Ab initio structural trends and torsional sensitivity in n-hexane and comparisons with crystallographic structural results

The molecular structures of n-hexane were determined by RHF/4-21G ab initio geometry optimization at 30° grid points in its three-dimensional τ₁(C11–C8–C5–C1), τ₂(C14–C11–C8–C5), τ₃(C17–C14–C11–C8) conformational space. Of the resulting 12×12×12=1728 grid structures, 468 are symmetrically non-equivalent and were optimized constraining the torsions τ₁, τ₂, and τ₃ to the respective grid points, while all other structural parameters were relaxed without any constraints. From the results, complete parameter surfaces were constructed using natural cubic spline functions, which make it possible to calculate parameter gradients, |P|=[(∂P/∂τ_i)²+(∂P/∂τ_j)²]^1/2, where P is a C–C bond length or C–C–C angle. The parameter gradients provide an effective measure of the torsional sensitivity of the system and indicate that dynamic activities in one part of the molecule can significantly affect the density of states, and thus the contributions to vibrational entropy, in another part. This opens the possibility of dynamic entropic conformational steering in complex molecules; i.e. the generation of free energy contributions from dynamic effects of one part of a molecule on another. When the conformational trends in the calculated C–C bond lengths and C–C–C angles are compared with average parameters taken from some 900 crystallographic structures containing n-hexyl fragments or longer C–C bond sequences, some correlation between calculated and experimental trends in angles is found, in contrast to the bond lengths for which the two sets of data are in complete disagreement. The results confirm experiences often made in crystallography. That is, effects of temperature, crystal structure and packing, and molecular volume effects are manifested more clearly in bond lengths than bond angles which depend mainly on intramolecular properties. Frequency analyses of the τ₁, τ₂ and τ₃ torsional angles in the crystal structures show conformational steering in the sense that, if τ₁ is trans peri-planar (170°≤τ₁≤180°; −180°≤τ₁≤−170°), the values of τ₂ and τ₃ are clustered closely around the ideal gauche (±60°) and trans (±180°) positions. In contrast, when τ₁ is in the region (50°≤τ₁≤70°), there is a definite increase in the populations of τ₂ and τ₃ at −90 and −150°.     

Adsorption of pyridine on the Lewis acid sites of microcrystalline γ-alumina: a quantum chemical cluster model study

Adsorption of pyridine on Lewis acid sites of microcrystalline γ-alumina was studied by quantum chemical cluster model approach at B3LYP and HF/6-31++G(d,p) levels of theory considering both the standard and the counterpoise-corrected potential energy surfaces (PESs). Harmonic vibrational frequency shifts of pyridine ν₈ and ν₁₉ internal mode components calculated at both levels of theory seem to excellently reproduce the experimental observations, the results for standard and counterpoise-corrected PESs being essentially identical. The interaction energies of pyridine with various clusters representing microcrystalline γ-Al₂O₃ were also calculated and the natural bond orbital and atoms in molecules analyses were performed.     

Theoretical study on the structure and UV–visible spectrum of pyridine–chloranil charge-transfer complex

The ground-state structure of the charge-transfer complex formed by pyridine (Py) as electron donor and chloranil (CA) as acceptor has been studied by full geometry optimization at the MP2 and DFT levels of theory. Binding energies were calculated and counterpoise corrections were used to correct the BSSE. Both MP2 and DFT indicate that the pyridine binds with chloranil to form an inclined T-shape structure, with the pyridine plane perpendicular to the chloranil. The CP and ZPE corrected binding energies were calculated to be 14.21 kJ/mol by PBEPBE/6-31G(d) and 23.21 kJ/mol by MP2/6-31G(d). The charge distribution of the ground state Py–CA complex was evaluated with the natural population analysis, showing a net charge transfer from Py to CA. Analysis of the frontier molecular orbitals reveals a σ–π interaction between CA and Py, and the binding is reinforced by the attraction of the O₇ atom of CA with the H₂₃ atom of Py. TD-DFT calculations have been performed to analyze the UV–visible spectrum of Py–CA complex, revealing both the charge transfer transitions and the weak symmetry-relieved chloranil π–π^* transition in the UV–visible region.     

