分子内氢键促进的大环合成:动力学和热力学控制途径

氢键诱导的线性芳酰胺寡聚体骨架可以采取折叠、螺旋、直线或"之"字型构象.这一结构预组织特征可以被应用于促进大环的合成.在芳酰胺骨架的两端引入适当反应基团,骨架的预组装构象可以诱导它们形成不同的空间取向和距离.当成环反应涉及到不可逆共价键、碳-金属键或配位键的形成时,前体的结构预组织构象可以促进目标大环形成的产率.当成环反应涉及亚胺及腙等可逆共价键时,在反应达到热力学平衡后,可以高产率或定量地形成大环.     

由氢键引导的、经强制可控折叠形成的含孔折叠分子结构

受蛋白折叠现象的启发,发展出了一类基于芳香寡聚酰胺的分子折叠体系。研究发现苯环单元带有邻位烷氧基的芳酰胺寡聚体,可经由高度稳定的分子内3中心氢键,使原本可自由转动的酰胺和芳环间的单键受到限制,导致整个分子骨架的平面及刚性化,并折叠成为向一侧弯曲的构象。不同长度的寡聚酰胺分子,在3中心氢键的引导与强制下折叠形成含有内部孔穴的弯月形或螺旋结构。进一步研究表明这些分子所含的内孔是非常稳定的。由于此类折叠分子骨架的刚性及其构象的稳定性,其内孔尺度大小可通过引入不同）间位及对位）取代的苯环单元,以调节寡聚酰胺骨架的弯曲度,从而加以精确调控。基于此策略,制备了中心孔径从9到30的弯月形或螺旋结构。稍后的研究发现,利用分子内3中心氢键的引导与强制作用,可实现具有同类芳酰胺骨架的刚性大环的一步高效合成。主要简介在芳香寡聚酰胺的强制可控折叠,及其应用于弯月形、螺旋折叠分子以及大环分子的制备方面的研究。     

芳酰胺折叠体分子内N—H…OMe氢键强度评估

为了评估分子内N—H…OMe氢键诱导的芳酰胺折叠体分子内氢键的稳定性, 我们从相应间-苯二胺和间-苯二甲酸前体出发构筑了3个三、五和七聚体芳酰胺折叠体, 并合成了3个并入这些折叠体片段的基于十六烷二胺的酰胺聚合物. ¹H NMR, 定量芳酰胺氢-氘交换和晶体结构研究揭示, 折叠体中间区域的氢键最弱, 而处于骨架两端的氢键最为稳定. 氢-氘交换实验测定出了不同酰胺氢发生这一过程的半衰期, 最大差别约为8倍. 对并入折叠体片段的聚合物的单分子力谱(SMFS)研究揭示, 折叠体片段内不同区域分子内氢键的稳定性与单个折叠体分子内相应位置氢键的稳定性一致. 通过SMFS实验, 我们还测定出了不同氢键的绝对力值. 结果显示, 并入到聚合物中的短的三聚体折叠体具有最强的分子内氢键, 而五聚体和七聚体折叠体的部分分子内氢键较弱, 其力值出现在较低位置.     

利用三中心氢键限制芳酰胺构象的核磁共振氢谱分析

设计并合成了9个可形成三中心氢键和6个可形成二中心氢键的N-芳基芳酰胺模型化合物, 基于它们在氯仿和二甲基亚砜(DMSO)中的一维核磁共振波谱, 系统地分析了羰基对βH和γH的去屏蔽效应. 将Δ(δ_βH)和Δ(δ_γH)的值结合在一起, 分析了三中心氢键对芳酰胺分子的构象限制效果, 发现N-(2-氟苯基)-2-氟苯甲酰胺、 N-(2-甲氧基苯基)-2-氟苯甲酰胺和N-(2-氟苯基)-2-甲氧基苯甲酰胺这3个N-芳基芳酰胺在酰胺基团的左右两侧都能展现出很好的构象控制效果, 因此认为这3种结构单元在构建折叠体方面具有更大的潜力. 此外, 本文还发现, 当NH与第二个氢键受体形成氢键时, 其和第一个氢键受体之间的氢键就被削弱了, 即在芳酰胺形成三中心氢键时, 2个氢键受体争相与NH形成氢键并取得了某种平衡.     

芳酰胺类大环一步高效合成及其成环机理研究进展

总结了最近发现的新型芳酰胺及芳酰肼大环一步合成反应,着重探讨了由分子内三中心氢键所引导的高效一步成环反应机理.这类反应是由未成环寡聚物前体的折叠构象所构筑,不仅高效,而且反应机理新颖,提供了传统成环反应难以得到的几类刚性大环的合成方法.这些大环化合物表现出对客体识别的高度专一性,并能形成具有高通量性的跨膜孔道.     

