Neutral and ionic hydrogen bonding in Schiff bases

Low-temperature, high-resolution X-ray studies of charge distributions in the three Schiff bases, the dianil of 2-hydroxy-5-methylisophthaldehyde, 3,5-dinitro-N-salicylidenoethylamine and 3-nitro-N-salicylidenocyclohexylamine, have been carried out. These structures exhibit interesting weak interactions, including two extreme cases of intramolecular hydrogen bonds that are ionic N(+)-H...O- and neutral O-H...N in nature. These two types of hydrogen bond reflect differences in geometrical parameters and electron density distribution. At the level of geometry, the neutral O-H...N hydrogen bond is accompanied by an increase in the length of the C(1)-O(1) bond, opening of the ipso-C(1) angle, elongation of the aromatic C-C bonds, shortening of the C(7)-N(2) bond and increased length of the C(1)-C(7) bond, relative to the ionic hydrogen bond type. According to the geometrical and critical point parameters, the neutral O-H...N hydrogen bond seems to be stronger than the ionic ones. There are also differences between charge density parameters of the aromatic rings consistent with the neutral hydrogen bond being stronger than the ionic ones, with a concomitant reduction in the aromaticity of the ring. Compounds with the ionic hydrogen bonds show a larger double-bond character in the C-O bond than appears in the compound containing a neutral hydrogen bond; this suggests that the electronic structure of the former pair of compounds includes a contribution from a zwitterionic canonical form. Furthermore, in the case of ionic hydrogen bonds, the corresponding interaction lines appear to be curved in the vicinity of the hydrogen atoms. In the 3-nitro-N-salicylidenocyclohexylamine crystal there exists, in addition to the intramolecular hydrogen bond, a pair of intermolecular O...H interactions in a centrosymmetric dimer unit.     

A Combined Experimental and Theoretical Electron Density Study of Intra‐ and Intermolecular Interactions in Thiourea S,S‐Dioxide

The thiourea S,S‐dioxide molecule is recognized as a zwitterion with a high dipole moment and an unusually long C? S bond. The molecule has a most interesting set of intermolecular interactions in the crystalline state—a relatively strong O???H? N hydrogen bond and very weak intermolecular C???S and N???O interactions. The molecule has C_s symmetry, and each oxygen atom is hydrogen‐bonded to two hydrogen atoms with O???H? N distances of 2.837 and 2.826 Å and angles of 176.61 and 158.38°. The electron density distribution is obtained both from Xray diffraction data at 110 K and from a periodic density functional theory (DFT) calculation. Bond characterization is made in terms of the analysis of topological properties. The covalent characters of the C? N, N? H, C? S, and S? O bonds are apparent, and the agreement on the topological properties between experiment and theory is adequate. The features of the Laplacian distributions, bond paths, and atomic domains are comparable. In a systematic approach, DFT calculations are performed based on a monomer, a dimer, a heptamer, and a crystal to see the effect on the electron density distribution due to the intermolecular interactions. The dipole moment of the molecule is enhanced in the solid state. The typical values of ρ_b and H_b of the hydrogen bonds and weak intermolecular C???S and N???O interactions are given. All the interactions are verified by the location of the bond critical point and its associated topological properties. The isovalue surface of Laplacian charge density and the detailed atomic graph around each atomic site reveal the shape of the valence‐shell charge concentration and provide a reasonable interpretation of the bonding of each atom.     

