Nature of halogen-centered intermolecular interactions in crystal growth and design: Fluorine-centered interactions in dimers in crystalline hexafluoropropylene as a prototype

The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design prompted this study, which includes a mini review of recent advances in the field. Particular emphasis is placed on providing compelling theoretical evidence of the formation of these interactions between sites of positive electrostatic potential, as well as between sites of negative electrostatic potential, localized on the electrostatic surfaces of the bound fluorine atoms in a prototypical system, hexafluoropropylene (C₃F₆), upon its interaction with another same molecule to form (C₃F₆)₂ dimers. The existence of σ- and π-hole interactions is shown for the stable dimers. Even so, weakly bound interactions locally responsible in holding the molecular fragments together cannot and should not be overlooked since they are partly responsible for determining the overall geometry of the crystal. The results of combined quantum theory of atoms in molecules, molecular electrostatic surface potential, and reduced density gradient noncovalent interaction analyses showed that these latter interactions do indeed play a role in the stability and growth of crystalline C₃F₆ itself and the (C₃F₆)₂ dimers. A symmetry adapted perturbation theory energy decomposition analysis leads to the conclusion that a great majority of the (C₃F₆)₂ dimers examined are the consequence of dispersion (and electrostatics), with nonnegligible contribution from polarization, which together competes with an exchange repulsion component to determine the equilibrium geometries. In a few structures of the (C₃F₆)₂ dimer, the fluorine is found to serve as a six-center five-bond donor/acceptor, as found for carbon in other systems (Malischewski and Seppelt, Angew. Chem. Int. Ed. 2017, 56, 368). © 2019 Wiley Periodicals, Inc.     

Theoretical study of the strong intramolecular hydrogen bond and metal-ligand interactions in group 10 (Ni, Pd, Pt) bis(dimethylglyoximato) complexes

The structural and bonding characteristics of the bis(dimethylglyoximato) complexes of group 10 transition metals ([M(dmg)₂], where M = Ni, Pd and Pt) were investigated by means of quantum chemical computations. The equilibrium geometries, energetic and bonding properties were computed using the B3P86 exchange-correlation density functional in conjunction with a 6-311+(+)G^∗∗ basis set. The computations revealed that the strong O⁻?H-O hydrogen bond exists only in the presence of the metal cations. The free (dmg)₂²⁻ ligand has significantly different geometry in which the O⁻?H-O interaction is replaced by N?O-H bonds. The characteristics of the metal-ligand interactions were determined by natural bond orbital analysis.     

Triangular Halogen Bond and Hydrogen Bond Supramolecular Complex Consisting of Carbon Tetrabromide,Halide, and Solvent Molecule： A Theoretical and Spectroscopic Study

The theoretical calculation and spectroscopic experiments indicate a kind of triangular three bonding supramolecular complexes CBr4…X^-…-H-C, which consist of carbon tetrabromide, halide, and protic solvent molecule （referring to dichloromethane, chloroform and acetonitrile）, can be formed in solution. The strength of halogen and hydrogen bonds in the triangular complexes using halide as common acceptor obeys the order of iodide〉bromide〉chloride. The halogen and hydrogen bonds work weak-cooperatively. Charge transfer bands of halogen bonding complexes between CBra and halide are observed in UV-Vis absorption spectroscopy in three solvents, and then the stoichiometry of 1：1, formation constants K and molar extinction coefficients ε of the halogen bonding complexes are obtained by Benesi-Hildebrand method. The K and ε show a dependence on the solvent dielectric constant and, on the whole, obey an order of iodide〉bromide〉chloride in the same solvents. Furthermore, the C-H vibrational frequencies of solvent molecules vary obviously with the addition of halide, which indicates the C-H…X- interaction. The experimental data indicate that the halogen bond and hydrogen bond coexist by sharing a common halide acceptor as predicted by calculation.     

Theoretical study of the calcium dication hydrates

Ab initio SCF calculations have been carried out for calcium dication surrounded by 1–4 or 6 water molecules using several basis sets. The structure of the hydrated ions is examined and the hydration energy estimated. The changes in the structure of water within the complex are qualitatively explained in terms of charge transfer and coulombic interactions among the atoms. Finally, the influence of electron correlations is discussed.     