两个非全氢键介质的芳酰肼七聚体对n-辛基-alpha-L-吡喃糖苷的络合作用

本文报道了两个芳酰肼七聚体的合成,它们分别由两个氢键介质的折叠片段组成.与其全氢键介质的类似物相比,这两个七聚体的骨架因中间的芳环减少了一个和两个分子内氢键而流动性增加.^1H NMR,园二色谱及荧光研究表明,这两个寡聚体能够在氯仿中中等程度地络合n-辛基-α-L-吡喃糖苷.     

非天然相互作用对均聚多肽链螺旋形成动力学过程的影响的计算机模拟研究

以螺旋结构的形成过程为研究对象,基于粗粒化的格子模型和动态蒙特卡罗模拟方法,初步探讨了非天然氢键相互作用对均聚多肽链螺旋折叠动力学过程的影响.研究发现,非天然氢键的引入虽然延缓了其热力学转变的发生,但也从整体上降低了折叠动力学过程的能垒,在某一特定温度之下,反而可以提高折叠速率.对其折叠路径分布的分析表明,非天然氢键可以减少慢速折叠路径的发生,而后者是导致折叠时间增加的主要因素.另一方面,比较特定温度下多肽链链构象及螺旋片断随时间的演化进程,发现非天然氢键在一定程度上影响了天然氢键的形成以及天然态构象的稳定存在,同时也加快了其部分解折叠过程.这说明,非天然相互作用的存在有利于蛋白质构象的快速动态调整,从而行使其相应的生物功能.     

β发卡多肽Trpzip4折叠的副本交换分子动力学模拟

采用副本交换分子动力学对β发卡Trpzip4重折叠进行研究,结果表明,构象空间存在较大能垒时,副本交换分子动力学(REMD)表现出比分子动力学(MD)更优的抽样效率.288 K下,Trpzip4势能、骨架均方根偏差、溶剂可及表面积(SASA)在REMD中呈逐渐降低趋势.采样得到两种特定形态的低势能构象:β发卡和螺旋-卷曲.β发卡中,第3组氢键Asp46容易与Thr49形成氢键;转角Thr49的羟基(OH)倾向于与Asp46的羧基(COO-)或主链上的C=O形成氢键,强化了Asp46与Thr49的相互作用,导致转角形成折回弯度;与Thr49相比,Thr51的羟基倾向与水分子作用,甲基朝内,因此与Asp46的侧链作用微小.螺旋-卷曲中,吲哚环-甲基为主要疏水形式.Trpzip4在折叠成β发卡过程中,转角氢键影响整个β发卡构象的形成.转角氢键具有距离优势和强侧链相互作用,最先形成.     

基于分子间卤键的超分子平面大环自组装

本工作报道了含卤键供体和受体片段的三种芳酰胺分子(化合物1~3)的设计和合成, 并对固相中卤键的不同作用模式进行了探索和分析. 化合物1的晶体数据显示, 由于没有分子内氢键, 组成分子的三个芳环相互扭转一定角度, 并且在分子间交替排列的N···I和O···I卤键的控制下, 组装成了一条线型的超分子组装体. 由于酰胺羰基和两个紧邻的氟原子之间的排斥作用, 化合物2未能形成分子内三中心氢键. 在此基础上, 将三氟碘代苯作为卤键供体片段引入到化合物3中, 并且在折叠体骨架中嵌入了嘧啶单元. 化合物3的晶体数据显示, 基于多组有效的分子内三中心氢键和分子间较强的卤键作用, 双分子间形成了[1+1]的超分子大环. 另外, 由于嘧啶环的引入, 使得该超分子大环接近共平面.     

C—H···O氢键驱动的1,2,3-三氮唑折叠体:评估分子间C—H···X~-(X=Cl,Br,I)和C—H···N氢键的稳定性

1,2,3-三氮唑芳香寡聚体可以通过分子内三中心C—H···O氢键诱导形成折叠或螺旋二级结构.通过~1H NMR实验研究这类人工二级结构在氯仿和二氯甲烷中进一步形成分子间C—H···Cl~-和C—H···N氢键的倾向性,发现分子内的两类C—H···O氢键可以通过进一步形成C—H···Cl~-氢键而被弱化.在过量Cl~-存在时,三氮唑N-1侧的六元环C—H···O氢键被显著破坏,由此形成分子间C—H···Cl~-氢键,从而诱导骨架形成另一类更加扩展的折叠构象.过量的Br~-和I~-也可以形成类似的分子间氢键.对其中一个八聚体研究揭示,1,2,3-三氮唑螺旋体的内侧2,3-位N原子还可以与三炔和二炔衍生物的炔基C—H形成分子间弱的C—H···N氢键,三氮唑折叠结构通过诱导N原子形成环形定位促进这一分子间弱氢键产生协同效应.     

