Showing papers on "Hydrogen bond published in 2008"

Chiral squaramide derivatives are excellent hydrogen bond donor catalysts.

Abstract: Thioureas represent the dominant platform for hydrogen bond promoted asymmetric catalysts. A large number of reactions, reported in scores of publications, have been successfully promoted by chiral thioureas. The present paper reports the use of squaramides as a highly effective new scaffold for the development of chiral hydrogen bond donor catalysts. Squaramide catalysts are very simple to prepare. The (−)-cinchonine modified squaramide (5), easily prepared through a two-step process from methyl squarate, was shown to be an effective catalyst, even at catalyst loadings as low as 0.1 mol%, for the conjugate addition reactions of 1,3-dicarbonyl compounds to β-nitrostyrenes. The addition products were obtained in high yields and excellent enantioselectivities.

Supramolecular control of reactivity in the solid state: from templates to ladderanes to metal-organic frameworks.

Abstract: We describe how reactivity can be controlled in the solid state using molecules and self-assembled metal-organic complexes as templates. Being able to control reactivity in the solid state bears relevance to synthetic chemistry and materials science. The former offers a promise to synthesize molecules that may be impossible to realize from the liquid phase while also taking advantage of the benefits of conducting highly stereocontrolled reactions in a solvent-free environment (i.e., green chemistry). The latter provides an opportunity to modify bulk physical properties of solids (e.g., optical properties) through changes to molecular structure that result from a solid-state reaction. Reactions in the solid state have been difficult to control owing to frustrating effects of molecular close packing. The high degree of order provided by the solid state also means that the templates can be developed to determine how principles of supramolecular chemistry can be generally employed to form covalent bonds. The paradigm of synthetic chemistry employed by Nature is based on integrating noncovalent and covalent bonds. The templates assemble olefins via either hydrogen bond or coordination-driven self-assembly for intermolecular [2 + 2] photodimerizations. The olefins are assembled within discrete, or finite, self-assembled complexes, which effectively decouples chemical reactivity from effects of crystal packing. The control of the solid-state assembly process affords the supramolecular construction of targets in the form of cyclophanes and ladderanes. The targets form stereospecifically, in quantitative yield, and in gram amounts. Both [3]- and [5]-ladderanes have been synthesized. The ladderanes are comparable to natural ladderane lipids, which are a new and exciting class of natural products recently discovered in anaerobic marine bacteria. The organic templates function as either hydrogen bond donors or hydrogen bond acceptors. The donors and acceptors generate cyclobutanes lined with pyridyl and carboxylic acid groups, respectively. The metal-organic templates are based on Zn(II) and Ag(I) ions. The reactivity involving Zn(II) ions is shown to affect optical properties in the form of solid-state fluorescence. The solids based on both the organic and metal-organic templates undergo rare single-crystal-to-single-crystal reactions. We also demonstrate how the cyclobutanes obtained from this method can be applied as novel polytopic ligands of metallosupramolecular assemblies (e.g., self-assembled capsules) and materials (e.g., metal-organic frameworks). Sonochemistry is also used to generate nanostructured single crystals of the multicomponent solids or cocrystals based on the organic templates. Collectively, our observations suggest that the organic solid state can be integrated into more mainstream settings of synthetic organic chemistry and be developed to construct functional crystalline solids.

PdII-Catalyzed Enantioselective Activation of C(sp2)H and C(sp3)H Bonds Using Monoprotected Amino Acids as Chiral Ligands†

