Ab initio and density function theory computational studies of the CH4 + H → CH3 + H2 reaction

The activation barrier for the CH₄ + H → CH₃ + H₂ reaction was evaluated with traditional ab initio and Density Functional Theory (DFT) methods. None of the applied ab initio and DFT methods was able to reproduce the experimental activation barrier of 11.0-12.0 kcal/mol. All ab initio methods (HF, MP2, MP3, MP4, QCISD, QCISD(T), G1, G2, and G2MP2) overestimated the activation energy. The best results were obtained with the G2 and G2MP2 ab initio computational approaches. The zero-point corrected energy was 14.4 kcal mol⁻¹. Some of the exchange DFT methods (HFB) computed energies which were similar to the highly accurate ab initio methods, while the B3LYP hybrid DFT methods underestimated the activation barrier by 3 kcal mol⁻¹. Gradient-corrected DFT methods underestimated the barrier even more. The gradient-corrected DFT method that incorporated the PW91 correlational functional even generated a negative reaction barrier. The suitability of some computational methods for accurately predicting the potential energy surface for this hydrogen radical abstraction reaction was discussed.     

Ab initio studies of methanol, methanethiol and methylamine dimer

Quantum chemical calculations are used to provide structural, vibrational and energetical information on the dimers of the methanol, methylamine and methanethiol systems. These systems were studied employing the DFT(B3LYP) and MP2 methods together with the 6-31+G^** and 6-311+G^** basis sets. We found two distinct potential minima for methylamine (one of them is a transition structure) and methanethiol, and one for the methanol dimer. The properties of these dimers are compared with those of the dimers (H₂O)₂, (NH₃)₂ and (CH₃SH)₂. The interactions in these dimers were analyzed using electron density properties at the bond critical point.     

从能量和信息理论视角理解单取代烷烃的异构化

对直链烷烃和支链烷烃的相对稳定性统一的解释仍然没有定论,并且一直在进行着。以单取代的烷烃体系C_nH_2n+1―R (n = 3, 4, 5, 6;R = OH, OCH₃, NH₂, NO₂, F, Cl, CN, CHO)为例,本文对支链效应的有效性和本质进行了研究。与传统的基于轨道的描述不同的是,本文采用了密度泛函理论的总能量和基于新能量分配方案的能量分量[见Liu, S. B. J. Chem. Phys. 2007, 126, 244103]。新型能量分解方法计算结果表明,静电效应和立体效应等对支链效应的存在都起着重要作用,但是它们均不能单独用来解释支链效应的本质。用双变量(静电势和空间位阻)组合,发现单取代烷烃衍生物的异构化反应主要影响因子是静电势作用,空间位阻效应的影响是次要的。此外还发现了香农熵差与Fisher信息差之间的线性关系,未能发现总能量差或者分能量差值和Fisher信息或者Shannon熵之间的关系。这与前人发现是一致的。     

多原子反应体系的高精度拟合势能面

本文介绍了近几年来我们组构建多原子反应体系的高精度拟合势能面的进展。我们基于神经网络(NN)方法,成功构建了多原子气相分子体系和气相分子在金属表面解离的一系列势能面。这些势能面的拟合精度相当高,并且经过了严格的量子动力学测试,能广泛应用到动力学研究中。我们还提出了一种新的置换不变势能面的拟合方法,即基本不变量神经网络方法(FI-NN)。基本不变量的使用极大地减少了神经网络输入层多项式的个数,有效提高了势能面的计算速度。     

Sc3C2@C80与[12]CPP纳米环之间非共价相互作用的理论研究

金属富勒烯嵌套于纳米环内形成主客体系, 二者产生的主客体作用可诱导内部金属团簇的取向, 影响分子的电子结构等性质. 本文基于密度泛函理论(DFT)计算, 对碳纳米环[12]CPP(CPP=环苯撑, 主体分子)与金属富勒烯Sc₃C₂@C₈₀(客体分子)形成的主客体配合物的结构和性质进行了研究. 计算结果表明, 在最稳定构型中, [12]CPP呈现椭圆形, Sc₃C₂@C₈₀与[12]CPP的质心不再重合. Sc₃C₂@C₈₀在[12]CPP内旋转对构型总体能量影响仅为13.51 kJ/mol. [12]CPP向Sc₃C₂@C₈₀转移了0.03 e, 主客体分子之间存在弱相互作用. 对二者相互作用的分析结果表明, 色散作用在弱相互作用中占主导地位.     

