Hydrogen-bonded structures for self-aggregates of 2,5-dimethylpyrrole and its binary clusters with pyrrole studied by IR cavity ringdown spectroscopy

N-H···π hydrogen-bonded (H-bonded) structures were studied by applying vibrational spectroscopy to self-aggregate clusters of 2,5-dimethylpyrrole (DMPy) and its binary clusters with pyrrole (Py). The NH stretching vibrations of jet-cooled clusters were observed by IR cavity ringdown spectroscopy. A combination of experiments and density functional theory calculations revealed the stable structures, intermolecular binding energies, and harmonic vibrational frequencies. The IR spectrum of the DMPy self-aggregate clusters was very similar in spectral features to that of the Py clusters in a previous work. The observed NH stretching vibrations at 3505, 3420, 3371, and 3353 cm(-1) are simultaneously red-shifted by ～25 cm(-1) from the Py monomer, dimer, trimer, and tetramer, respectively. Based on a spectral analogy of DMPy with Py, and a consistency of the calculated harmonic frequencies with experiments, the H-bonded structures of the DMPy clusters were determined to be of a T-shape for a dimer and a cyclic for a trimer and a tetramer. For the DMPy-Py binary clusters, we discussed the stability and geometry of the N-H···π interactions in the T-shaped dimer and the cyclic trimer. The binary dimer showed the only single NH stretch at 3419 cm(-1) in the IR spectrum. A vibrational analysis of the H-bonded NH stretches as well as the calculated stabilization energies deduced that only the binary dimer by DMPy as an acceptor and Py as a donor can exist in a supersonic jet. For binary trimers, NH stretches were observed due to both (DMPy)(2)-(Py)(1) and (DMPy)(1)-(Py)(2). They were found to have different vibrational patterns from each other; the former showed three dispersed NH stretches, and the other had two quasi-degenerate NH stretches. Throughout this study, we also considered the intermolecular geometries, such as the H-bond distance and the angle in terms of the methyl group substitution effect.     

"Union is strength": how weak hydrogen bonds become stronger

Recently reported rotational spectroscopic studies on small dimers and oligomers bound by weak hydrogen bonds show that the driving forces, the spatial arrangement and the dynamical features displayed are very different from those involved in stronger and conventional hydrogen bonds. The very small binding energies (similar to those of van der Waals interactions) imply that the stabilization of the dimer is often obtained by networks of weak hydrogen bonds. Even in the presence of multiple bonds the partner molecules show a high degree of internal freedom within the complex. This paper analyses several examples of molecular adducts bound by weak hydrogen bonds formed in free jet expansions and recently characterized by rotational spectroscopy. They include weakly bound complexes of weak donors with strong acceptors (C-H···O,N, S-H···O,N), strong donors (O-H, N-H) with weak acceptors such as the halogen atoms and π systems but also the elusive interactions between weak donors and weak acceptors (C-H···π and C-H···halogen). Examples are also given where rotational spectroscopy highlights that weak hydrogen bonds are extremely important in chiral recognition phenomena and as driving forces of the conformational landscape of important biomolecules.     

Competition between hydrogen bonding and dispersion interactions in the indole···pyridine dimer and (indole)2···pyridine trimer studied in a supersonic jet

Structures of the indole···pyridine dimer and (indole)2···pyridine trimer have been investigated in a supersonic jet using resonant two-photon ionization (R2PI) and IR-UV double resonance spectroscopic techniques combined with quantum chemistry calculations. R2PI spectra of the dimer and the trimer recorded by electronic excitation of the indole moiety show that the red-shift in the band origin of the dimer with respect to the 0(0)(0) band of the monomer is larger compared to that of the trimer. The presence of only one conformer in the case of both the dimer and the trimer has been confirmed from IR-UV hole-burning spectroscopy. The structures of the dimer and the trimer have been determined from resonant ion dip infrared (RIDIR) spectra combined with ab initio as well as DFT/M05-2X and DFT/M06-2X calculations. It has been found that the dimer, observed in the experiment, has a V-shaped geometry stabilized by N–H···N and C–H···N hydrogen bonding interactions, as well as C–H···π and π···π dispersion interactions. The geometry of the trimer has been found to be a cyclic one stabilized by N–H···N, N–H···π, C–H···π, and C–H···N interactions. The most important finding of this current study is the observation of the mixed dimer and trimer, which are stabilized by hydrogen bonding as well as dispersion interactions.     

