DFT Investigation on the Trans-cis Photoisomerization of Pentamethine Cyanine Dye Model Molecule

The trans-cis photoisomerization of pentamethine cyanine dye (Cy5) has been theoretically investigated by the analysis on an analogical molecule model. All possible isomers have been searched by rotating the different bridge C-C bonds of the model. The relative stability of the isomers for the ground and first excited states as well as the corresponding excitation mechanism has been envisaged by DFT and time-dependent DFT method. The results show different conjugation degree of the isomers resulting in different absorption energy upon the different C-C bridge bond rotation. From the analyses of electronic density distribution of the frontier orbitals, it is predicted that there is charge transfer besides the π-π* excitation for the cyanine dye model, which makes the mechanism and photo-properties different form those of other conjugated molecules.     

Electron density based characterization of π bonds in planar molecules

A new method has been developed to detect and analyze molecular π systems. The concept of bonding critical point is generalized to electronic π systems, and it is shown how a π bond can be characterized via the corresponding bond critical point (BCP) in planar molecules. In this context, charge density and its Laplacian at the BCP(π) of a strongly delocalized π system can be distinguished from that of a localized one. The presented formalism is applied to three types of nanoconductors as conjugated polyenes, which revealed the alternative pattern of the double bonds. Also, several cyclic conjugated molecules are considered to explore their π electronic structure and aromaticity.     

Further test of the isolated pentagon rule: Thermodynamic and kinetic stabilities of C84 fullerene isomers

Thermodynamic and kinetic stabilities of 73 C₈₄ fullerene isomers were estimated from the MM3 heats of formation and the recently defined bond resonance energies (BREs), respectively. The BRE represents the contribution of a given π bond in a molecule to the topological resonance energy (TRE). All π bonds shared by two pentagons turned out to be highly reactive without exceptions. C₈₄ fullerene isomers with such π bonds must be incapable of survival during harsh synthetic processes. Thus, the isolated pentagon rule (IPR) proved to be applicable to such large fullerene cages. For sufficiently large fullerenes like C₈₄, some isolated-pentagon isomers are also predicted to be very unstable with highly antiaromatic π bonds. © 1996 by John Wiley & Sons, Inc.     

有机化学基本理论问题新的研究方法、新的观念和新 的思维模式

有机化学基本理论研究的总结和回顾。15年来,在国家自然科学基金委员会的支持下,为了认识电子离域的本质,在量子化学领域,我们建立和发展了新的作用能分解方法和大型计算程序,发展和完善了轨道定域化程序。我们的方法可以为任何一个共轭分子(无论是平面的还是非平面的,是含共轭双键的还是含累积双键的),提供一个π与σ体系彻底分离的片断分子轨道基组。这个轨道基组不仅满足分子特殊的对称性,而且还具有确切的电子占据数。与Hückel理论完全不同,我们强调：π电子的离域除了对它原先的定域π体系有强烈的失稳定作用外,它还可通过π-σ空间作用,对σ构架产生强烈的稳定作用。据此,我们提出了芳环化合物新的分类准则,揭示了芳香环流起因的必要条件,定义环的刚度为芳香性一个新判据。发现,分子内基团间的局部作用(CT和EX)同它们对分子整体性能的影响是完全相反的。就构象而言,稳定的CT作用是相斥的,失稳定的EX作用是相吸的;就电子转移而言,大的EX作用是电荷转移的助动力。其助动性在于,它能降低因CT作用而产生的给体自身对电荷转移的阻力。论证了,在二苯乙烯类分子中,π-π共轭,π-σ超共轭和σ-σ非键轨道作用都是失稳定的。与σ-σ和π-σ作用相比,π-π作用对于分子构像的影响是非常微弱的。与经典的思维模式相反,有机分子总是倾向于较小的失稳定,而不是较大的稳定。为了维持尽可能最稳定的电子总能量,在σ-σ作用的驱动下,共轭基团应该尽量地偏离共平面。阻止分子扭曲的(非电子作用力)是核排斥力。因此,一个空间拥挤的构象可以是能量有利的构象。在我们的研究中,经典有机结构理论的整体因果关系已经全面地被颠倒。     

Quantum-chemical modeling of ethylene and acetylene adsorption on gold clusters

The interaction of ethylene and acetylene molecules with planar (2D) and nonplanar (3D) gold clusters Au _n (n = 10, 12, 20) was studied by the density functional theory (DFT) method. The coordination of hydrocarbons at the vertices, edges, and fragments of the Au₃ cluster was shown to form π, di-σ, and μ type complexes, respectively. The standard Gibbs energy and the C-C bond length of the hydrocarbon change during its adsorption in the series μ > di-σ > π complexes. The highest selectivity in adsorption of acetylene relative to that of ethylene was achieved on Au₁₂ (3D) and Au₂₀ (2D) clusters.     

