Self-assembly of vesicles from the stacking of a dipodal F?H-N hydrogen bonded arylamide foldamer

In this paper, we report the synthesis and self-assembling behavior of an F?H-N hydrogen bonding-induced arylamide-based dipodal foldamer. SEM, AFM, TEM, and XRD studies reveal that this preorganized oligomer stacks to form vesicles in methanol-chloroform (10-70%) binary solvents due to the strong stacking interaction of the folded segments and the supramolecular polymeric feature of the dipodal molecule in the stacked state. In contrast, a simple folded molecule can give rise to vesicles only when the chloroform content is 45-55%.     

Highly selective adenine recognition by a macrocyclic host molecule employing multiple hydrogen bonding and π-π stacking interactions

A new macrocyclic host, which contains a 2,6-bis(oxazol-2-yl)pyridine unit and a 2,7-dialkoxynaphthalene unit tethered by the appropriate length of alkyl side chains is prepared. This host undergoes highly selective complex formation with an adenine nucleobase, accompanied by a fluorescence response in CHCl₃ by a combination of multiple hydrogen bonding and π-π stacking interactions.     

Theoretical study of hydrogen bonded clusters of water and cyanic acid: Hydrogen bonding in terms of the molecular structure

Ab initio and density functional calculations were used to analyze the interaction between a molecule of cyanic acid (HOCN) and up to 4 molecules of water at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. The cooperative effect (CE) is increased with the increasing size of the studied clusters. Red shifts of the H–O stretching frequency for complexes involving HOCN as an H-donor were predicted. The strength of the hydrogen bonds in terms of molecular structures could be deduced from a comparison of HOCN–H₂O with HCNO–H₂O, HONC–H₂O and HNCO–H₂O HB clusters. The atom in molecules (AIM) method was used to analyze the cooperative effects on topological parameters.     

Crystal and molecular structure, hydrogen bonding and electrostatic interactions of bis(pyridine betaine) perchlorate

Bis(pyridine betaine) perchlorate, (PB)₂H·ClO₄, has been characterized by X-ray diffraction, B3LYP and MP2 calculations, FTIR, Raman and NMR spectroscopy and DSC. The complex crystallizes in space group C2/c. A pair of PB molecules is bridged by a short symmetric O·H·O hydrogen bond of the length 2.456(5) Å. Three conformers (I-III), with respect to the N⁺?O distances, of (PB)₂H cation have been analyzed at the DFT and MP2 level of theory and compared with the C(1)?O distances in the (PhCH₂COO)₂H anion. The calculated O?O distances for the analyzed cations are slightly shorter than that in the crystal. The type of hydrogen bond depends on the cation conformation and the method of calculations. The FTIR spectra of (PB)₂H·ClO₄ and (PBd₅)₂H·ClO₄ (bis(pyridine-d₅ betaine) perchlorate) show a broad and intense absorption in the 1500-400 cm⁻¹ range, which is similar to the type A acid salts of carboxylic acids and other 2:1 betaine complexes with mineral acids. In the Raman and second FTIR-derivative spectra (d²) the broad absorption is absent. A linear unit-slope correlation between d² negative band and Raman band is found. This confirms that derivative spectrometry can be used to estimate frequencies of the narrow bands covered by the broad absorption due to the O·H·O stretching and bending vibrations.     

A hydrogen bond between a calixarene (as host and its guest: Crystal and molecular structure of thep-t-butyldihomooxacalix[4]arene : Triethylamine (1 : 2) complex/clathrate

The structure of thep-t-butyldihomooxacalix[4]arene triethylamine (1 : 2 complex has been determined by X-ray crystallography. Crystals are monoclinic, space groupCc,a = 22.821(3),b = 15.257(3),c = 16.365(2) Å, = 97.44(1)°,V = 5650(1) ų,Z = 4,D _calc = 1.03 g cm^–3. One triethylamine (Et₃N) molecule has one of its ethyl groups pointing inside the cavity of a calixarene molecule; its nitrogen atom is directed exo to this calixarene molecule and is involved in a hydrogen bond with one of the hydroxy groups of a neighbouring calixarene molecule. This scheme leads to columns of alternating host and guest molecules. The other Et₃N molecule is in the interhost space. This feature allows us to define the title compound as a complex/clathrate hybrid.Supplementary data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82144 (8 pages).     

