Differences in structure, energy, and spectrum between neutral, protonated, and deprotonated phenol dimers: comparison of various density functionals with ab initio theory

We have carried out extensive calculations for neutral, cationic protonated, anionic deprotonated phenol dimers. The structures and energetics of this system are determined by the delicate competition between H-bonding, H-π interaction and π-π interaction. Thus, the structures, binding energies and frequencies of the dimers are studied by using a variety of functionals of density functional theory (DFT) and M?ller-Plesset second order perturbation theory (MP2) with medium and extended basis sets. The binding energies are compared with those of highly reliable coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)) at the complete basis set (CBS) limit. The neutral phenol dimer is unique in the sense that its experimental rotational constants have been measured. The geometry of the neutral phenol dimer is governed by the hydrogen bond formed by two hydroxyl groups and the H-π interaction between two aromatic rings, while the structure of the protonated/deprotonated phenol dimers is additionally governed by the electrostatic and induction effects due to the short strong hydrogen bond (SSHB) and the charges populated in the aromatic rings in the ionic systems. Our salient finding is the substantial differences in structure between neutral, protonated, and deprotonated phenol dimers. This is because the neutral dimer involves in both H(π)···O and H(π)···π interactions, the protonated dimer involves in H(π)···π interactions, and the deprotonated dimer involves in a strong H(π)···O interaction. It is important to compare the reliability of diverse computational approaches employed in quantum chemistry on the basis of the calculational results of this system. MP2 calculations using a small cc-pVDZ basis set give reasonable structures, but those using extended basis sets predict wrong π-stacked structures due to the overestimation of the dispersion energies of the π-π interactions. A few new DFT functionals with the empirical dispersion give reliable results consistent with the CCSD(T)/CBS results. The binding energies of the neutral, cationic protonated, and anionic deprotonated phenol dimers are estimated to be more than 28.5, 118.2, and 118.3 kJ mol(-1), respectively. The energy components of the intermolecular interactions for the neutral, protonated and deprotonated dimers are analyzed.     

Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components

The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and the aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) monomers containing the biological backbone (either the protein backbone or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that the protein backbone strengthens, while the deoxyribose sugar either strengthens or weakens, the interaction calculated using truncated models, the reasons for these effects were unknown. The present work explains these observations by dissecting the interaction energy of the extended complexes into individual backbone···π and π···π components. Our calculations reveal that the total interaction energy of the extended complex can be predicted as a sum of the backbone···π and π···π components, which indicates that the biological backbone does not significantly affect the ring system through π-polarization. Instead, we find that the backbone can indirectly affect the magnitude of the π···π contribution by changing the relative ring orientations in extended dimers compared with truncated dimers. Furthermore, the strengths of the individual backbone···π contributions are determined to be significant (up to 18 kJ mol(-1)). Therefore, the origin of the energetic change upon model extension is found to result from a balance between an additional (attractive) backbone···π component and differences in the strength of the π···π interaction. In addition, to understand the effects of the biological backbone on the stacking interactions at DNA-protein interfaces in nature, we analyzed the stacking interactions found in select DNA-protein crystal structures, and verified that an additive approach can be used to examine the strength of these interactions in biological complexes. Interestingly, although the presence of attractive backbone···π contacts is qualitatively confirmed using the quantum theory of atoms in molecules (QTAIM), QTAIM electron density analysis is unable to quantitatively predict the additive relationship of these interactions. Most importantly, this work reveals that both the backbone···π and π···π components must be carefully considered to accurately determine the overall stability of DNA-protein assemblies.     

双齿甜菜碱衍生物大环及双环镉(Ⅱ)配位化合物的合成与晶体结构

利用甜菜碱衍生物1,5-二(4-羧基吡啶基)-N-甲基二乙胺(L)合成了两种镉(Ⅱ)的配位化合物[Cd2Cl4(H2O)2L2].2H2O和[Cd2(SCN)4(μ-H2O)L2]。用X-射线单晶衍射仪测定了配合物的单晶结构,并对它们进行了元素分析、红外光谱、1H NMR、热重等表征。结构分析表明,前者具有三十六元大环框架,而后者为双环结构。由于缺乏分子之间的强烈相互作用,弱相互作用决定了这两种化合物在晶格中的堆积模式:前者由相邻分子间的π-π和C-H…π相互作用而堆积形成二维砖墙的结构;后者由配位的SCN-阴离子通过S…S弱相互作用联接成一维链状结构。     

