Oxyanion-encapsulated caged supramolecular frameworks of a tris(urea) receptor: evidence of hydroxide- and fluoride-ion-induced fixation of atmospheric CO2 as a trapped CO3(2-) anion

A tris(2-aminoethyl)amine-based tris(urea) receptor, L, with electron-withdrawing m-nitrophenyl terminals has been established as a potential system that can efficiently capture and fix atmospheric CO(2) as air-stable crystals of a CO(3)(2-)-encapsulated molecular capsule (complex 1), triggered by the presence of n-tetrabutylammonium hydroxide/fluoride in a dimethyl sulfoxide solution of L. Additionally, L in the presence of excess HSO(4)(-) has been found to encapsulate a divalent sulfate anion (SO(4)(2-)) within a dimeric capsular assembly of the receptor (complex 2) via hydrogen-bonding-activated proton transfer between the free and bound HSO(4)(-) anions. Crystallographic results show proof of oxyanion encapsulation within the centrosymmetric cage of L via multiple N-H···O hydrogen bonds to the six urea functions of two inversion-symmetric molecules. The solution-state binding and encapsulation of oxyanions by N-H···O hydrogen bonding has also been confirmed by quantitative (1)H NMR titration experiments, 2D NOESY NMR experiments, and Fourier transform IR analyses of the isolated crystals of the complexes that show huge spectral changes relative to the free receptor.     

The gold-ammonia bonding patterns of neutral and charged complexes Au m 0+/-1-(NH3)n. I. Bonding and charge alternation

The gold-ammonia bonding patterns of the complexes which are formed between the ammonia clusters (NH(3))(1< or =n< or =3) and gold clusters of different sizes that range from one gold atom to the tri-, tetra-, and 20-nanogold clusters are governed by two basic and fundamentally different ingredients: the anchoring Au-N bond and the nonconventional N-H...Au hydrogen bond. The latter resembles, by all features, a conventional hydrogen bond and is formed between a typical conventional proton donor N-H group and the gold cluster that behaves as a nonconventional proton acceptor. We provide strong computational evidence that the gold-ammonia bonding patterns exhibit distinct characteristics as the Z charge state of the gold cluster varies within Z=0,+/-1. The analysis of these bonding patterns and their effects on the N-H...N H-bonded ammonia clusters are the subject of this paper.     

Structural studies of ammonia and metallic lithium-ammonia solutions

The technique of hydrogen/deuterium isotopic substitution has been used to extract detailed information concerning the solvent structure in pure ammonia and metallic lithium-ammonia solutions. In pure ammonia we find evidence for approximately 2.0 hydrogen bonds around each central nitrogen atom, with an average N-H distance of 2.4 A. On addition of alkali metal, we observe directly significant disruption of this hydrogen bonding. At 8 mol % metal there remains only around 0.7 hydrogen bond per nitrogen atom. This value decreases to 0.0 for the saturated solution of 21 mol % metal, as all ammonia molecules have then become incorporated into the tetrahedral first solvation spheres of the lithium cations. In conjunction with a classical three-dimensional computer modeling technique, we are now able to identify a well-defined second cationic solvation shell. In this secondary shell the nitrogen atoms tend to reside above the faces and edges of the primary tetrahedral shell. Furthermore, the computer-generated models reveal that on addition of alkali metal the solvent molecules form voids of approximate radius 2.5-3.0 A. Our data therefore provide new insight into the structure of the polaronic cavities and tunnels, which have been theoretically predicted for lithium-ammonia solutions.     

Theoretical investigation of in-plane hydrogen-bonded complexes of ammonia with partially substituted fluorobenzenes

Systematic investigation of in-plane hydrogen-bonded complexes of ammonia with partially substituted fluorobenzenes has revealed that fluorobenzene, difluorobenzene, and trifluorobenzene favor formation of cyclic complexes with a C-H...N-H...F-C binding motif. On the other hand, tetrafluorobenzene and pentafluorobenzene favor formation of linear C-H...N hydrogen-bonded complexes. The complete absence of exclusively linear N-H...F hydrogen-bonded complexes for the entire series indicates that C-F bond in fluorobenzenes is a reluctant hydrogen-bond acceptor. However, fluorine does hydrogen bond when cooperatively stabilized with C-H...N hydrogen bonds for the lower fluoro analogues. The propensity of fluorobenzenes to adapt to the C-H...N-H...F-C binding motif decreases with the progressive fluorination of the benzene ring and disappears completely when benzene ring is substituted with five or more fluorine atoms.     