Three‐electron two‐center bonding in cycloimmonium ylides

We explore the possibility that a 3‐electron‐2‐center bonding exists in cycloimmonium ylides. To detect this bonding in a polyatomic system, 3‐electron‐1‐hole density operators, characterizing a Pauling 3‐electron bond, are used in the framework of second quantization formalism. The weights of 3‐electron resonance structures are calculated and compared with the weights of 2‐electron structures for the ylide bond of pyridinium dicyanomethylide; the correlations of (↑↓) and (↑) electronic events, involved in the 3‐electron resonance structures, are also investigated. The calculations are performed in various approximation levels, and both orthogonal and nonorthogonal natural atomic orbitals are adopted. All calculations show that a 3‐electron bond exists between N and C atoms of ylide bond, but this bonding is not extended in C atoms of the pyridinium group. The interactions of α,β electrons (at the configuration interaction [CI] level) increase the localization of electrons, the weights of 3‐electron resonance structures, and thus the probability for 3‐electron bonding. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

杂氮硼三环类化合物的UPS及化学键的理论研究

报道了六种杂氮硼三环类化合物的紫外光电子能谱(UPS).采用RHF/3-21G优化了各分子的优势构型,根据化合物UPS的谱带特征结合RHF/6-31G^*的计算结果对化合物的UPS进行了解析和指认,精确给出了各化合物中σN-B配键电子的电离峰位置.利用电子密度拓扑分析方法对各化合物的成键情况的研究显示:在该类化合物中B原子具有较为明显的阳离子的特征,N,B原子间均存在键鞍点.从实验和理论上证实了该类体系中σN-B的存在.各化合物的UPS,SCFMO计算和电子密度拓扑分析都表明,在该类体系中环上CH~3,CH~2的引入削弱了B,N间的成键作用;环上羰基的引入增强了B,N间的成键作用。     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

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。     

Functional groups expressed as graphs extracted from the Laplacian of the electron density

The valence charge concentration shell, as determined by the Laplacian of the electron density, is used as a source of quantum topological graphs, called L‐graphs. A considerable number of such graphs are extracted from the ab initio wave functions of 31 molecules calculated at the B3LYP/6‐311+G(2d,p)//B3LYP/6‐311+G(2d,p) level, covering common functional groups in organic chemistry. We show how L‐graphs can be constructed from a largely transferable subgraph called atomic L‐graph. We investigate the topological stability of the L‐graphs as a function of the basis set. Reliable and consistent atomic L‐graphs are only obtained with basis sets of triple‐zeta quality or higher. The recurrence of invariant motifs or subgraphs in the L‐graphs enables the isolation of 16 atomic L‐graphs. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Theoretical Studies on the Hydrogen‐bonding and π‐Stacking Interactions in the m‐Nisoldipine Polymorphism Dimers

The intermolecular interactions in the dimers of m‐nisoldipine polymorphism were studied by B3LYP calculations and quantum theory of "atoms in molecules" (QTAIM) studies. Four geometries of dimers were obtained: dimer I (a‐dimer, O···H? N), dimer II (b‐dimer, O···H? N), dimer III (b‐dimer, π‐stacking‐c), and dimer IV (b‐dimer, π‐stacking‐p). The interaction energies of the four dimers are along the sequence of II>I>III>IV. The intermolecular distance of the interactions follows the order: I (O···H? N)II>III>IV, and the electrostatic character decreases along the sequence: I>II>III>IV.     

硫代双烯酮与硫甲醛环加成反应机理的理论研究

采用从头算HF/6-31G^*和密度泛函B3LYP/6-31++G^*^*方法研究了硫代双烯酮与硫甲醛两种可能的环加成反应的机理,并对反应各驻点进行了电子密度拓扑分析研究.结果表明,这两个生成不同四元杂环产物的平行反应均为有一两性离子中间体的分步反应.两个反应均较易进行,但反应(1)更容易一些,结果与实验一致.     

SiP Double Bonds: Experimental and Theoretical Study of an NHC‐Stabilized Phosphasilenylidene