Quantum-chemical study on reactions of isocyanates with methanol associates: VI. Quantum-chemical characterization of the relative reactivity of linear and cyclic methanol trimers in the addition to methyl isocyanate

Quantum-chemical study on the reaction of methyl isocyanate with cyclic methanol trimer at the B3LYP/6-311++G(df,p) level of theory showed that the process involves concerted asymmetric transition state in which the formation of new N-H bond outstrips the formation of new C-O bond. The reaction of methyl isocyanate with linear methanol trimer was found to be both kinetically and thermodynamically more favorable than with cyclic trimer.     

超分子化合物[UO2Cl4][phenH]2的合成、晶体结构、荧光性质及[UO2Cl4][phenH]2/PVA薄膜的发光性能

水热条件下合成了一种含铀的超分子化合物[UO2Cl4][phenH]2(phen=1,10-邻菲罗啉),进行了X射线单晶衍射、红外光谱、紫外光谱和荧光光谱分析。 晶体结构分析表明,该化合物由2个[phenH]+阳离子和1个阴离子[UO2Cl4]2-组成。 红外光谱和X射线单晶衍射表明,标题化合物的三维框架是由N-H…Cl、C-H…Cl和C-H…O弱氢键相互作用所构建。 中心U原子是六配位,有4个Cl原子和2个O原子。 此外,没参与配位的phen利用氢键和π…π堆积与[UO2Cl4]2-相互作用。 含U原子的阴离子是一种扭曲八面体结构。 利用溶胶-凝胶法合成了化合物的PVA薄膜。 标题化合物和薄膜均有较强的荧光性。CCDC:713149     

π-Hydrogen bonding wins over conventional hydrogen bonding interaction: a jet-cooled study of indole···furan heterodimer

In this study, we have explored the conformational landscape of the indole···furan dimer in a supersonic jet by using resonant two-photon ionization (R2PI) and IR-UV double-resonance spectroscopic techniques combined with dispersion-corrected density functional theory (DFT) calculations. Only one conformer of the dimer has been observed in the experiment. DFT/B97-D level calculation shows that N-H···π hydrogen-bonded conformer (T') is energetically more stable than the N-H···O hydrogen-bonded conformer (HB). Natural bond orbital (NBO) calculation also shows that the hydrogen-bonding interaction in the HB conformer is very weak. Finally, the structure of the observed dimer has been determined to be tilted T-shaped N-H···π hydrogen-bonded (T') from very excellent agreement between experimental and theoretical N-H stretch frequency. The most significant finding of this study is the first-time observation of a N-H···π bound conformer of a dimer, which wins over a conventional hydrogen-bonded conformer of the dimer.     

Cooperative effects and strengths of hydrogen bonds in open-chain cis-triaziridine clusters (n = 2-8): a DFT investigation

We employ DFT/B3LYP method to investigate linear open-chain clusters (n = 2-8) of the cis-triaziridine molecule that is a candidate molecule for high energy density materials (HEDM). Our calculations indicate that the pervasive phenomena of cooperative effects are observed in the clusters of n = 3-8, which are reflected in changes in lengths of N...H hydrogen bonds, stretching frequencies, and intensities of N-H bonds, dipole moments, and charge transfers as cluster size increases. The n(N) --> sigma*(N-H) interactions, i.e., the charge transfers from lone pairs (n(N)) of the N atoms into antibonds (sigma*) of the N-H bonds acting as H-donors, can be used to explain the observed cooperative phenomena. The approaches based upon natural bond orbital (NBO) method and theory of atoms in molecule (AIM) to evaluating N...H strengths are found to be equivalent. In the process of N...H bonding, cooperative nature of n(N) --> sigma*(N-H) interactions promotes formation of stronger N...H bonds as reflected in increases in the capacities of cis-triaziridine clusters to concentrate electrons at the bond critical points of N...H bonds. The calculated nonadditive energies also show that the cooperative effects due to n(N) --> sigma*(N-H) interactions indeed provide additional stabilities for the clusters.     