Abstract: Enantioselective C H activation has been a longstanding challenge in catalysis and organic chemistry. The insertion of metal-bound carbenes or nitrenes into C H bonds has been employed to develop highly enantioselective carbon–carbon and carbon–nitrogen bond-forming reactions. The enantioselective lithiation of C(sp) H bonds adjacent to the nitrogen atom in N-tert-butyloxycarbonylpyrrolidine using secBuLi/( )sparteine has provided a broadly useful method for the differentiation of prochiral C(sp) H bonds. Investigations into the biomimetic oxidation of C H bonds using chiral metal–porphyrin complexes and other synthetic catalysts continue to provide inspiration for the development of methods for the asymmetric oxidation of C H bonds. Remarkable progress in understanding the fundamental mechanisms of C H activation by means of metal insertion has spurred the development of metal-catalyzed carbon– carbon and carbon–heteroatom bond-forming reactions in organic molecules containing functional groups. Such reactions will impact synthetic and medicinal chemistry in the context of retrosynthetic analysis by providing unprecedented and more efficient strategic disconnections. A major hurdle remaining in Pd-catalyzed C H activation reactions, however, is the need for an external ligand that coordinates to the Pd species and controls the chemo-, regio-, and stereoselectivity of its insertion into C H bonds. With this in mind, we embarked on the development of a Pd-catalyzed enantioselective C H activation/C C coupling reaction, a process previously unknown owing to the difficulty in differentiating prochiral C H bonds through metal insertions. Herein we demonstrate a proof of concept by the design of a Pd/amino acid complex capable of catalyzing asymmetric activation of prochiral C(sp) H and C(sp) H bonds to form chiral products with new C C bonds in excellent enantioselectivity [Eq. (1)].

Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding

Abstract: The mechanism of denaturation of proteins by urea is explored by using all-atom microseconds molecular dynamics simulations of hen lysozyme generated on BlueGene/L Accumulation of urea around lysozyme shows that water molecules are expelled from the first hydration shell of the protein We observe a 2-stage penetration of the protein, with urea penetrating the hydrophobic core before water, forming a "dry globule" The direct dispersion interaction between urea and the protein backbone and side chains is stronger than for water, which gives rise to the intrusion of urea into the protein interior and to urea's preferential binding to all regions of the protein This is augmented by preferential hydrogen bond formation between the urea carbonyl and the backbone amides that contributes to the breaking of intrabackbone hydrogen bonds Our study supports the "direct interaction mechanism" whereby urea has a stronger dispersion interaction with protein than water

Conformational polymorphism in organic crystals.

Abstract: Polymorphs are different crystalline modifications of the same chemical substance. When different conformers of the same molecule occur in different crystal forms, the phenomenon is termed conformational polymorphism. Occasionally, more than one conformer is present in the same crystal structure. The influence of molecular conformation changes on the formation and stability of polymorphs is the focus of this Account. X-ray crystal structures of conformational polymorphs were analyzed to understand the interplay of intramolecular (conformer) and intermolecular (lattice) energy in the crystallization and stability of polymorphs. Polymorphic structures stabilized by strong O−H···O/N−H···O hydrogen bonds, weak C−H···O interactions, and close packing were considered. 4,4-Diphenyl-2,5-cyclohexadienone (1) and bis(p-tolyl) ketone p-tosylhydrazone (3) are prototypes of C−H···O and N−H···O hydrogen-bonded structures. Distance−angle scatter plots of O−H···O and C−H···O hydrogen bonds extracted from the Cambridge St...

Control of H‐ and J‐Type π Stacking by Peripheral Alkyl Chains and Self‐Sorting Phenomena in Perylene Bisimide Homo‐ and Heteroaggregates

Abstract: The synthesis, self-assembly, and gelation ability of a series of organogelators based on perylene bisimide (PBI) dyes containing amide groups at imide positions are reported. The synergetic effect of intermolecular hydrogen bonding among the amide functionalities and pi-pi stacking between the PBI units directs the formation of the self-assembled structure in solution, which beyond a certain concentration results in gelation. Effects of different peripheral alkyl substituents on the self-assembly were studied by solvent- and temperature-dependent UV-visible and circular dichroism (CD) spectroscopy. PBI derivatives containing linear alkyl side chains in the periphery formed H-type pi stacks and red gels, whereas by introducing branched alkyl chains the formation of J-type pi stacks and green gels could be achieved. Sterically demanding substituents, in particular, the 2-ethylhexyl group completely suppressed the pi stacking. Coaggregation studies with H- and J-aggregating chromophores revealed the formation of solely H-type pi stacks containing both precursor molecules at a lower mole fraction of J-aggregating chromophore. Beyond a critical composition of the two chromophores, mixed H-aggregate and J-aggregate were formed simultaneously, which points to a self-sorting process. The versatility of the gelators is strongly dependent on the length and nature of the peripheral alkyl substituents. CD spectroscopic studies revealed a preferential helicity of the aggregates of PBI building blocks bearing chiral side chains. Even for achiral PBI derivatives, the utilization of chiral solvents such as (R)- or (S)-limonene was effective in preferential population of one-handed helical fibers. AFM studies revealed the formation of helical fibers from all the present PBI gelators, irrespective of the presence of chiral or achiral side chains. Furthermore, vortex flow was found to be effective in macroscopic orientation of the aggregates as evidenced from the origin of CD signals from aggregates of achiral PBI molecules.