An experimental and theoretical study of the first compound featuring a Si?P bond to a two‐coordinate silicon atom is reported. The NHC‐stabilized phosphasilenylidene (IDipp)Si?PMes* (IDipp=1,3‐bis(2,6‐diisopropylphenyl)imidazolin‐2‐ylidene, Mes*=2,4,6‐tBu₃C₆H₂) was prepared by SiMe₃Cl elimination from SiCl₂(IDipp) and LiP(Mes*)SiMe₃ and characterized by X‐ray crystallography, NMR spectroscopy, cyclic voltammetry, and UV/Vis spectroscopy. It has a planar trans‐bent geometry with a short Si? P distance of 2.1188(7) Å and acute bonding angles at Si (96.90(6)°) and P (95.38(6)°). The bonding parameters indicate the presence of a Si?P bond with a lone electron pair of high s‐character at Si and P, in agreement with natural bond orbital (NBO) analysis. Comparative cyclic voltammetric and UV/Vis spectroscopic experiments of this compound, the disilicon(0) compound (IDipp)Si?Si(IDipp), and the diphosphene Mes*P?PMes* reveal, in combination with quantum chemical calculations, the isolobal relationship of the three double‐bond systems.     

取代1-氯蒽醌中分子内卤键的电子密度拓扑分析

运用量子化学密度泛函B3LYP方法,在6-311＋＋G（d,p）基组水平上对邻位和间位取代1-氯葸醌的分子内卤键进行了研究．用电子定域函数和“分子中的原子,,理论对分子内卤键的性质进行了电子密度拓扑分析．通过对计算得到的密度矩阵进行σ-π兀分离,得到了π-键的键径和分子图,并讨论了。电荷密度和兀电荷密度对卤键的影响．结果表明,键鞍点和环鞍点处的电子密度拓扑性质均可作为衡量分子内卤键强度的量度．键鞍点和环鞍点处的电荷密度P越大,键鞍点与环鞍点的距离越大,卤键强度越大．除σ电荷密度外,π电荷密度对分子内卤键的性质也有明显影响．     

Theoretical investigations of the reactivities of four-membered N-heterocyclic carbene analogues of the group 13 elements

The potential energy surfaces for the chemical reactions of four‐membered N‐heterocyclic group 13 heavy carbeneoid species have been studied using density functional theory (Becke, 3‐parameter, Lee‐Yang‐Parr (B3LYP)/Los Alamos National Laboratory 2‐Double‐Zeta (LANL2DZ)). Five four‐membered group 13 heavy carbeneoid species, iPr₂NC(NAr)₂E:, where E = B, Al, Ga, In, and Tl, have been chosen as model reactants in this work. Also, three kinds of chemical reactions, C? H bond insertion, alkene cycloaddition, and dimerization, have been used to study the chemical reactivities of these group 13 four‐membered N‐heterocyclic carbeneoid species. In principle, our present theoretical work predicts that the larger the ∠NEN bond angle of the four‐membered group 13 iPr₂NC(NAr)₂E: species, the smaller the singlet–triplet splitting, the lower the activation barrier, and, in turn, the more rapid its chemical reactions to various chemical species. Moreover, our theoretical investigations suggest that the relative carbenic reactivity decreases in the following order: B > Al > Ga > In > Tl. That is, the heavier the group 13 atom (E), the more stable its four‐membered carbeneoid toward chemical reactions is. As a result, our computations predict that the four‐membered heavy group 13 iPr₂NC(NAr)₂E: species (E = Al, Ga, In, and Tl) should be both kinetically and thermodynamically stable, and can be readily synthesized and isolated at room temperature. Furthermore, the singlet–triplet energy splitting of the four‐membered group 13 iPr₂NC(NAr)₂E: species, as described in the configuration mixing model attributed to the work of Pross and Shaik, can be used as a diagnostic tool to predict their reactivities. The results obtained allow a number of predictions to be made. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

硫代双烯酮与异氰酸环加成反应的理论研究

采用从头算ＲＨＦ／６－３１Ｇ方法研究了硫代双烯酮与异氰酸之间两种可能的环加成反应的机理,并对反应各驻点进行了电子密度拓扑分析研究．结果表明,这两个生成不同四元杂环产物的平行反应均为非同步的协同反应,但两个反应进行的难易程度不同,形成硫氮杂环的反应更容易一些,而形成氮杂环反应的产物在热力学上更稳定一些     

