Isomerization of B6, B6 − and B6 + clusters

The interconversions between isomers with the same spin multiplicity of neutral B₆ and charged B₆ ^? and B₆ ⁺ clusters have been investigated at the B3LYP/6-311+G* level of theory, including determination of the minimum energy pathways with transition states connecting the corresponding reactants and products. In dynamic calculations, 26 isomers were optimized, including 11 novel isomers. In order to further refine the energies, single-point B3LYP/6-311+G(3df) calculations were carried out on the corresponding B3LYP/6-311+G* geometries of all isomers of B₆, B₆ ^? and B₆ ⁺ and the corresponding isomerization transition states. The stability of each isomer of B₆ (singlet and triplet states), B₆ ^? (doublet state) and B₆ ⁺ (doublet state) was analyzed from both thermodynamic and dynamic viewpoints.     

B4O分子异构化稳定性的理论研究

采用CCSD(T)/6-311+G(2df)//B3LYP/6-311+G(d)方法, 系统研究了B₄O体系各个异构体的结构和能量, 以及重要异构体的解离和异构化稳定性. 结果表明, 单态平面三角形含-BO单元的异构体cB₃-BO ¹1能量最低, 其次是带状的异构体B₄O ¹2(10.9 kJ/mol), 并且¹1和¹2结构都具有良好的动力学稳定性. 因此对于B₄O体系, ¹1和¹2都是有可能存在的. 而文献报道的三态直线型结构BBBBO(146.0 kJ/mol)的能量比异构体¹1和¹2高得多.     

NMR spectra, GIAO and charge density calculations of five-membered aromatic heterocycles

The B3LYP/6-31+G(d) molecular geometry optimized structures of 17 five-membered heterocycles were employed together with the gauge including atomic orbitals (GIAO) density functional theory (DFT) method at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants. The method of geometry optimization for pyrrole (1), N-methylpyrrole (2) and thiophene (7) using the larger 6-311++G(d,p) basis sets at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,p) and B3LYP/cc-pVTZ levels of theory gave little difference between calculated and experimental values of coupling constants. In general, the (1)H and 13C chemical shifts for all compounds are in good agreement with theoretical calculations using the smaller 6-31 basis set. The values of nJHH(n=3, 4, 5) and rmnJ(CH)(n=1, 2, 3, 4) were predicted well using the larger 6-31+G(d,p) and 6-311++G(d,p) basis sets and at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p) levels of theory. The computed atomic charges [Mülliken; Natural Bond Orbital Analysis (NBO); Merz-Kollman (MK); CHELP and CHELPG] for the B3LYP/6-311++G(d,p) geometry optimized structures of 1-17 were used to explore correlations with the experimental proton and carbon chemical shifts.     

丁烯和丁烷自由基阳离子的分子结构和超精细结构的 理论研究

用密度函数理论B3LYP方法和6-31G(d,p),6-311G(d,p)及6-311+G(d,p)基组，分别对1-C4H^+~8,2-C4H^+~8和C4H^+~10进行了构型优化和频率分析计算，预言1-C4H^+~8具有非平面构型，与以往报道的从头算和密度函数理论计算结果不同。在各自由基阳离子的B3LYP构型上，进行了B3LYP、MP2及MRSDCI方法的超精细偶合常数计算，得到了比以往更好的结果，特别是MP2/B3LYP计算值是至今与实验值符合得最好的理论计算结果。     

Structural elucidation of nitro-substituted five-membered aromatic heterocycles utilizing GIAO DFT calculations

The GIAO (Gauge Including Atomic Orbitals) DFT (Density Functional Theory) method is applied at the B3LYP/6-31+G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311+G (2d,p)//B3LYP/6-31+G(d) and B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants for 25 nitro-substituted five-membered heterocycles. Difference (1D NOE) spectra in combination with long-range gHMBC experiments were used as tools for the structural elucidation of nitro-substituted five-membered heterocycles. The assigned NMR data (chemical shifts and coupling constants) for all compounds were found to be in good agreement with theoretical calculations using the GIAO DFT method. The magnitudes of one-bond (1JCH) and long-range (nJCH, n>1) coupling constants were utilized for unambiguous differentiation between regioisomers of nitro-substituted five-membered heterocycles.     

The C7-C10 cycloalkanes revisited

The conformers of cycloheptane through cyclodecane have been examined at the B3LYP/6-311+G* and MP2/6-311+G* theoretical levels, with some additional calculations at the CCD/6-311+G* and CCSD(T)/6-311++G** levels. With cyclooctane, B3LYP predicts that the boat-chair and crown conformers have similar energies, whereas MP2 and CCSD(T) predict that the crown conformer is 2 kcal/mol higher in energy. The latter is in agreement with the electron diffraction data. With cyclononane, B3LYP predicts that two of the higher-energy conformers found in molecular mechanics calculations should convert to one of the lower-energy conformers. However, MP2/6-311+G* optimizations find them to be true minima on the potential energy surface. B3LYP systematically predicts larger C-C-C bond angles for these compounds than either MP2 or CCD. The results of molecular mechanics MM4 calculations are generally in good agreement with those obtained using MP2.     