Structural studies of C-amidated amino acids and peptides: crystal structures of Z-Gly-Phe-NH2, Tyr-Lys-NH2, and Asp-Phe-NH2

As part of the series investigating the structural features of C-terminal amidated amino acids and peptides, three crystal structures of Z-Gly-Phe-NH2, Tyr-Lys-NH2, and Asp-Phe-NH2 were analyzed by the X-ray diffraction method, and their molecular conformations and intermolecular interactions were investigated. Although the respective dipeptides exhibited an energetically allowable torsion angle concerning each backbone or side chain, the observed extended (Z-Gly-Phe-NH2, Asp-Phe-NH2) and folded (Tyr-Lys-NH2) conformations were considerably different from those of the corresponding unamidated peptides, due to the conformational flexibility of the respective dipeptides. The comparison between the crystal packings of the amidated and unamidated dipeptides indicated that the C-terminal amides tend to associate with the same neighboring group through hydrogen bonds, in which both the amide NH and O=C groups participate, while the unamidated peptides prefer a linear molecular connection, where both or either of the two carboxyl oxygens participate in the hydrogen bond formation. The difference in hydrogen bonding ability between the C-terminal amide and carboxyl groups has been considered to be based on the structural data of the related peptides analyzed so far.     

Dependence of amide vibrations on hydrogen bonding

The effect of hydrogen bonding on the amide group vibrational spectra has traditionally been rationalized by invoking a resonance model where hydrogen bonding impacts the amide functional group by stabilizing its [(-)O-C=NH (+)] structure over the [O=C-NH] structure. However, Triggs and Valentini's UV-Raman study of solvation and hydrogen bonding effects on epsilon-caprolactum, N, N-dimethylacetamide (DMA), and N-methylacetamide (NMA) ( Triggs, N. E.; Valentini, J. J. J. Phys. Chem. 1992, 96, 6922-6931) casts doubt on the validity of this model by demonstrating that, contrary to the resonance model prediction, carbonyl hydrogen bonding does not impact the AmII' frequency of DMA. In this study, we utilize density functional theory (DFT) calculations to examine the impact of hydrogen bonding on the C=O and N-H functional groups of NMA, which is typically used as a simple model of the peptide bond. Our calculations indicate that, as expected, the hydrogen bonding frequency dependence of the AmI vibration predominantly derives from the C=O group, whereas the hydrogen bonding frequency dependence of the AmII vibration primarily derives from N-H hydrogen bonding. In contrast, the hydrogen bonding dependence of the conformation-sensitive AmIII band derives equally from both C=O and N-H groups and thus, is equally responsive to hydrogen bonding at the C=O or N-H site. Our work shows that a clear understanding of the normal mode composition of the amide vibrations is crucial for an accurate interpretation of the hydrogen bonding dependence of amide vibrational frequencies.     

Investigating the effect of hydrogen bonding environments in amide cleavage reactions at zinc(II) complexes with intramolecular amide oxygen co-ordination

Amide oxygen co-ordination to a zinc(II) ion around a hydrogen bonding microenvironment is a common structural/functional feature of metalloproteases. We report two strategies to position hydrogen bonding groups in the proximity of a zinc(II)-bound amide oxygen, and we investigate their effect on the stability of the amide group. Polydentate tripodal ligands (6-R1-2-pyridylmethyl)-R2 (R1= NHCOtBu, R2= N(CH2-py-6-X)2 X = H L1, X = NH2, H L2, X = NH2 L3) form [(L)Zn]2+ cations (L =L1, 1; L2, 2; L3, 3) with intramolecular amide oxygen co-ordination (1-3), and intramolecular N-H...O=C(amide) hydrogen bonding (2, 3) rigidly fixed by the ligand framework. 1-3 undergo cleavage of the tert-butyl amide upon addition of Me4NOH.5H2O (1 equiv.) in methanol at 50(1) degrees C. Under these conditions the half-life, t(1/2), of the amide bond is 0.4 h for 1, 9 h for 2 and 320 h for 3. Mononuclear zinc(II) complexes of (6-NHCOtBu-2-pyridylmethyl)-R2(R2= N(CH2CH2)2S) L4 and chelating N2 ligands without hydrogen bonding groups (1,10-phenanthroline L5, 2-(aminomethyl)pyridine L6) as control compounds, and with an amino hydrogen bonding group (6-amino-2-(aminomethyl)pyridine L7) have been synthesised. Amide cleavage is in this case faster at the zinc(II) complex with the amino hydrogen bonding group. Thus, hydrogen bonding environments can both accelerate and slow down amide bond cleavage reactions at zinc(II) sites. Importantly, the magnitude of the effect exerted by the hydrogen bonding environments was found to be significant; 800-fold rate difference. This result highlights the importance of hydrogen bonding environments around metal centres in amide cleavage reactions, which may be relevant to the chemistry of natural metalloproteases and applicable to the design of more efficient artificial protein cleaving agents.     

