Showing papers on "Hydrogen bond published in 2003"
TL;DR: In this paper, a linear relationship between the contact angle and the water monomer binding energy on graphite was established and a new route to calibrate interaction potential parameters was presented, which was obtained by applying a carbon−oxygen Lennard-Jones potential with parameters eCO = 0.392 kJ mol-1 and σCO = 3.19 A.
Abstract: A systematic molecular dynamics study shows that the contact angle of a water droplet on graphite changes significantly as a function of the water−carbon interaction energy. Together with the observation that a linear relationship can be established between the contact angle and the water monomer binding energy on graphite, a new route to calibrate interaction potential parameters is presented. Through a variation of the droplet size in the range from 1000 to 17 500 water molecules, we determine the line tension to be positive and on the order of 2 × 10-10 J/m. To recover a macroscopic contact angle of 86°, a water monomer binding energy of −6.33 kJ mol-1 is required, which is obtained by applying a carbon−oxygen Lennard-Jones potential with the parameters eCO = 0.392 kJ mol-1 and σCO = 3.19 A. For this new water−carbon interaction potential, we present density profiles and hydrogen bond distributions for a water droplet on graphite.
1,155 citations
TL;DR: This work uses hydrogen bonding to guide the assembly of two types of molecules into a two-dimensional open honeycomb network that then controls and templates new surface phases formed by subsequently deposited fullerene molecules, and finds that the open network acts as aTwo-dimensional array of large pores of sufficient capacity to accommodate several large guest molecules.
Abstract: Selective non-covalent interactions have been widely exploited in solution-based chemistry to direct the assembly of molecules into nanometre-sized functional structures such as capsules, switches and prototype machines1,2,3,4,5. More recently, the concepts of supramolecular organization have also been applied to two-dimensional assemblies on surfaces6,7 stabilized by hydrogen bonding8,9,10,11,12,13,14, dipolar coupling15,16,17 or metal co-ordination18. Structures realized to date include isolated rows8,13,14,15, clusters9,10,18 and extended networks10,11,12,17, as well as more complex multi-component arrangements16. Another approach to controlling surface structures uses adsorbed molecular monolayers to create preferential binding sites that accommodate individual target molecules19,20. Here we combine these approaches, by using hydrogen bonding to guide the assembly of two types of molecules into a two-dimensional open honeycomb network that then controls and templates new surface phases formed by subsequently deposited fullerene molecules. We find that the open network acts as a two-dimensional array of large pores of sufficient capacity to accommodate several large guest molecules, with the network itself also serving as a template for the formation of a fullerene layer.
1,047 citations
TL;DR: This result shows that the presence of ions does not lead to an enhancement or a breakdown of the hydrogen-bond network in liquid water.
Abstract: The effects of ions on bulk properties of liquid water, such as viscosity, have suggested that ions alter water's hydrogen-bonding network We measured the orientational correlation time of water molecules in Mg(ClO4)2, NaClO4, and Na2SO4 solutions by means of femtosecond pump-probe spectroscopy The addition of ions had no influence on the rotational dynamics of water molecules outside the first solvation shells of the ions This result shows that the presence of ions does not lead to an enhancement or a breakdown of the hydrogen-bond network in liquid water
850 citations
TL;DR: H-H bonding is shown to be distinct from "dihydrogen bonding", a form of hydrogen bonding with a hydridic hydrogen in the role of the base atom.
