their corresponding neutral species.     

The C−NO2 bond dissociation energies of some nitroaromatic compounds: DFT study

The C−NO₂ bond dissociation energies in nitrobenzene; 3-amino-nitrobenze; 4-amino-nitrobenze; 1,3-dinitrobenzene; 1,4-dinitrobenzene; 2-methyl-nitrobenzene; 4-methyl-nitrobenzene; and 1,3,5-trinitrobenzene nitroaromatic molecules, are computed using B3LYP, B3PW91, B3P86 three-parameter hybrid Density Functional Theory (DFT) methods in conjunction with 6-31G^** basis set. By comparing the computed energies and experimental ones, it is found that B3P86/6-31G^** is not capable of predicting the satisfactory bond dissociation energy (BDE). The BDEs computed with both B3LYP/6-31G^** and B3PW91/6-31G^** for the nitroaromatic molecules are closer to the experimental ones than those obtained with B3P86/6-31G^**. But, when compared with the experimental one, the BDE from the B3LYP/6-31G^** has the maximum deviation, which is completely outside our desired target accuracy for chemical predictions (less than 2.00 kcal mol⁻¹). Therefore, we suggest B3PW91/6-31G^** method as a reliable method of computing the BDE for removal of the nitrogen dioxide group in the nitroaromatic compounds. In addition, the C−NO₂ BDEs for 2,4,6-trinitrotoluene (TNT), triaminotrinitrobenzene (TATB), diaminotrinitrobenzene (DATB), and picramide are studied with B3PW91/6-31G^** method.     

Theoretical studies of bond dissociation energies for removal of the nitrile group in some nitrile compounds

The CCN bond distances and bond dissociation energies (BDEs) are estimated by utilizing quantum chemical calculations for 16 nitrile compounds. Since DFT methods have been researched to have low basis sets sensitivity for small and medium molecules in our earlier work [Jun Zhao, Xinlu Cheng, Xiangdong. Yang, J. Mol. Struct. (Theochem) 766 (2006) 87] 16 nitrile compounds are studied by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86) and the complete basis set (CBS-Q) method in conjunction with the 6-311G^** basis set. The obtained results are compared with the available experimental data. It is demonstrated that CBS-Q method, which can produce reasonable BDEs for some systems, seems unable to predict accurate BDEs here. While, the B3P86 calculated results agree very well with the experimental values. So B3P86 method is suitable for computing the reliable BDEs of CCN bond for nitrile compounds.     

Cyanovinyl radical: an illustration of the poor performance of unrestricted perturbation theory and density functional theory procedures in calculating radical stabilization energies

Stabilization energies for the 1-cyanovinyl radical (CH₂=CCN) have been calculated using a variety of conventional ab initio (M?ller–Plesset, quadratic configuration interaction and coupled-cluster) and density functional theory (B-LYP, B3-LYP) procedures, as well as with a range of compound methods. Compared with a high-level benchmark value (that predicts a stabilization energy of 17.1 kJ mol⁻¹), UMP2 and UMP4 give the wrong sign and magnitude of the stabilization energy (both methods predicting desta- bilization instead of stabilization), while B-LYP and B3-LYP overestimate the degree of stabilization. The RMP2, RMP4, QCISD(T) and CCSD(T) techniques, and several, but not all, variants of G2 and CBS theories give radical stabilization energies in good agreement with the benchmark value. Received: 15 June 1998 / Accepted: 19 August 1998 /  Published online: 15 February 1999     

Structural and electronic properties of stable Aun (n = 2–13) clusters: A density functional study