沥青质杂环模型分子间相互作用及溶剂化效应的理论研究

重质油中沥青质组分易发生聚沉形成团簇,严重影响重质油的加工和利用效率,但目前对于沥青质聚沉的研究较少,其机理尚不明确。本文采用理论计算对沥青质杂环模型分子间相互作用和溶剂化效应进行研究,以此为重质油沥青质聚沉现象的研究及聚沉抑制剂的研发提供一定的数据和理论支持。(1)在M062X/6-31G(d)水平上,计算得到了11种由沥青质杂环分子片段组成的二元体系的全优化稳定构型,讨论分析了构型的几何结构、NBO电荷、Mulliken重叠布居、相互作用能和分子轨道能,得到了最稳定的两种构型。(2)在B3LYP/6-31G(d)水平上,运用SMD模型对沥青质大分子在13种溶剂中进行溶剂化效应的建模和理论计算,通过对静电溶剂化自由能(ΔGelec)、非静电溶剂化自由能(ΔGnonelec)、总溶剂化自由能(ΔGsolv)的分析可知,沥青质溶解性大小的关键在于溶剂对它的远程静电作用的大小。     

Theoretical study of intermolecular proton transfer reaction in isolated 5-hydroxyisoxazole–water complexes

A systematic investigation in isolated 5-hydroxyisoxazole–water complexes (5-HIO · (H₂O)_nn = 1–3) is performed at the DFT level, employing B3LYP/6-31G(d, p) basis set. Single-point energy calculations are also performed at the MP2 level using B3LYP/6-31G(d, p) optimized geometries and the 6-311++G(d, p) basis set. The computational results show that the keto tautomer K₂ is the most stable isomer in the gas phase, and the tautomer K₁ to be the next most stable tautomer. Hydrogen bonding between HIO and the water molecule(s) will dramatically lower the barrier by a concerted multiple proton transfer mechanism. The proton transfer process of 3WE_cis ↔ 3WK₁ and 2WE_trans ↔ 2WK₂ is found to be more efficient in two tautomerization, and the barrier heights are 7.03 and 14.15 kcal/mol at B3LYP/6-31G(d, p) level, respectively. However, the proton transfer reaction between E_cis and K₁ cannot happen without solvent-assisted.     

Theoretical study on intermolecular interaction of epoxyethane dimer

Ab initio calculations at Hartree–Fock and fourth‐order Mø ller–Plesset (MP4) correlation correction levels with 6‐31G* basis set have been performed on the epoxyethane dimer. Dimer binding energies have been corrected for the basis set superposition error (BSSE) and the zero‐point energy. The greatest corrected dimer binding energy is −8.36 kJ/mol at the MP4/6‐31G*//HF/6‐31G* level. The natural bond orbital analysis has been performed to trace the origin of the weak interactions that stabilize dimer. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 94–98, 2000     

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: ab initio fragment molecular orbital study

The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP-cAMP with each base pair, DNA duplex with each amino acid residue, and each base pair with each residue. In addition, base-base interactions were analyzed including hydrogen bonding and stacking of DNA. In the interaction between DNA and CRP-cAMP, there was a significant charge transfer (CT) from the DNA to CRP, and this CT interaction played an important role as well as the electrostatic interactions. It is necessary to apply a quantum mechanical approach beyond the "classical" force-field approach to describe the sequence specificity. In the DNA intramolecular interaction, the dispersion interactions dominated the stabilization of the base-pair stacking interactions. Strong, attractive 1,2-stacking interactions and weak, repulsive 1,3-stacking interactions were observed. Comparison of the intramolecular interactions of free and complexed DNA revealed that the base-pairing interactions were stronger, and the stacking interactions were weaker, in the complexed structure. Therefore, the DNA duplex stability appears to change due to both the electrostatic and the CT interactions that take place under conditions of DNA-CRP binding.     

有机半导体Terazulene单晶双极电荷传输性质的理论研究

利用密度泛函方法计算Terazulene单晶的重组能和分子间电子耦合,结合Marcus电荷转移速率理论以及随机行走技术模拟电荷迁移率,分别研究Terazulene单晶中电子与空穴的角分辨各向异性迁移率及平均迁移率.结果表明,Terazulene单晶具有均衡的电子与空穴传输性质,并分析了具体原因.由于p型有机半导体Naphthodithiophene(NDT)的分子共轭长度与Terazulene接近,通过比较Terazulene单晶和NDT单晶中电荷传输的差异,从理论上理解分子结构对有机半导体材料电荷传输性能的影响.     

A systematic study of ligand intermolecular interactions in crystals of copper(II) complexes of bidentate guanidino derivatives

The synthesis and X-ray structures of four neutral copper(II) complexes and one cationic complex incorporating bidentate alkyl N-(4-oxo-5,5-diphenyl-4,5-dihydro-1H-imidazol-2-yl)imidocarbamate ligands are reported. The neutral complexes, which possess potential doublet (DA) hydrogen bonding motifs, form supramolecular structures based on synthons involving hydrogen bonding or phenyl embraces. The formation of sheets within the crystal through combination of these synthons, and the occurrence of guest molecules trapped in cavities between the sheets, are described. The cationic complex forms an extended hydrogen-bonded structure that incorporates nitrate ions. The structures of the five complexes are compared with others reported previously for complexes of related ligands.     