Synthesis and Structural Studies of 6-（2,5-Dimethyl-1H-pyrrol-1-yl）pyridin-2-amine

6-(2,5-Dimethyl-1H-pyrrol-1-yl)pyridin-2-amine (1) was synthesized and characte-rized by elemental analyses,1H-NMR and 13C-NMR,FTIR,Uv-Vis,mass spectral studies and single-crystal X-ray diffraction.All data obtained from spectral studies support the structural properties of 1.Intermolecular N-H…N hydrogen bonds produce an R22(8) ring.An extensive three-dimensional network formed by C-H…π and N-H…π-facial hydrogen bonds is responsible for the crystal stabilization.The combination of C-H…π interactions produces R33(12),R43(19) and R44(20) rings.     

Molecule-substrate interaction channels of metal-phthalocyanines on graphene on Ni(111) surface

Molecule-substrate interaction channels of metal-phthalocyanines (MPcs, including NiPc, CuPc, ZnPc, FePc, and CoPc) on graphene on Ni(111) were investigated by employing high-resolution electron energy loss spectroscopy (HREELS). Except the expected IR-active modes, some Raman-active modes were also observed in all of MPcs, which are considered in this study. From the origination of the Raman-active features, it was deduced that MPcs are coupled with the substrate mainly through their central metal atom. The Raman-active modes appear as symmetric peaks in the HREELS in the case of MPcs with Ni, Cu, and Zn, whereas they are asymmetric and appear as a Fano line shape in the case of MPcs with Fe and Co. This spectroscopic difference indicates that the molecule-substrate coupling is completely different in the two cases mentioned above. The molecule-substrate interaction strength is considerably weak and comparable with the π-π interaction between molecules in the case of MPcs with Ni, Cu, and Zn, whereas it is much stronger in the case of MPcs with Fe and Co. From the HREELS observations, it can be suggested that the whole molecule can be effectively decoupled from the underneath Ni(111) by inserting a single layer of graphene between them in the case of MPcs with Ni, Cu, and Zn, whereas only benzene rings can be completely decoupled in the case of MPcs with Fe and Co.     

Interpretation of hydrogen bonding in the weak and strong regions using conceptual DFT descriptors

Hydrogen bonding is among the most fundamental interactions in biology and chemistry, providing an extra stabilization of 1-40 kcal/mol to the molecular systems involved. This wide range of stabilization energy underlines the need for a general and comprehensive theory that will explain the formation of hydrogen bonds. While a simple electrostatic model is adequate to describe the bonding patterns in the weak and moderate hydrogen bond regimes, strong hydrogen bonds, on the other hand, require a more complete theory due to the appearance of covalent interactions. In this study, conceptual DFT tools such as local hardness, eta(r) and local softness, s(r), have been used in order to get an alternative view on solving this hydrogen-bonding puzzle as described by Gilli et al. [J. Mol. Struct. 2000, 552, 1]. A series of both homonuclear and heteronuclear resonance-assisted hydrogen bonds of the types O-H...N, N-H...O, N-H...N, and O-H...O with strength varying from weak to very strong have been studied. First of all, DeltaPA and DeltapK(a) values were calculated and correlated to the hydrogen bond energy. Then the electrostatic effects were examined as hard-hard interactions accessible through molecular electrostatic potential, natural population analysis (NPA) charge, and local hardness calculations. Finally, secondary soft-soft interaction effects were entered into the picture described by the local softness values, providing insight into the covalent character of the strong hydrogen bonds.     