2]Catenanes and inclusion complexes derived from self-assembled rectangular Pd(II) and Pt(II) metallocycles

New inclusion complexes and [2]catenanes were self-assembled from a fluorescent diazapyrenium based ligand, a Pd(II) or Pt(II) complex, and cyclic or acyclic electron rich aromatic guests in aqueous and organic media. The molecular rectangles display a π-deficient cavity suitable to incorporate π-donor aromatic systems. The inclusion complexes between the metallocycles and phenylenic () and naphthalenic () derivatives were studied by NMR, UV-vis and fluorescence spectroscopy. The crystal structure of () ? ·6PF(6) confirmed the insertion of the guest into the cavity of the metallocycle. Following the same self-assembly strategy, the use of polyethers , as π-donors resulted in the self-assembly of the [2]catenanes (,)·6PF(6). Single-crystal X-ray analysis of ()·6PF(6) revealed the [2]catenane structure being stabilized by π-stacking and [C-HO] interactions.     

A novel thiophene-fused polycyclic aromatic with a tetracene core: synthesis, characterization, optical and electrochemical properties

FeCl?-mediated oxidative cyclization was successfully used to construct an extended thiophene-pendant pyrene skeleton and synthesize a novel thiophene-fused polycyclic aromatic (THTP-C) with a tetracene core. The identity of the compound was confirmed by 1H-NMR, 13C-NMR, MS, and elemental analysis. Meanwhile, a single crystal of THTP-C was obtained and analyzed by X-ray single-crystal diffraction. THTP-C has a "saddle" shaped π-conjugated 1-D supramolecular structure, and favors highly ordered self-assembly by π-π interactions as evidenced by its concentration-dependent 1H-NMR spectra in solution. The optical properties of THTP-C were investigated by ultraviolet-visible (UV-Vis) and photoluminescence (PL) spectroscopy and its electrochemical properties were investigated by cyclic voltammetry (CV). The relatively large band gap (2.86 eV), low E(HOMO) level (-5.64 eV) and intermolecular π-π interactions imply that THTP-C has a high stability against photo-degradation and oxidation, and may be a promising candidate for stable hole-transporting materials.     

一维链状锰配位聚合物的合成、晶体结构与性能研究

本文合成了1个新的一维链状锰的配位聚合物{[Mn(HL)(phen)(H2O)2].1.5H2O}n,(H3L=2-羟基-5-羧基苯磺酸),并且进行了元素分析、红外、热重、荧光、紫外、粉末XRD及单晶X射线衍射等表征及研究。标题化合物属于单斜晶系,C2/c空间群,a=0.840 57(17)nm,b=1.757 5(4)nm,c=2.873 4(6)nm,β=92.54(3)°,V=4.240 7(16)nm 3,Z=4,R=0.027 0。每个Mn(Ⅱ)离子与邻菲咯啉配体的2个N原子、磺酸配体中的1个磺酸基O原子和羧基O原子以及2个配位水分子配位,展示出扭曲的八面体几何构型。2个相邻的Mn(Ⅱ)八面体单元通过1个磺酸基氧原子和1个羧基氧原子连接形成一维链状结构,该一维链进一步通过氢键作用构筑成三维网状结构。     

瓜环与含羟基功能基二胺包结配合物的晶体结构及相互作用的研究

合成并表征了含羟基功能基的二胺1,3-二(2-氨基苯氧基)-2-丙醇(客体). 利用X射线衍射方法研究了客体与八元瓜环Q[8]所形成包结配合物的晶体结构. 结果表明主客体间形成了1∶2的包结配合物, 两个客体分子分别从瓜环的两个端口进入瓜环内腔, 在腔内两个客体分子中的苯环间存在着π-π相互作用. 利用1H NMR技术及紫外-可见吸收光谱对主客体间的相互作用进行考察, 所得结果与晶体结构吻合.     

Conformational control of benzyl-o-carboranylbenzene derivatives and molecular encapsulation of acetone in the dynamically formed space of 1,3,5-tris(2-benzyl-o-carboran-1-yl)benzene