Density functional theory investigations on the conformational stability and vibrational spectra of the model compound of vitamin K

Becke 3-Lee–Yang–Parr density functional theory (DFT/B3LYP) using 6-31G(d) and 6-311G(d) basis sets and the scaled quantum mechanics (SQM) force field method are used to study molecular conformations and vibrational spectra of a model compound of vitamin K (VK). In this molecule, there are six conformers on the torsional potential energy map of the dihedral angles C₈C₁₄C₁₅C₁₆ () and C₇C₈C₁₄C₁₅ (β). It is shown that the VK_1 conformer ( = 237.7° and β = 274.2°) is the most stable form. For this lowest energy conformer, the harmonic force fields calculated by B3LYP/6-311G(d) and B3LYP/6-31G(d) methods are scaled with one scale factor of 0.9623 and a set of different scale factors transferred from the previous studies for the other similar molecules, respectively. The vibrational frequencies, IR intensities, and Raman activities are obtained for the lowest energy conformer. On the basis of B3LYP calculations, the normal mode analysis is performed to assign the vibrational fundamental frequencies according to the potential energy distributions. The computational frequencies are in good agreement with the observed results.     

5-巯基-1, 3, 4-噻二唑-2-硫酮微溶剂团簇的光谱和理论计算研究

微溶剂作用(即溶剂化过程)广泛存在于所有物理、 化学和生命过程中. 在液相化学反应体系中, 几乎是一切化学反应的基础. 通过傅里叶变换拉曼光谱(FT-Raman)并结合密度泛函理论(DFT), 表征了固态5-巯基- 1, 3, 4-噻二唑-2-硫酮(MTT)的结构, 并进一步确认了MTT在乙腈、 甲醇和水中微溶剂团簇的大小和氢键位点. 通过探究MTT在不同溶剂及pH条件下的紫外-可见吸收光谱(UV-Vis), 结合含时密度泛函理论(TD-DFT)计算, 揭示了溶剂和pH对MTT电子跃迁带的影响, 进一步解释了其光谱位移. 结合能量计算可以得出, MTT分别与1个乙腈、 2个甲醇和2个水分子形成MTT(CH₃CN), MTT(CH₃OH)₂ 和MTT(H₂O)₂团簇.     

Highlevel ab initio and hybrid density functional theory study of the energy profile for the CO+CO reaction

Two complete basis set and three hybrid density functional computational studies were applied in the exploration of the ¹CO+²CO⁺ reaction potential energy surface. One molecular carbon monoxide–carbon monoxide cation molecular associate was elucidated as the structure with the lowest energy on the potential energy surface. Ionization energies, bond dissociation energies, and enthalpies of formation for every di and tri-atomic molecule on the potential energy surface were estimated with the two complete basis sets and the three hybrid density functional theory methods. Six different endothermic channels for the ¹CO+²CO⁺ reaction were evaluated with ab initio and DFT methods. The computed energies and structural parameters are compared with experimental values where available. Some new energies for this reaction system were suggested.     

Theoretical Studies on Structural and Spectroscopic Properties of Photoelectrochemical Cell Ruthenium Sensitizers-the Derivatives of N3

A series of dye molecules was designed theoretically. Particularly, azoles and their derivatives were chosen as the modifying groups linking to ancillary ligands of [Ru(dcbpyH₂)₂(NCS)₂](N3, dcbpy=4,4′-dicarboxy- 2,2′-bipyridine; NCS=thiocyanato). Density functional theory(DFT) based approaches were applied to exploring the electronic structures and properties of all these systems. The dye molecule with 1,2,4-triazole groups which exhibits a very high intensity of absorption in visible region, was obtained. Time-dependent DFT(TD-DFT) results indicate that the ancillary ligand dominates the molecular orbital(MO) energy levels and masters the absorption transition nature to a certain extent. The deprotonation of anchoring ligand not only affects the frontier MO energy levels but also controls the energy gaps of the highest occupied MO(HOMO) to the lowest unoccupied MO(LUMO) and LUMO to LUMO+1 orbital. If the gap between LUMO-LUMO+1 is small enough, the higher efficiency of dye-sensitized solar cell(DSSC) should be expected.     