Density functional theory study of the properties of N-H...N, non-cooperativities, and intermolecular interactions in linear trans-diazene clusters up to ten molecules

We investigate aspects of N-H...N hydrogen bonding in the linear trans-diazene clusters (n=2-10) such as the N...H and N-H lengths, n(N) --> sigma(N-H) interactions, N...H strengths, and frequencies of the N-H stretching vibrations utilizing the DFT/B3LYP theory, the natural bond orbital (NBO) method, and the theory of atoms in molecules (AIM). Our calculations indicate that the structure and energetics are qualitatively different from the conventional H-bonded systems, which usually exhibit distinct cooperative effects, as cluster size increases. First, a shortening rather than lengthening of the N-H bond is found and thus a blue rather than red shift is predicted. Second, for the title clusters, any sizable cooperative changes in the N-H and N...H lengths, n(N) --> sigma(N-H) charge transfers, N...H strengths, and frequencies of the N-H stretching vibrations for the linear H-bonded trans-diazene clusters do not exist. Because the n(N) --> sigma(N-H) interaction hardly exhibits cooperative effects, the capability of the linear trans-diazene cluster to localize electrons at the N...H bond critical point is almost independent of cluster size and thereby leads to the noncooperative changes in the N...H lengths and strengths and the N-H stretching frequencies. Third, the dispersion energy is sizable and important; more than 30% of short-range dispersion energy not being reproduced by the DFT leads to the underestimation of the interaction energies by DFT/B3LYP. The calculated nonadditive interaction energies show that, unlike the conventional H-boned systems, the trans-diazene clusters indeed exhibit very weak nonadditive interactions.     

Theory Studies on the Intermolecular Interactions of Urea Nitrate with RDX

Six fully optimized geometries of urea nitrate cation and RDX complexes have been obtained with DFT-B3LYP and MP2 methods at the 6-311++G** level. The intermolecular interaction energies have been calculated with basis set superposition error (BSSE) and zero point energy (ZPE) correction. The nature of intermolecular interaction has been revealed by the analysis of AIM and NBO. The results indicate that the greatest binding energy of urea nitrate with RDX is –82.47kJ/mol. The O–H…O and N–H…O hydrogen bonds are important intermolecular interactions of urea nitrate cation with RDX, and the origin of hydrogen bonds is the oxygen atom offering its lone-pair electrons to the σ(O-H)* or σ(O-H)* antibonding orbital. The intermolecular interactions strengthen the N–NO2 bond, leading to the reduced sensitivity of urea nitrate and RDX mixture explosive.     

Ammonium cyanate shows N-H...N hydrogen bonding, not N-H...O

The transformation of ammonium cyanate into urea, first studied over 170 years ago by W?hler and Liebig, has an important place in the history of chemistry. To understand the nature of this solid state reaction, knowledge of the crystal structure of ammonium cyanate is a prerequisite. Employing neutron powder diffraction, we demonstrate conclusively that, in the structure of ammonium cyanate, the NH(4)(+) cation forms N-H...N hydrogen bonds to four cyanate N atoms at alternate corners of a distorted cube, rather than our previously proposed alternative arrangement with N-H...O hydrogen bonds to cyanate O atoms at the other four corners.     

Thermal desorption of hydrogen from ammonia borane: unexpected role of homopolar B-H···H-B interactions

The solid-state structure of ammonia borane is held together by an intricate N-H···H-B proton-hydride bonding network. These intermolecular interactions have long been considered to mediate the release of hydrogen from this material. Here we reveal the silent but important role played by B-H···H-B interactions in the thermal decomposition of this leading hydrogen storage candidate.     

