Molecular Recognition of Nucleic Acid Bases in Water by Hydrogen Bonding of Poly(vinyldiaminotriazine)

Poly(2-vinyl-4,6-diamino-1,3,5-triazine) efficiently binds nucleic acid bases and nucleosides in water by using complementary hydrogen bonding. The binding activity decreases in the order: U, T > A C, G. The corresponding monomer shows virtually no activity, indicating a predominant role of polymer effect for the molecular recognition in water.     

Density functional study of HO(H2O)n (n = 1–3) clusters

The hydrogen bonding complexes HO(H₂O)_n (n = 1–3) were completely investigated in the present study using DFT and MP2 methods at varied basis set levels from 6‐31++G(d,p) to 6‐311++G(2d,2p). For n = 1 two, for n = 2 two, and for n = 3 five reasonable geometries are considered. The optimized geometric parameters and interaction energies for various complexes at different levels are estimated. The infrared spectrum frequencies and IR intensities of the most stable structures are reported. Finally, thermochemistry studies are also carried out. The results indicate that the formation and the number of hydrogen bonding have played an important role in the structures and relative stabilities of different complexes. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Conjugation and proton exchange equilibria I. Significant role of proton exchange and homoconjugation equilibria in protonic hetero systems

The significant role of the proton exchange and homoconjugation (formation of AHA^– and A₁HA ₁ ^– complexes) equilibria in protonic hetero systems (HA+A ₁ ^– ) has been shown from analysis of published data and from my own simple experiments. It is concluded that there is a need to reconsider some basic hydrogen bond problems. One of these problems-the existence of heteroconjugates in polar solvents — has been verified and illustrated with suitable experimental evidence (IR and UV-VIS spectra). The most accepted experimental evidence for the double minimum potential in the hydrogen bridge has been questioned as being in disagreement with the equilibrium law. A simple relation between the heteroconjugation constant, the parent homoconjugation constants and the proton exchange constant is also postulated. This relation fulfills important theoretical requirements, however, it is not applicable in extreme cases.To the memory of Bogdan Przybyszewski.     

Novel Host Compounds, 1,1′-Binaphthyl-2,2′-Dihydroxy-5,5′- and 6,6′-Dicarboxylic Acid, which Trap Guest Molecules Tightly in their Inclusion Crystals

The host compounds 1,1’-binaphthyl-2,2′-dihydroxy-5,5′-dicarboxylic acid (1) and 1,1′-binaphthyl-2,2′-dihydroxy-6,6′-dicarboxylic acid (2) have been synthesized, and their inclusion properties have been studied. Inclusion complexes formed by 1 and 2 with volatile guests such as acetone and methanol release the guests only at much higher temperatures than their boiling points. The crystal structures of the inclusion complexes have been determined from single crystal X-ray diffraction data and show different host lattices.     

Dansyl-Modified γ-Cyclodextrin as a fluorescent sensor for molecular recognition

The crystal structure of thiamine iodide sesquihydrate has been determined by X-ray diffraction methods as a host-guest model for coenzyme-substrate interactions. The asymmetric unit contains two chemical units. Both the thiamine molecules A and B, which are crystallographically independent, assume the usualF conformation and have a disordered hydroxyethyl side chain. An iodide anion (or a water molecule) bridges the pyrimidine and thiazolium rings of molecule A (or B) by forming a hydrogen bond with the amino group and an electrostatic contact with the thiazolium ring to stabilize the molecular conformation. In the crystal the thiamine molecules self-associate to form a pipe-like polymeric structure, in which four thiamine hosts surround an iodide guest and hold it through C(2)-H...I hydrogen bonds and thiazolium...I electrostatic interactions. Crystal data: C₁₂H₁₇N₄OS⁺·I^– · 1.5 H₂O, monoclinic,P2₁/c, a=12.585(2), b=25.303(5), c=12.030(2) Å, =115.15(1)°,V=3468(1) ų,Z=8,D _c=1.606 g cm^–3,R=0.045 for 3328 observed reflections. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP. 82156 (13 pages).     