Ab initio and DFT computer studies of complexes of trimethylphosphine and products of substituted phosphonium cations with hydroxide, chloride and fluoride anions: Phosphorus analogues of choline and acetylcholine

Theoretical calculations (DFT, MP2) are reported for up to four sets of reaction products of trimethylphosphine, (CH₃)₃P, each with H₂O, HCl and HF together with DFT calculations on up to three sets of reaction products of substituted phosphonium cations, (CH₃)₃P–R⁺. These products comprise (a) P(III) normal complexes (CH₃)₃PHY, (b) P(IV) ‘reverse’ complexes Y(H–CH₂)₃P–R, (c) P(IV) ylidic complexes YHCH₂(CH₃)₂P–R and (d) P(V) covalent compounds Y–P(CH₃)₃–R for Y=HO, Cl and F and R=H, CH₃, C₂H₅, C₂H₄OH and C₂H₄OC:OCH₃. Calculations are carried out at the B3LYP/6-31+G(d,p) level in all cases and also at the MP2/6-31+G(d,p) level for systems in which R=H. Minimum energy structures are determined for predicted complexes or structures and geometrical properties, harmonic vibrations and BSSE corrected binding energies are reported and compared with the limited experimental information available. Potential energy scans predict equilibria between covalent trigonal bipyramidal P(V) forms and reverse complexes comprising hydrogen bonded or ion pair, tetrahedral P(IV) forms separated by low potential energy barriers. Similar scans are also reported for equilibria between reverse complexes and ylidic complexes for Y=OH and R=CH₃, C₂H₅, C₂H₄OH and C₂H₄OC:OCH₃. Corrected binding energies, structures and values of harmonic modes are discussed in relation to bonding The names ‘pholine’ and ‘acetylpholine’ are suggested for phosphorus analogues to choline and acetylcholine.     

Multiply Charged Anions,Maximum Charge Acceptance,and Higher Electron Affinities of Molecules,Superatoms,and ClustersSCI北大核心CSCD

The addition of electrons to form gas-phase multiply charged anions (MCAs) normally requires sophisticated experiments or calculations.In this work, the factors stabilizing the MCAs, the maximum electron uptake of gas-phase molecules, X, and the electronic stability of MCAs X^Q-, are discussed. The drawbacks encountered when applying computational and/or conceptual density functional theory (DFT) to MCAs are highlighted. We develop and test a different model based on the valence-state concept. As in DFT, the electronic energy, E(N, v_ex), is a continuous function of the average electron number, N, and the external potential, v_ex, of the nuclei. The valence-state-parabola is a second-order polynomial that allows extending E(N, v_ex) to dianions and higher MCAs. The model expresses the maximum electron acceptance, Q_max, and the higher electron affinities, A_Q, as simple functions of the first electron affinity, A₁, and the ionization energy, I, of the "ancestor" system. Thus, the maximum electron acceptance is Q_{max, calc} = 1 + 12A₁/7(I -A₁). The ground-state parabola model of the conceptual DFT yields approximately half of this value, and it is termed Q_{max, GS} = ${}^{1}\!\!\diagup\!\!{}_{2}\; $ + A₁/(I -A₁). A large variety of molecules are evaluated including fullerenes, metal clusters, super-pnictogens, super-halogens (OF₃), super-alkali species (OLi₃), and neutral or charged transition-metal complexes, AB_mL_n^0/+/-. The calculated second electron affinity A_{2, calc} = A₁-(7/12)(I -A₁) is linearly correlated to the literature references A_{2, lit} with a correlation coefficient R = 0.998. A₂ or A₃ values are predicted for further 24 species. The appearance sizes, n_ap^3-, of triply charged anionic clusters and fullerenes are calculated in agreement with the literature.     