Conformational structure of tyrosine, tyrosyl-glycine, and tyrosyl-glycyl-glycine by double resonance spectroscopy

We investigated the variation in conformation for the amino acid tyrosine (Y), alone and in the small peptides tyrosine-glycine (YG) and tyrosine-glycine-glycine (YGG), in the gas phase by using UV-UV and IR-UV double resonance spectroscopy and density functional theory calculations. For tyrosine we found seven different conformations, for YG we found four different conformations, and for YGG we found three different conformations. As the peptides get larger, we observe fewer stable conformers, despite the increasing complexity and number of degrees of freedom. We find structural trends similar to those in phenylalanine-glycine-glycine (FGG) and tryptophan-glycine-glycine (WGG); however, the effect of dispersive forces in FGG for stabilizing a folded structure is replaced by that of hydrogen bonding in YGG.     

Crystal engineering of hydroxy group hydrogen bonding: design and synthesis of new diol lattice inclusion hosts

The diols 7-11 have been synthesized, and their X-ray crystal structures determined, to learn how to influence and control lattice hydroxy group hydrogen bonding using crystal engineering ideas. To obtain new lattice inclusion hosts precise structural rules can be defined which enable the necessary supramolecular interactions to be duplicated. In this manner the helical tubuland 10 and ellipsoidal clathrate 11 hosts were obtained for the first time and their chloroform inclusion compounds characterized. New synthetic routes were utilized to obtain the bicyclo[3.3.2]decane and 9-thiatricyclo[4.3.1.1(3,8)]undecane frameworks present in these compounds. The solid-state conformations of bicyclo[3.3.2]decane derivatives 9 and 10 are compared with prior predictions and studies made on this uncommon ring system.     

基于非生物折叠体的分子识别

利用分子自组装的方法控制大分子量的线性有机分子的构象是物理有机化学一个富于挑战性的研究课题. 近年来, 化学家已经成功利用不同的分子内非共价键作用力如氢键和疏溶剂作用等诱导线性分子的折叠乃至螺旋构象的产生. 综述了近年来这种新的非生物二级结构形式在分子识别研究中的应用.     

Vesicles and organogels from foldamers: a solvent-modulated self-assembling process

Nonamphiphilic, hydrogen-bonded hydrazide foldamers appended with four or six long flexible chains were revealed to spontaneously assemble to form vesicles in methanol and organogels in aliphatic hydrocarbons. SEM, AFM, TEM, DLS, and fluorescence microscopy were all used to identify the structures of the vesicles. It was proposed that intermolecular pi stacking of the folded frameworks and hydrogen bonding of the amide units in the appended chains induced the molecules to produce cylindrical aggregates. In polar methanol, these aggregates packed together to generate one-layered vesicles owing to hydrophobically induced entanglement of the peripheral chains, while in nonpolar hydrocarbons, the peripheral chains entwined across stacked cylinders to form three-dimensional networks and thus immobilize the liquid molecules.     

Alcohol‐Mediated Resistance‐Switching Behavior in Metal–Organic Framework‐Based Electronic Devices

Metal‐organic frameworks (MOFs) have drawn increasing attentions as promising candidates for functional devices. Herein, we present MOF films in constructing memory devices with alcohol mediated resistance switching property, where the resistance state is controlled by applying alcohol vapors to achieve multilevel information storage. The ordered packing mode and the hydrogen bonding system of the guest molecules adsorbed in MOF crystals are shown to be the reason for the alcohol mediated electrical switching. This chemically mediated memory device can be a candidate in achieving environment‐responsive devices and exhibits potential applications in wearable information storage systems.     

Molecular Tectonics: A Node-and-Linker Building Block Approach to a Family of Hydrogen-Bonded Frameworks

While numerous hydrogen-bonded organic frameworks (HOFs) have been reported, typically these cannot be prepared predictably or in a modular fashion. In this work, we report a family of nine diamondoid crystalline porous frameworks assembled via hydrogen bonding between poly-amidinium and poly-carboxylate tectons. The frameworks are prepared at room temperature in either water or water/alcohol mixtures. Importantly, both the cationic and anionic components can be varied and additional functionality can be incorporated into the frameworks, which show good stability including to prolonged heating in DMSO or water.     

Synthesis of nano-scale shape-persistent macrocycles via hydrogen bonding-promoted formation of amide and hydrazone bonds

This paper describes the synthesis of two series of rigid macrocycles from hydrogen bonding-induced folded aryl amide and hydrazone oligomers that bear two amines or one amine and one aldehyde. The diamines reacted with diacyl chloride to produce amide macrocycles, whereas the latter underwent self-coupling reactions to afford imine macrocycles. DFT calculations revealed that the new macrocycles possess rigid planar conformations and their cavity diameters were estimated to be 1.86 nm–2.75 nm.