Hydrogen bonding without borders: an atoms-in-molecules perspective

It is shown that the electron density at the hydrogen bond critical point increases approximately linearly with increasing stabilization energy in going from weak hydrogen bonds to moderate and strong hydrogen bonds, thus serving as an indicator of the nature and gradual change of strength of the hydrogen bond for a large number of test intermolecular complexes.     

The all non-metal homodinuclear and heterodinuclear sandwich-like compounds C2(η3-L3)2 and BN(η3-L3)2 (L = BCO, BNN and CBO)

Density functional theory studies on the all non-metal homodinuclear and heterodinuclear sandwich-like compounds C(2)(η(3)-L(3))(2) and BN(η(3)-L(3))(2) (L = BCO, BNN and CBO) have been performed. The staggered conformations of both C(2)(η(3)-L(3))(2) and BN(η(3)-L(3))(2) are predicted to be stable. The non-metal direct C-C and B-N bonds are covalent with σ interactions, which are formed by the interactions of s and p(z) orbitals of the center atoms. Different from the ionic metal-ligand bond in the traditional metal center sandwich-like compounds, the C-L, B-L, and N-L bonds are covalent in these all non-metal sandwich-like compounds. The NICS values indicate that the ligands of C(2)(η(3)-L(3))(2) and BN(η(3)-L(3))(2), as well as their bare rings, display multiple aromaticity (σ and π aromaticity). Both σ and π aromaticity of the ring ligands towards the center atoms become stronger after complexation with the center atoms, while the π aromaticity against the center atoms is reduced. The π aromaticity of the ligands bonded to different center atoms follows a trend of B > C > N, and the (CBO)(3)(+) ligands bonded to B possess the strongest π aromaticity. The dissociation reactions and possible synthetic reactions analysis show that these all non-metal sandwich-like compounds are stable, and the homodinuclear species are more stable than the heterodinuclear ones. These all non-metal binuclear sandwich-like compounds can be regarded as potential synthetic targets according to the highly negative free energies of the possible synthetic reactions. The isomerization reactions demonstrate that the CBO-based compounds should be more possible to synthesize in experiments than their BCO-based isomers.     

Influence of copper substitution on the interaction of ethylene over iron clusters: a theoretical study

We report the results of density functional theory (DFT) calculations of ethylene adsorption over the most stable pure and bimetallic clusters of Fe(n)Cu(m) (2 ≤ m+n ≤ 4), in two adsorption modes of π and di-σ. Our results show that the quality of interaction of ethylene with iron center in bimetallic clusters of iron-copper is characteristically different from what is found over pure iron. Over the range of our studies for dimers, trimers, and tetramers, whether for π or di-σ mode, alloying iron clusters results in a substantial improvement in adsorption of ethylene over cluster and exhibits a notable increase in binding and interaction energies compared with pure iron clusters. One of the interesting features of this adsorption is that ethylene never orients toward di-σ mode for Cu-Cu or Fe-Cu bonds, and π orientation is strongly preferred. Ethylene adsorption in di-σ coordination is accompanied by the sever restructuring, larger deformation energy, and the larger interaction energy. In the next part, we answer this question of how electronic perturbations induced by copper atoms can enhance the activity of iron toward ethylene. This interpretation is done within the framework of natural bond orbital (NBO) and natural resonance theory (NRT) analyses. Different reaction pathways detected by NRT analysis (donor-acceptor, metallacyclic, and carbanion) reveal interesting aspects of differences between the nature of metal-alkene coordination in bimetallic and purely metallic clusters.     

An Excursion from Normal to Inverted C?C Bonds Shows a Clear Demarcation between Covalent and Charge‐Shift C?C Bonds