Theoretical Study of Stability and Electronic Characteristics in Various Complexes of Psoralen as an Anticancer Drug in Gas Phase,Water and CCl4 Solutions

The present research employs density functional theory(DFT) computations to analyze the structure and energy of complexes formed by psoralen drug with alkali(Li⁺, Na⁺, K⁺) and alkaline earth(Be²⁺, Mg²⁺, Ca²⁺) metal cations. The computations are conducted on M06-2X/aug-cc-pVTZ level of theory in the gas phase and solution. The Atoms in Molecules(AIM) and natural bond orbital(NBO) analyses are applied to evaluating the characterization of bonds and the atomic charge distribution, respectively. The results show that the absolute values of binding energies decrease with going from the gas phase to the solution. Furthermore, the considered complexes in the water(as a polar solvent) are more stable than the CCl₄(as a non-polar solvent). The DFT based chemical reactivity indices, such as molecular orbital energies, chemical potential, hardness and softness are also investigated. The outcomes show that the considered complexes have high chemical stability and low reactivity from the gas phase to the solution. Finally, charge density distributions and chemical reactive sites of a typical complex explored in this study are obtained by molecular electrostatic potential surface.     

EMIM离子液体离子簇模型的量子化学计算

以1-乙基-3-甲基咪唑(EMIM)卤化物、氟硼酸盐、三溴化物和二碘溴酸盐、氯铝酸和溴铝酸盐等不同种类EMIM离子液体为研究对象,对多阳离子、多阴离子的离子簇模型进行了量子化学计算研究.首先在B3LYP/6-311++G(d, p)水平上(I使用6-311G(d, p)基组)对{[EMIM]X_n}^(n-1)- (X = Cl, Br, I, BF₄, AlCl₄, AlBr₄, Br₃, IBrI, FHF; n = 2, 3)和{[EMIM]₂X_n'}^(n'-2)- (n' = 3, 4, 5)离子簇进行构型优化,并对卤化物和氟硼酸盐进行了振动光谱计算.结果表明所采用理论模型在键长、键角等结构参数及红外振动光谱方面均与实验结果符合较好.同时对不同离子簇模型中阴、阳离子间相互作用能与实验熔点之间的关系进行了研究,发现采用{[EMIM]₂X_n'}^(n'-2)--模型时EMIM离子液体实验熔点与阴、阳离子间相互作用能之间呈现近线性关系.     

The potential energy surfaces and the radiationless dynamics of excited states of benzene and pyrazine

The potential energy surfaces of the lowest excited states of benzene and pyrazine are investigated as a function of some of the symmetry-adapted internal coordinates by means of the INDO/S method. A large stabilization of the T₂ (ππ*) state of pyrazine (≈ 0.5 eV) along the S_8b vibrational coordinate is found. The calculated potential energy in some excited states (T₁ in benzene, T₂ and S₂ in pyrazine) is a very flat function of the S_16b vibrational coordinate, leading to a crossing with the potential energy of the ground state at relatively small excess of vibrational energy (≈ 1 eV). Thus the ν_16b vibrational mode is postulated to play an important role in the radiationless relaxation to the ground states of these systems. No such crossing has been found near the “channel three” threshold of benzene.     

A DFT study of the generation of interstellar species XN (X = Cl, and Br) activated by molecular sieve clusters

A cluster DFT (B3LYP) calculation study of ClN₃ and BrN₃ dissociation pathways catalyzed by molecular sieve is reported. A three-tetrahedral molecular sieve cluster (Al(OHSiH₃)(OSiH₃)(OH)₂, called T3) has been chosen in this study. Triplet-state products ClN and BrN are more easily produced with T3 molecular sieve cluster. Although the potential energy surfaces with T3 molecular sieve cluster are similar with those without T3 molecular sieve cluster, the dissociation process of ClN₃ and BrN₃ with T3 molecular sieve cluster becomes easier, which can be attributed to smaller energy gaps from the ground state reactant to the intersystem crossing point.     