A 1,3,5-substituted benzene platform has been widely used in the fields of supramolecular chemistry and molecular recognition. Here, we show that 1,3,5-tris(2-benzyl-o-carboran-1-yl)benzene 6 exhibits solvent-dependent conformation in the crystalline state. Recrystallization from dichloromethane-n-pentane gave the anti conformation 6-anti, while recrystallization from methanol-acetone gave the syn conformation 6-syn, in which the three benzyl-o-carboranyl moieties are located to one side of the central benzene ring. Interestingly, one acetone molecule is captured in the π-rich space of 6-syn and two complexes facing each other encapsulate two acetone molecules in a π-rich container formed by the eight benzene rings. The inclusion involves several weak interactions, that is, T-shaped C-H···π interactions, and C-H···O and C-H···π interactions. Two C-H···O interactions involving benzylic C-H hydrogens activated by the electron-withdrawing character of the o-carborane cage and the oxygen atom of the acetone seem to be the most important. DFT calculations indicate that the binding energy for entrapment of acetone is 6.6 kcal/mol. Inclusion of acetone is achieved through not only multiple C-H···O interactions but also a number of C-H···π interactions. The third benzyl-o-carborane moiety is fixed in the syn conformation by intramolecular and intermolecular C-H···π interactions.     

Unprecedented π···π interaction between an aromatic ring and a pseudo-aromatic ring formed through intramolecular H-bonding in a bidentate Schiff base ligand: crystal structure and DFT calculations

A combination of a single crystal X-ray diffraction study and density functional theory calculations has been applied to a bidentate Schiff base compound to elucidate different cooperative non-covalent interactions involved in the stabilization of the keto form over the enol one in the solid state. The single crystal X-ray structure reveals a remarkable supramolecular assembly of the keto form through a cyclic hydrogen bonded dimeric motif. The most interesting feature in the supramolecular assembly is the formation of a 'dimer of dimer' motif by π···π, CH···π and N···O/O···O interactions in which the π···π interaction involving the aromatic phenyl ring and the intramolecularly hydrogen bonded pseudo-aromatic ring of the keto form lying just above or below the phenyl ring of the other dimer seems to be unprecedented. The optimized geometry of the hydrogen bonded dimeric motif of the keto form of the organic molecule has been obtained by DFT calculations and agrees very well with that found within the crystalline state. The X-ray crystallographic geometry of the 'dimer of dimer' has also been computed, which shows that in the HOMO, the π electrons are localized in the phenyl rings away from each other, while in the LUMO, there is a strong π-π interaction between the phenyl ring of one dimer with the pseudo-aromatic ring of another dimer with an energy estimated to be 7.95 kJ mol(-1). Therefore, on HOMO → LUMO excitation there is localization of π electrons in the central part of the complex moiety which plays a stabilizing role of the dimer of dimer motif in the solid state.     

Communication: Competition between π···π interaction and halogen bond in solution: a combined 13C NMR and density functional theory study

Competition between π···π interaction and halogen bond in solution has been investigated by using carbon nuclear magnetic resonance spectroscopy ((13)C NMR) combined with density functional theory calculation. Both experimental and theoretical results clearly show that there are no C-Cl···π or C-Br···π halogen bonds and only the π···π interactions exist in the binary liquid mixtures of C(6)D(6) with C(6)F(5)Cl and C(6)F(5)Br, respectively. The case is totally different for the binary liquid mixtures of C(6)D(6) with C(6)F(5)I in which the C-I···π halogen bonds not the π···π interactions are present. The important role of entropy in the competition between π···π interaction and halogen bond in solution was also discussed.     

Chiral porphyrin dimer with a macrocyclic cavity for intercalation of aromatic guests

Chiral diporphyrin receptor 1, which has a macrocyclic cavity to sandwich aromatic guest molecules via double π-π stacking interactions, enabled the naked-eye detection of an aromatic explosive as well as chiral discrimination in NMR.     

Configurational studies of complexes of various tea catechins and caffeine in crystal state

Crystals of the complexes of (+)-catechin (CA) of non-galloylated catechin and (-)-catechin-3-O-gallate (Cg) of galloylated catechin with caffeine were prepared, and their stereochemical structures and intermolecular interactions were determined by X-ray crystallographic analysis. CA formed a 1 : 1 complex with caffeine by intermolecular hydrogen bonds, whereas Cg formed a 1 : 2 complex with caffeine, which was formed by face-to-face and offset π-π interactions and intermolecular hydrogen bonds. A solution of two kinds of non-galloylated catechin, CA and (-)-epicatechin (EC), and caffeine (molar ratio 1 : 1 : 2) in water afforded a 1 : 1 : 2 complex, the crystal structure of which had two layers, one layer in which CA and caffeine formed alternate lines and an other layer in which EC and caffeine formed alternate lines. The 1 : 1 : 2 complex was formed by offset π-π and CH-π interactions and intermolecular hydrogen bonds.     