戊烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p)、6-31＋G(d,p)、6-311G(d,p)及6-311＋G(d,p)基组，分别对2-C5H10＋和1-C5H10＋的各种构象进行了几何构型优化，并用B3LYP/6-311G(d,p)进行了频率分析计算.计算预言1-C5H10＋具有非平面构型，与以往报导的从头算计算结论相反.在两个自由基阳离子的各种构象的B3LYP几何构型上，进行了B3LYP和UMP2(full)方法的超精细偶合常数计算，得到了比以往更好的结果.     

Investigation on Structure and Bonding of As_4S_4 Isomers

Mineral medicine, especially those containing heavy metals, is one of the characteristics of traditional Chinese medicine. A famous mineral medicine, realgar, containing heavy metal arsenic with a chemical formula of As_4S_4, has the function of detoxification, killing bacteria and viruses, and eliminating dampness and phlegm. Different As_4S_4 isomers are likely to have different drug effects and pharmacological actions. Therefore, it is of great scientific significance to find more stable As_4S_4 isomers. In view of this, ab initio molecular orbital theory and density functional theory(DFT) have been used to study ten isomers of As_4S_4 at the B3LYP/6-31 G*, B3LYP/6-311+G*, B3LYP/6-311+G(3 df, 2 p) and MP2/(6-311+G*, LanL2 MB) levels of theory. In addition to the two isomers having been studied previously, eight new isomers were investigated in the present paper. All the ten As_4S_4 isomers were proved to be true local minima on their potential energy surfaces. The calculated NICS values and molecular orbital analyses showed that, the D_(2d) symmetric As_4S_4, isomer 1, may be s-aromatic. The study proves that ten As_4S_4 isomers are stable thermodynamically, and are highly desirable for the future theoretical study of realgar.     

硫氧分子阴离子的QCISD方法研究

使用二次组态相互作用（QCISD）方法和6－311G（d),6-311+G(d),6-311G(2d) 及6－311＋G(2d)基组研究了SO2^-和SO3^-的分子结构，超精细偶数常数（hfcc)及 其对应的分子的绝热电子亲合势（AEA）。发现在QCISD／6－311＋G（2d)水平上计 算的两个分子离子的结构，hfcc值（在^33S和^17O上的）和AEA值与实验值符合得 都很好（除SO^3-中的在^33S上的hfcc值比实验值小23％）。作为比较，我们使用 相同基组作了B3LYP方法计算，得到的超精细偶合常数和AEA值却都与实验符合得不 好。     

NC2S+离子的结构和稳定性的理论研究

在密度泛函和从头算理论水平下计算了单重态的NC2S+离子的结构、能量、光谱以及稳定性. 在B3LYP/6-311G(d)水平下, 得到8个异构体, 它们由15个过渡态相连接. 在CCSD(T)/6-311+G(2df)//QCISD/6-311G(d)+ZPVE水平下, 得到能量最低的异构体是直线型的具有1Σ电子态的NCCS+(1)(0.0 kJ/mol), 其次是直线型的异构体CNCS+(2)(54.8 kJ/mol). 两个低能量的异构体1和2及另外一个高能量的直线型异构体CCNS+(3)(323.8 kJ/mol)都具有相当大的动力学稳定性, 这三个异构体在具备一定条件的实验室和星际条件下是可以进行观测的. 分析了这3个异构体的成键性质.     

Theoretical Studies on Structures and Stabilities of C4H2+ Isomers

The structures, energies, stabilities and spectroscopies of doublet C₄H₂⁺ cations were explored at the DFT/B3LYP/6-311G(d,p), CCSD(T)/6-311+G(2df,2pd)(single-point), and G3B3 levels. Ten minimum isomers including the chainlike, three-member-ring, and four-member-ring structures are interconverted by means of 15 interconversion transition states. The potential energy surface was investigated. At the CCSD(T)/6-311+G(2df,2pd) and G3B3 levels, the global minimum isomer was found to be a linear HCCCCH. The structures of the stable isomer and its relevant transition state are further optimized at the QCISD/6-311G(d,p) level. The bonding nature and structure of isomer HCCCCH were analyzed.     

已烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p),6-31+G(d,p),6-311G(d,p)及6- 311+G(d,p)基组,分别对1-C_6H_(12)~+,2-C_6H_(12)~+和3-C_6H_(12)~+的各种构 象进行了几何构型优化,并在B3LYP/6-311G(d,p)水平上进行了频率分析计算,在 各优化构型上,使用B3LYP和MP2(full)方法进行了超精细结构的计算。计算的3- C_6H_(12)~+的超精细偶合常数比以往的计算结果更好;1-C_6H_(12)~+和2-C_6H_ (12)~+的超精细偶合常数目前尚无实验数据报道,本计算预言了它们的超精细偶合 常数和最稳定构型。     

Redox potentials of dopamine and its supramolecular complex with aspartic acid

Dopamine (DA) can be oxidized to dopamine quinone (DAquinone) through a one-step, two-electron redox reaction. The electron transfer property of DA and its supramolecular complex with aspartic acid (Asp) has been investigated by the theoretical calculations. We calculated the standard redox potentials (E ^o) of DA/DAquinone at the MP2/6-31G(d,p)//B3LYP/6-31G(d,p), MP2/6-31+G(d,p)//B3LYP/6-31+G(d,p), MP2/6-31G(d,p)//B3LYP/6-311G(d,p), and MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) levels. Comparing the experimental value, the redox potentials of DA/DAquinone obtained at MP2//B3LYP/6-311G(d,p) and MP2//B3LYP/6-311+G(d,p) levels can be considered as the upper and lower estimates. DA can form supramolecular complex (DA-Asp) with Asp through hydrogen bond (H-bond). Therefore, the values of 0.631 and 0.628 V obtained at MP2//B3LYP/6-311G(d,p) and MP2//B3LYP/6-311+G(d,p) levels for DA-Asp/DAquinone-Asp can be proposed as the upper and lower estimates of a probable (about 0.630 V) value of the corresponding redox potential. The calculated E ^o values of DA-Asp/DAquinone-Asp at the four theoretical levels are upper than those of DA/DAquinone, which indicates that the formation of H-bonds weaken the electron-donating ability of DA.     

S2O2分子稳定结构的密度泛函理论研究

采用密度泛函理论中的B3LYP方法,在6-311+G(3df)和Aug-cc-pVTZ水平上,研究了单态S2O2分子的各种可能的异构体及其相对稳定性。结果表明,具有C2v对称性的三角平面分叉异构体的热力学稳定性要高于目前实验上唯一被发现的具有C2v对称性的cis-OSSO异构体,同时trans-OSSO的稳定性与顺式异构体十分接近,这2种异构体应该可以在实验上被观察到。同时本文还讨论了3个最稳定构型的前线分子轨道和链型OSSO的内扭转势能。     

Theoretical Study on Hydrogen Interaction between 5-Fluorouracil and Glycine

The geometries,electronic structure,IR spectrum and other properties of hydrogen interaction between 5-fluorouracil and glycine were studied at the B3LYP/6-31+G* level.Single point energy calculations were executed at the B3LYP/6-311++G** and B3LYP/aug-cc-pvdz levels,and natural bond orbital (NBO) analysis was carried out at the B3LYP/6-31+G* level.Finally,the hydrogen bonds were discussed via AIM electronic density topology analysis.     

Molecular structure of the trans and cis isomers of metal-free phthalocyanine studied by gas-phase electron diffraction and high-level quantum chemical calculations: NH tautomerization and calculated vibrational frequencies

The molecular structure of the trans isomer of metal-free phthalocyanine (H2Pc) is determined using the gas electron diffraction (GED) method and high-level quantum chemical calculations. B3LYP calculations employing the basis sets 6-31G**, 6-311++G**, and cc-pVTZ give two tautomeric isomers for the inner H atoms, a trans isomer having D2h symmetry and a cis isomer having C2v symmetry. The trans isomer is calculated to be 41.6 (B3LYP/6-311++G**, zero-point corrected) and 37.3 kJ/mol (B3LYP/cc-pVTZ, not zero-point corrected) more stable than the cis isomer. However, Hartree-Fock (HF) calculations using different basis sets predict that cis is preferred and that trans does not exist as a stable form of the molecule. The equilibrium composition in the gas phase at 471 degrees C (the temperature of the GED experiment) calculated at the B3LYP/6-311++G** level is 99.8% trans and 0.2% cis. This is in very good agreement with the GED data, which indicate that the mole fraction of the cis isomer is close to zero. The transition states for two mechanisms of the NH tautomerization have been characterized. A concerted mechanism where the two H atoms move simultaneously yields a transition state of D2h symmetry and an energy barrier of 95.8 kJ/mol. A two-step mechanism where a trans isomer is converted to a cis isomer, which is converted into another trans isomer, proceeds via two transition states of C(s) symmetry and an energy barrier of 64.2 kJ/mol according to the B3LYP/6-311++G** calculation. The molecular geometry determined from GED is in very good agreement with the geometry obtained from the quantum chemical calculations. Vibrational frequencies, IR, and Raman intensities have been calculated using B3LYP/6-311++G**. These calculations indicate that the molecule is rather flexible with six vibrational frequencies in the range of 20-84 cm(-1) for the trans isomer. The cis isomer might be detected by infrared matrix spectroscopy since the N-H stretching frequencies are very different for the two isomers.     