金属串配合物[MM′M″(dpa)4(Cl)2](M=Co,Ni;M′,M″=Co,Rh)电子输运的理论研究

采用密度泛函理论DFT/BP86方法研究金属串配合物[MM'M″(dpa)₄(Cl)₂] [MM'M″=CoCoCo(1), CoCoRh(2), CoRhRh(3), NiCoRh(4)] 的结构和电子输运性质. 结果表明, 配合物1, 2和4的最稳定自旋态均存在1个(MM'M″)⁶⁺的离域$\sigma_{3}^{3}$键($\sigma^{2}\sigma_{nb}^{1}\sigma^{*0}$); 但配合物3具有1个(MM'M″)⁶⁺的离域$\sigma_{3}^{4}$键($\sigma^{2}\sigma_{nb}^{2}\sigma^{*0}$)和2个$\pi_{3}^{5}$键($\pi^{4}\pi_{nb}^{4}\pi^{*2}$), 故Rh—Rh键和Co—Rh键较强; Rh的引入使M—M键增强, Ni的引入则使M—M键减弱, 键强次序为Rh—Rh>Co—Rh>Co—Co>Ni—Co. 配合物14的传输通道均含有π和σ型轨道. 正偏压下, 配合物2和3的电流大于配合物1和4的. 负偏压下, 配合物4中出现负微分电阻效应. 配合物3中形成传输通道的σ_nbα/β和π^*α/β轨道能级分裂明显, (MM'M″)⁶⁺对β自旋的π^*轨道的贡献(88%)比α自旋(74%)的大, 使β自旋的电子更易传输, 具有较好的自旋过滤效应(70%80%).     

The lipid-mediated hypothesis of fumonisin B1 toxicodynamics tested in model membranes

The disruption of lipidic metabolism was considered a good candidate to explain FB1 toxicity mechanism. In the present work we investigated molecular organizational changes induced by FB1–biomembrane interaction possibly involved in mycotoxic effects.

FB1 was self-aggregated with a critical micellar concentration of 1.97 mM. FB1 (0–81.4 μM), decreased in a dose-dependent manner, the fluorescence anisotropy of TMA-DPH (from 0.349 ± 0.003 to 0.1720 ± 0.0035) in dpPC bilayers, whilst no differences were registered with DPH. At 5.6 μM in the subphase, FB1 increased the lateral surface pressure (π) of a Langmuir film to an extent that depended on the monolayer composition (Δπ_{dpPC:DOTAP 3:1} > Δπ_dpPC:dpPA3:1 > Δπ_dpPC), the molecular packing (Δπ decreased linearly as a function of the initial π) and the subphase pH (Δπ_{pH 2.6} > Δπ_{pH 7.4} and maximal π allowing the drug penetration π_cut-off was 34.3 and 27.7 mN/m at pH 2.63 and 7.4, respectively). FB1 increased the surface potential of dpPC and dpPC:DOTAP monolayers and decreased that of dpPC:dpPA. This suggested that FB1 acquired different orientations and/or foldings depending on the surface electrostatics and the toxin charge state. Moreover, FB1–lipid interactions were transduced into long-range effects at the mesoscopic level affecting the lipidic self-separated lateral domains shape and density.     

A monolayer study on three binary mixed systems of dipalmitoyl phosphatidyl choline with cholesterol, cholestanol and stigmasterol

The monolayer behavior of three mixed systems of dipalmitoyl phosphatidyl choline (DPPC) with sterols; cholesterol (Ch), stigmasterol (Stig), and cholestanol (Chsta) formed at the interface of air/water (phosphate buffer solution at 7.4 with addition of NaCl) was investigated in terms of surface pressure (π) and molecular occupation surface area (A) relation. A series of π–A curves at every 0.1 mol fraction of each sterol for the three combinations of mixed systems were obtained at 25.0 °C.

On the basis of the π–A curves, the additivity rule in regard to A versus sterol mole fraction (X_st) was examined at discrete surface pressures such as 5, 10, 15, 20, 25, 30 mN m⁻¹, and then from the obtained A–X_st curves the partial molecular areas (PMA) were determined. The A–X_st relation exhibited a marked negative deviation from ideal mixing in the pressure range below 10 mN m⁻¹, i.e. in the expanded liquid film region (below the transition pressure of DPPC).

