Weak C—H...X (X = O,N) hydrogen bonds in the crystal structure of dihydroberberine

Dihydroberberine (systematic name: 9,10‐dimethoxy‐6,8‐dihydro‐5H‐1,3‐dioxolo[4,5‐g]isoquinolino[3,2‐a]isoquinoline), C₂₀H₁₉NO₄, a reduced form of pharmacologically important berberine, crystallizes from ethanol without interstitial solvent. The molecule shows a dihedral angle of 27.94 (5)° between the two arene rings at the ends of the molecule, owing to the partial saturation of the inner quinolizine ring system. Although lacking classical O—H or N—H donors, the packing in the crystalline state is clearly governed by C—H...N and C—H...O hydrogen bonds involving the two acetal‐type C—H bonds of the 1,3‐dioxole ring. Each dihydroberberine molecule is engaged in four hydrogen bonds with neighbouring molecules, twice as donor and twice as acceptor, thus forming a two‐dimensional sheet network that lies parallel to the (100) plane.     

Ab initio investigation of water clusters (H2O)n (n = 2–34)

Various properties of typical structures of water clusters in the n = 2–34 size regime with the change of cluster size have been systematically explored. Full optimizations are carried out for the structures presented in this article at the Hartree–Fock (HF) level using the 6‐31G(d) basis set by taking into account the positions of all atoms within the cluster. The influence of the HF level on the results has been reflected by the comparison between the binding energies of (H₂O)_n (n = 2–6, 8, 11, 13, 20) calculated at the HF level and those obtained from high‐level ab initio calculations at the second‐order Møller–Plesset (MP2) perturbation theory and the coupled cluster method including singles and doubles with perturbative triples (CCSD(T)) levels. HF is inaccurate when compared with MP2 and CCSD(T), but it is more practical and allows us to study larger systems. The computed properties characterizing water clusters (H₂O)_n (n = 2–34) include optimal structures, structural parameters, binding energies, hydrogen bonds, charge distributions, dipole moments, and so on. When the cluster size increases, trends of the above various properties have been presented to provide important reference for understanding and describing the nature of the hydrogen bond. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

C—H···X (X = N,O, S) intramolecular interaction in 1‐vinyl‐2‐(2′‐heteroaryl)pyrroles as monitored by 1H and 13C NMR spectroscopy

¹H and ¹³C NMR spectroscopy of a series of 1‐vinyl‐2‐(2′‐heteroaryl)‐pyrroles were employed for the analysis of their electronic and spatial structure. The C—H···N intramolecular interaction between the α‐hydrogen of the vinyl group and the pyridine nitrogen, a kind of hydrogen bonding, was detected in 1‐vinyl‐2‐(2′‐pyridyl)pyrrole, which disappeared in its iodide methyl derivative. It was shown that this interaction is stronger than the C—H···O and C—H···S interactions in 1‐vinyl‐2‐(2′‐furyl)‐ and ‐2‐(2′‐thienyl)‐pyrroles. Copyright © 2001 John Wiley & Sons, Ltd.     

NiFe2O4 as a magnetically recoverable nanocatalyst for odourless C–S bond formation via the cleavage of C–O bond in the presence of S8 under mild and green conditions

We present green methodologies for one‐pot and odourless syntheses of unsymmetric and symmetric diaryl sulfides via C─O bond activation using NiFe₂O₄ magnetic nanoparticles as a reusable heterogeneous nanocatalyst. The synthesis of unsymmetric sulfides is performed using the cross‐coupling reaction of phenolic esters such as acetates, triflates and tosylates with arylboronic acid/S₈ or triphenyltin chloride/S₈ as thiolating agents in the presence of base and NiFe₂O₄ magnetic nanoparticles as a catalyst in poly(ethylene glycol) as solvent at 60–85°C. Also, the synthesis of symmetric diaryl sulfides from phenolic compounds using S₈ as the sulfur source and NiFe₂O₄ as catalyst in dimethylformamide at 120°C is described. Using these protocols, the syntheses of various unsymmetric and symmetric sulfides become easier than using the available protocols due to the use of a magnetically reusable bimetallic nanocatalyst and avoiding the use of thiols and aryl halides.     