Quantum Differences between Heavy and Light Water.

Abstract: The structures of heavy and light water at ambient conditions are investigated with the combined techniques of x-ray diffraction, neutron diffraction, and computer simulation. It is found that heavy water is a more structured liquid than light water. We find the OH bond length in H2O is approximately 3% longer than the OD bond length in D2O. This is a much larger change than current predictions. Corresponding to this, the hydrogen bond in light water is approximately 4% shorter than in heavy water, while the intermolecular HH distance is approximately 2% longer.

The smallest amphiphiles: nanostructure in protic room-temperature ionic liquids with short alkyl groups.

Abstract: Room-temperature ionic liquids (ILs) are low-melting-point organic salts that, until recently, were thought to have homogeneous microstructure. In this work, we investigate nanoscale segregation of short (

Time-dependent density functional theory study on hydrogen-bonded intramolecular charge-transfer excited state of 4-dimethylamino-benzonitrile in methanol.

Abstract: The time-dependent density functional theory (TDDFT) method was carried out to investigate the hydrogen-bonded intramolecular charge-transfer (ICT) excited state of 4-dimethylaminobenzonitrile (DMABN) in methanol (MeOH) solvent. We demonstrated that the intermolecular hydrogen bond C[triple bond]N...H-O formed between DMABN and MeOH can induce the C[triple bond]N stretching mode shift to the blue in both the ground state and the twisted intramolecular charge-transfer (TICT) state of DMABN. Therefore, the two components at 2091 and 2109 cm(-1) observed in the time-resolved infrared (TRIR) absorption spectra of DMABN in MeOH solvent were reassigned in this work. The hydrogen-bonded TICT state should correspond to the blue-side component at 2109 cm(-1), whereas not the red-side component at 2091 cm(-1) designated in the previous study. It was also demonstrated that the intermolecular hydrogen bond C[triple bond]N...H-O is significantly strengthened in the TICT state. The intermolecular hydrogen bond strengthening in the TICT state can facilitate the deactivation of the excited state via internal conversion (IC), and thus account for the fluorescence quenching of DMABN in protic solvents. Furthermore, the dynamic equilibrium of these electronically excited states is explained by the hydrogen bond strengthening in the TICT state.

Nature and physical origin of CH/π interaction: significant difference from conventional hydrogen bonds

Abstract: Recently reported high-level ab initio calculations and gas phase spectroscopic measurements show that the nature of CH/π interactions is considerably different from conventional hydrogen bonds, although the CH/π interactions were often regarded as the weakest class of hydrogen bonds. The major source of attraction in the CH/π interaction is the dispersion interaction and the electrostatic contribution is small, while the electrostatic interaction is mainly responsible for the attraction in the conventional hydrogen bonds. The nature of the “typical” CH/π interactions is similar to that of van der Waals interactions, if some exceptional “activated” CH/π interactions of highly acidic C–H bonds are excluded. Shifts of C–H vibrational frequencies and electronic spectra also support the similarity. The hydrogen bond is important in controlling structures of molecular assemblies, since the hydrogen bond is sufficiently strong and directional due to the large electrostatic contribution. On the other hand, the directionality of the “typical” CH/π interaction is very weak. Although the “typical” CH/π interaction is often regarded as an important interaction in controlling the structures of molecular assemblies as in the cases of conventional hydrogen bonds, the importance of the “typical” CH/π interactions is questionable.