聚醚氨酯红外N—H伸缩振动谱带分析

通过快速淬火实验,直接观察到聚醚氨酯中由硬段N—H基与软段—O—形成氢键的N—H伸缩振动谱带位于约3295cm~(-1),低于与硬段本身C=O形成氢键的N—H伸缩振动谱带(约3330cm~(-1))。这两种氢键键连的N—H伸缩振动谱带的位置从聚醚氨酯-四氢呋喃溶液的红外光谱得到证实。在此基础上讨论了三种聚醚氨酯试样的红外光谱中N—H伸缩振动谱带的差异。     

Nature of urea-fluoride interaction: incipient and definitive proton transfer

1,3-bis(4-nitrophenyl)urea (1) interacts through hydrogen bonding with a variety of oxoanions in an MeCN solution to give bright yellow 1:1 complexes, whose stability decreases with the decreasing basicity of the anion (CH3COO- > C6H5COO- > H2PO4- > NO2- > HSO4- > NO3-). The [Bu4N][1.CH3COO] complex salt has been isolated as a crystalline solid and its molecular structure determined, showing the formation of a discrete adduct held together by two N-H...O hydrogen bonds of moderate strength. On the other hand, the F- ion first establishes a hydrogen-bonding interaction with 1 to give the most stable 1:1 complex, and then on addition of a second equivalent, induces urea deprotonation, due to the formation of HF2-. The orange-red deprotonated urea solution uptakes carbon dioxide from air to give the tetrabutylammonium salt of the hydrogencarbonate H-bond complex, [Bu4N][1.HCO3], whose crystal and molecular structures have been determined.     

Probing C-H...X hydrogen bonds in amide-functionalized imidazolium salts under high pressure

We have probed under high pressure the C-H hydrogen bonds formed by N,N(')-disubstituted imidazolium ions having PF(6) (-) and Br(-) counterions. High-pressure infrared spectral profiles, x-ray crystallographic analysis, and ab initio calculations allow us to make a vibrational assignment of these compounds. The appearance of a signal for the free-NH unit (or weakly bonded N-H...F unit) in the infrared spectrum of the PF(6) (-) salt indicates that conventional N-H...O and N-H...N hydrogen bonds do not fully dominate the packing. It is likely that the charge-enhanced C(2)-H...F interactions, combined with other weak hydrogen bonds, disturb the formation of N-H hydrogen bonds in the PF(6) (-) salt. This finding is consistent with the pressure-dependent results, which reveal that the C(2)-H...F interaction is enhanced upon increasing the pressure. In contrast to the PF(6) (-) salt, the imidazolium C-H bonds of the Br(-) salt have low sensitivity to high pressure. This finding suggests that the hydrogen bonding patterns are determined by the relative hydrogen bond acceptor strengths of the Br(-) and PF(6) (-) ions.     

PET suppression of acridinedione dyes by urea derivatives in water and methanol

Spectroscopic investigations involving the interaction of acridinedione dyes with urea and its derivatives in water and methanol were carried out by absorption, steady-state fluorescence, and time-resolved fluorescence measurements. The hydrogen-bonding properties of urea and derivatives in aqueous solutions are found to be distinctly different from those observed in methanol. Urea, which can serve both as a hydrogen bond donor as well as an acceptor and has a unique hydrogen-bonding feature, helps in studying urea interaction with fluorophores in aqueous solutions, micelles, and alcohol. In our studies, we have used acridinedione dyes as the probe. We report that the hydrophobic interaction of urea with dye predominates by weakening of the hydrogen-bonding interaction of the solvent and urea derivatives with increase in the hydrophobicity of urea derivatives. In methanol, the hydrogen bonding between solvent and urea derivatives predominating over the hydrophobicity of the urea derivatives is observed. The presence of alkyl group substitution in the N-H moiety with a function of increasing concentration resulting in the creation of a more favorable hydrophobic environment to the dye molecule to reside in the hydrophobic shell phase rather than in the bulk aqueous phase is illustrated. The hydrophobic interaction of dye with urea in aqueous solution predominates because of the weakening of the hydrogen bonding of the solvent and urea derivatives, and the photoinduced electron transfer (PET) process is used as a marker to identify the hydrophobic interaction illustrated in our studies.     