The presentation of an approach for estimating the intramolecular hydrogen bond strength in conformational study of β-Aminoacrolein

All the plausible conformations of β-aminoacrolein (AMAC) have been investigated by the Bekes-Lee-Yang-Parr (B3LYP) nonlocal density functional with extended 6-311++G** basis set for studying the stability order of conformers and the various possibilities of intramolecular hydrogen bonding formation. In general the ketoamine (KA) conformers of AMAC, by mean average, are more stable than the corresponding enolimine (EI) and ketoimine (KI) analogues and this stability is mainly due to the π-electron resonance in these conformers that established by NH2 functional group. The contribution of resonance to the stability of chelated KA conformers is about 75.6 kJ/mol, which is greater than that of the hydrogen bond energy (E_HB=35.0 kJ/mol). The relative decreasing order of the various hydrogen bond energies was found to be: O–HN_imine(strong)>N_amine-HO_keto (normal)>N_imine-HO_hydroxyl (weak) > N_imine-HO_keto (weak). Hydrogen bond energies for all systems were obtained from the method that we called related rotamers method (RRM). The topological properties of the electron density contributions for various type of intramolecular hydrogen bond have been analyzed in term of the Bader theory of atoms in molecules (AIM). The results of these calculations support the previous calculations, which obtained by the related rotamer methods.     

Density functional calculations for Rh(I)‐catalyzed C–C bond activation of siloxyvinylcyclopropanes and diazoesters

Density functional theory was employed to investigate rhodium(I)‐catalyzed C–C bond activation of siloxyvinylcyclopropanes and diazoesters. The B3LYP/6‐31G(d,p) level (LANL2DZ(f) for Rh) was used to optimize completely all intermediates and transition states. The computational results revealed that the most favorable pathway was the channel forming the methyl‐branched acyclic product p1 in path A (cyclooctadiene (cod) as the ligand), and the oxidative addition was the rate‐determining step for this channel. It proceeded mainly through the complexation of diazoester to rhodium, rhodium–carbene formation, coordination of siloxyvinylcyclopropane, oxidative addition (C2–C3 bond cleavage) of siloxyvinylcyclopropane, carbene migratory insertion, β‐hydrogen elimination and reductive elimination. The complexation of diazoester to rhodium occurred prior to the coordination of siloxyvinylcyclopropane. Also, the role of the ligands cod, chlorine and 1,4‐dioxane, the effect of di‐rhodium catalyst and the solvent effect are discussed in detail.     

Crystal and molecular structure of (r-2, c-4)-3-benzyl-2,4,5,5-tetraphenyl1,3-thiazolidine, intramolecular C–HS hydrogen bonds

The crystal and molecular structures of (r-2, c-4)-3-benzyl-2,4,5,5-tetraphenyl-1,3-thiazolidine are investigated showing the existence of C(sp²)–HS and C(sp²)–HN intramolecular contacts. The analysis of geometrical parameters shows that C–HS contacts may be treated as hydrogen bonds but C–HN do not fulfil the geometrical criteria of the existence of H-bonds. The B3LYP/6-311+G* single point calculations were performed to obtain wave functions applied later for ‘atoms in molecules’ (AIM) study. The analysis of bond critical points based on the Bader theory (AIM) supports the existence of intramolecular C–HS H-bonds.     

Theoretical Studies on Structures and Properties of Endohedral Fullerenes Complexes： XHn@C32（X=F,O, N,C; n=l-4）

Theoretical studies on structures and properties of endohedral fullerene complexes formed by encapsulating small molecules of HF, H20, NH3, and CH4 in a C32 fullerene cage, were carried out by ab initio method. Current calculations reveal that these processes to encase them in fullerene are energetically unfavorable because of the small cavity size of C32. The red shift in the F-H stretching frequency indicates the potential existence of hydrogen bonding between the HF molecule and the carbon cage.     