The PMA of Ch at π=5 mN m⁻¹, for example, was found to be conspicuously negative in the range of X_Ch=0–0.2 (about −0.4 nm² per molecule) and slightly positive (ca. 0.1 nm² per molecule) in the range X_Ch=0.2 to 0.4. Above X_Ch=0.5, Ch’s PMA was almost the same as the surface area of pure Ch, while DPPC’s PMA was reduced to 60% of that of the pure system.

Excess Gibbs energy (ΔG_(ex)) as a function of X_st was estimated at different pressures. Applying the regular solution theory to thermodynamic analysis of ΔG_(ex), the activity coefficients (f₁ and f₂) of DPPC and the respective sterols as well as the interaction parameter (I_p) in the mixed film phase were evaluated; the results showed a marked dependence on X_st.

Compressibility C_s and elasticity C_s⁻¹ were also examined. These physical parameters directly reflected the mechanical strength of formed monolayer film.

Phase diagrams plotting the collapse pressure (π_c) against X_st were constructed, and the π_c versus X_st curves were examined for the respective mixed systems in comparison with the simulated curves of ideal mixing based on the Joos equation.

Comparing the monolayer behavior of the three mixed systems, little remarkable difference was found in regard to various aspects. In common among the three combinations, the mole fraction dependence in monolayer properties was classified into three ranges: 0<X_st<0.2, 0.2<X_st<0.4 and 0.5<X_st<1. How the difference in the chemical structure of the sterols influenced the properties was examined in detail.     

卟啉-碳硼烷-硼亚甲基二吡咯三元化合物二阶非线性光学性质的理论研究

采用密度泛函理论(DFT)方法对卟啉-碳硼烷-硼亚甲基二吡咯(BODIPY)三元化合物的几何结构、 吸收光谱及二阶非线性光学(NLO)特性进行计算分析. 结果表明, V型化合物的静态第一超极化率(β_tot)大于相应直线型化合物, 且延长共轭链可提高体系的β_tot. 分析体系的电子密度差分图得出, 化合物氧化还原态的电荷转移方式与本征态相比发生了改变, 从而使其二阶NLO性质发生明显变化. 含频第一超极化率计算结果表明, 在一定范围内频率对化合物有较小的色散效应. 因此, 通过延长二维化合物的共轭链及氧化还原反应, 可以有效调控其二阶NLO响应.     

Theoretical study on the aromaticity of the bimetallic clusters X2M2 (X=Si, Ge, M=Al, Ga)

Four neutral bimetallic clusters X₂M₂ (X=Si, Ge, M=Al, Ga) are investigated using density functional theory (DFT) and post-HF methods. The calculated results show that each of four X₂M₂ species has two energetically close stable isomers with rhombic structure (D_2h symmetry) and trapezoidal structure (C_2v symmetry) respectively. For the Ge₂Al₂ species the rhombic (D_2h) isomer is the ground state, whereas for other three species Ge₂Ga₂, Si₂Al₂, and Si₂Ga₂, the trapezoidal (C_2v) isomers are the ground states. The calculated magnetic susceptibility anisotropy (χ_anis) and nucleus-independent chemical shift (NICS) indicate that a strong diatropic ring current exists in the two heterocyclic planar isomers, suggesting they are highly aromatic. A detailed molecular orbital analysis further reveals that both heterocyclic isomers possess multiple aromaticity derived from one delocalized π MOs and two delocalized σ MOs.     

Structure and bonding in a series of cyano complexes: RuCp(PPh3) 2CN, [RuCp(PPh3) 2(CNH)]CF3SO3, and H-bridged [Ru2(Cp) 2(PPh3) 4CNHNC]CF3SO3

The three title cyanoruthenium complexes have been characterized by means of X-ray diffraction analysis, IR and NMR solution spectroscopies, as well as extended Hückel molecular orbital calculations examining the properties of the cyanide fragment changing with complexation and with the co-ligands Cp and PPh₃. Explanations are given for crystallographic results of the C-N bond shortening upon complexation, the supershort (2.573 Å) bond length of N(H) N in the bridged complex, as well as the Ru-C-N and C-N-H-N-C bendings. Although the crystallographically found asymmetry of coordinated Cp is not significant, the MO calculations suggest a distorted endocyclic bond-length pattern indicative of the relative importance of σ and π bonding in the metalcyclopentadienyl interactions.     