Theoretical study of quinolines-I(2) intermolecular interaction and implications on dye-sensitized solar cell performance

The monomer and intermolecular charge-transfer complexes of 13 different quinoline derivatives with diiodine were studied using ab initio molecular orbital (MO) and density functional theory (DFT) methods. Calculations revealed that the sigma* orbital of iodine interacts with the nitrogen lone pair in the quinoline ring. The open-circuit photovoltage (V(oc)) values of an Ru(II) complex dye-sensitized nanocrystalline TiO(2) solar cell with an I(-)/I(3) (-) redox electrolyte in acetonitrile using quinoline additives were compared to the computational calculations on the intermolecular interaction between quinolines and I(2). The optimized geometries, frequency analyses, Mulliken population analyses, natural bond orbital (NBO) analyses, and interaction energies indicate that the V(oc) value of the solar cell is higher when quinoline complexes more favorably interact with I(2). Therefore, the interaction between the quinoline additives and iodine redox electrolyte is an important factor for controlling dye-sensitized solar cell performance.     

Steric conditions for donor–acceptor interactions in C60 complexes with planar organic donors

Charge transfer complexes of fullerene C₆₀ with planar donors of tetrathiafulvalene, dithiadiazafulvalene and pyranylidene family were investigated by IR- and UV-VIS-NIR spectroscopy. The analysis of IR and X-ray data shows that the charge transfer complexes of fullerene with the planar donors are involved in polarization interactions of van der Waals type. Charge transfer is very weak in these compounds and is hindered by unfavourable steric factors. As a result, the CT rate does not correlate with the ionization potential of the donor; the charge transfer absorption bands are very weak too.     

Theoretical and experimental studies of the structure and intermolecular interactions in 2-biphenylmethanole

The crystalline structure of 2-biphenylmethanol has been investigated by the radiographic method at room temperature, and its IR transmission spectra were measured in the 400–4000 cm^?1 range. Structural-dynamic models of free molecules of 2-biphenylmethanol, biphenyl and methanol, hydrogen-bonded complexes of 2-biphenylmethanol with methanol and a tetramer of methanol molecules have been built by the density functional method (B3LYP/6-31G*). The structure, the energy, mechanical and electro-optical parameters, the frequency and intensity of normal vibrations in IR spectra of each of the mentioned molecular systems were calculated. The crystalline structure of 2-biphenylmethanol, its features determined by the hydrogen bond formation in the crystal has been found, its structure-forming role and energy were assessed, and IR spectra interpreted on the basis of single crystal X-ray diffraction data, the analysis of measured IR spectra, and results of molecular modeling.     

Structural tuning of low band gap intermolecular push/pull side-chain polymers for organic photovoltaic applications

A series of novel low band gap donor-acceptor (D-A) type organic co-polymers (BT-F-TPA,BT-CZ-TPA and BT-SI-TPA) consisting of electron-deficient acceptor blocks both in main chains (M1) and at the pendant (M2) were polymerized with different electron rich donor (M3-M5) blocks,i.e.,9,9-dihexyl-9H-fluorene,N-alkyl-2,7-carbazole,and 2,6-dithinosilole,respectively,via Suzuki method.These polymers exhibited relatively low band gaps (1.65-1.88 eV) and broad absorption ranges (680-740 nm).Bulk heterojunction (BHJ) solar cells incorporating these polymers as electron donors,blended with [6,6]-phenyl-C61-butyric acid methyl ester (PC61BM) or [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) as electron-acceptors in different weight ratios were fabricated and tested under 100 mW/cm2 of AM 1.5 with white-light illumination.The photovoltaic device containing donor BT-SI-TPA and acceptor PC71BM in 1:2 weight ratio showed the best power conversion efficiency (PCE) value of 1.88％,with open circuit voltage (Voc) =0.75 V,short circuit current density (Jsc) =7.60 mA/cm2,and fill factor (FF) =33.0％.     