Synthesis and Crystal Structure of N-Benzyl-N'-(2-pyridyl)urea and Its Mononuclear Cu(II) Complex

A new ligand of N-benzyl-N'-(2-pyridyl)urea L and its self-assembly product with CuCl2, [Cu(II)LCl2]∞ 1, have been synthesized and structurally characterized by IR, 1H NMR and single-crystal X-ray diffraction analysis. In the structure of L, the urea groups adopt Z,E conformation to form dimers through intermolecular hydrogen bonds; while in complex 1, it assumes Z,Z conformation to fit for the coordination sphere of the Cu(II) ions. The coordinated units are connected through intermolecular N-H…Cl hydrogen bonds to form an extended 2D framework. Finally, a 3D structure is obtained via π-π stacking interactions between pyridyl rings.     

Aromaticity-controlled tautomerism and resonance-assisted hydrogen bonding in heterocyclic enaminone-iminoenol systems

The contribution of aromaticity and intramolecular hydrogen bonding to relative stability, for a set of (1H-azahetero-2-ylidene)-acetaldehyde and 2-azahetero-2-yl-ethanol tautomeric pairs, has been investigated by means of quantum chemical DFT and ab initio methods up to the MP4(SDTQ)/AUG-cc-pVDZ and MP2/AUG-cc-pVTZ levels of theory. It is found that the relative energy of the tautomers is governed by the change in the degree of heterocycle aromaticity upon intramolecular hydrogen transfer. An analysis of geometrical parameters of a hydrogen-bonded system reveals a clear relationship between the aromaticity of the heterocycle, the conjugation in a resonant spacer, and the strengths of the intramolecular hydrogen bonds. This allows the conclusion to be drawn that intramolecular N-H...O and O-H...N hydrogen bonds formed are found to be resonance-assisted and their strength is dependent on the pi-donating/accepting properties of the heterocycle. On the basis of the results of the calculations, a simple model describing the mechanism of resonance assistance of hydrogen bonding has been suggested.     

尿素-富马酸根-水分子为主体晶格的四乙基铵离子包合物的合成与晶体结构

合成一种新的尿素-阴离子复合主体晶格包合物,(C₂H₅)₄N⁺[C₄H₂O₄^2-]1/2·CO(NH₂)₂·H₂O,并进行了X射线晶体结构分析.晶体为单斜晶系,C₂/_c(No.15)空间群,a=1.7909(5)nm,b=1.4431(4)nm,c=1.4443(3)nm,β=126.76(2)°,V=2.9905(13)nm³,Z=4,R₁=0.0647,_wR=0.0735.包合物中,两个尿素分子通过一对N-H…O氢键以通常的“肩并肩”方式连接起来,形成一个二聚体.这些二聚体沿c轴方向依次排列,每两个相邻二聚体间生成的氢键将它们连接成一个沿(001)方向延伸的锯齿形扭带.由c滑移面相关连的富马酸阴离子以水分子为桥,由O(W)-H…O氢键连成一条宽带,沿c轴方向延伸.这些富马酸根-水分子复合氢键宽带与尿素纽带交替平行排列,由此形成了一个平行于ac面的氢键层.四乙基铵离子层填充在b=1/4和b=3/4处的主体晶格的层间空隙处,构成“三明治”式夹层结构的包合物.     

Supercritical ammonia: a molecular dynamics simulation and vibrational spectroscopic investigation

Combining infrared spectroscopy and molecular dynamics simulations, we have investigated the structural and dynamical properties of ammonia from liquid state (T = 220 and 303 K) up to the supercritical domain along the isotherm T = 423 K. Infrared spectra show that the N-H stretching and bending modes are significantly perturbed which is interpreted as a signature of the change of the local environment. In order to compare the experimental spectra with those obtained using molecular dynamics simulation, we have used a flexible four sites model which allows to take into account the anharmonicity in all the vibration modes particularly that of the inversion mode of the molecule. A good agreement between our experimental and calculated spectra has been obtained hence validating the intermolecular potential used in this study to simulate supercritical ammonia. The detailed analysis of the molecular dynamics simulation results provides a quantitative insight of the relative importance of hydrogen bonding versus nonhydrogen bonded interactions that governs the structure of fluid ammonia.     