Experimental support for the role of dispersion forces in aromatic interactions

Herein a core scaffold of 1-phenylnaphthalenes and 1,8-diphenylnaphthalenes with different substituents on the phenyl rings was used to study substituent effects on parallel-displaced aromatic π???π interactions. The energetics of the interaction was evaluated in gas phase based on the standard molar enthalpies of formation, at T=298.15?K, for the compounds studied; these values were derived from the combination of the results obtained by combustion calorimetry and Knudsen/Quartz crystal effusion. A homodesmotic gas-phase reaction scheme was used to quantify and compare the intramolecular interaction enthalpies in various substituted 1,8-diphenylnaphthalenes. The application of this methodology allowed a direct evaluation of aromatic interactions, and showed that substituent effects on the interaction enthalpy cannot be rationalized solely on classical electrostatic grounds, because no correlation with the σ(meta) or σ(para) Hammett constants was observed. Moreover, the results obtained indicate that aromatic π???π interactions are significantly enhanced by substitution, in a way that correlates with the ability of the interacting aryl rings to establish dispersive interactions. A combined experimental and computational approach for calculation of the true aromatic π???π interaction energies in these systems, free of secondary effects, was employed, and corroborates the rationale derived from the experimental results. These findings clearly emphasize the role of dispersion and dilute the importance of electrostatic forces on this type of interactions.     

Effects of extending the computational model on DNA-protein T-shaped interactions: the case of adenine-histidine dimers

The MP2/6-31G*(0.25) π-π or π(+)-π T-shaped (edge-to-face) interactions between neutral or protonated histidine and adenine were considered using computational models of varying size to determine the effects of the protein and DNA backbones on the preferred dimer structure and binding strength. The overall consequences of the backbones are reasonably subtle for the neutral adenine-histidine T-shaped dimers. Furthermore, the minor changes in the binding strengths of these dimers upon model extension arise from additional (attractive) backbone-π (bb-π) contacts and changes in the preferred π-π orientations, which is verified by the quantum theory of atoms in molecules (QTAIM). Since the binding strength of the extended dimer equals the sum of the individual backbone-π and π-π contributions, the π-π component is not appreciably affected by polarization of the ring upon inclusion of the biological backbone. In contrast, the larger effect of the backbone on the protonated histidine dimers cannot simply be predicted as the sum of changes in the π-π and bb-π components regardless of the dimer type or model. This suggests, and QTAIM qualitatively supports, that the magnitude of the π(+)-π contribution changes, which is likely due to alterations in the electrostatic landscape of the monomer rings upon inclusion of the biological backbone that largely affect T-shaped dimers. These findings differ from those previously reported for (neutral) π-π stacked and (metallic) cation-π interactions, which highlights the distinct properties of each (π-π, π(+)-π, and cation-π) classification of noncovalent interaction. Furthermore, these results emphasize the importance of considering backbone-π interactions when analyzing contacts that appear in experimental crystal structures and cautions the use of truncated models when evaluating the magnitude of the π(+)-π contribution present in large biological complexes.     

Etude du Groupe Azomethine par RMN du Carbone-13. Cétimines et Dibenzo[b,f] diazocines[1,4]

Carbon-13 chemical shifts (substituents effects, variations of shielding and deshielding related to the magnitude of n.π or π.π interactions) not only confirm the non-planar conformation of ketimines of the benzalaniline type, but provide torsional angles of the aromatic rings. Carbon-13 chemical shifts of dibenzo[b,f] diazocines[1,4] confirm the tub-like conformations and the presence of n.π and π.π interactions.     

Crystal structure of pyrimidinophane containing two uracil moieties with a <Emphasis Type="Italic">cis</Emphasis>-orientation of the carbonyl groups

The molecular and crystal structure of an isomer of crystalline pyrimidinophane containing two uracil moieties, as well as the intermolecular π-π interactions in crystal, were studied by X-ray diffraction analysis.     