Synthesis and Crystal Structure of Bis{2-bromo- 4-chloro-6-[(2-isopropylammonioethylimino)-methyl]phenolato}bisthiocyanatozinc(Ⅱ)

A Schiff base zinc(Ⅱ) complex [Zn(C12H16BrClN2O)2(NCS)2] was prepared and characterized by elemental analysis, IR and single-crystal X-ray diffraction. The crystal belongs to the triclinic system, space group P with a = 8.414(1), b = 9.124(1), c = 22.212(3) (A), α = 79.177(2), β = 86.296(2), γ = 89.899(2)o, V = 1671.3(4) (A)3, Z = 2, Dc = 1.631 g/cm3, Mr = 820.79, λ(MoKα) = 0.71073 (A), μ = 3.444 mm-1, F(000) = 824, R = 0.0646 and wR = 0.1179. A total of 7371 unique reflections were collected, of which 3904 with I＞2σ(I) were observed. The complex crystallizes with two half-molecules per asymmetric unit and each mononuclear molecule is centrosymmetric. The Zn atom lying at the inversion centre is six-coordinated in a slightly distorted octahedral geometry by two phenolate O atoms and two imine N atoms from two Schiff base ligands, as well as two N atoms from two thiocyanate anions. In the crystal structure, the combination of π-π stacking interactions and intermolecular hydrogen bonds (N-H…Br, N-H…O, N-H…N, C-H…O, C-H…S and C-H…Cl) leads to a three-dimensional network.     

Synthesis of cyclic chlorophyll oligomers

As a new model of photosynthetic light-harvesting antennas, cyclic dimer, trimer, and tetramer of chlorophyllous moieties were prepared by intermolecular transesterification of a hydroxy-methoxycarbonyl-chlorin using 1,3-dichlorotetrabutyl distannoxane as a catalyst. ¹H NMR and UV-vis spectra showed that the cyclic oligomers tended to form stacked conformers through intramolecular π-π interactions of the chlorin macrocycles. It was demonstrated that the cyclic trimer could form a complex with fullerenes in CDCl₃.     

A new polymorph of methimazole: Single crystal and powder X-ray diffraction study

A new polymorph of 1-methyl-4-imidazoline-2-thione has been first discovered and studied by X-ray diffraction. The crystal of the new polymorph is monoclinic, the asymmetric part of the cell contains three independent molecules. In the crystal, the key compound is in the form of planar hydrogen-bonded dimers due to the interactions of the N-H…S type. The new modification is of an intensely yellow color in contrast to the previously known colorless forms, is characterized by a lower density but stronger hydrogen bonds; it is formed as a minor impurity to main triclinic polymorph.     

Crystal Structure of 2,6-Dihistidine Dimethyl Ester Pyridine Acylamine Monohydrate

The crystal structure of the title compound,C21H25N7O7,has been determined in the orthorhombic space group C222(1) with a=8.993(10),b=12.149(14),c=22.20(2) and Z=4.There exist intramolecular C-H…O and N-H…N hydrogen bonds in the title crystal structure.The intermolecular N-H…N and C-H…O hydrogen bonds together with π-π stacking interactions(face-to-face) link the molecules into an infinite three-dimensional supramolecular network.     

Contrasting the supramolecular structures in the isomeric pair 5‐bromo‐3‐nitrosalicylaldehyde phenylhydrazone and 3‐bromo‐5‐nitrosalicylaldehyde phenylhydrazone

Isomeric 5‐bromo‐3‐nitrosalicylaldehyde phenylhydrazone and 3‐bromo‐5‐nitrosalicylaldehyde phenylhydrazone, C₁₃H₁₀BrN₃O₃, both crystallize with two molecules in the asymmetric unit. In both isomers, an intramolecular O—H...N hydrogen bond links the hydroxy group and the imine N atom. In the 5‐bromo‐3‐nitro isomer, there are two independent N—H...O hydrogen‐bonded chains, each molecule in the asymmetric unit forming its own chain. These chains are then linked to form a three‐dimensional framework by a combination of weak C—H...O, C—H...Br, C—H...π and π–π stacking interactions. In the 3‐bromo‐5‐nitro isomer, N—H...O hydrogen bonds link the independent molecules alternately into a zigzag chain, which is reinforced by a weak C—H...O interaction. Individual chains are linked by a C—H...Br interaction and a three‐dimensional framework is generated by π–π stacking interactions.     