Overtone bands in aniline and its chloro-derivatives--a low concentration study

Overtone spectra of aniline and its o-and m- chloro-derivatives mixed with carbon tetrachloride have been studied at different dilutions. Vibrational frequency and anharmonicity constants for the C-H stretch vibration and for the symmetric and asymmetric N-H stretch vibrations have been determined. The presence of intermolecular hydrogen bonding has been noted in all the three molecules. Intramolecular hydrogen bonding involving N-H...Cl has also been detected in o-chloroaniline.     

Photodissociation of pyrrole-ammonia clusters below 218 nm: Quenching of statistical decomposition pathways under clustering conditions

The excited state hydrogen transfer (ESHT) reaction in pyrrole-ammonia clusters (PyH[middle dot](NH(3))(n), n = 2-5) at excitation wavelengths below 218 nm down to 199 nm, has been studied using a combination of velocity map imaging and non-resonant detection of the NH(4)(NH(3))(n-1) products. Special care has been taken to avoid evaporation of solvent molecules from the excited clusters by controlling the intensity of both the excitation and probing lasers. The high resolution translational energy distributions obtained are analyzed on the base of an impulsive mechanism for the hydrogen transfer, which mimics the direct N-H bond dissociation of the bare pyrrole. In spite of the low dissociation wavelengths attained (～200 nm) no evidence of hydrogen-loss statistical dynamics has been observed. The effects of clustering of pyrrole with ammonia molecules on the possible statistical decomposition channels of the bare pyrrole are discussed.     

准确快速计算含多肽酰胺和核酸碱基的氢键复合物的氢键强度和氢键作用势能曲线

N-H···O=C、C-H···O=C、N-H···N和C-H···N等氢键作用是蛋白质a-螺旋结构、b-折叠结构和DNA双螺旋结构形成的主要因素,在生物分子识别、蛋白质复制以及遗传信息传递等过程中起重要作用。准确快速计算生物体系中存在的N-H···O=C、C-H···O=C、N-H···N和C-H···N等氢键作用强度以及氢键强度随分子几何结构(距离和角度)变化的势能曲线对正确模拟(从而正确认识和理解)蛋白质折叠机制和DNA双螺旋结构形成机制等生物过程意义重大,对设计合成具有特殊功能的生物分子材料有重要指导价值。本文主要介绍了近年来建立的偶极-偶极氢键作用模型及其在快速预测多肽-多肽分子间和核酸碱基-多肽分子间氢键作用强度和氢键作用势能曲线方面的应用。     

Moderate and advanced intramolecular proton transfer in urea-anion hydrogen-bonded complexes

The study of the interactions of the three urea-based receptors AH, BH(+) and CH(2+) with a variety of anions, in MeCN, has made it possible to verify the current view that hydrogen bonding is frozen proton transfer from the donor (the urea N-H fragment in this case) to the acceptor (the anion X(-)). The poorly acidic, neutral receptor AH establishes two equivalent hydrogen bonds N-H···X(-), with all anions, including CH(3)COO(-) and F(-), in which moderate proton transfer from N-H to the anion takes place. The strongly acidic, dicationic receptor CH(2+) forms, with most anions, complexes in which two inequivalent hydrogen bonds are present: one involving moderate proton transfer (N-H···X(-)) and one in which advanced proton transfer has taken place, described as N(-)···H-X. The degree of proton advancement is directly related to the basic tendencies of the anion. The cationic receptor BH(+) of intermediate acidic properties only forms complexes with two inequivalent hydrogen bonds (moderate+advanced proton transfer) with CH(3)COO(-) and F(-), and complexes with two equivalent hydrogen bonds (moderate proton transfer) with all the other anions. Moreover, [B···HF] and [C···HF](+), on addition of a second F(-) ion, lose the bound HF molecule to give HF(2)(-). Release of CH(3)COOH, with the formation of [CH(3)COOH···CH(3)COO](-), also takes place with the [B···CH(3)COOH] complex in the presence of a large excess of anion.