What is the nature of the C? C bond? Valence bond and electron density computations of 16 C? C bonds show two families of bonds that flesh out as a phase diagram. One family, involving ethane, cyclopropane and so forth, is typified by covalent C? C bonding wherein covalent spin‐pairing accounts for most of the bond energy. The second family includes the inverted bridgehead bonds of small propellanes, where the bond is neither covalent nor ionic, but owes its existence to the resonance stabilization between the respective structures; hence a charge‐shift (CS) bond. The dual family also emerges from calculated and experimental electron density properties. Covalent C? C bonds are characterized by negative Laplacians of the density, whereas CS‐bonds display small or positive Laplacians. The positive Laplacian defines a region suffering from neighbouring repulsive interactions, which is precisely the case in the inverted bonding region. Such regions are rich in kinetic energy, and indeed the energy‐density analysis reveals that CS‐bonds are richer in kinetic energy than the covalent C? C bonds. The large covalent–ionic resonance energy is precisely the mechanism that lowers the kinetic energy in the bonding region and restores equilibrium bonding. Thus, different degrees of repulsive strain create two bonding families of the same chemical bond made from a single atomic constituent. It is further shown that the idea of repulsive strain is portable and can predict the properties of propellanes of various sizes and different wing substituents. Experimentally (M. Messerschmidt, S. Scheins, L. Bruberth, M. Patzel, G. Szeimies, C. Paulman, P. Luger, Angew. Chem. 2005 , 117, 3993–3997; Angew. Chem. Int. Ed. 2005 , 44, 3925–3928), the C? C bond families are beautifully represented in [1.1.1]propellane, where the inverted C? C is a CS‐bond, while the wings are made from covalent C? C bonds. What other manifestations can we expect from CS‐bonds? Answers from experiment have the potential of recharting the mental map of chemical bonding.     

Mechanisms of reductive eliminations in square planar Pd(II) complexes: nature of eliminated bonds and role of trans influence

The trans influence of various phosphine ligands (L) in direct as well as dissociative reductive elimination pathways yielding CH(3)CH(3) from Pd(CH(3))(2)L(2) and CH(3)Cl from Pd(CH(3))(Cl)L(2) has been quantified in terms of isodesmic reaction energy, E(trans), using the MPWB1K level of density functional theory. In the absence of a large steric effect, E(trans) correlated linearly with the activation barrier (E(act)) of both direct and dissociation pathways. The minimum of molecular electrostatic potential (V(min)) at the lone pair region of phosphine ligands has been used to assess their electron donating power. E(trans) increased linearly with an increase in the negative V(min) values. Further, the nature of bonds that are eliminated during reductive elimination have been analyzed in terms of AIM parameters, viz. electron density (ρ(r)), Laplacian of the electron density (?(2)ρ(r)), total electron energy density (H(r)), and ratio of potential and kinetic electron energy densities (k(r)). Interestingly, E(act) correlated inversely with the strength of the eliminated metal-ligand bonds measured in terms of the bond length or the ρ(r). Analysis of H(r) showed that elimination of the C-C/C-Cl bond becomes more facile when the covalent character of the Pd-C/Pd-Cl bond increases. Thus, AIM details clearly showed that the strength of the eliminated bond is not the deciding factor for the reductive elimination but the nature of the bond, covalent or ionic. Further, a unified picture showing the relationship between the nature of the eliminated chemical bond and the tendency of reductive elimination is obtained from the k(r) values: the E(act) of both direct and dissociative mechanisms for the elimination of CH(3)CH(3) and CH(3)Cl decreased linearly when the sum of k(r) at the cleaved bonds showed a more negative character. It means that the potential electron energy density dominates over the kinetic electron energy density when the bonds (Pd-C/Pd-Cl) become more covalent and the eliminated fragments attain more radical character leading to the easy formation of C-C/C-Cl bond.     

Direct estimate of the strength of conjugation and hyperconjugation by the energy decomposition analysis method