Abstract: Bond paths linking two bonded hydrogen atoms that bear identical or similar charges are found between the ortho-hydrogen atoms in planar biphenyl, between the hydrogen atoms bonded to the C1–C4 carbon atoms in phenanthrene and other angular polybenzenoids, and between the methyl hydrogen atoms in the cyclobutadiene, tetrahedrane and indacene molecules corseted with tertiary-tetra-butyl groups. It is shown that each such H–H interaction, rather than denoting the presence of “nonbonded steric repulsions”, makes a stabilizing contribution of up to 10 kcal mol−1 to the energy of the molecule in which it occurs. The quantum theory of atoms in molecules—the physics of an open system—demonstrates that while the approach of two bonded hydrogen atoms to a separation less than the sum of their van der Waals radii does result in an increase in the repulsive contributions to their energies, these changes are dominated by an increase in the magnitude of the attractive interaction of the protons with the electron density distribution, and the net result is a stabilizing change in the energy. The surface virial that determines the contribution to the total energy decrease resulting from the formation of the H–H interatomic surface is shown to account for the resulting stability. It is pointed out that H–H interactions must be ubiquitous, their stabilization energies contributing to the sublimation energies of hydrocarbon molecular crystals, as well as solid hydrogen. H–H bonding is shown to be distinct from “dihydrogen bonding”, a form of hydrogen bonding with a hydridic hydrogen in the role of the base atom.
646 citations
TL;DR: An unusual buried metal-receptor site in CueR restricts the metal to a linear, two-coordinate geometry and uses helix-dipole and hydrogen-bonding interactions to enhance metal binding, which is rare among metalloproteins but well suited for an ultrasensitive genetic switch.
Abstract: The earliest of a series of copper efflux genes in Escherichia coli are controlled by CueR, a member of the MerR family of transcriptional activators. Thermodynamic calibration of CueR reveals a zeptomolar (10(-21) molar) sensitivity to free Cu+, which is far less than one atom per cell. Atomic details of this extraordinary sensitivity and selectivity for +1transition-metal ions are revealed by comparing the crystal structures of CueR and a Zn2+-sensing homolog, ZntR. An unusual buried metal-receptor site in CueR restricts the metal to a linear, two-coordinate geometry and uses helix-dipole and hydrogen-bonding interactions to enhance metal binding. This binding mode is rare among metalloproteins but well suited for an ultrasensitive genetic switch.
622 citations
TL;DR: An orientation-dependent hydrogen bonding potential based on the geometric characteristics of hydrogen bonds in high-resolution protein crystal structures is developed and evaluated using four tests related to the prediction and design of protein structures and protein-protein complexes.
511 citations
TL;DR: An overview of coordination complexes connected via simple hydrogen bonding substituents, e.g. carboxylic acids and carboxamides, is given, and analogous organic and inorganic hydrogen bonding networks are discussed as mentioned in this paper.
461 citations
416 citations
TL;DR: Although the inhibitor did not directly coordinate to the molybdenum ion, numerous hydrogen bonds as well as hydrophobic interactions with the protein matrix were observed, most of which are also used in substrate recognition.
359 citations
TL;DR: In this paper, the authors used terahertz time-domain spectroscopy to measure the full dielectric function of the monosaccharides glucose and fructose and the disaccharide sucrose in the frequency range 0.5-4.0 THz.
351 citations
TL;DR: Proton transfer along 1D chains of water molecules inside carbon nanotubes is studied by simulations and an empirical valence bond model yield similar structures and time scales.
Abstract: Proton transfer along 1D chains of water molecules inside carbon nanotubes is studied by simulations. Ab initio molecular dynamics and an empirical valence bond model yield similar structures and time scales. The proton mobility along 1D water chains exceeds that in bulk water by a factor of 40, but is reduced if orientational defects are present. Excess protons interact with hydrogen-bonding defects through long-range electrostatics, resulting in coupled motion of protons and defects.
TL;DR: In this article, the synthesis of neutral macrocyclic anion receptors and their anion binding properties is discussed. But the synthesis is not restricted to macro-cyclic scaffolds.
TL;DR: In this article, the role of metal centers in hydrogen bonding has been highlighted, the inorganic and organometallic sides of hydrogen bonding, and the potential importance and applications of metal involvement.
