Double H-bonds Research Articles

New Two-Dimensional Ice Models

This paper presents a new approach for enumerating all hydrogen bond arrange- ments of ice-like systems with periodic boundary conditions. It is founded on a topological procedure for the dimensional reduction and a new variant of the transfer matrix method based on small conditional transfer matrices. We consider a couple of new two-dimensional ice models on very unusual lattices. One of them is the twisted square ice model with cross- ing H-bonds. The other is the digonal-hexagonal model with double H-bonds. In spite of their uncommonness, these models are quite realistic, because from the standpoint of com- binatorics and topology they are equivalent to the layers of usual hexagonal ice Ih under periodic boundary conditions in one of the directions. The exact proton configuration statis- tics for a number of 2D-expanded unit cells of hexagonal ice Ih and the residual entropy of the new ice models in the large system limit are presented.

Time-Dependent Density Functional Theory Study on Excited-State Hydrogen Bonding Dynamics of Acetic Acid Hydrates

The time-dependent density functional theory (TDDFT) method was performed to investigate the hydrogen-bonding dynamics of acetic acid (AA) hydrates in aqueous solution. For AA, it tends to be both active hydrogen acceptor and donor and denote double H-bonds as OA···HW and HA···OW, resulting in ring structure hydrates. The ground-state geometry optimizations and electronic transition energies and corresponding oscillation strengths of the low-lying electronically excited states for the isolated AA monomer and the hydrogen-bonded ring structure hydrates are calculated by the density functional theory and TDDFT methods, respectively. Different types of intermolecular hydrogen bonds are formed between one AA molecule and water molecules. According to Zhao’s rule on the excited-state hydrogen bonding dynamics, it can be found that the intermolecular hydrogen bonds OA···HW and HA···OW are strengthened in electronically excited states of the hydrogen-bonded ring structure hydrates, with the excitation energy of a related excited state being lowered and electronic spectral redshifts being induced. Moreover, the hydrogen bond strengthening in the electronically excited state is crucial to the photophysics and photochemistry of hydrates with AA in aqueous solution.

Coupling Interactions between Sulfurous Acid and the Hydroperoxyl Radical

Radical-molecule complexes associated with the hydroperoxyl radical (HOO) play an important role in atmospheric chemistry. Herein, the nature of the coupling interactions between sulfurous acid (H(2)SO(3)) and the HOO radical is systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, the natural bond orbital (NBO) method, and energy decomposition analyses (EDA). Eight stable stationary points possessing double H-bonding features were located on the H(2)SO(3)...HOO potential energy surface. The largest binding energies of -12.27 and -11.72 kcal mol(-1) are observed for the two most stable complexes, where both of them possess strong double intermolecular H-bonds of partially covalence. Moreover, the characteristics of the IR spectra for the two most stable complexes are discussed to provide some help for their possible experimental identification.

Enantioselective Organocatalytic Direct Michael Addition of Nitroalkanes to Nitroalkenes Promoted by a Unique Bifunctional DMAP-Thiourea

A new catalyst is designed, synthesized, and evaluated for the asymmetric Michael addition of nitroalkanes to nitroalkenes. The obdurate nature of this reaction has made this a formidable challenge to subdue by asymmetric catalysis. The catalyst design includes a thiourea function to activate the nitroalkene by a double H-bond and a 4-dimethylaminopyridine unit to deprotonate the nitroalkane and to bind the resulting nitronate anion also by a double H-bond. The chiral scaffold for the catalyst is 2,2'-diamino-1,1'-binaphthalene (BINAM), and a bis-conjugate is prepared by the attachment of the thiourea unit and the dimethylaminopyridine moiety (DMAP) via the two amino groups. The resulting catalyst will effect the reaction of nitroalkanes to a variety of nitrostyrenes and gives excellent asymmetric inductions (91-95% ee) over a range of 10 substrates. Remarkably, the asymmetric induction increases with decreasing catalyst loading with the optimal compromise between rate and induction at a loading of 2 mol %.

An unusual Cu(II) polymeric compound with tridentate dehydronated and bidentate neutral ligand bis(pyrimidin-2-yl)amine (=Hdipm) and uncoordinated Hdipm in a complicated H-bonding system. Synthesis, characterization and X-ray structure of {[Cu(dipm)(Hdipm)](Hdipm)(CF 3SO 3)(C 2H 5OH)(H 2O)} n

A highly unusual polymeric copper(II) compound with formula {[Cu(dipm)(Hdipm)](Hdipm)(CF 3SO 3)(C 2H 5OH)(H 2O)} n (in which Hdipm = bis(pyrimidin-2-yl)amine) has been synthesized and characterized by X-ray crystallography, infrared spectroscopy and EPR. The Cu(II) ion is surrounded by five nitrogen atoms. The basal plane is formed by two nitrogen atoms from a neutral Hdipm ligand and two nitrogen atoms from a dehydronated (dipm) − ligand with Cu–N distances which vary from 1.990(3) to 2.093(3) Å. The fifth nitrogen atom originate from a neighbouring anionic ligand with a Cu–N distance of 2.183(4) Å, forming a distorted trigonal bipyramidal geometry around the Cu(II) ion. Furthermore the lattice are contains an uncoordinating Hdipm ligand (stacked on other ligands), one triflate anion, one ethanol molecule and one water molecule. The 2D system of Hydrogen bonds consists of Watson–Crick-type intermolecular double H-bonds between pairs of dipm molecules and H-bonds between the triflate anion, the ethanol and water molecules. The ligand-field and EPR spectra are uneventful and agree with the found coordination geometry. Cu(II) hyperfine splitting remains unresolved.