Photochemical Generation of Chiral N,B,X‐Heterocycles by Heteroaromatic C−X Bond Scission (X=S,O) and Boron Insertion

Chiral organoboron compounds with a chelate backbone and mesityl/heterocycle substituents (thienyl, furyl, and derivatives thereof) undergo a quantitative phototransformation that yields rare, chiral N,B,X‐containing heterocycles, such as base‐stabilized 1,2‐thiaborinines and 1,2‐oxaborinines. Boriranes were observed as intermediates in some of these transformations. The oxaborinines display further reactivity, generating 4a,12b‐dihydrobenzo[h][1,2]oxaborinino[4,3‐f]quinolines through a sequential conrotatory electrocyclization and a [1,5]‐H shift. The N,B,X‐containing heterocycles display strong blue‐green to orange‐red emission in the solid state. Combined DFT//CASP2T calculations suggest that a common biradical intermediate is responsible for the formation of these compounds as well as their interconversion.     

Studies of intramolecular hydrogen bonds (IMHB): crystal and molecular structure of 2-(2′-hydroxy-phenyl)imidazoles

The molecular and crystal structure of 2-(2′-hydroxyphenyl)imidazole (2) and 1-methyl-2-(2′-hydroxyphenyl)imidazole (5) have been determined by X-ray analysis. Compound (2) presents a strong intramolecular hydrogen bond (IMHB) responsible for the planarity of the molecule. In both compounds the molecules form chains through N---H…O (compound 2) and O---H…N hydrogen bonds (compound 5) but giving rise to the same packing mode. Ab initio calculations (6–31G**) have been carried out on both compounds in order to study the effect of the IMHB on the structure.     

Quantum chemical investigation of linear hydrogen bonding in ONCCN···HX (X = F,Cl, Br) dimers

Linear hydrogen bonding formed between the nitrogen end of cyanogen‐N‐oxide (ONCCN) and hydrogen halides HX (X = F, Cl, Br) has been observed in their ground Σ states. The order of agreement of energetic stabilities between the correlated functionals used in this calculation is: B3LYP < PBE0 < PBE < PW91 in conjunction with the 6–311++G(3df,3pd) basis set. Analysis of various parameters describing the existence of H‐bonds in these dimers follows the conventional trend: ONCCN···HF > ONCCN···HCl > ONCCN···HBr in the series, except H‐bond lengths and static dipole polarizabilities which are in reverse order. The atomic charges obtained from the Mulliken and natural population analysis is used to assess the charge transfer effects that accompany the dimer formation. It is found from the investigation that the dimers having highest binding energy are accompanied by the highest transfer of charge. The ¹⁴N nuclear quadrupole coupling constants of the monomer ON¹CCN² are found to be decreased upon complection and in the series it increases from F through Br. We observed enhancements in the values of the dimer dipole moment and intrinsic dipole polarizabilities compared with the sum of the monomer values by intermolecular electrical interaction. Investigation reveals vibrational spectral shifts of HX and CN stretching modes similar to the conventional red‐shifted H‐bonded dimers; for the former case, the infrared band intensity increases significantly. Finally, the new vibrational modes originated from the intermolecular interaction are outlined. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

An ab initio study of solvent polarity and hydrogen bonding effects on the nitrogen NMR shieldings of N,N‐dimethylacetamidine

Density functional theory combined with the polarizable continuum model (PCM) and continuous set of gauge transformations method is applied to investigate the effects of solvent polarity on the nitrogen NMR shieldings of N, N‐dimethylacetamidine. Hydrogen bonding effects on shielding are likewise calculated using a supermolecule approach, where the imino group of the solute is hydrogen bonded with solvent. Theoretical results are compared with published experimental data. The PCM shielding calculations utilizing PCM‐optimized solute geometries yield results comparable to those obtained with the supermolecule approach. Geometry optimization of the solute appears to be more important in PCM shielding calculations than in the supermolecule approach. The large solvent shifts observed in water can only be reproduced when the N·H distance used in the calculation indicates full proton transfer from water to the imino nitrogen of the solute. Copyright © 2002 John Wiley & Sons, Ltd.     