Stress relaxation behaviour of dipalmitoyl phosphatidylcholine monolayers spread on the surface of a pendant drop

Dipalmitoyl phosphatidylcholine (DPPC) monolayers were characterised by surface pressure/area isotherms (π/A) and surface dilational rheological parameters at temperatures 20–40°C. The methods used were the Langmuir trough and the pendant drop micro-film balance. The latter allows accurate measurements at higher temperatures and transient drop deformation. Stable DPPC monolayers were found only for low surface pressures, π<15 mN m⁻¹. At higher monolayer compression π decreases over a long time, mainly caused by molecular rearrangement processes in the monolayer starting in the coexisting region. At π>25 mN m⁻¹ and 20°C relaxation experiments give evident of rupturing, brittle monolayer structures. At higher temperatures the monolayers became more fluid-like. π/A-isotherms determined by using both methods principally agree with each other, but show also remarkable differences, which cannot be explained so far satisfactory. Transient drop relaxation experiments were analysed for the short time range (600 s). At 20°C the dilational modulus (_r) and the surface dilational viscosity (ξ_r) passes a stationary maximum at 0.54 nm² molecule⁻¹ and increase strongly at higher surface coverage, thus indicating crystalline monolayer structure. Increasing temperature from 20 to 30°C causes a rapid decrease of _r and ξ_r and a shift of the stationary maximum to lower surface coverage. No evidence for crystalline structure is found. Further increase of temperature causes _r and ξ_r increase again. This increase is caused by a rising relaxation time, while the elasticity does not change in the same manner. Such intermediate decrease of _r and ξ_r in the range 30–40°C appears to be unusual and can be interpreted as a consequence of strong DPPC interactions and strongly pronounced retardation of monolayer deformation. The study is discussed in connection to the physiology of breathing. For pulmonary surfactants the observed behaviour seems to be understandable. It is however interesting that such complex behaviour is observed for monolayers consisting of DPPC only.     

Structure and conformation of 2,3,4-triphenyl-1-oxa-4-azabutadiene

2,3,4-triphenyl-1-oxa-4-azabutadine (C20H15NO) has been studied by X-ray analysis and AM1 molecular orbital methods. It crystallises in the triclinic space group P-1 with a=9.414(3), b=10.479(3), c=8.385(2) Å, =103.31(3)°, β=97.10(3)°, γ=74.09(1)°, V=772.5(4) ų, Z=2, D_c=1.227 gcm⁻³, and μ(MoK)=0.075 mm⁻¹ and F₀₀₀=300. The structure was solved by direct methods and refined to R=0.043 for 2672 reflections [I>2σ(I)]. The conformational analysis of the title compound were investigated by semi-empirical quantum mechanical AM1 calculations. The minimum conformation energies were calculated as a function of the three torsion angles θ₁(O(1)C(7)C(8)N(1)), θ₂(C(8)N(1)C(15)C(16)) and θ₃(C(14)C(9)C(8)N(1)). The results are compared with the X-ray results. C=O and C=N groups are twisted about each other by 95.5(2)°.     

Ab initio and DFT studies on 1-(thionitrosomethylene) hydrazine: conformers, energies, and intramolecular hydrogen-bond strength

In the current study, we present an intramolecular HB, molecular structure, π-electrons delocalization and vibrational frequencies analysis of 25 possible conformers of 1-(thionitrosomethylene) hydrazine by means of DFT (B3LYP), MP2 methods in conjunction with the 6-311++G** and augmented correlation-consistent polarized-valence triple-zeta basis sets and G2MP2 theoretical level. The influence of the solvent on the stability order of conformers and the strength of intramolecular hydrogen-bonding was considered using the Tomasi’s polarized continuum model. Statistical analyses of quantitative definitions of aromaticity, nucleus independent chemical shift, harmonic oscillator model of aromaticity, aromatic fluctuation index, and the π-electron delocalization parameter (Q) as a geometrical indicator of a local aromaticity, evaluated for this conformers. Further verification of the obtained transition state structures were implemented via intrinsic reaction coordinate (IRC) analysis. Calculations of the ¹H NMR chemical shift at GIAO/B3LYP/6-311++G** levels of theory are also presented. The calculated highest occupied molecular orbital (MO) and lowest unoccupied MO energies show that charge transfer occur within the molecule. Hydrogen-bond energies for H-bonded conformers were obtained from Espinosa method and the natural bond orbital theory and the atoms in molecules theory were also applied to get a more precise insight into the nature of such H-bond interactions.     