两个含1-(1-萘甲基)咪唑的化合物：晶体结构和弱相互作用

1-(1-萘甲基)咪唑(L)和盐酸反应生成1-(1-萘甲基)咪唑盐酸盐L·HCl (1),在这个化合物中通过π-π堆积相互作用和氢键形成了二维超分子层。1-(1-萘甲基)咪唑(L)和AgPF₆反应生成单核银配合物[L]₂AgPF₆ (2),在这个化合物中通过2个类型的π-π堆积相互作用形成了二维超分子层。测定了L,1和2的荧光发射光谱。     

Zinc paddlewheel dimers containing a strong π···π stacking supramolecular synthon: designed single-crystal to single-crystal phase changes and gas/solid guest exchange

The ligand 4-(1,8-naphthalimido)benzoate, L(C4)(-), containing a linear link between the strong π···π stacking 1,8-naphthalimide supramolecular synthon and the carboxylate donor group, reacts with Zn(O(2)CCH(3))(2)(H(2)O)(2) in the presence of dimethylsulfoxide (DMSO) to yield [Zn(2)(L(C4))(4)(DMSO)(2)]·2(CH(2)Cl(2)). This compound contains the "paddlewheel" Zn(2)(O(2)CR)(4) secondary building unit (SBU) that organizes the rigid phenylene and naphthalimide rings of the carboxylate ligands in a square arrangement. The supramolecular architecture is dominated by π···π stacking interactions between naphthalimide rings of one dimer with four adjacent dimers, essentially at right angles, forming an open three-dimensional network structure. Two symmetry equivalent networks of this type interpenetrate generating overall a densely packed three-dimensional, 2-fold interpenetrated architecture in which the CH(2)Cl(2) solvate molecules are trapped in isolated pockets. Upon cooling, single crystals of [Zn(2)(L(C4))(4)(DMSO)(2)]·2(CH(2)Cl(2)) undergo two distinct crystallographic phase transitions, as characterized by X-ray diffraction at different temperatures, without loss of crystallinity. These two new phases have supramolecular structures very similar to the room temperature structure, but changes in the ordering of the CH(2)Cl(2) solvate cause shifting of the naphthalimide rings and a lowering of the symmetry. Crystals of [Zn(2)(L(C4))(4)(DMSO)(2)]·2(CH(2)Cl(2)) undergo a single-crystal to single-crystal gas/solid guest exchange upon exposure to atmospheric moisture, or faster if placed under vacuum or heated under dry gas to 100 °C, followed by atmospheric moisture, to yield [Zn(2)(L(C4))(4)(DMSO)(2)]·3.9(H(2)O). The molecular and supramolecular structures of this new compound are very similar to the dichloromethane adduct, with now the water molecules encapsulated into the framework. The remarkable feature of both the phase changes and exchange of solvates is that this robust network is not porous; local distortions (ring slippage and tilting changes) of the π···π stacking interactions of the naphthalimide rings that organize these structures allow these changes to take place without the loss of crystallinity. The complexes [Zn(2)(L(C4))(4)(DMSO)(2)]·2(CH(2)Cl(2)) and [Zn(2)(L(C4))(4)(DMSO)(2)]·3.9(H(2)O) show green emission in the solid state.     

Direct measurements of electric fields in weak OH···π hydrogen bonds

Hydrogen bonds and aromatic interactions are of widespread importance in chemistry, biology, and materials science. Electrostatics play a fundamental role in these interactions, but the magnitude of the electric fields that support them has not been quantified experimentally. Phenol forms a weak hydrogen bond complex with the π-cloud of benzene, and we used this as a model system to study the role of electric fields in weak OH···π hydrogen bonds. The effects of complex formation on the vibrational frequency of the phenol OH or OD stretches were measured in a series of benzene-based aromatic solvents. Large shifts are observed and these can be converted into electric fields via the measured vibrational Stark effect. A comparison of the measured fields with quantum chemical calculations demonstrates that calculations performed in the gas phase are surprisingly effective at capturing the electrostatics observed in solution. The results provide quantitative measurements of the magnitude of electric fields and electrostatic binding energies in these interactions and suggest that electrostatics dominate them. The combination of vibrational Stark effect (VSE) measurements of electric fields and high-level quantum chemistry calculations is a general strategy for quantifying and characterizing the origins of intermolecular interactions.     

Unique photochromism of two solid-emissive boron difluoride-based diarylethenes with isomeric structures

Two solid-emissive boron difluoride-based diarylethenes with isomeric structures are synthesized and the boron-difluoride chromophores are one part of the photoisomerization units in both diarylethenes. These two diarylethenes show similar fluorescent properties in the solid state as in dilute chloroform solutions because intermolecular planar π-π interactions are significantly alleviated as verified by their X-ray single crystal structures. However, only one of these two diarylethenes exhibits typical reversible absorption and fluorescence changes upon UV or visible light irradiation, and their diverse response to light irradiation is investigated by X-ray single crystal analysis and also DFT calculation. The investigation presented here provides valuable insight into the designing and development of diarylethene-based fluorescent switches in the solid state.