The intrinsic strength of pi interactions in conjugated and hyperconjugated molecules has been calculated using density functional theory by energy decomposition analysis (EDA) of the interaction energy between the conjugating fragments. The results of the EDA of the trans-polyenes H2C=CH-(HC=CH)n-CH=CH2 (n = 1-3) show that the strength of pi conjugation for each C=C moiety is higher than in trans-1,3-butadiene. The absolute values for the conjugation between Si=Si pi bonds are around two-thirds of the conjugation between C=C bonds but the relative contributions of DeltaE pi to DeltaE orb in the all-silicon systems are higher than in the carbon compounds. The pi conjugation between C=C and C=O or C=NH bonds in H2C=CH--C(H)=O and H2C=CH-C(H)=NH is comparable to the strength of the conjugation between C=C bonds. The pi conjugation in H2C=CH-C(R)=O decreases when R = Me, OH, and NH2 while it increases when R = halogen. The hyperconjugation in ethane is around a quarter as strong as the pi conjugation in ethyne. Very strong hyperconjugation is found in the central C-C bonds in cubylcubane and tetrahedranyltetrahedrane. The hyperconjugation in substituted ethanes X3C-CY3 (X,Y = Me, SiH3, F, Cl) is stronger than in the parent compound particularly when X,Y = SiH3 and Cl. The hyperconjugation in donor-acceptor-substituted ethanes may be very strong; the largest DeltaE pi value was calculated for (SiH3)3C-CCl3 in which the hyperconjugation is stronger than the conjugation in ethene. The breakdown of the hyperconjugation in X3C-CY3 shows that donation of the donor-substituted moiety to the acceptor group is as expected the most important contribution but the reverse interaction is not negligible. The relative strengths of the pi interactions between two C=C double bonds, one C=C double bond and CH3 or CMe3 substituents, and between two CH3 or CMe3 groups, which are separated by one C-C single bond, are in a ratio of 4:2:1. Very strong hyperconjugation is found in HC[triple bond]C-C(SiH3)3 and HC[triple bond]C-CCl3. The extra stabilization of alkenes and alkynes with central multiple bonds over their terminal isomers coming from hyperconjugation is bigger than the total energy difference between the isomeric species. The hyperconjugation in Me-C(R)=O is half as strong as the conjugation in H2C=CH-C(R)=O and shows the same trend for different substituents R. Bond energies and lengths should not be used as indicators of the strength of hyperconjugation because the effect of sigma interactions and electrostatic forces may compensate for the hyperconjugative effect.     

Adjacent Lone Pair (ALP) Effect: A Computational Approach for Its Origin

The adjacent lone pair (ALP) effect is an experimental phenomenon in certain nitrogenous heterocyclic systems exhibiting the preference of the products with lone pairs separated over other isomers with lone pairs adjacent. A theoretical elucidation of the ALP effect requires the decomposition of intramolecular energy terms and the isolation of lone pair–lone pair interactions. Here we used the block‐localized wavefunction (BLW) method within the ab initio valence bond (VB) theory to derive the strictly localized orbitals which are used to accommodate one‐atom centered lone pairs and two‐atom centered σ or π bonds. As such, interactions among electron pairs can be directly derived. Two‐electron integrals between adjacent lone pairs do not support the view that the lone pair–lone pair repulsion is responsible for the ALP effect. Instead, the disabling of π conjugation greatly diminishes the ALP effect, indicating that the reduction of π conjugation in deprotonated forms with two σ lone pairs adjacent is one of the major causes for the ALP effect. Further electrostatic potential analysis and intramolecular energy decomposition confirm that the other key factor is the favorable electrostatic attraction within the isomers with lone pairs separated.     

硫叶立德化合物优势构型和键结构的量子拓扑研究

采用MP4（SDTQ）/6-311++G（d,p）和B3LYP/6-311++G（d,p）对所选四种化合 物进行构型优化，从量子拓扑学的角度对各稳定构型进行电子密度拓扑分析，讨论 了C-S键的特性。研究发现：（1）类硫叶立德自由基（·CHSH_2）和硫叶立德（ CH_2SH_2）基态的稳定构型都不具有C_s对称性；（2）类硫叶立德自由基和硫叶立 德中C-S键的性质类似，硫叶立德中π键由两个电子形成，类硫叶立德自由基中π 键由一个电子形成，所以前者的π键性质明显，后者的π键性质不明显；（3）类 硫叶立德自由基（·CHSH_2）中单电子π键中的电子主要在碳原子附近运动，属于 单电子π（C → S）配键，所以其C-S键的强度比相应的产物要弱。     

Theoretical study on the bromomethane-water 1:2 complexes

Bromomethane-water 1:2 complexes have been theoretically studied to reveal the role of hydrogen bond and halogen bond in the formation of different aggregations. Four stable structures exist on the potential energy surface of the CH3Br(H2O)2 complex. The bromine atom acts mainly as proton acceptor in the four studied structures. It is also capable of participating in the formation of the halogen bond. The properties and characteristics of the hydrogen bond and the halogen bond are investigated employing several different quantum chemical analysis methods. Cooperative effects for the pure hydrogen bonds or the mixed hydrogen bonds with halogen bonds and the possibility of describing cooperative effects in terms of the topological analysis of the electronic density or the charge-transfer stabilization energy are discussed in detail. An atoms-in-molecules study of the hydrogen bond or the halogen bond in the bromomethane-water 1:2 complexes suggests that the electronic density topology of the hydrogen bond or the halogen bond is insensitive to the cooperative effect. The charge-transfer stabilization energy is proportional to the cooperative effect, which indicates the donor-acceptor electron density transfer to be mainly responsible for the trimer nonadditive effect.     

