Probing weak molecular orbital interactions in non-conjugated diene molecules by means of near-edge X-ray absorption spectroscopy

Carbon and oxygen near-edge X-ray absorption fine structure (NEXAFS) spectra of 1,4-cyclohexadiene, p-benzoquinone, norbornadiene, norbornadienone, and cis-cis-[4,4,2]propella-3,8-diene-11,12-dione were calculated by means of Hartree-Fock and hybrid density functional theory using the static-exchange (STEX) approximation. The NEXAFS spectra are used as a probe to identify weak molecular interactions between the two non-conjugated ethylenic pi* orbitals present in these molecules. We show that the X-ray absorption spectrum of 1,4-cyclohexadiene exhibits some particular spectral structures in the discrete energy region that evidence diene through-bond orbital interaction, whereas absorption peaks are identified in the norbornadiene and norbornadienone spectra that indicate effective through-space orbital interactions. The molecular structure of the cis-cis-[4,4,2]propella-3,8-diene-11,12-dione isomer is such that the indirect through-bond or through-space diene orbital interactions are too weak to be assigned by its C1s NEXAFS spectrum.     

分子内孤对(n)轨道间相互作用的又一例证——某些杂氮环己烷系列化合物的气相H_eI_α紫外光电子能谱(UPS)研究

人们知道,原子和分子的气相紫外光电子能谱(UPS)谱带的分离结构是电子能级量子化的反映.谱峰相应的电子结合能(或电离能)是正则(自洽场)分子轨道计算方法给出的本征值(-ε_i),所以UPS是目前用以获得原子或分子能级直接量度的最好技术.就是说:量子化学理论可以提供UPS解译的必要模型,而UPS谱本身反过来又可以检验分子轨道理论的正确性,并作为各种近似分子轨道理论计算中经验参数化(如SPINDO)的基础.因而UPS     

分子内孤对(n)轨道间相互作用的又一例证——某些杂氮环已烷系列化合物的气相HeIα紫外光电子能谱(UPS)研究

Ione pair orbital and their interaction in some nitrogen heterocyclic compound series have been interpreted in terms of through-space and through-bond mechanisms through the study of their gas phase ultraviolet photoelectron spectrocopy. The HAM/3 molecular orbital calculations on each molecule of the studied series were also carried out. The order of experimental vertical ionization potentials of the molecules can be not only predicated, but the spacing of through-space and through-bond interactions splitting of the studied compounds are consistent with the results of HAM/3 calculations.     

An analysis of the through bond interaction using the localised molecular orbitals—III : Long range effect of lone pair orbital to the optical rotatory strength of the carbonyl n-π* transition in 3-ketopiperidines

The optical rotatory strengths of the carbonyl n-π^* transitions of (1R)-3-ketopiperidine and (1S)-3-ketopiperidine were subjected to the analysis in terms of the through-space and the through-bond interactions according to the procedure using localised molecular orbitals we proposed in the preceding papers. As a result of the present analysis, the optical rotatory strengths of the molecules were found to be influenced by the direction of the remote nitrogen lone pair orbital. This influence was found to be illustrated by the coupling between the CO group and the nitrogen lone pair orbital as well as the N-H bond localized orbital via a path containing the through-bond and the through-space interactions. That is, the positive coupling and the negative coupling paths were determined by the present analysis and the sign of the optical rotatory strength was found to correspond to the sum of the contributions of both coupling paths.     

The magnetochemistry of verdazyl radical-based materials

Stable organic radicals have received much attention as building blocks for the construction of molecular magnetic materials because they are readily functionalized using modern synthetic techniques. In this context, the nitroxide radical family has been the dominant class of radicals in molecular magnetochemistry. However, other stable radical systems have also been explored. One such example is the verdazyl family of radicals. Their high chemical stability and synthetic versatility make verdazyls one of the more attractive alternatives to nitroxides in molecular magnet design. This article reviews the magnetism of verdazyl-based systems, including through-bond coupling in polyradicals, coordination complexes and intermolecular interactions in the solid state.     