取代苯酚中共振增强的分子内氢键

根据晶体结构资料，计算了59个邻位取代苯酚中分子内氢键的几何．在STO－3G水平上计算了一些分子中原子部分电荷．结果表明，酚基氧与苯环上碳之间的键长，酚基上氢原子的部分电荷，酚基所在位置处的苯环环内角与取代苯酚的酸常数pKa均有近似线性关系，当邻位上存在硝基或羰基时，内氢键由于共振而得到显著的增强，据此可说明这一类酚的显著酸性     

Application of the pKa rule to synthesize salts of bezafibrate

ABSTRACT

Co-crystallization frequently employs forces such as hydrogen bonds, halogen bonds, and π-π stacking to assemble molecules in a multi-component crystal. In an effort to increase the strength of the intermolecular interaction between the anti-cholesterol drug bezafibrate (BEZA), a wastewater contaminant, and hydrogen-bond-acceptor molecules, we modified the pK_a values of the acceptors. Here, we describe the first series of salts incorporating BEZA and achieve a variety of supramolecular architectures including discrete assemblies, 1D chains, tapes, and 2D sheets. We discuss exceptions to the pK_a rule, and demonstrate that the presence of hydrogen-bond-donor atoms on the acceptor molecule supports salt formation.     

Structure of the 18-Crown-6 Complex with Ammonium Hexafluorosilicate and Water

The crystalline host–guest type complex [(18-crown-6NH₄)₂][SiF₆]4H₂Ohas been obtained as the result of the interaction of SiF₄2NH₃ with 18-crown-6 (18C6) in an aqueous medium. Crystal data: monoclinic, space groupC 2 c, a=26.541(2), b=8.363(2), c=20.469(2) Å, = 122.43(1)°and Z=4. The final R-value is 0.070 for 3253 reflections with I 2(I).The crystals consist of the complex [NH₄18C6]⁺ cations, [SiF₆]^2-anions and water molecules. The ammonium cation is hydrogen bonded by three of its H-atoms to the crown ether oxygen atoms with N(1) O separations2.923(5)–2.940(5) Å and by the fourth H-atom to the fluorine atom of thehexafluorosilicate anion, the N(1)F(4) distance being 2.797(6) Å.The conformation of the macrocycle and the hydrogen-bond geometry in thecomplex cation closely resemble those in related adducts between 18-crown-6and ammonium salts. All crystal components are connected via a system of hydrogen bonds into a ribbon along the b axis in the unit cell.     

A structural analysis of the complexes of (S,S)-dimethylpyridino-18-crown-6 with (R) and (S)-[α-(1-naphthyl)ethyl]ammonium perchlorate by NMR techniques and molecular modeling

Significant - interaction is found in the complexes of (S, S)-dimethylpyridino-18-crown-6 with (R)- and (S)-[-(1-naphthyl)ethyl]ammonium perchlorate. This finding is supported by the¹H NOESY NMR spectral technique, greater chemical shift changes of aromatic protons in both host and guest molecules upon complexation, and by molecular mechanics calculations. Because of the flexibility of the ligand, the tripod hydrogen bonding causes¹³C relaxation times of all periphery carbons to decrease without significant selectivity. Rotational energy barrier calculations of the methyl groups of the complexed ligand also show that the (S, S)-host-(R)-guest is the more stable complex.     

Isocytosine as a hydrogen-bonding partner and as a ligand in metal complexes

Isocytosine (ICH; 1) exists in solution in an equilibrium of tautomers 1a and 1b with the N1 and N3 positions carrying the acidic proton, respectively. In the solid state, both tautomers coexist in a 1:1 ratio. As we show, the N3H tautomer 1b can selectively be crystallized in the presence of the model nucleobase 1-methylcytosine (1-MeC). The complex 1b x (1-MeC)2 x H2O (2) forms pairs through three hydrogen bonds between the components; hydrogen bonds between identical molecules are also formed, leading to an infinite tape structure. On the other hand, the N1H tautomer 1a co-crystallizes with protonated ICH to give [1a x ICH2]NO3 (3), again with three hydrogen bonds between the partners, yet the acidic proton is disordered over the two entities. With M(II)(dien) (M=Pt, Pd; dien=diethylenetriamine) preferential coordination of tautomer 1a through the N3 position is observed. DFT calculations, which were also extended to Pt(II)(tmeda) linkage isomers (tmeda=N,N,N',N'-tetramethylethylenediamine), suggest that intramolecular hydrogen bonding between the ICH tautomers and the co-ligands at M, while adding to the preference for N3 coordination, is not the major determining factor. Rather it is the inherently stronger Pt-N3 bond which favors complexation of 1a. With an excess of M(II)(dien), dinuclear species [M2(dien)2(IC-N1,N3)]3+ (M=Pd(II), 4 and Pt(II), 5) also form and were isolated as their ClO4(-) salts and structurally characterized. In strongly acidic medium 5 is converted to [Pt(dien)(ICH-N1)]2+ (6), that is, to the Pt(II) complex of tautomer 1b.