All-electron scalar relativistic calculations have been performed to investigate the electronic structures of neutral gold clusters (Au_n, n = 2–13) in the gas phase using density functional theory with the generalized gradient approximation. Full geometry optimizations of topologically different clusters and clusters belonging to different symmetry groups have been carried out. Binding energies, ionization potentials, electron affinities, and chemical hardness values are calculated and they are found to be comparable with the available experimental and theoretical results. The most stable structure of each of the cluster has a two-dimensional planar configuration. A three dimensional distorted Y shaped structure (4b) for Au₄, a tri-capped triangle (6b), a chair (6f), and a see-saw structure (6j) for Au₆, an eclipsed sandwich structure (7g) for Au₇, a condensed trigonal bipyramid (9e) and a boat shaped structure (9f) for Au₉, a staggered sandwich (11c) and an eclipsed sandwich structure (11d) for Au₁₁, a ladderane structure (12d) for Au₁₂, and a staggered (13d) and a distorted sandwich structure (13e) for Au₁₃ are characterized for the first time in this work.     

The evaluation of bond dissociation energies for simple sulphur containing molecules using ab initio and density functional methods

The S–H and C–S bond dissociation energies for simple alkylthiols and dialkylsulphides, along with the S–S bond dissociation energy for dimethyl disulphide, compounds which have been used in the metal–organic chemical vapour deposition (MOCVD) growth of wide band gap II–VI (12–16) Zn- and Cd-based compound semiconductors, have been computed using the ab initio (ROHF and MP2) and density functional theory (DFT) methods (BHandH, BHandHLYP, B3LYP, B3P86, B3PW91, BLYP and BP86) with the 6-311+G(2d,p) basis set along with high accuracy complete basis set, CBS-4 and CBS-Q energy computations. The computed energies are compared with experimental results and the suitability of the DFT methods, for the computational study of these systems, is discussed.     

Valence ionization potentials and cation radicals of prototype porphyrins. The remarkable performance of nonlocal density functional theory

Nonlocal density functional theory (NLDFT) has been used to calculate the lower ionized states of the free-base forms of porphin, bacteriochlorin, and porphyrazine and also zinc porphin. For porphin, the calculated vertical ionization potentials (IPs) quantitatively reproduce the low-energy end of the experimental gas-phase ultraviolet photoelectron spectrum, which suggests that NLDFT could be an exceptionally useful tool for studying IPs and cation radical states of a variety of porphyrinic materials. Received: 7 January 1997 / Accepted: 6 May 1997     

Density functional computations of the energetic and spectroscopic parameters of quercetin and its radicals in the gas phase and in solvent

Quercetin and its radicals were investigated at the B3LYP density functional level with the aim of determining the energetic and spectroscopic parameters and the factors that influence their antioxidant activity in the gas phase and in aqueous solution. The results indicated that the antioxidant ability of quercetin is mainly due to the orthodiphenolic moiety but also to the presence of the C=C double bond of the pyrone ring. Differences in the stability order of the isomers of quercetins radicals were found in going from vacuum to solvent. Hyperfine coupling constants were computed to help the interpretation of the intricate ESR spectrum of quercetin.Contribution to the Jacopo Tomasi Honorary Issue     

Catalytic hydrogenolysis of alkyl halides by sulfido-bridged molybdenum clusters: A density functional study

Density functional theory has been used to explore the mechanism of cleavage of H₂ at a sulfido-bridged molybdenum cluster, CpMo(μ-SH)(μ-S)(μ-S₂CH₂)MoCp. The addition occurs across a single Mo-S bond, and the disruption of the strong Mo-S π bonding in the ground state leads to a very high-lying transition state (+43 kcal mol⁻¹). Once formed, the adsorbed hydrogen migrates over the cluster via a series of hops from metal to sulphur, formally corresponding to a switch from hydridic to protic character. The low barrier (+15 kcal mol⁻¹) for migration leads to facile hydrogenolysis of coordinated substrates.     

A short-range correlation energy density functional with multi-determinantal reference

We introduce a short-range correlation density functional defined with respect to a multi-determinantal reference which is meant to be used in a multi-determinantal extension of the Kohn–Sham scheme of density functional theory based on a long-range/short-range decomposition of the Coulomb electron–electron interaction. We construct the local density approximation for this functional and discuss its performance on the He atom.     