A FTIR and 2D-IR Spectroscopic Study on the Microdynamics Phase Separation Mechanism of the Poly(N-isopropylacrylamide) Aqueous Solution

Abstract: The thermal behavior of PNIPAM in its concentrated D2O solution (20 wt %) was studied by FTIR and 2D-IR correlation spectroscopy. The spectral data of the C−H groups and the Amide I region provide details about the changes of the hydrophobic and hydrophilic parts in the polymer respectively during a heating−cooling cycle. The reversal of peak positions of the C−H bands upon cooling indicates the reversibility of temperature-induced dehydration of the hydrophobic groups. The change in hydrogen bonding of CO···D−N constructed between dehydrated CO and N−D groups, as derived from the Amide I region, does not revert precisely in the cooling process due to the newly formed hydrogen bonds in the collapsed state, and a hysteresis phenomenon is observed. In our concentrated solution (20 wt %), the strength of those intra- and interchain hydrogen bonds even prevent the polymers from dissociating completely below the LCST during the cooling process. The microdynamics phase separation mechanism was obtained by appli...

A hydrogen bond accepting (HBA) scale for anions, including room temperature ionic liquids

Abstract: A hydrogen bond accepting (HBA) ability scale for anions of room temperature ionic liquids (RTILs) has been determined by means of 1H NMR spectroscopy and a solvatochromic UV/vis probe.

Structures and interaction energies of stacked graphene–nucleobase complexes

Abstract: The noncovalent interactions of nucleobases and hydrogen-bonded (Watson–Crick) base-pairs on graphene are investigated with the DFT-D method, i.e., all-electron density functional theory (DFT) in generalized gradient approximation (GGA) combined with an empirical correction for dispersion (van der Waals) interactions. Full geometry optimization is performed for complexes with graphene sheet models of increasing size (up to C150H30). Large Gaussian basis sets of at least polarized triple-ζ quality are employed. The interaction energies are extrapolated to infinite lateral size of the sheets. Comparisons are made with B2PLYP-D and SCS-MP2 single point energies for coronene and C54H18 substrates. The contributions to the binding (Pauli exchange repulsion, electrostatic and induction, dispersion) are analyzed. At a frozen inter-fragment distance, the interaction energy surface of the rigid C96H24 and base monomers is explored in three dimensions (two lateral and one rotational). Methodologically and also regarding the results of an energy decomposition analysis, the complexes behave like other π-stacked systems examined previously. The sequence obtained for the interaction energy of bases with graphene (G > A > T > C > U) is the same for all methods and supports recent experimental findings. The absolute values are rather large (about −20 to −25 kcal mol−1) but in the expected range for π-systems of that size. The relatively short equilibrium inter-plane distance (about 3 A) is consistent with atomic force microscopy results of monolayer guanine and adenine on graphite. In graphene⋯Watson–Crick pair complexes, the bases lie differently from their isolated energy minima leading to geometrical anti-cooperativity. Together with an electronic contribution of 2 and 6%, this adds up to total binding anti-cooperativities of 7 and 12% for AT and CG, respectively, on C96H24. Hydrogen bonds themselves are merely affected by binding on graphene.

Palladium-catalyzed method for the synthesis of carbazoles via tandem C-H functionalization and C-N bond formation.

Abstract: The development of a new method for the assembly of unsymmetrical carbazoles is reported. The strategy involves the selective intramolecular functionalization of an arene C-H bond and the formation of a new arene C-N bond. The substitution pattern of the carbazole product can be controlled by the design of the biaryl amide substrate, and the method is compatible with a variety of functional groups. The utility of the new protocol was demonstrated by the concise synthesis of three natural products from commercially available materials.