High level of ab initio and density functional theory computational study of structural and energetic properties of tetrafluorhydrazine rotamers

The HF, MP2, MP3, MP4, and QCISD ab initio methods were compared with local, hybrid, and gradient-corrected density functional theory (DFT) methods for computing structures and energies of N2F4 rotamers. In all DFT calculations 6-311 + G(2d) basis set was used. The generated structures energies of trans- and gauche-N₂F₄ rotamers, and their dissociation energies to nitrogen difluoride were compared with experimental data. Suitable hybrid and gradient-corrected DFT methods for determining structures and energies for these and similar molecular systems were discussed.     

A case study in performance evaluation of Density Functional Tight Binding method in two-layer ONIOM method

A performance evaluation of Density Functional Tight Binding (DFTB) in the two-layer ONIOM method is presented in an effort to estimate DFTB effectiveness as an inexpensive low level quantum mechanical layer. Ground state geometries, geometry error, S-values and energy error for: (H₂O)_x(MeOH)_y, [(η⁵-C₅Me_nH_5−n)₂Ti]₂(μ₂, η²,η²-N₂), n = 4, and complexes of Cu⁺ with tyrosine, were compared to target calculations at B3LYP level of theory for all three of the systems and second order Moller-Plesset (MP2) target level of theory for the first two systems. The calculated root-mean-square errors (RMS) of the ONIOM optimized geometries relative to the target are found to be small. The DFTB level of theory was unable to reproduce the target geometry structure for one of the isomers of tyrosine–Cu⁺ complex, while the ONIOM combinations were able to reproduce all target structures. The absolute value of the geometry error was determined to be smaller then the corresponding energy error except for the (H₂O)_x(MeOH)_y system at the ONIOM(MP2/6-31G(d,p):DFTB) level of theory. The S-values were relatively small and close in value contributing to relatively small energy errors. Both method combinations ONIOM(MP2:DFTB) and ONIOM(DFT:DFTB) show similar performance compared to the corresponding target level of theory. The results also suggest that it is safe to use ONIOM(DFT:DFTB) for investigations of [(η⁵-C₅Me_nH_5−n)₂Ti]₂(μ₂, η²,η²-N₂) complexes.     

Structure, ordering, and bonding of half antiperovskites: PbNi3/2S and BiPd3/2S

In a model study the crystal structures of shandite (Pb₂Ni₃S₂), parkerite (Bi₂Ni₃S₂) and their Pd homologues are investigated in terms of ordered half antiperovskites AM_3/2S (A = Pb, Bi; M = Ni, Pd). This addresses fundamental questions on the structural relations, ordering and chemical bonding. From crystal structure investigations a new cubic parkerite variant is presented for Bi₂Pd₃S₂ that fits in an ordering model equivalently to shandite and parkerite. Type–antitype relations to ordered oxygen deficit perovskites are presented. With the relation to the superconductor Ni₃MgC a model is deduced that provides the complete crystal structure and symmetry in terms of the Ni and Pd ordering in antiperovskite superstructures. Therein a systematic ab initio investigation on the relative stability of shandite and parkerite structures is carried out for the first time. From the DFT modelling results the preferences of the ordering variants and the distinct differences in the atomic coordination spheres are discussed. The bonding in the systems is investigated by site projected density of states and covalent bond energy calculations.     

Hydrogen-atom production channels of acetaldehyde photodissociation: Direct DFT molecular dynamics study

Direct density-functional (DFT) molecular dynamics (MD) calculations have been carried out for the following two hydrogen-atom production channels in acetaldehyde photodissociation on the lowest triplet-state (T₁) potential energy surface (PES): CD₃CHO → CD₂CHO + D (1) and CD₃CHO → CD₃CO + H (2). The employed DFT method was B3LYP with the cc-pVDZ basis set. The average product hydrogen kinetic energies estimated from the results of the direct DFT MD calculations were 18.3 and 16.6 kcal mol⁻¹ for reactions 1 and 2, respectively, and these were half – two thirds of the previously measured values [T.Y. Kang, S.W. Kang, H.L. Kim, Chem. Phys. Lett. 434 (2007) 6]. This is because of the low reverse barrier heights predicted at the B3LYP/cc-pVDZ level. The present results for the product hydrogen kinetic energies, however, agree qualitatively with the experimental measurements and strongly supports the mechanisms taking place on the T₁ PES.