Synthesis,characterization and crystal structure of the new pentahydrate of bis(2,2′‐bipyridine‐κ2N,N′)(oxalato‐κ2O1,O2)nickel(II)

The reaction of NiCl₂, K₂C₂O₄·H₂O and 2,2′‐bipyridine (bpy) in water–ethanol solution at 281 K yields light‐purple needles of the new pentahydrate of bis(2,2′‐bipyridine)oxalatonickel(II), [Ni(C₂O₄)(C₁₀H₈N₂)₂]·5H₂O or [Ni(ox)(bpy)₂]·5H₂O, while at room temperature, deep‐pink prisms of the previously reported tetrahydrate [Ni(ox)(bpy)₂]·4H₂O [Román, Luque, Guzmán‐Miralles & Beitia (1995), Polyhedron, 14 , 2863–2869] were gathered. The asymmetric unit in the crystal structure of the new pentahydrate incorporates the discrete molecular complex [Ni(ox)(bpy)₂] and five solvent water molecules. Within the complex molecule, all three ligands are bonded as chelates. The complex molecules are involved in an extended system of hydrogen bonds with the solvent water molecules. Additionally, π–π interactions also contribute to the stabilization of the extended structure. The dehydration of the pentahydrate starts at 323 K and proceeds in at least two steps as determined by thermal analysis.     

Hydrogen bond and σ‐hole interaction in M2C=S···HCN (M = H,F, Cl,Br, HO,H3C,H2N) complex: Dual roles of C=S group and substitution effect

An ab initio computational study of the dual functions of C?S group in the M₂C?S ··· HCN (M = H, F, Cl, Br, HO, H₃C, H₂N) complex has been performed at the MP2(Full)/aug‐cc‐pVTZ level. The C?S group can act as both the electron donor and acceptor, thus two minima complexes were found for each molecular pairs. The interaction energy of hydrogen bond in the F, Cl, or Br substituted complexes is less negative than that in the corresponding H₂CS one, while the interaction energy of the σ‐hole interaction is more negative. The OH substitution weakens the hydrogen bond, whereas the H₃C and H₂N substitution strengthens it. The σ‐hole interaction in the HO, H₃C, and H₂N complexes is very weak. The substitution effect has been understood with electrostatic induction and conjugation effects. The energy decomposition analysis has been performed for the halogen‐substituted complexes. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012.     

Ab initio and DFT energetics of silylenic X–CNSi (X=H, F, Cl, and Br)

Singlet–triplet energy splitting for 24 silylenic reactive intermediates, X–CNSi (where X=H, F, Cl and Br), are compared and contrasted at 11 levels of theory: B1LYP/6-31++G**, B3LYP/6-31++G**, B1LYP/6-311++G**, B3LYP/6-311++G**, MP3/6-31G*, MP3/6-311++G**, MP2/6-31+G**, MP2/6-311++G**, MP4 (SDTQ)/6-311++G**, QCISD(T)/6-311++G** and CCSD(T)/6-311++G**. Each X-substituted silylenic species may either be singlet (s) or triplet (t), with one of the following three structures: 3-X-2-aza-1-silacyclopropenylidene (1_s-X, 1_t-X); [(X-imino)methylene]silylene (2_s-X, 2_t-X); and X-cyanosilylene (3_s-X, 3_t-X). For all X–CNSi species studied, orders of singlet–triplet energy separations (ΔE_s-t,X), appear as a function of electro-negativity (F>Cl>Br>H). For the six H–CNSi isomers (X=H), stability order is: 3_s-H>1_s-H>2_t-H>3_t-H>2_s-H>1_t-H. Likewise, stability order for the six isomers with X=F, is: 3_s-F>3_t-F>1_s-F>1_t-F>2_s-F>2_t-F. For X=Cl, the order of stability is: 3_s-Cl>1_s-Cl>3_t-Cl>2_t-Cl>1_t-Cl>2_t-Cl. Finally, the order of stability for six isomers of Br–CNSi is: 3_s-Br>3_t-Br>1_s-Br>2_s-Br>2_t-Br>1_t-Br. The lowest energy minimum, among all 24 species scrutinized, appears to be the singlet acyclic 3_s-X. Triplet silylene 2_t-H is suggested to be more stable than its corresponding 2_s-H at MP3, MP2 and DFT levels of theory. Comparisons between relative stabilities; multiplicities and geometrical parameters of 1–3 are discussed.     