A density functional study of alizarin two of its isomers and its transition metals and rare-earth complexes

Electronic structure of Alizarin, two of its isomers, 11 different transition metal complexes and five rare-earth complexes are studied using density functional theory (DFT). Complexation energies are evaluated and it is found that chelation has a negligible influence on the structure of the anthraquinone backbone; the molecule keeps a planar conformation except for some metals such as Cr, Al, and Zn where the metal atom M and the oxygen atoms are slightly out of the plane by few degrees. The M–O bonds involve p or d metal orbitals depending on whether the d shell is full or empty. The complexation effect leads to a red shift and hence to a colour change of the solutions of the complexes.

The calculated complexation energies are of the same order for metal transition and for rare-earth elements.     

Exploring odd-even effects of simple oligomer-like DRCNnT series: a study based on density functional theory/time-dependent density functional theory calculations

Odd-even effects of short-circuit current density and power conversion efficiency (PCE) are an interesting phenomenon in some organic solar cells. Although some explanations have been given, why they behave in such a way is still an open question. In the present work, we investigate a set of acceptor-donor-acceptor simple oligomer-like small molecules, named the DRCNnT (n = 5-9) series, to give an insight into this phenomenon because the solar cells based on them have high PCE (up to 10.08%) and show strong odd-even effects in experiments. By modeling the DRCNnT series and using density functional theory, we have studied the ground-state electronic structures of the DRCNnT (n = 5-9) series in condensed phase. The calculated results reproduce the experimental trends well. Furthermore, we find that the exciton-binding energies of the DRCNnT series may be one of the key parameters to explain this phenomenon because they also show odd-even effects. In addition, by studying the effects of alkyl branch and terminal group on odd-even effects of dipole moment, we find that eliminating one or two alkyl branches does not break the odd-even effects of dipole moments, but eliminating one or two terminal groups does. Finally, we conclude that removing one alkyl branch close to the terminal group of DRCN5T can decrease highest occupied molecular orbital (HOMO) energy (thus increasing open circuit voltage) and increase dipole moment (thus enhancing charge separation and short-circuit current). This could be a new and simple method to increase the PCE of DRCN5T-based solar cells.     

Computational studies of bond dissociation energies, ionization potentials, and heat of formation for NH and NH+. Are hybrid density functional theory methods as accurate as quadratic complete basis set and Gaussian-2 ab initio methods?

Ionization potentials, bond dissociation energies, and heat of formation for NH and NH⁺ molecular species as well as for their elements were computed with highly reliable quadratic complete basis set and Gaussian-2 ab initio methods. The results are compared with experimental results and the assurance of these ab initio approaches is assessed. The same studies were also performed with three hybrid density functional methods (B3LYP, B3P86, and B3PW91) in combination with variously sized basis sets. The computational results are discussed in light of density functional theory reliability for exploring the potential energy of small polar molecular systems. Received: 21 July 1997 / Accepted: 8 December 1997     

Vibrational spectra and density functional study of propylgermane

Raman and infrared spectra of propylgermane, CH₃CH₂CH₂GeH₃, and its Ge-deuterated analog, CH₃CH₂CH₂GeD₃, were investigated in their gaseous, liquid and solid states. The normal coordinate treatment was carried out by density functional theory (DFT) calculation, using B3LYP/6-31G^* and 6-311++G^** basis sets, and the corresponding fundamental vibrations were assigned. The trans (T) and gauche (G) forms around the central C–C bond coexisted in the gaseous and liquid states and only the T form existed in the solid state. From the temperature dependent measurements of the Raman spectra in the liquid state, the enthalpy difference was found to be ΔH(T−G)=−0.36±0.02 kcalmol⁻¹ with the T form being more stable. The energy differences between the isomers obtained by DFT calculations were ΔE(T−G)=−0.46 kcalmol⁻¹ and ΔE(T−G)=−0.87 kcalmol⁻¹ by the 6-31G^* basis set and 6-311++G^** basis set, respectively.     