The HRuCCH, RuCCH2, and Ru-η2-C2H2 molecules: infrared spectra and density functional calculations

Laser-ablated ruthenium atoms undergo reaction with acetylene during condensation in excess neon and argon matrices to form a metallacycle complex, insertion into the C-H bond, and rearrangement to the vinylidene complex. The subject molecules were identified by (13)C(2)H(2) and C(2)D(2), isotopic substitutions and density functional theory (DFT) frequency calculations. The HRuCCH molecule is described by Ru-H, CH, and CC stretching modes and CCH deformation modes. A very strong CC double bond stretching, weak CH stretching, and CCH deformation frequencies were observed for the Ru═C═CH(2) complex. The metallacycle Ru-η(2)-(C(2)H(2)) is characterized through CC double bond stretching, CH stretching and CCH deformation modes. The reaction mechanism for formation of the Ru═C═CH(2) complex was investigated by B3LYP internal reaction coordinate calculations, and the hydrido-alkyny complex is the rate-determining step. The delocalized three-center-four-electron π bond using the Ru 4d(xz) electron pair contributes to the C-C π* orbital and provides stabilization energy (ΔE((2)), second-order perturbation) for the vinylidene Ru═C═CH(2) complex.     

A photoelectron spectroscopy and ab initio study of B21-: negatively charged boron clusters continue to be planar at 21

The structures and chemical bonding of the B(21)(-) cluster have been investigated by a combined photoelectron spectroscopy and ab initio study. The photoelectron spectrum at 193 nm revealed a very high adiabatic electron binding energy of 4.38 eV for B(21)(-) and a congested spectral pattern. Extensive global minimum searches were conducted using two different methods, followed by high-level calculations of the low-lying isomers. The global minimum of B(21)(-) was found to be a quasiplanar structure with the next low-lying planar isomer only 1.9 kcal/mol higher in energy at the CCSD(T)/6-311-G* level of theory. The calculated vertical detachment energies for the two isomers were found to be in good agreement with the experimental spectrum, suggesting that they were both present experimentally and contributed to the observed spectrum. Chemical bonding analyses showed that both isomers consist of a 14-atom periphery, which is bonded by classical two-center two-electron bonds, and seven interior atoms in the planar structures. A localized two-center two-electron bond is found in the interior of the two planar isomers, in addition to delocalized multi-center σ and π bonds. The structures and the delocalized bonding of the two lowest lying isomers of B(21)(-) were found to be similar to those in the two lowest energy isomers in B(19)(-).     

Peierls instability and vibrational spectra of polyacetylene

It is shown that the Peierls instability in conjugated polymers is modified by the interaction of π electrons. This modification gives rise to the absence of a soft mode of stretching C? C vibrations. Taking into account electron correlations we obtain reasonable agreement between the calculated and measured frequencies of the carbon skeleton of polyacetylene with all the C? C bonds being equal in length. It is shown that the conclusion for the bond length alternation in polyacetylene does not follow from the experimental data on the vibrations of polyacetylene.     

第一过渡系金属硅烯配合物的理论研究

以HF/6-311+G^*基组研究了硅烯SiH₂同第一过渡系金属的配合物MSiH₂的分子轨道特征及键解离能.MSiH₂为共平面构型.其中基态的3TiSiH₂和4CoSiH₂带有明显的双键特征.M-Si键具有共价性质.M-Si的键解离能,从Sc到Cu呈现周期性变化,这种变化趋势同M的金属离子激发能之间存在近似的线性关系.     

木质素模化物键离解能的理论研究

采用密度泛函理论B3P86方法,在6-31G(d,p)基组水平上,对木质素结构中的6种连接方式(β-O-4、α-O-4、4-O-5、β-1、α-1、5-5)的63个木质素模化物的醚键(C-O)和C-C键的键离解能E_B进行了理论计算研究。分析了不同取代基对键离解能的影响以及键长与键离解能的相关性。计算结果表明,C-O键的键离解能通常比C-C键的小,在各种醚键中C_α-O键的平均键离解能最小,为182.7 kJ/mol;其次是β-O-4连接中的C_β-O键,苯环和烷烃基上的取代基对醚键的键离解能有较强的弱化作用,C-O键的键长和键离解能的相关性较差。与C-O键相比,C-C键的键离解能受苯环上取代基的影响很小,而烷烃基上的取代基对C-C键的键离解能有较大的影响,C-C键的键离解能和键长之间存在较强的线性关系,C-C键的键长越长,其键离解能越小。