Abstract: The hydrogen bond is commonly considered to lie within the domain of organic or biological chemistry, involving interactions of a hydrogen atom with two electronegative p-block elements. However, recent work, particularly in the past decade, has highlighted the role of metal centres in hydrogen bonding, the inorganic and organometallic sides of hydrogen bonding. This Perspective provides a personal view of the varied roles that metals, particularly transition metals, can play in hydrogen bonding and the potential importance and applications of metal involvement. It draws upon work in this area conducted in my research group over the past decade as well as related work from the literature.
TL;DR: The observed rupture of these hydrogen bonds are studied in a molecular dynamics calculation as an alternative to using thermodynamics and it is suggested that such a direct calculation can be useful for the prediction of hydrogen bond strengths in various environments of interest.
Abstract: Hydrogen bonds and their relative strengths in proteins are of importance for understanding protein structure and protein motions. The correct strength of such hydrogen bonds is experimentally known to vary greatly from ≈5–6 kcal/mol for the isolated bond to ≈0.5–1.5 kcal/mol for proteins in solution. To estimate these bond strengths, here we suggest a direct novel kinetic procedure. This analyzes the timing of the trajectories of a properly averaged dynamic ensemble. Here we study the observed rupture of these hydrogen bonds in a molecular dynamics calculation as an alternative to using thermodynamics. This calculation is performed for the isolated system and contrasted with results for water. We find that the activation energy for the rupture of the hydrogen bond in a β-sheet under isolated conditions is 4.76 kcal/mol, and the activation energy is 1.58 kcal/mol for the same β-sheet in water. These results are in excellent agreement with observations and suggest that such a direct calculation can be useful for the prediction of hydrogen bond strengths in various environments of interest.
TL;DR: Six new coordination polymers, synthesized by hydrothermal reactions of lanthanide chlorides with three isomers of benzenedicarboxylic acid and 1,10-phenanthroline (phen), were investigated, and characterized by single-crystal X-ray diffraction.
Abstract: Six new coordination polymers, [Eu(1,2-BDC)(1,2-HBDC)(phen)(H2O)]n (1), [Eu2(1,3-BDC)3(phen)2(H2O)2]n·4nH2O (2), [Eu(1,4-BDC)3/2(phen)(H2O)]n (3), [Yb2(1,2-BDC)3(phen)(H2O)2]n·3.5nH2O (4), [Yb2(1,3-BDC)3(phen)1/2]n (5), and [Yb2(1,4-BDC)3(phen)2(H2O)]n (6), were synthesized by hydrothermal reactions of lanthanide chlorides with three isomers of benzenedicarboxylic acid (H2BDC) and 1,10-phenanthroline (phen), and characterized by single-crystal X-ray diffraction. 1 has a 2-D herringbone architecture with a Z-shaped cavity. 2 and 5 have different 3-D networks, but both are formed by 1,3-BDC anions bridging metal centers (Eu or Yb) via carboxylate groups. 3 and 6 possess similar layer structures which are further constructed to form 3-D networks by hydrogen bonds and/or π−π aromatic interactions. 4 comprises 1-D chains that are further interlinked via hydrogen bonds, resulting in a 3-D network. In the three europium complexes, all the europium ions are eight-coordinated, while the coordination numbers of the...
TL;DR: In this paper, the role of guest molecules in templating the isomeric network structures with one set of molecular components is discussed, showing that the materials that are designed based on strong hydrogen bonds and coordination bonds exhibited zeolite-like and clay-like properties.
Abstract: This article highlights the importance of crystal engineering in designing functional materials. Various rational design strategies will be discussed for controlling the molecular architectures of the materials using C–H⋯O, C–H⋯π, O–H⋯O, N–H⋯O and O–H⋯N hydrogen bonds and co-ordination bonds. The results described here show the role of guest molecules in templating the isomeric network structures with one set of molecular components. In particular, the materials that are designed based on strong hydrogen bonds and coordination bonds exhibited zeolite like and clay like properties.