Reversible thermochromism in self-layered hydrogen-bondedpolydiacetylene assembly

We structurally designed and synthesized a novel class of self-layered supramolecular polymers containing DA derivatives that can be obtained as film-forming materials and processed into a various forms. We found that double H-bonds between the acid hard cores together with a remarkable molecular DA recognition allow for retaining more favorable packing of the reactive groups in spin-coated films or even in dispersed solutions with a high degree of local ordering, suitable for topochemical polymerization. The sample molecularly designed here could be topochemically polymerized by UV irradiation through 1,4 addition of the conjugated triple bonds between adjacent stacking molecules. A reversible thermochromism in the absorption characteristics of spin-coated terephthalic acid/diacetylene polymers was also observed.

Probing the Watson−Crick, Wobble, and Sugar-Edge Hydrogen Bond Sites of Uracil and Thymine

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.

Infrared Signatures of a Water Molecule Attached to Triatomic Domains of Molecular Anions: Evolution of the H-bonding Configuration with Domain Length

We present mid-IR argon predissociation spectra for a series of complexes, M-·H2O (M = CS2-, OCS-, SO2-, CH3NO2-, CH3CO2-, and NO2-), chosen to explore how changes in the triatomic binding site affect the H-bonding configuration of the attached water molecule. With the exception of NO2-, the calculated global minima on the potential surfaces of all of the complexes occur in a configuration where both OH groups are attached to the anion. The observed spectra, on the other hand, fall into three distinct categories. Simple spectra characteristic of the double ionic H-bonding arrangement are observed for the monohydrates of SO2-, OCS-, and CS2-, whereas the CH3NO2-·H2O and CH3CO2-·H2O spectra are complicated, displaying a progression of closely spaced bands with a broad, bell-shaped envelope beginning several hundred wavenumbers below the calculated fundamentals. Although the spectrum of the NO2-·H2O complex is the most red-shifted, it is again simple, reflecting the expected asymmetric (single ionic H-bonded) motif. These data indicate that the transition from single to double ionic H-bonding occurs at a critical domain length of about 2.2 Å. We explore the potential surfaces governing the interconversion between the two forms with density functional calculations and construct vibrationally adiabatic potential surfaces to assess the cause of the spectral complexity displayed by the methylated anion hydrates.

Structure and dynamics of metallomacrocycles: recognition of zinc xylyl-bicyclam by an HIV coreceptor.

As platforms for the design of metal-based therapeutic and diagnostic agents, macrocycles are rigid enough to provide strong metal binding sites and orient functional groups stereoselectively, yet flexible enough to accommodate structural changes required for induced-fit recognition of biological targets. We consider the recognition of the Zn(II) complex of the bis-tetraazamacrocycle xylyl-bicyclam, a potent anti-HIV agent, by the coreceptor CXCR4, a G-protein-coupled receptor used by HIV for membrane fusion and cell entry. NMR studies show that the macrocycles of Zn(II)(2)-xylyl-bicyclam perchlorate exist in aqueous solution as two major configurations, trans-I (nitrogen chirality R,S,R,S), and trans-III (S,S,R,R). Acetate addition induced a major structural change. X-ray crystallography shows that the acetate complex contains the unusual cis-V cyclam configuration (R,R,R,R and folded) with bidentate coordination of acetate to Zn(II) plus second-coordination-sphere double H-bond formation between diagonal NH protons on the opposite cyclam face and acetate carboxylate oxygens. Detailed 1D and 2D NMR studies show that the major configuration of Zn(II)(2)-xylyl-bicyclam acetate in aqueous solution is cis-V/trans-I. Molecular modeling shows that an analogous cis-V site can be formed when Zn(II)(2)-xylyl-bicyclam binds to CXCR4, involving the carboxylate groups of Asp262 (Zn(II) coordination) and Glu288 (double H-bonding). The second cyclam can adopt the trans-I (or trans-III) configuration with Zn(II) binding to Asp171. These interactions are consistent with the known structure-activity relationships for bicyclam anti-HIV activity and receptor mutation. Consideration of the anti-HIV activity of xylyl-bicyclam complexes of other metal ions suggests that affinity for carboxylates, configurational flexibility, and kinetic factors may all play roles in receptor recognition. For example, Pd(II) cyclam complexes interact only weakly with axial ligands and are inflexible and inactive, whereas Co(III) cyclams bind carboxylates strongly, are configurationally flexible, and yet have low activity. Our findings should aid the design of new generations of active macrocycles including highly specific chemokine receptor antagonists.

Teaching molecular 3‐D literacy

Teaching molecular 3‐D literacy

Characterisation of sorbed water molecules on neutral and ionic polysaccharides

Ionic and neutral polysaccharides with well-defined structures were chosen to investigate the mechanism of water sorption at different relative humidities. From an experimental point of view, the freezing water was determined by DSC when the total sorbed water was obtained from thermogravimetry. The isotherms of sorption and enthalpies of interaction were determined using the combination of a microbalance and a microcalorimeter. It is shown that freezing water appears for P/ P 0 > 0.85 especially with the neutral polymers. The differential molar enthalpy of interaction is higher for P/ P 0 < 0.85 corresponding to the fixation of two water molecules forming double H-bonds; this result is confirmed by molecular modelling; saturation is obtained experimentally for 4 water molecules interacting per glucose unit. On ionic polymers, the water retention increases especially over P/P 0 ∼ 0.8 and the enthalpy of interaction is higher for the first water molecules sorbed. For P/ P 0 ≅ 0.8, the numbers of bound water molecules found are 2 per glucopyranosyl unit for neutral polysaccharides, 5 for glucuronan and 9–10 for carboxymethylcellulose (CMC) of D S = 2 and hyaluronan (HA)