An analysis of the through-bond interaction using the localized molecular orbitals—II : Long-range proton hyperfine coupling in bridgehead alkyl radicals: bicyclo[1.1.1]pent-1-yl,bicyclo[2.1.1]hex-1-yl and bicyclo[2.2.1]hept-1-yl radicals

The INDO calculations were performed on three bridgehead alkyl radicals; bicyclo[1.1.1]pent-1-yl, bicyclo[2.1.1]hex-l-yl and bicyclo[2.2.1]hept-1-yl radicals. We have transformed the canonical molecular orbitals obtained by the INDO method into the localized molecular orbitals. With the use of the obtained localized molecular orbitals, the variation in the hyperfine coupling constant at the bridgehead proton in these radicals was pursued in terms of the through-bond (and/or the through-space) interaction according to the method by which we selectively can pick up a particular interaction between the specified localized molecular orbitals in a radical. As a result of this analysis, it was found that the hyperfine coupling constants in these radicals can be expressed by the summation of several terms; through-virtuals, through-space, through-bond, and some other coupling terms.     

A quantitative analysis of the through-space and the through-bond interactions between lone-pairs in azines: pyridazine,pyrimidine and pyrazine

The INDO calculations were performed on the three azines: pyridazine, pyrimidine, and pyrazine. The cannonical molecular orbitais obtained by these calculations were then transformed into the localized molecular orbitals. With the use of the localized molecular orbitals, the variation in the lone-pair orbital energies of these molecules were pursued in the light of the through-space and/or the through-bond interactions between the specified localized molecular orbitals in a molecule selectively. The interactions were expressed by the summation of several terms: through-space, through-bond, through-virtuals and coupling terms.     

An analysis of the through-bond interaction using the localized molecular orbitals with ab initio calculations—I : Lone-pair orbital interactions in cis- and trans-hydrazines

Ab initio SCF MO calculations using STO-3G basis set were performed on the cis- and trans- hydrazines. The cannonical MOs obtained by these calculations were then transformed into the localized MOs. With the use of the localized MOs thus obtained, the variation in the lone-pair orbital energies of the molecules were pursued in the light of the through-space and/or the through-bond interactions between the specified localized MOs. As a result of this analysis, it was found that ; (a) the effect of the inner shell orbitais, l s electrons of N atoms, is not negligibly small, (b) the effect of the through-bond interaction is not so larger than the through-space interaction, and (c) the large contribution of the through-space interaction is caused from the indirect as well as direct interactions between two lone-pairs.     

Effect of double-hyperconjugation on the apparent donor ability of sigma-bonds: insights from the relative stability of delta-substituted cyclohexyl cations

A combination of electronic, structural, and energetic analyses shows that a somewhat larger intrinsic donor ability of the C-H bonds compared to that of C-C bonds can be overshadowed by cooperative hyperconjugative interactions with participation of remote substituents (double hyperconjugation or through-bond interaction). The importance of double hyperconjugation was investigated computationally using two independent criteria: (a) relative total energies and geometries of two conformers ("hyperconjomers") of delta-substituted cyclohexyl cations (b) and natural bond orbital (NBO) analysis of electronic structure and orbital interactions in these molecules. Both criteria clearly show that the apparent donor ability of C-C bonds can vary over a wide range, and the relative order of donor ability of C-H and C-C bonds can be easily inverted depending on molecular connectivity and environment. In general, relative donor abilities of sigma bonds can be changed by their through-bond communication with remote substituents and by greater polarizability of C-X bonds toward heavier elements. These computational results can be confirmed by experimental studies of conformational equilibrium of delta-substituted cyclohexyl cations.     