Non-fused polyaromatic hydrocarbons: interactions of aromatic and antiaromatic rings through a CC bond

The interaction of the moieties of benzene, cyclobutadiene, cyclopentadinyl anion, and the cyclopentadianide cation upon each other and upon a CC bond connecting pairs of these rings is investigated computationally. The resulting non-fused bicycles include biphenyl, phenylcyclobutadiene, phenylcyclopentadienylium, phenylcyclopentadienide, pentafulvalene, cyclobutadienyl–cyclopentadienylium, cyclobutadienyl–cyclopentadienide, and bicyclobutadiene. The relative stability and aromaticity are assessed from hydrogenation energies, aromatic stabilization energies, ring separation energies, nucleus-independent chemical-shift, harmonic oscillator model of aromaticity, and natural bond orbital analysis. Calculations are performed with density functional theory (B3LYP) and Møller–Plesset perturbation theory of second order (MP2). Enthalpy quantities are also determined by G3. When both rings are aromatic in character, the bridging bond is mostly σ in character. When one or both of the rings is antiaromatic, the bridging bond has significant π character. Systems with contrasting aromaticities have CC bridging bonds of lengths between CC single bond lengths and CC double bond lengths and where the systems were charged, the charge is evenly distributed between the rings.     

Molecular weights of polystyrenes in toluene solutions by light scattering. Comparison between classical values and values deduced from a new method

Light scattering measurements in toluene solutions are performed for a series of monodisperse polystyrenes with a molecular weight M_w range from 4×10³ to 8×10⁶. The scattered polarized intensities I_v and the natural depolarization ratios ρ_n are registered with different apparatus at λ=633 or 488 nm and the M_w values are deduced through different formulae. The complete Carr and Zimm formula (CL_a), from I_v and ρ_n, and the usual simplified formula (CL_b), from I_v, are considered for the classical method. An already demonstrated formula is considered for the new method (New). Values of M_w and related parameters do not depend on the experimental systems used but deviations appear when using different formulae. The deviations are generally low (about 10%) but often systematic: M_w(CL_a)<M_w(CL_b)<M_w(New). The most important difference concerns the effect of destructive interferences for M_w>5×10⁵: the new formula leads to a lower increase from θ=90° to θ→0 for M_w values (θ is the observation angle). For instance, in the 8×10⁶ sample, M_w(θ→0)/M_w(θ=90°)=3.6 instead of 6.1, which implies a revision of the usual determination of the radius of gyration, R_g.     

Computational study of hydrogen bonding interaction between formamide and nitrosyl hydride

The hydrogen bonding interaction of formamide–nitrosyl hydride complex has been investigated using density functional theory (DFT) and ab initio method. The natural bond orbital (NBO) analysis and atom in molecules (AIM) theory were applied to understand the nature of the interaction. Two stable geometries are found on the potential energy surface, a six-membered cyclic structure of complex A and a seven-membered cyclic structure of complex B, characterized by AIM analysis. Complex A is less stable than complex B. It is confirmed that there are contractions of CH (compared with the monomer HCONH₂), NH bonds (compared with the monomer HNO) and the corresponding stretching vibrational frequencies are blue-shifted, while there is an elongation of the NH bond and the corresponding stretching vibrational frequency is red-shifted, relative to those of the monomer HCONH₂. From NBO analysis, it is evident that the electron densities in the σ^* (CH) and σ^*(NH) of the complex A are less than those of the monomers HCONH₂ and HNO, which strengthen CH and NH bonds. Furthermore, the increases in s-characters of X also strengthen XH bonds.     