Structure of 7-azaindole···2-fluoropyridine dimer in a supersonic jet: competition between N-H···N and N-H···F interactions

In the present work, we have investigated the structure of 7-azaindole···2-fluoropyridine dimer in a supersonic jet by employing resonant two photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques combined with quantum chemistry calculations. The R2PI spectrum of the dimer is recorded by electronic excitation of the 7-azaindole moiety, and a few low frequency intermolecular vibrations of the dimer are clearly observed in the spectrum. The electronic origin band of the dimer is red-shifted by 1278 cm(-1) from the S(1) ← S(0) origin band of 7-azaindole monomer. The presence of a single conformer of the dimer is confirmed by IR-UV and UV-UV hole-burning spectroscopic techniques. RIDIR (Resonant ion dip infrared) spectrum of the dimer shows a red-shift of 265 cm(-1) in the N-H stretching frequency with respect to that of the 7-azaindole monomer. Two planar double hydrogen bonded cyclic structures of the dimer have been predicted from DFT calculations. Comparison of experimental and theoretical N-H stretching frequencies confirms that the observed dimer is stabilized by N-H···N and C-H···N hydrogen bonding interactions. The less stable conformer with N-H···F and C-H···N interactions are not observed in the experiment. The competition between N-H···N and N-H···F interactions in the two dimeric structures are discussed from natural bond orbital (NBO) analysis. The current results demonstrate that fluorine makes a hydrogen bond of intermediate strength through cooperative interaction of another hydrogen bond (C-H···N) present in the dimer, although fluorine is believed to be very weak hydrogen bond acceptor.     

2-(2-苯并咪唑基)吡啶双核镉(Ⅱ)配合物的水热合成、晶体结构及荧光性质

通过水热反应,合成了2-(2-苯并咪唑基)吡啶(BMPY)镉(Ⅱ)配合物[Cd2Cl4(BMPY)2]。对它进行了元素分析、热重、红外光谱及电子光谱表征,并用X-射线单晶衍射测定了配合物的晶体结构。配体2-(2-苯并咪唑基)吡啶中的2个氮原子与3个氯原子与镉(Ⅱ)配位,形成五配位的畸变四角锥构型,2个配位镉(Ⅱ)离子通过双氯桥键结合成双核镉的配合物。该配合物通过分子间N-H…Cl,C-H…Cl氢键和π-π作用形成一维链状结构。热重-微分热重(TG-DTG)分析结果表明,[Cd2Cl4(BMPY)2]在320℃以下无分解反应,耐热性好。室温固态荧光测试显示,配合物在408.9 nm(λmax)处具有较强的荧光发射。     

Theoretical study of properties of H bonds and intermolecular interactions in linear cis-,trans-cyclotriazane clusters (n = 2-8)

Our calculations based upon Becke's three-parameter functional of density-functional theory (DFT) with the correlation of Lee, Yang, and Parr (B3LYP), natural bond orbital, and atoms in molecule indicate that in drastic contrast to most H-bonded systems, the anticooperative and cooperative effects coexist in the linear H-bonded cis-,trans (c,t)-cyclotriazane clusters (n = 2-8). As cluster size increases, the properties along the H-bonded chains at trans-positions take on the unexpectedly anticooperative changes which are reflected in elongation of the N...H hydrogen bonds, frequency blueshift in the N-H stretching vibrations, decay in the n(N)-->sigma*(N-H) charge transfers, and weakening of strengths of the N...H bonds. And the cooperative changes in the corresponding properties for the cis- H-bonded chains are observed to be concurrent with the anticooperativities. The rise and fall in the n(N)-->sigma*(N-H) interactions cause increment and decrement in capacities of the clusters to concentrate electrons at the bond critical points of the N...H bonds, and thereby leading to the cooperative and the anticooperative changes especially in the N...H lengths and the N-H stretching frequencies. In terms of three-body symmetry-adapted perturbation theory (three-body SAPT), the first exchange nonadditivity plays a more important role in stabilizing trimer than the nonadditive induction. However, the dominance of the first exchange nonadditivity in three-body interaction unexpectedly triggers the anticooperative effect that counteracts the concurrent cooperative effect. According to the SAPT(DFT), which is a combination of SAPT with asymptotically corrected DFT, DFT/B3LYP is able to succeed in describing the electrostatic, exchange, and induction components, but fails to yield satisfactory interaction energies due to the fact that about 40% of short-range dispersion energy is neglected by the DFT, which is different from many H-bonded described well by the DFT. A quantum cluster equilibrium model illustrates that the c,t-cyclotriazane liquid phase exhibits a weak cooperative effect.     