Mono‐ and dinuclear oxime palladacycles bearing diphosphine ligands: An unusual coordination mode for dppe

Three new oxime‐based palladacycles, namely [Pd{C,N‐C₆H₄{C(Me)?NOH}‐2}(dppm)]ClO₄ ( 1 ), [Pd₂{C,N‐C₆H₄{C(Me)?NOH}‐2}₂(dppe)₂(μ‐dppe)](ClO₄)₂ ( 2 ) and [Pd{C,N‐C₆H₄{C(Me)?NOH}‐2}(dppmS₂)]ClO₄ ( 3 ), were synthesized by the reaction of dinuclear oxime complex [Pd{C,N‐C₆H₄{C(Me)?NOH}‐2}(μ‐Cl)]₂ with different diphosphine ligands (dppm, dppe and dppmS₂). The synthesized complexes were characterized using Fourier transform infrared, ³¹P NMR, ¹H NMR and ¹³C NMR spectroscopic methods and elemental analyses, and their molecular structures were elucidated using X‐ray crystallography. The structure of 2 is worthy of note as it is the first oxime palladacycle where there are both bridging (P–) and chelating (P^P) dppe ligands, giving rise to a dinuclear complex. The palladium atom is in a five‐coordinate, square pyramidal P₃NC environment, while in 3 the palladium atom is in a distorted square planar environment, coordinated by the oxime ligand and a chelating (S^S) dppmS₂ ligand. These complexes were employed as efficient catalysts for the Suzuki–Miyaura cross‐coupling reaction of several aryl bromides with phenylboronic acid. The in vitro cytotoxicity of the compounds was also evaluated against human tumour cell lines (HT29, A549 and HeLa) using the MTT assay method. The results indicate that the dinuclear complex 2 has greater catalytic and anticancer activity in comparison with the mononuclear complexes 1 and 3 .     

An alternative way of characterising the bonding in compounds featuring main-group elements and with the potential for multiple bonding: on the dissociation of binary main-group hydrides

Herein the bonding in compounds featuring main-group elements and with the potential for multiple bonding is studied theoretically by examination of their fragmentation into two fragments that still exhibit the same structure as they had in the molecule prior to dissociation. The fragments were calculated both in their electronic ground state and in an excited electronic state, in which the number of unpaired electrons is equal to the maximal number of bonds in the compounds before dissociation. The energies of the fragmentation processes (DeltaE(frag)) can be more directly linked to the bond strengths than the dissociation energies (DeltaE(diss)), because of the absence of any secondary effects like relaxation of the electronic state or of the geometry of the fragments. These relaxation energies of the fragments (DeltaE(frag)) are also studied herein. The energies derived in this work allow for an accurate comparison of the bonding properties in main-group-element hydrides. The trends of the fragmentation and relaxation energies are discussed in detail. It will be shown that the relaxation energies allow for a classification of the bonds ("classical" sigma and pi bonds or donor-acceptor interactions), while the fragmentation energies are good quantitative measures for the total bond strength. Similar calculations are on the way to explore the bonding in systems in which the hydrogen atoms are replaced by organic groups or halogen atoms.     

Experimental and Theoretical Studies on Arene‐Bridged Metal–Metal‐Bonded Dimolybdenum Complexes

The bis(hydride) dimolybdenum complex, [Mo₂(H)₂{HC(N‐2,6‐iPr₂C₆H₃)₂}₂(thf)₂], 2 , which possesses a quadruply bonded Mo₂^II core, undergoes light‐induced (365 nm) reductive elimination of H₂ and arene coordination in benzene and toluene solutions, with formation of the Mo^I₂ complexes [Mo₂{HC(N‐2,6‐iPr₂C₆H₃)₂}₂(arene)], 3?C₆H₆ and 3?C₆H₅Me , respectively. The analogous C₆H₅OMe, p‐C₆H₄Me₂, C₆H₅F, and p‐C₆H₄F₂ derivatives have also been prepared by thermal or photochemical methods, which nevertheless employ different Mo₂ complex precursors. X‐ray crystallography and solution NMR studies demonstrate that the molecule of the arene bridges the molybdenum atoms of the Mo^I₂ core, coordinating to each in an η² fashion. In solution, the arene rotates fast on the NMR timescale around the Mo₂‐arene axis. For the substituted aromatic hydrocarbons, the NMR data are consistent with the existence of a major rotamer in which the metal atoms are coordinated to the more electron‐rich C?C bonds.     