A novel C?C bond cleavage reaction of 2, 2′‐pyridil in solution

2,2′‐Pyridil reacted with CuCl₂ to give C–‐C bond cleavage product (picolinate)₂Cu, and its structure has been unambiguously confirmed by an X‐ray structural analysis.     

Experimental and theoretical study of the intramolecular C–H···N and C–H···S hydrogen bonding effects in the 1H and 13C NMR spectra of the 2‐(alkylsulfanyl)‐5‐amino‐1‐vinylpyrroles: a particular state of amine nitrogen

In the ¹H NMR spectra of the 1‐vinylpyrroles with amino‐ and alkylsulfanyl groups in 5 and 2 positions, an extraordinarily large difference between resonance positions of the H_A and H_B terminal methylene protons of the vinyl group is discovered. Also, the one‐bond ¹J(C_β,H_B) coupling constant is surprisingly greater than the ¹J(C_β,H_A) coupling constant in pyrroles under investigation, while in all known cases, there was a reverse relationship between these coupling constants. These spectral anomalies are substantiated by quantum chemical calculations. The calculations show that the amine nitrogen lone pair is removed from the conjugation with the π‐system of the pyrrole ring so that it is directed toward the H_B hydrogen. These factors are favorable to the emergence of the intramolecular C–H_B???N hydrogen bonding in the s‐cis(N) conformation. On the other hand, the spatial proximity of the sulfur to the H_B hydrogen provides an opportunity of the intramolecular C–H_B???S hydrogen bonding in the s‐cis(S) conformation. Presence of the hydrogen bond critical points as well as ring critical point for corresponding chelate ring revealed by a quantum theory of atoms in molecules (QTAIM) approach confirms the existence of the weak intramolecular C–H???N and C–H???S hydrogen bonding. Therefore, an unusual high‐frequency shift of the H_B signal and the increase in the ¹J(C_β,H_B) coupling constant can be explained by the effects of hydrogen bonding. Copyright © 2013 John Wiley & Sons, Ltd.     

High-level ab initio versus DFT calculations on (H2O2)2 and H2O2–H2O complexes as prototypes of multiple hydrogen bond systems

The performance of B-LYP, B-P86, B3-LYP, B3-P86, and B3-PW91 density functionals to describe multiple hydrogen bond systems was studied. For this purpose we have chosen the dimers of hydrogen peroxide and the hydrogen peroxide–water complexes. The geometries and vibrational frequencies obtained with a 6-311+G(d,p) basis set were compared with those obtained at the MP2 level using the same basis set expansion. The corresponding dimerization energies were obtained using a 6-311+G(3df,2p) basis set and compared with those obtained using the G2(MP2) theory. Red shiftings of the OH donor stretching frequencies were predicted by all approaches investigated; however, in all cases, the DFT values were sizably larger than the MP2 ones. Similarly, the blue shifting of the torsion of the hydrogen peroxide subunit was larger when evaluated at the DFT level. All functionals reproduced the G2(MP2) relative stabilities of the different local minima quite well. With the exception of the B-LYP and B3-PW91 approaches, all functionals yielded binding energies which deviated from the G2(MP2) values by less than 0.5 kcal/mol, provided that G2-type basis sets were used and that the corresponding BSSE corrections were included. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1124–1135     

Rg—HX(Rg=He,Ne;X=F,Cl,Br)分子间势的精确量子化学从头计算研究III.He—HBr

在用非迭代的三重激发项来校正CCSD的CCSD（T）理论水平下，采用aug-cc- pVQZ基函数对He—HBr的分子间势进行了系统的研究。结果表明：He—HBr以线型结 构存在。在极限基的情况下，复合物两种线型极小点结构He—H—Br和He—Br—H势 阱深分别为28.792 cm~(-1)和35.707 cm~(-1)，对应He原子到HBr分子质心的距离 R分别为0.407 nm和0.343 nm。讨论了不同的基函数和理论方法在研究此类弱束缚 态复合物的分子间势时的可靠性及其对结果的影响，同时也给出了热函数的解析形 式。