Hollow Crescents, Helices, and Macrocycles from Enforced Folding and Folding-Assisted Macrocyclization

Abstract: This Account reviews the progress made by us on creating porous molecular crescents, helices, and macrocycles based on aromatic oligoamides. Inspired by natural pore- or cavity-containing secondary structures, work described in this Account stemmed from the development of foldamers consisting of benzene rings linked by secondary amide groups. Highly stable, three-center intramolecular hydrogen bonds involving the amide linkages are incorporated into these aromatic oligoamides, which, along with meta-linked benzene units that introduce curvatures into the corresponding backbones, leads to tape-like, curved backbones. Depending on their chain lengths, aromatic oligoamides that fold into crescent and helical conformations have been obtained. Combining results from modeling and experimentally measured data indicates that the folding of these oligomers is readily predictable, determined by the localized intramolecular three-center H-bonds and is independent of side-chain substitution. As a result, a variety of...

Structure of the transmembrane region of the M2 protein H(+) channel.

Abstract: The transmembrane domain of the M2 protein from influenza A virus forms a nearly uniform and ideal helix in a liquid crystalline bilayer environment. The exposure of the hydrophilic backbone structure is minimized through uniform hydrogen bond geometry imposed by the low dielectric lipid environment. A high-resolution structure of the monomer backbone and a detailed description of its orientation with respect to the bilayer were achieved using orientational restraints from solid-state NMR. With this unique information, the tetrameric structure of this H+ channel is constrained substantially. Features of numerous published models are discussed in light of the experimental structure of the monomer and derived features of the tetrameric bundle.

In-situ X-ray photoelectron spectroscopy studies of water on metals and oxides at ambient conditions

Abstract: X-ray photoelectron spectroscopy (XPS) is a powerful tool for surface and interface analysis, providing the elemental composition of surfaces and the local chemical environment of adsorbed species. Conventional XPS experiments have been limited to ultrahigh vacuum (UHV) conditions due to a short mean free path of electrons in a gas phase. The recent advances in instrumentation coupled with third-generation synchrotron radiation sources enables in-situ XPS measurements at pressures above 5 Torr. In this review, we describe the basic design of the ambient pressure XPS setup that combines differential pumping with an electrostatic focusing. We present examples of the application of in-situ XPS to studies of water adsorption on the surface of metals and oxides including Cu(110), Cu(111), TiO2(110) under environmental conditions of water vapor pressure. On all these surfaces we observe a general trend where hydroxyl groups form first, followed by molecular water adsorption. The importance of surface OH groups and their hydrogen bonding to water molecules in water adsorption on surfaces is discussed in detail.

Blue shifts vs red shifts in σ-hole bonding

Abstract: σ-Hole bonding is a noncovalent interaction between a region of positive electrostatic potential on the outer surface of a Group V, VI, or VII covalently-bonded atom (a σ-hole) and a region of negative potential on another molecule, e.g., a lone pair of a Lewis base. We have investigated computationally the occurrence of increased vibration frequencies (blue shifts) and bond shortening vs decreased frequencies (red shifts) and bond lengthening for the covalent bonds to the atoms having the σ-holes (the σ-hole donors). Both are possible, depending upon the properties of the donor and the acceptor. Our results are consistent with models that were developed earlier by Hermansson and by Qian and Krimm in relation to blue vs red shifting in hydrogen bond formation. These models invoke the derivatives of the permanent and the induced dipole moments of the donor molecule.