Time‐dependent density functional theory study on the electronic excited‐state geometric structure,infrared spectra,and hydrogen bonding of a doubly hydrogen‐bonded complex

The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S₁ state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm^?1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S₁ state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

核酸中碱基的氢键作用机理及电子特征理论研究

采用耦合簇量子化学方法 CCSD/aug-cc-pVDZ研究了嘧啶与嘌呤之间的相互作用,利用基函数叠加误差法(BSSE)消除相互作用能误差,并进行了几何结构优化;采用Gaussian 03程序包中的NBO程序分析了二阶稳定化能及自然键轨道.与此同时,应用约化密度函数(RDG)填色等值面图对体系进行了图形化分析,分析了氢键相互作用所在的空间位置和相对强度,以及氢键相互作用的性质,以进一步了解二者的相互作用.结果表明,嘧啶-嘌呤体系的相互作用属于闭合壳层静电相互作用.电子密度跃迁矩阵分析结果表明,激发区域主要集中在N原子和O原子处,涉及的空间广度很大,第一激发态主要涉及前线分子轨道,属于σ→π*或n→π*类型跃迁.     

Temperature‐dependent changes in the hydrogen bonded hard segment network and microphase morphology in a model polyurethane: Experimental and simulation studies

Hydrogen bonding between hard segments has a critical effect on the morphology and properties of polyurethanes. Influence of temperature on hydrogen bonded urethane network and melting behavior of a model semicrystalline segmented polyurethane was investigated by experiments and simulations. Polyurethane was synthesized by the stoichiometric reaction between p‐phenylene diisocyanate and poly(tetramethylene oxide) (PTMO) with a molecular weight of 1000 g/mol. Simulations were carried out using dissipative particle dynamics (DPD) and molecular dynamics (MD) approaches. Experimental melting behavior obtained by various techniques was compared with simulations. DPD simulations showed a room temperature microphase morphology consisting of a three‐dimensional hydrogen‐bonded urethane hard segment network in a continuous and amorphous PTMO matrix. The first‐order melting transitions of crystalline urethane hard segments observed during the continuous isobaric heating in DPD and MD simulations (340–360 K) were in reasonably good agreement with those observed experimentally, such as AFM (320–340 K), WAXS (330–360 K), and FTIR (320–350 K) measurements. Quantitative verification of the melting of urethane hard segments was demonstrated by sharp discontinuities in energy versus temperature plots obtained by MD simulations due to substantial decrease in the number of hydrogen bonds above 340 K. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 182–192     

Crystal structure of a non-stoichiometric channel inclusion complex of 1-benzyl-6-phenylpiperidin-2-one-5-carboxylic acid with acetonitrile

C₁₉H₁₉NO₃·x CH₃CN (x=0.3),M _r=643.35, hexagonal, space groupP6₁ (No. 169),a=23.027(5),c=5.775(1) Å,V=2652(1) ų,Z=6. The structure was solved by direct methods and refined toR=0.077 for 1562 observed MoK reflections. The title heterocyclic carboxylic acid was established as thetrans isomer, with the phenyl and carboxyl substituents occupying pseudo-equatorial and equatorial positions, respectively, of the piperidin-2-one ring in a half-chair conformation. Acid host molecules related by the 6₁ screw operation are linked by intermolecular O–H...O (cyclic amide) hydrogen bonds to generate an open channel bounded by coaxial intertwined helices each having a pitch of 5c. Within each channel of free diameterca. 6.0 Å the acetonitrile molecules partially occupy highly disordered sites which do not lie on thec axis. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82067 (13 pages).     