Terms representing the reorganization of bonding within charge‐bond order matrices of reacting molecules

The usual way of obtaining charge‐bond order (CBO) matrices of molecules by summing up the MO LCAO coefficients over occupied molecular orbitals (MOs) is extended to derive terms representing the reorganization of bonding in reacting systems. The CBO matrix of a certain molecule (reactant) under influence of another one (reagent) is expressed in the form of power series with respect to intermolecular interaction. Terms of this series responsible for the internal reorganization of bonding in the reactant are also shown to be representable by sums of MO LCAO coefficients of the relevant isolated compound. As opposed to the case of a single molecule, the new sums embrace all MOs of the reactant and their pairs. This result is conditioned by the fact that the actual occupation numbers of MOs differ from either two or zero in the bimolecular system because of the intermolecular charge transfer, and bond orders arise between pairs of MOs in addition. Partial increments to the final reorganization of bonding related to individual MOs and to their pairs are then studied separately. These increments may be classified on the basis of criteria applied to MOs they originate from. In particular, symmetric and antisymmetric increments are distinguished with respect to any symmetry operation of the isolated reactant lost under influence of an approaching reagent. Increments of the same symmetry are subsequently collected into separate groups representable by specific graphical schemes. Consequently, the final pattern of charge and bond order redistribution in the reactant under influence of an approaching reagent follows from superposition of a few principal schemes. The results are illustrated by consideration of specific examples, in particular of addition of electrophile to the butadiene molecule. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Suppressing one‐bond homonuclear 13C,13C scalar couplings in the J‐HMBC NMR experiment: application to 13C site‐specifically labeled oligosaccharides

Site‐specific ¹³C isotope labeling is a useful approach that allows for the measurement of homonuclear ¹³C,¹³C coupling constants. For three site‐specifically labeled oligosaccharides, it is demonstrated that using the J‐HMBC experiment for measuring heteronuclear long‐range coupling constants is problematical for the carbons adjacent to the spin label. By incorporating either a selective inversion pulse or a constant‐time element in the pulse sequence, the interference from one‐bond ¹³C,¹³C scalar couplings is suppressed, allowing the coupling constants of interest to be measured without complications. Experimental spectra are compared with spectra of a nonlabeled compound as well as with simulated spectra. The work extends the use of the J‐HMBC experiments to site‐specifically labeled molecules, thereby increasing the number of coupling constants that can be obtained from a single preparation of a molecule. Copyright © 2014 John Wiley & Sons, Ltd.     

Intriguing E…E' bonding in [Nap(EPh)(E'Ph)]•+ (E,E'=O,S, Se,Te)

The nature of E···E' bonding in homonuclear (E = E') and heteronuclear (E ≠ E') [Nap(EPh)(E'Ph)]^?+ (E, E' = O, S, Se, and Te) radical cations has been investigated by quantum chemistry and the topological analysis of electron density. The calculation results show that the E···E' bonding in the title compounds occurs through attractive interactions; O···E' (E'=O, S, Se, and Te) bonding are electrostatic interactions, and the others have a partial covalent character. The nature of E···E' bonding varies periodically, with the changes of E' atoms going from the lighter to the heavier (O, S, Se, and Te). Both in homonuclear and heteronuclear [Nap(EPh)(E'Ph)]^?+, for the same E atom, a heavier E' atom means stronger E···E/E' bonding, a more covalent character of the E···E' bond, and more spin electron density transfers from benzene rings to the E···E' group. © 2016 Wiley Periodicals, Inc.