Polyethers: Structural analysis of the 1,4,5,8-tetraoxadecalins and 2,2'-bis(1,3-dioxolane) by photoelectron spectroscopy,molecular mechanics and molecular orbital calculations

The photoelectron (PE) spectrum of cis-1,4,5,8-tetraoxadecalin exhibits in contrast to most polyoxa compounds an extremely well resolved low energy pan due to large ‘through-bond’ interactions between the oxygen lone pairs and the ideally oriented C-C bonds. The ‘through-bond’ interactions of the cis- as well as the unknown trans-1,4,5,8-tetraoxadecalin are discussed based on simple perturbation molecular orbital theory and PRDDO molecular orbital calculations. Additionally the PE spectrum of 2,2'-bis (1,3-dioxolane) is reported. Molecular mechanics (MM1 and MM2) and molecular orbital (PRDDO) calculations of the different conformations of the 1,4,5,8-telraoxadecalin and 2,2'-bis(1,3-dioxolane) systems allow the absence of the trans-1, 4,5,8-tetraoxadecalin, and the cis-trans energy difference in the series decalin, 1,8-dioxadecalin and 1,4,5,8-tetraoxadecalin systems to be explained.     

An analysis of the through-bond interaction using the localized molecular orbitals with ab initio calculations—II : Lone-pair orbital energies in bicyclo compounds: 7-azabicyclo[2.2.1]heptane and 2-azabicyclo[2.2.2]octane,and their n-methyl derivatives

Ab intio SCF MO calculations using STO-3G basis set were performed on 7-azabicyclo[2.2.1]heptane, N-methyl-7-azabicyclo[2.2.1]heptane, 2-azabicyclo[2.2.2)octane, N-methyl-2-azabicyclo[2.2.2)octane, and their model molecules. The orbital energies obtained by these calculations were compared with the experimental ionization potentials The canonical MOs obtained for the model molecules were then transformed into the localized Mos. With the use of the localized MOs thus obtained, the lone-pair orbital energies were pursued in the light of the through-space and/or the through-bond interactions between thw specified localized MOs. As a result of this analysis, it was found that the effects of the inner shell orbitals, 1s electrons of the N atom, and of the neighbouring N-C bonds of the skeleton (through-bond interaction) play a dominant role in the interaction with the lone-pair orbitals. It was also found that the effect of the N-Me group on the lone-pair orbital energy is considerably important.     

The fulvenediyls and related biradicals: Molecular and electronic structure

The structures, stabilities, and electronic properties of the nine fulvenediyls have been investigated and compared to the isomeric benzynes using density functional theory (DFT) and ab initio multireference configuration interaction methods (MRCI). Given the significant biradical character of several singlet fulvenediyls, the BLYP method reproduces the relative energies of these systems rather accurately. In contrast, some triplet states (3A'-12, 3A'-13, and 3B2-14) suffer from artifactual symmetry breaking towards a nonplanar geometry at the DFT level. The structures and properties of the title biradicals are readily rationalized within the framework of through-space and through-bond molecular orbital interactions. The degree of coupling between the formally unpaired electrons strongly depends on the number and arrangement of intervening sigma-bonds, and often parallels the trends observed for annellated arynes of similar topology. In some cases, novel structural patterns can be identified that are characteristic of five-membered-ring systems. These similarities and differences between five- and six-membered-ring arynes are discussed on the basis of molecular orbital arguments.     

哌嗪二酮的气相Hel光电子能谱及其量化计算

给出了哌嗪二酮的气相HeI紫外光电子能谱(UPS), 并进行了化合物分子的HAM/3, MNDO, MINDO/3, INDO, CNDO/2和EHMO等量子化学计算研究. UPS谱低电离能(<11.00 eV)区的四重峰被指认为分子体系中氧-氧, 氮-氮原子孤对轨道间的通过键相互作用导致的分裂峰. 表明HAM/3和MNDO计算法是预指该化合物实验电离能正确次序、轨道对称性类型以及通过键相互作用导致分裂大小的较好方法.     