Diphenylbutadiene-bridged gadolinium complex [GdCl2(THF) 3]2(μ-Ph2C4H4) · 3THF: The synthesis and crystal structure

The diphenylbutadiene-bridged gadolinium complex [GdCl₂(THF)₃]₂(μ-Ph₂C₄H₄) · 3THF (1) has been obtained by the reaction of Gd(III) chloride with diphenylbutadienepotassium. The molecular structure of 1 was determined by X-ray diffraction. The complex 1 has a binuclear structure in which a bridging diphenylbutadiene ligand is η⁴-bonded to the Gd atoms connecting two GdCl₂(THF)₃ units. Both Gd atoms have a distorted octahedral environment. At the Gd atom the two Cl atoms are in trans positions and the four other coordination sites are occupied by the three O atoms of THF molecules and the η⁴-bonded C₄H₄ fragment of a diphenylbutadiene ligand. In the two η⁴-bonded GdC₄H₄ fragments one of the Gd-C η⁴-distances is significantly elongated (2.86(3) and 2.97(3) Å) compared with other three (2.65(3)–2.69(3) and 2.67(3)—2.77(3) Å). The magnetic moment of Gd, equal to 8.1 BM, is typical for Gd³⁺ compounds that is evidence for a formal charge of DPBD ligand of −2 in complex 1. However, the expected distribution of the C-C bond of the diene fragment as long—short—long is not realized.     

The effects of fluorine and chlorine substitution on bond lengths in ethanes and disilanes: comparisons of ab initio and experimental information

Ab initio and some density functional theory calculations of bond lengths in fluoro- and chloro-ethanes and disilanes are reported with a precision of ±0.0001 Å under strictly comparable conditions. The resulting changes in MH and MX (M=C, Si; X=F, Cl) bond length are analysed for the effects of halogens substituted in geminal (), or vicinal (gauche or trans) positions. The shortening effect of halogen on an MH bond is markedly reduced or even reversed by the introduction of electron correlation at the MP2 or B3LYP level. MX bonds are little affected. gauche halogen consistently shortens both MH and MX bonds, while trans halogen has no effect on an MH bond but a small and variable effect on the MX bond.

The reality of these calculated changes in bond length is tested in two ways. MH bond lengths are plotted against experimental values of the isolated stretching frequencies ν^isMH, which themselves correlate well with experimental r₀ bond lengths. Agreement on the resulting substituent effects is generally good for the gauche and trans effects of halogen but variable for effects. Unobserved ν^isMH values are predicted from computed bond lengths in fluoroethanes, chloroethanes and chlorodisilanes.

Calculated MX and MM bond lengths are compared with experimental values, notably those from electron diffraction studies amongst the ethanes. Most calculations underestimate the changes found experimentally in CF and CCl bond lengths. CC bond length changes are underestimated in fluoroethanes and overestimated in the chloro-compounds.

The ‘offset’ value (r_e(calc)−r_e(true)) for a CH or SiH bond calculated with a given basis set and level of theory in most cases varies markedly throughout the series of compounds. The same is true for CF, CCl, CC and SiSi bonds if the corresponding offset values for the r_a lengths are constant.

The need is stressed for extended experimental work on many of the compounds, especially the disilanes. It is recommended that structures should be refined with ab initio derived constraints on the bond lengths involved and differences between spectroscopic and diffraction-based geometries reconciled through the calculation of r_z structures.     

异丙醇对氯化镨化学键配位活化的量子化学研究

用醇类作为配位试剂,可使LnCl₃-R₃Al的催化活性显著提高。不言而喻,从电子结构的层次上阐明配位活化的机理,是具有一定意义的。王佛松等曾在4f轨道参与成键的假设条件下用群论的方法讨论了不同稀土元素的催化活性并计算了NdCl₃(OC₃-H₃)₃配合物的电子结构讨论了它们与配位活化之间的关系。本文为上述工作的继续,以PrCl₃(OC₃H₃)₃为研究对象。     

Interplay between cation-π and hydrogen bonding interactions

The interplay between two important non-covalent interactions involving aromatic rings is studied by means of ab initio calculations (MP2/6-31++G^**). They demonstrate that synergetic effects are present in complexes where cation-π and hydrogen bonding interactions coexist. These synergetic effects have been studied using the ‘atoms-in-molecules’ theory and the molecular interaction potential with polarization partition scheme.