An Iron(II) Spin‐Crossover Complex with a 70 K Wide Thermal Hysteresis Loop

Abstract: Spin-crossover (SCO) complexes are a fascinating class of molecules that can be switched on the molecular level by the use of temperature, pressure, or light. For potential applications, these compounds should exhibit a cooperative spin transition with a wide thermal hysteresis loop that is centered at room temperature. In the past few years, several strategies were discussed as to how geometry changes occurring during the spin transition can be transmitted effectively through the crystal lattice, as these cooperative interactions are the key factor for the appearance of wide thermal hysteresis loops. One promising strategy is the use of covalent linkers to form coordination polymers, as suggested by Kahn et al. 3] However, no real breakthrough has occurred in the last decade. This is not surprising considering that we could demonstrate for the bridging ligand 4,4’bipyridine that different SCO properties are not based on the covalent linker but are due to interactions (e.g. van der Waals forces) between the polymer chains. Over the last few years, we have investigated the properties of several SCO complexes with N4O2 coordination spheres. 6] The properties of the spin transition curve correlate well with the number and intensity of the intermolecular contacts, and thermal hysteresis loops up to 18 K wide could be obtained, owing to a 3D network of short van der Waals contacts. The widest hysteresis loops observed to date for a structurally characterized SCO complex are about 40 K. In both examples, this hysteresis arises from p–p interactions between ligands with extended aromatic structures. In other compounds with thermal hysteresis loops 70 K wide or up to 92 K wide, p stacking is also considered to play a central role; however, no X-ray structure analyses are available for these compounds. To date, we have not succeed in applying this strategy to our N4O2 ligand system. [10] Therefore, we decided to use hydrogen bonds as intermolecular contacts, as these should be stronger than van der Waals contacts but more flexible than covalent linkers. Although the possibility to transmit cooperative interactions through H bonds has not been drawn into questioned, to date relatively few examples of H-bond-linked SCO complexes are known. Recently, indications were found that the 35 K wide thermal hysteresis loop in the SCO coordination polymer [Fe(NH2trz)3](NO3)2 (trz = 4-amino-1,2,4-triazole) is due to a network of hydrogen bonds. The reaction of imidazole with the iron complex [FeL(MeOH)2] (Scheme 1) in methanol was first investigated by M ller et al. and resulted in the formation of an iron

A Hydrogen Bond Surrogate Approach for Stabilization of Short Peptide Sequences in α-Helical Conformation

Abstract: α-Helices constitute the largest class of protein secondary structures and play a major role in mediating protein−protein interactions. Development of stable mimics of short α-helices would be invaluable for inhibition of protein−protein interactions. This Account describes our efforts in developing a general approach for constraining short peptides in α-helical conformations by a main-chain hydrogen bond surrogate (HBS) strategy. The HBS α-helices feature a carbon−carbon bond derived from a ring-closing metathesis reaction in place of an N-terminal intramolecular hydrogen bond between the peptide i and i + 4 residues. Our approach is centered on the helix−coil transition theory in peptides, which suggests that the energetically demanding organization of three consecutive amino acids into the helical orientation inherently limits the stability of short α-helices. The HBS method affords preorganized α-turns to overcome this intrinsic nucleation barrier and initiate helix formation. The HBS approach is an a...

Temperature-responsive polymers in mixed solvents: competitive hydrogen bonds cause cononsolvency.

Abstract: If two good solvents become poor for a polymer when mixed, the solvent pair is called a cononsolvent pair. The sharp reentrant coil-to-globule-to-coil transition of a $\mathrm{\text{poly}}(N\mathrm{\text{-isopropylacrylamide}})$ chain observed in the mixed solvent of water and methanol is shown to be caused by the competitive hydrogen bonding by water and methanol molecules onto the polymer chain. On the basis of a new statistical-mechanical model for competitive hydrogen bonds, the mean square end-to-end distance is theoretically calculated and compared with experiment. The chain sharply collapses at the molar fraction ${x}_{m}\ensuremath{\simeq}0.2$ of methanol, stays collapsed up to ${x}_{m}\ensuremath{\simeq}0.4$, and finally recovers the swollen state at ${x}_{m}\ensuremath{\simeq}0.6$. Such a reentrant coil-globule transition takes place because the total number of hydrogen bonds along the chain exhibits a similar square-well-type depression as a result of the competition.

The Reaction Mechanism for the Organocatalytic Ring-Opening Polymerization of l-Lactide Using a Guanidine-Based Catalyst: Hydrogen-Bonded or Covalently Bound?

Abstract: We have investigated two alternative mechanisms for the ring-opening polymerization of l-lactide using a guanidine-based catalyst, the first involving acetyl transfer to the catalyst, and the second involving only hydrogen bonding to the catalyst. Using computational chemistry methods, we show that the hydrogen bonding pathway is considerably preferred over the acetyl transfer pathway and that this is consistent with experimental information.