Non-bonded interactions in 2,2,4,4-tetramethyl-1,3-cyclobutanedithione and 2,2,4,4-tetramethyl-3-thio-1,3-cyclobutanedione

Electronic absorption and emission spectra as well as He(I) photoelectron spectra of 2,2,4,4-tetramethyl-1,3-cyclobutanedithione and 2,2,4,4-tetramethyl-1-3-thio-1,3-cyclobutanedione have been interpreted on the basis of molecular orbital calculations. The results show that the non-bonded orbital of the dithione is split owing to through-bond interaction, the magnitude of splitting being 0.4 eV. The π* orbital of the dithione appears to be split by about 0.2 eV. Electronic absorption spectra show evidence for the existence of four n—π* transitions, arising out of the splitting of the orbitals referred to above, just as in the case of 2,2,4,4-tetramethyl-1,3-cyclobutanedione. Electronic and photoelectron spectra of the thio-dione show evidence for weak interaction between the CS and C&.zdbnd;O groups, probably via π* orbitals. Infrared spectra of both the dithione and the thio-dione are consistent with the planar cyclobutane ring; the ring-puckering frequency responsible for non-bonded interactions is around 67 cm^?1 in both the dithione and the thio-dione, the value not being very different from that in the dione. The 1,3-transannular distance is also similar in the three molecules.     

Direct Measurement of Through-Bond Effects in Molecular Multivalent Interactions

Multivalent interactions occur throughout biology, and have a number of characteristics that monovalent interactions do not. However, it remains challenging to directly measure the binding force of molecular multivalent interactions and identify the mechanism of interactions. In this study, the specific interaction between bivalent aptamer and thrombin has been measured directly and quantitatively by force-induced remnant magnetization spectroscopy to investigate the binding force and through-bond effects of the multivalent interactions. The measured differential binding forces enable through-bond effects in thrombin–aptamer complexes to be identified, where aptamer binding at exosite II produces visible effects on their binding at exosite I and vice versa. This method might be suitable for practical applications in the design of high-performance ligands.     

环芳类化合物分子轨道相互作用的研究

建立模型分子描述环芳类分子中二苯环、二乙炔的π轨道间的相互作用,应用多重散主射Ｘα自洽场方法对模型分子的电子结构进行计算,得到分子轨道通过空间相互作用的大小随二苯环、二乙炔间距离的增加呈指数下降,在环芳类经合物分子电子结构研究基础上,分析了分子轨道通过键的相互作用,表明,分子轨道通过空间相互作用与通过键相互作用相互抵消,采用过滤态方法计算环芳类化合物分子前线分子轨道电离能,与实验符合较好。     

Symmetry and bonding in metalloporphyrins. A modern implementation for the bonding analyses of five- and six-coordinate high-spin iron(III)-porphyrin complexes through density functional calculation and NMR spectroscopy

Bonding interactions between the iron and the porphyrin macrocycle of five- and six-coordinate high-spin iron(III)-porphyrin complexes are analyzed within the framework of approximate density functional theory with the use of the quantitative energy decomposition scheme in combination with removal of the vacant pi orbitals of the porphyrin from the valence space. Although the relative extent of the iron-porphyrin interactions can be evaluated qualitatively through the spin population and orbital contribution analyses, the bond strengths corresponding to different symmetry representations can be only approximated quantitatively by the orbital interaction energies. In contrast to previous suggestions, there are only limited Fe --> P pi back-bonding interactions in high-spin iron(III)-porphyrin complexes. It is the symmetry-allowed bonding interaction between d(z)2 and a(2u) orbitals that is responsible for the positive pi spin densities at the meso-carbons of five-coordinate iron(III)-porphyrin complexes. Both five- and six-coordinate complexes show significant P --> Fe pi donation, which is further enhanced by the movement of the metal toward the in-plane position for six-coordinate complexes. These bonding characteristics correlate very well with the NMR data reported experimentally. The extraordinary bonding interaction between d(z)2 and a(2u) orbitals in five-coordinate iron(III)-porphyrin complexes offers a novel symmetry-controlled mechanism for spin transfer between the axial ligand sigma system and the porphyrin pi system and may be critical to the electron transfer pathways mediated by hemoproteins.     