Noncovalent interactions under extreme conditions: high-pressure and low-temperature diffraction studies of the isostructural metal-organic networks (4-chloropyridinium)2[CoX4] (X = Cl, Br)

The crystal structures of the two isostructural metal-organic salts, (4-chloropyridinium) 2[CoX 4], X = Cl ( 1), Br ( 2), have each been determined at nine temperatures from 30 to 300 K and at nine pressures from atmospheric pressure to 4.2 GPa. A 5% reduction in unit cell volume is observed upon temperature reduction, whereas an 18-19% reduction is observed upon increasing the pressure over the ranges studied. The structures adopt a tape arrangement propagated by bifurcated N-H...X 2Co hydrogen bonds and by Co-X...Cl-C halogen bonds. Intertape interactions include type I Co-X...Cl-C and C-Cl...Cl-C halogen-halogen interactions as well as offset pi-stacking between the aromatic rings of the cations. Although little anisotropy in compression is seen upon temperature reduction, marked anisotropy in compression is observed upon pressure increase. Compression between tapes far exceeds compression along the tape, consistent with the strong attractive nature of the intratape N-H...X 2Co and Co-X...Cl-C interactions and the weaker dispersion dominated Co-X...Cl-C and C-Cl...Cl-C halogen-halogen interactions and pi-stacking interactions. Increased distortion of the [CoX 4] (2-) anions from idealized tetrahedral geometry arises upon pressure increase, consistent with local changes in the electric field that result from compression of the pairs of pi-stacked cations. The study of the isostructural pair of compounds permits a rare opportunity for quantitative evaluation of the "internal" or "chemical" pressure exerted by changing the [CoBr 4] (2-) anion for the smaller [CoCl 4] (2-) anion. Thus, crystal structures of 1 and 2 with equivalent unit cell volumes require an additional pressure of ca. 1 GPa exerted upon the structure containing the larger [CoBr 4] (2-) anion ( 2). This internal pressure increases to ca. 1.9 GPa at the highest pressures used in this study. Most significant is that examination of the isovolumetric pairs of structures shows that the structures containing the [CoCl 4] (2-) anion are contracted along the <101> vector, the direction of tape propagation, by ca. 1.2% and correspondingly expanded in other directions, relative to those containing the [CoBr 4] (2-) anion. Since the effect of difference in anion size has been removed by application of pressure, this anisotropy in dimensions clearly indicates that the N-H...X 2Co hydrogen bonds and Co-X...Cl-C halogen bonds are more strongly attractive for X = Cl rather than X = Br. Use of internal pressure thereby provides unique insight into the relative strength of intermolecular interactions.     

Hydrogen bond strength modulates the mechanical strength of ferric-thiolate bonds in rubredoxin

It has long been recognized that hydrogen bonds formed by protein backbone amides with cysteinyl S(γ) atoms play important roles in modulating the functional and structural properties of the iron-sulfur centers in proteins. Here we use single molecule atomic force microscopy, cyclic voltammetry, and protein engineering techniques to investigate directly how the strength of N-H···S(γ) hydrogen bonds in the secondary coordination sphere affects the mechanical stability of Fe(III)-thiolate bonds of rubredoxin. Our results show that the mechanical stability of Fe(III)-thiolate bonds in rubredoxin correlates with the strength of N-H···S(γ) hydrogen bonds as reflected by the midpoint reduction potential, providing direct evidence that N-H···S(γ) hydrogen bonds play important roles in modulating the mechanical and kinetic properties of the Fe(III)-thiolate bonds of iron-sulfur proteins and corroborating the important roles of the protein environment in tuning the properties of metal-thiolate bonds.