Characterization of two types of intermolecular interactions on halogen monoxide monohydrates

Monohydrates of halogen monoxides ClO·H₂O and BrO·H₂O have been studied by means of DFT (B3LYP) and ab initio (MP2) correlated calculations with aug‐cc‐pVnZ basis sets ranging from triple‐ up to quintuple‐ζ. These complexes might be formed in the troposphere and stratosphere and participate in chemical reactions involved in ozone depletion. Two stable structures are found that differ in the intermolecular interaction which takes place, namely: conventional XO…HOH hydrogen bond and OX…OH₂ halogen bond. We demonstrate that both types of interactions participate in the formation of these complexes yet all the computational methods tested predict a slightly greater stability for the latter OX…O link. Both intermolecular interactions are characterized upon analyzing electron density distribution, charge transfer effects, and electron localization domains. These analyses reveal the central role played by electron redistribution. Because of this, the greater spatial extent of the electron density in Cl or Br as compared to H could be the main cause to yield a slightly greater stability for the O? X…O halogen bond with respect to the O…H? O hydrogen bond. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Concerning virial-based estimations of strength of bonding intermolecular interactions in molecular crystals and supramolecular complexes

It is shown that the electronic virial-based correlation should be used to estimate bonding contributions to the rigidity of molecular vibrations in crystals.     

Palladium site ordering and the occurrence of superconductivity in Bi2Pd3Se2−xSx

The crystallographic and electronic structures of compounds related to parkerite (Bi₂Ni₃S₂) are investigated with respect to the recently reported occurrence (Bi₂Pd₃Se₂) and absence (Bi₂Pd₃S₂) of superconductivity. Similarities and differences of the crystal structures are discussed within the series of solid solutions Bi₂Pd₃S_2−xSe_x from powder and single crystal diffraction data. From crystal structure refinements, the question of different structures and settings of parkerite is discussed. Similar and different 2D and 3D partial Pd-Ch (Ch=S, Se) structures are related to half antiperovskite ordering schemes. To investigate the relation of low dimensional structures and the occurrence of superconductivity, electronic structures are analyzed by scalar-relativistic DFT calculations, including site projected DOS, ECOV and Fermi surfaces.     

Theoretical study on the interactions of halogen‐bonds and pnicogen‐bonds in phosphine derivatives with Br2, BrCl,and BrF

The MP2 ab initio quantum chemistry methods were utilized to study the halogen‐bond and pnicogen‐bond system formed between PH₂X (X = Br, CH₃, OH, CN, NO₂, CF₃) and BrY (Y = Br, Cl, F). Calculated results show that all substituent can form halogen‐bond complexes while part substituent can form pnicogen‐bond complexes. Traditional, chlorine‐shared and ion‐pair halogen‐bonds complexes have been found with the different substituent X and Y. The halogen‐bonds are stronger than the related pnicogen‐bonds. For halogen‐bonds, strongly electronegative substituents which are connected to the Lewis acid can strengthen the bonds and significantly influenced the structures and properties of the compounds. In contrast, the substituents which connected to the Lewis bases can produce opposite effects. The interaction energies of halogen‐bonds are 2.56 to 32.06 kcal·mol^?1; The strongest halogen‐bond was found in the complex of PH₂OH???BrF. The interaction energies of pnicogen‐bonds are in the range 1.20 to 2.28 kcal·mol^?1; the strongest pnicogen‐bond was found in PH₂Br???Br₂ complex. The charge transfer of lp(P) ? σ*(Br? Y), lp(F) ? σ*(Br? P), and lp(Br) ? σ*(X? P) play important roles in the formation of the halogen‐bonds and pnicogen‐bonds, which lead to polarization of the monomers. The polarization caused by the halogen‐bond is more obvious than that by the pnicogen‐bond, resulting in that some halogen‐bonds having little covalent character. The symmetry adapted perturbation theory (SAPT) energy decomposition analysis showes that the halogen‐bond and pnicogen‐bond interactions are predominantly electrostatic and dispersion, respectively.     

卤键在化学传感和分子识别中的应用

卤键是一种新的分子间非共价作用力,它存在于卤素原子(路易斯酸)和具有孤电子对的原子或π-电子体系(路易斯碱)之间,在超分子化学、材料科学、生物识别和药物设计等领域已经显示出独特的优势。本文主要从卤键的特征和在化学传感和分子识别中的应用以及发展前景等几方面进行了介绍,期望引起人们对卤键的更多关注。     

环芳有机分子中分子轨道的通过空间相互作用

本文给出了描述环芳类化合物分子轨道通过空间相互作用的模型, 进一步采用离散变分X~α自洽场方法研究它们的电子结构, 并计算三类环芳有机分子轨道的通过空间相互作用, 计算结果表明环芳类有机分子的通过空间相互作用的大小随分子中苯环, 乙炔、乙烯间距离的增大而衰减, 本文的结果与定性分析是一致的。