Lone-pair orbital interactions in polythiaadamantanes

The electronic structures of a series of polythiaadamantanes from thiaadamantane through 2,4,6,8,9,10-hexathiaadamantane (HTA) have been analyzed using density functional theory calculations in conjunction with Hückel and natural bond orbital analysis. The effects of multiple sulfur p-type lone-pair orbital interactions on ionization potentials, hole mobilities, and electronic coupling have been determined. An overall increase in the average energy of the lone-pair orbitals as the number of sulfur atoms increases is predicted, with the exact positioning of the HOMO depending on specific lone-pair interactions. Separation of through-bond (TB) and through-space (TS) interactions between intramolecular sulfur atoms has been performed using localized molecular orbitals and model systems based on interacting hydrogen sulfide molecules. TB interations were found to reduce orbital splitting, while TS interactions were found to increase orbital splitting. TS interactions were more or less constant from one polythiaadamantane to the next, and the contributions of TB effects to individual orbital energies vary depending on the relative orientation of sulfur atoms as determined by the sigma molecular framework. Electronic coupling between intermolecular sulfur lone-pair orbitals was determined by investigating unique dimer pairs observed in the crystal structure of HTA. Electronic coupling is not as strong as expected given the short intermolecular S-S distances observed in the crystal structure. In general, B3LYP/6-31G(d) and B3LYP/6-311+G(d,p) give very similar orbital energies and splittings.     

A computational study of the Dougherty model for the prediction of high-spin states in organic chemistry

The model proposed by Dougherty for the design of high-spin organic systems has been studied from a quantitative point of view using a Heisenberg Hamiltonian formalism. This analysis leads to a decomposition of the phenomenological coupling parameter, J, into contributions from individual active orbital sites and a decomposition of the spin multiplicity into terms from the ferromagnetic coupling unit and the spin-containing units. An analysis of the origin of quintet stability has been carried out for four molecular systems with quintet ground states that have previously been synthesized by Dougherty and by Adam. The results indicate that the ferromagnetic coupling unit plays the dominant role in determining high-spin stability as suggested by Dougherty and gives some insights that may be useful in the rational design of high-spin systems. Received: 31 July 1998 / Accepted: 21 September 1998 / Published online: 23 February 1999     

Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method

The ab initio fragment molecular orbital calculations were performed for molecular interactions of the whole estrogen receptor (ER) ligand-binding domain with a natural ligand, 17beta-estradiol (EST). The interaction energies of the ligand at the residue level were calculated using HF and MP2 methods with several basis sets. The charge-transfer (CT) interactions were also analyzed based on configuration analysis for fragment interaction. Strong electrostatic interactions were observed between the EST and surrounding charged/polarized residues, Glu353, Arg394, His524, and Thr347. Weak electrostatic and significant van der Waals dispersion interactions were observed between the EST and the many surrounding hydrophobic residues. Together with the experimental interpretations, both interactions equally contributed to the total binding energies, and it was found that the inclusion of electron correlation was essential to obtain an appropriate picture of the interaction. The strongest interaction energy was observed between Glu353 and the EST, and the CT interactions from the lone-pair orbital of the carbonyl oxygen of Glu353 to the sigma(OmicronEta) orbital of the hydroxyl group of EST were found to be important. The CT interactions from the lone-pair orbital of EST to the sigma(NuEta) of Arg394 and from the lone-pair orbital of EST to the sigma(NuEta) of His524 were also observed. These CT interactions occurred through the hydrogen-bond networks between the ER and EST. Therefore, electron donations from the ER to the EST and electron back-donations from EST to the ER were characteristic of ER-ligand binding. Our approach provides a powerful tool to understanding detailed molecular interactions at the quantum mechanical level.