Synthesis and Crystal Structure of[Ni(C5H2N2O4)(2, 2'-bipy)(H2O)2]·2H2O

The crystal structure of [Ni(C5H2N2O4)(2, 2?-bipy)(H2O)2]·2H2O 1 has been determined by X-ray diffraction. Crystal data: triclinic system, space group P ī with a = 7.9424(3), b = 9.9417(3), c = 12.1867(3) (A。）, α = 84.771(1), β = 77.375(2), γ = 68.993(2)°, C15H18N4O8Ni, Mr = 440.7, V = 876.16(5) (A。）3, Z = 2, Dc = 1.672 g/cm3, F(000) = 456, ((MoK() = 1.162 mm-1, the final R = 0.0464 and wR = 0.1055 for 3026 observed reflections with I > 2((I). In the title compound, the nickel ion is coordinated by a nitrogen atom and an oxygen atom from the orotate ligand, two nitrogen atoms from 2, 2'-bipy and two oxygen atoms from the coordinated water molecules in a distorted octahedral geometry. The presence of intermolecular hydrogen bonding and (-( stacking interaction of aromatic rings from 2, 2'-bipy results in a 3D structure.     

基于5-氯烟酸的锌(Ⅱ)和镉(Ⅱ)配合物的合成、晶体结构及荧光性质(英文)

通过水热方法,以5-氯烟酸(5-ClnicH)和2,2′-联咪唑(2,2′-biimidazole)分别与Zn(NO3)2·6H2O和Cd(NO3)2·4H2O反应,合成了2个配合物[Zn(5-Clnic)2]n(1)和[Cd(5-Clnic)2(H2biim)2](2),并对其结构和荧光性质进行了研究。结构分析结果表明配合物1和2分别属于单斜晶系,C2c空间群和三斜晶系,P1空间群。配合物1具有二维层状结构,而且这些层通过Cl…Cl卤键作用进一步形成了三维超分子框架。2为单核镉配合物,通过分子间N-H…O、C-H…N和C-H…Cl氢键作用,单核的分子被进一步连接成了三维超分子结构。配合物1和2在室温下能分别发出很强的紫色和绿色荧光。     

Telomere structure and stability: covalency in hydrogen bonds, not resonance assistance, causes cooperativity in guanine quartets

We show that the cooperative reinforcement between hydrogen bonds in guanine quartets is not caused by resonance-assisted hydrogen bonding (RAHB). This follows from extensive computational analyses of guanine quartets (G(4)) and xanthine quartets (X(4)) based on dispersion-corrected density functional theory (DFT-D). Our investigations cover the situation of quartets in the gas phase, in aqueous solution as well as in telomere-like stacks. A new mechanism for cooperativity between hydrogen bonds in guanine quartets emerges from our quantitative Kohn-Sham molecular orbital (MO) and corresponding energy decomposition analyses (EDA). Our analyses reveal that the intriguing cooperativity originates from the charge separation that goes with donor-acceptor orbital interactions in the σ-electron system, and not from the strengthening caused by resonance in the π-electron system. The cooperativity mechanism proposed here is argued to apply, beyond the present model systems, also to other hydrogen bonds that show cooperativity effects.     

Hydrogen versus fluorine: effects on molecular structure and intermolecular interactions in a platinum isocyanate complex

At the molecular level, the enantiomerically pure square‐planar organoplatinum complex (SP‐4‐4)‐(R)‐[2‐(1‐aminoethyl)‐5‐fluorophenyl‐κ²C¹,N][(R)‐1‐(4‐fluorophenyl)ethylamine‐κN](isocyanato‐κN)platinum(II), [Pt(C₈H₉FN)(NCO)(C₈H₁₀FN)], and its congener without fluorine substituents on the aryl rings adopt the same structure within error. The similarities between the compounds extend to the most relevant intermolecular interactions, i.e. N—H…O and N—H…N hydrogen bonds link neighbouring molecules into chains along the shortest lattice parameter in each structure. Differences between the crystal structures of the fluoro‐substituted and parent complex become obvious with respect to secondary interactions perpendicular to the classical hydrogen bonds; the fluorinated compound features short C—H…F contacts with an F…H distance of ca 2.6 Å. The fluorine substitution is also reflected in reduced backbonding from the metal cation to the isocyanate ligand.     