V2CO2 MXene负载过渡金属单原子催化剂氧还原和氢氧化活性的DFT研究

开发廉价且高性能的电催化剂对推动燃料电池的商业应用具有重要意义.二维(2D) MXenes和单原子(SAs)催化剂是催化研究中的两个前沿领域.2D MXenes材料具有独特的几何和电子结构,能够有效调节负载SAs的催化性能.而负载的SAs又会反过来影响2D MXenes材料的本征活性,使2D MXenes形成更加丰富的活性位,进而提升其催化性能.为了拓展2D负载SAs催化剂在燃料电池中的应用,本文采用密度泛函理论(DFT)计算,系统地研究了V2CO2 MXenes负载过渡金属(TM,包括一系列3d、部分4d和5d金属)SAs催化剂的稳定结构、电子结构及其催化氧还原(ORR)和氢氧化(HOR)的催化活性,并筛选出潜在的可替代贵金属铂的ORR/HOR的双功能催化剂.稳定结构计算结果表明,3d TM SAs倾向于以锚定的形式负载于V2CO2表面与O原子作用,而4d,5d TM原子倾向于以掺杂的形式负载于含氧空穴的V2CO2表面与V原子作用;同时,Sc,Ti,V,Rh,Pd,Pt,Ag和Au SAs在V2CO2表面因具有较高扩散能垒,不易团聚,具有较高的热力学稳定性.电子结构计算结果表明,锚定型的TM SAs与O形成共价键,伴随发生明显的电荷转移,带较多正电荷;掺杂型的TM SAs与V形成金属键,因TM-V和V-O键间电荷转移的协同影响,导致TM SAs仅带有少量的电荷.TM-V2CO2电子结构与ORR/HOR中间物种的吸附关系为,TM位点为ORR中间物种(O,OH和OOH)的吸附位点,且d电子数为1、5、10的TM比其他TM对ORR物种的吸附更弱;而TM-V2CO2表面的O原子为HOR中间物种(H)的有效吸附位点,且H的吸附强弱与O位点的电荷有关,即O位点负电荷越多,对H的吸附越弱.TM-V2CO2催化剂各活性位对ORR和HOR反应物种的选择性吸附结果表明,催化剂有利于形成丰富多样的活性位,并具备作为双功能催化剂的内在优势.TM-V2CO2催化剂ORR和HOR理论活性筛选发现:与Pt(111)相比,Sc-、Mn-、Rh-和Pt-V2CO2具有较高的ORR活性,而Sc-、Ti-、V-、Cr-和Mn-V2CO2表现出较高的HOR活性.其中,Sc-V2CO2和Mn-V2CO2因同时具有较高的ORR和HOR活性和稳定性,有望成为高效和低成本的燃料电池双功能催化剂.本文从研究TM-V2CO2性质和活性出发,深入研究了SAs与2D MXenes间相互作用及其对ORR与HOR催化活性的影响机制,筛选出了高效、低成本的ORR/HOR双功能催化剂,为合理设计燃料电池双功能催化剂提供了理论指导.     

On the performance of time-dependent density functional theory and polarizable continuum model in the study of aqueous formaldehyde

In this paper Time-Dependent Density Functional Theory (TD-DFT) with Becke's three-parameter hybrid method using the Lee–Yang–Parr correlation functional (B3LYP) in conjunction with different basis sets is applied to calculate the solvatochromic shift on the lowest singlet transition of formaldehyde in vacuum and in solution. Our results, in excellent agreement with solvent excitation energy shift of acetone in water at 298–300 K (no experimental data on formaldehyde in water are available so far) and with previous high level quantum chemical calculations, help in appreciating the potentialities of the combined DFT/PCM approach on aquo-complexes for the study of structural and spectroscopic properties of molecule in solution.     

黄酮类化合物的密度泛函理论研究

在混合密度泛函B3LYP理论下,用6-31G*基函数研究了几种典型黄酮类化合物分子的几何结构、电子结构和分子的静电势,讨论了电子结构和分子活性部位的关系.