Vibrational spectra and assignments using ab initio and density functional theory analysis on the structure of biotin

Density functional theory (DFT) and Hartree-Fock calculations were performed using the following models: HF/6-311G(d), B3LYP/6-311G(d), B3LYP/6-311+G(d) and B3PW91/6-311G(d) calculations were performed for biotin. It has been characterized by IR and X-ray. The calculated results show that the predicted geometry can well reproduce the structural parameters. Predicted vibrational frequencies have been assigned and compared with experimental IR spectra and they supported each other. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between Cp,m degrees, Sm degrees, Hm degrees and temperatures.     

Electron momentum spectroscopy of CF2Cl2: experimental and theoretical momentum profiles for outer valence orbitals

Electron momentum distributions for outer valence orbitals of CF2Cl2 have been obtained by (e,2e) electron momentum spectroscopy at an incident energy of 1200 eV + binding energy. The experimental electron momentum profiles are compared with Hartree-Fock and density functional theory (DFT) calculations using B3LYP hybrid functional with the 6-31G and 6-311+G* basis sets. Generally, the shapes of the experimental momentum profiles are well reproduced by DFT calculations using larger basis sets 6-311 + G*. An attempt has been made to clarify the ordering of the outer valence orbitals, which have been in controversy, by comparing experimental results with B3LYP/6-311 + G* calculations.     

Inductive effects in radicals calculated from DFT energies; substituted bicyclo[2.2.2]octan-1-yloxy radicals

Energies of a series of 4-substituted 1-oxybicyclo[2.2.2]octan-1-yloxy radicals with 18 various substituents were calculated within the framework of the DFT theory at the levels UB3LYP/6-311+G(d,p)//UB3LYP/6-311+G(d,p) and UB3LYP/6-311++G(2df,p)//UB3LYP/6-311+G(d,p) and compared with similar series of the parent alcohols, their deprotonated and protonated forms calculated at the levels B3LYP/6-311+G(d,p)//B3LYP/6-311+G(d,p) and B3LYP/6-311++G(2df,p)//B3LYP/6-311+G(d,p). The two levels are of the same performance and both are sufficient for molecules of this type according to comparison with scarce experimental gas-phase acidities and basicities. The substituent effects were analyzed in terms of isodesmic equations. In addition to strong dependence on the substituent inductive effect, a slight dependence on the electronegativity of the first atom of the substituent was proven in certain cases. In all aspects, there is no qualitative difference between the effects on radicals and on similar closed shell species. Radicals behave as slightly electron deficient; the substituent effect is weaker than that on the ions but stronger than on neutral molecules.     

Comprehensive density functional theory study on serine and related ions in gas phase: conformations, gas phase basicities, and acidities

Density functional theory (DFT) calculations have been performed to investigate the gas-phase conformations of serine and its three related ions (serineH(+), serine(-), and serine(2-)). The full ensemble of possible conformations, 324 conformations for serine, 108 for serineH(+), 162 for serine(-) and 54 for serine(2-), were first surveyed at B3LYP/6-31G level, and then the obtained unique conformations were further refined at B3LYP/6-311+G level. From full optimizations, 74 unique conformations for seine, 14 for serineH(+), 11 for serine(-), and 4 for serine(2-) were located, and their relative energies were also determined at B3LYP/6-311+G level. Atoms in molecules (AIM) analysis was carried out to establish rigorous definition of hydrogen bonds. Six types of intramolecular H-bonds in conformers of serine, six types in serineH(+), three types in serine(-), and two types in serine(2-) were identified within the framework of AIM theory and their relative strengths were determined based on topological properties at bond critical points (BCPs) of H-bonds. The intramolecular H-bonds were demonstrated to play an important role in deciding the relative stability of conformations of amino acids and the related ions. The enthalpies and Gibbs free energies of protonation and deprotonation reactions of serine and its related ions were calculated at B3LYP/6-311+G//B3LYP/6-31G, and B3LYP/6-311+G//B3LYP/6-311+G level. The calculated results are both in excellent agreement with the experimental data. We demonstrate in this study that B3LYP is an efficient and accurate method to predict the thermochemical and structural parameters of amino acids and the related ions.