Crystal structure of the 1 : 1 : 6 complex between 18-crown-6, hydroquinone and water

Hydroquinone forms a 1 : 1 : 6 complex with 18-crown-6 and water. Crystals of this complex are monoclinic, space groupP2₁/a witha = 14.289(1),b = 7.972(1),c = 11.596(1) Å, = 97.72(1)°,Z = 2,D _c = 1.22 g cm^–3. The hydroquinone and crown ether molecules lie on centres of symmetry with the crown in theD _3d conformation. The water molecules act as a bridge between hydroquinone and the crown ether. The structure consists of molecules linked by a 3-dimensional network of hydrogen bonds: the hydroquinone and two water molecules lie roughly in the (001) plane; the crown ether and four water molecules form bipyramidal structures which are stacked in layers alternating with the previous planes.     

两个包含联苯三羧酸配体的铜(II)和锰(II)配合物的合成、晶体结构及磁性质

采用水热方法,用联苯三羧酸配体(H3dppa)和4,4′-联吡啶(4,4′-bipy)分别与CuCl_2·2H_2O和MnCl_2·4H_2O反应,合成了一个具有零维双核铜结构的配合物[Cu_2(Hdppa)_2(4,4′-bipy)(H_2O)_4]·4,4′-bipy·6H_2O(1)和一个基于双螺旋链单元的三维配位聚合物{[Mn_3(μ_5-dppa)_2(4,4′-bipy)(H_2O)_2]·4H_2O}_n(2),并对其结构和磁性质进行了研究。结构分析结果表明2个配合物分别属于三斜和单斜晶系,P1和C2/c空间群。配合物1具有零维双核铜结构,而且这些双核铜单元通过O-H…O/N氢键作用进一步形成了三维超分子框架。而配合物2中存在一个双螺旋锰链单元,这些锰链单元又通过配体进一步连接成了三维结构。研究表明,配合物2中相邻锰离子间存在反铁磁相互作用。     

Transition metal impurities in fluorides: Role of electronic structure of fluorine on spectroscopic properties

This work examines the relation between optical properties of a MF₆^q− complex (M = transition-metal cation) and the chemical bonding paying especial attention to the role played by the electronic structure of fluorine. A main goal of the present study is to understand why if the effective Racah parameters, B and C, as well as the cubic splitting parameter, 10Dq, all depend on the covalency nevertheless the latter one is much more sensitive to a hydrostatic pressure than the former ones. The analysis carried out in this work, together with the results of ab initio calculations on CrF₆³⁻ embedded in the cubic elpasolite K₂NaScF₆, demonstrates that, although the 2s-2p separation for fluorine is 23 eV, 10Dq does not come mainly from the dominant 3d(Cr)-2p(F) covalency but from the tiny admixture of deep 2s(F) levels of fluorine in the antibonding e_g(∼3z² − r², x² − y²) orbital. By contrast, it is pointed out that the reduction of Racah parameters essentially reflects the global covalency in the bonding. The way of measuring the 2p(F) and 2s(F) admixtures into the mainly 3d(Cr) level through Electron Paramagnetic Resonance data for MF₆^q− complexes with unpaired σ electrons in the ground state is also explained in some detail. At the same time the reasons avoiding its measurement from optical spectra are pointed out as well. The present results stress that the microscopic origin of an optical parameter like 10Dq can certainly be very subtle.     

The effect of hydrogen bonding on oligoleucine structure in water: A molecular dynamics simulation study

Molecular dynamics simulations were conducted in order to improve our understanding of the forces that determine polyleucine chains conformations and govern polyleucine self-assembly in aqueous solutions. Simulations of 10 repeat unit oligoleucine in aqueous solution were performed using the optimized potential for liquid simulations (OPLS) - all atom force field using the canonical ensemble for a minimum of 1.3 ns. These simulations provided information on conformations, chain collapse and intermolecular aggregation. Simulations indicate that single isotactic oligoleucine chains in dilute solution assume tightly packed, regular hairpin conformations while atactic oligoleucine assumes a much less regular and less compact structure. The regular, compact collapsed isotactic chain exhibited a greater degree of intramolecular hydrogen bonding and an increased level of hydrophobic t-butyl functional group aggregation compared to the atactic chain. This occurs at the expense of reduced leucine-water hydrogen bonding.