TL;DR: A linear coordination polymeric structure under hydrothermal conditions where each metal ion shows 9-coordination with an approximate D3 symmetry and coordinated water dimers are hydrogen-bonded to the hexamers.
Abstract: Ce(NO3)3·6H2O or Pr(NO3)3·6H2O and pyridine-2,6-dicarboxylic acid form a linear coordination polymeric structure under hydrothermal conditions. Hexameric water clusters join these linear chains through bonding to the metal ions. Other coordinated water and the carboxylate oxygen form an intricate array of hydrogen bonding resulting in a 3D network where each metal ion shows 9-coordination with an approximate D3 symmetry. Dimeric water clusters are also located in the void spaces. In the structure containing Pr(III), the water dimers are hydrogen-bonded to the hexamers, whereas in the Ce(III) structure, the dimers and the hexamers are far apart.
TL;DR: Higher amounts of water can be absorbed when the anion of the RTIL can strongly interact and hence stabilize absorbed water molecules by forming hydrogen bonds with them or inducing hydrogen bonds among water molecules.
Abstract: Near-infrared (NIR) spectrometry was successfully used for the non-invasive and in situ determination of concentrations and structure of water absorbed by room-temperature ionic liquids (RTILs). It was found that RTILs based on 1-butyl-3-methylimidazolium, namely, [BuMIm]+ [BF4]-, [BuMIm]+ [bis((trifluoromethyl)sulfonyl)amide, or Tf2N]- and [BuMIm]+ [PF6]-, are hydroscopic and can quickly absorb water when they are exposed to air. Absorbed water interacts with the anions of the RTILs, and these interactions lead to changes in the structure of water. Among the RTILs studied, [BF4]- provides the strongest interactions and [PF6]- the weakest. In 24 hours, [Bu-MIm]+ [BF4]- can absorb up to 0.320 M of water, whereas [Bu-MIm]+ [PF6]- can only absorb 8.3 x 10(-2) M of water. It seems that higher amounts of water can be absorbed when the anion of the RTIL can strongly interact and hence stabilize absorbed water molecules by forming hydrogen bonds with them or inducing hydrogen bonds among water molecules. More importantly, the NIR technique can be sensitively used for the noninvasive, in situ determination of absorbed water in RTILs, without any pretreatment, and at limits of detection as low as 3.20 x 10(-3) M.
TL;DR: In this paper, a 1:2 and 1: 1:1 cocrystallization of α,ω-alkanedicarboxylic acids (HOOC−(CH2)n-2−COOH, n = 2−6) with isonicotinamide (IN) is carried out in 1: 2 and 1 : 1 stoichiometry.
Abstract: Crystallization of α,ω-alkanedicarboxylic acids (HOOC−(CH2)n-2−COOH, n = 2−6) with isonicotinamide (IN) is carried out in 1:2 and 1:1 stoichiometry. Five cocrystals of (diacid)·(IN)2 composition (diacid = oxalic acid, malonic acid, succinic acid, glutaric acid, and adipic acid) are characterized by X-ray diffraction at 153(2) K. Tapes of acid−pyridine O−H···N and amide−amide N−H···O hydrogen bond synthons stabilize these five crystal structures as predicted by the hierarchic model: the best donor (COOH) and best acceptor group (pyridine N) hydrogen bond as acid−pyridine and the second best donor−acceptor group (CONH2) aggregates as an amide dimer. Glutaric acid and adipic acid cocrystallize in 1:1 stoichiometry also, (diacid)·(IN), with acid−pyridine and acid−amide hydrogen bonds. Synthon energy calculations (ΔEsynthon, RHF/6-31G**) explain the observed hydrogen bond preferences in 1:2 (five examples) and 1:1 (two examples) cocrystals. The acid−pyridine hydrogen bond is favored over the acid−amide dimer ...
TL;DR: This work shows that a crucial factor in predicting and rationalizing protein–protein interfaces can be inferred by assessing the extent of intramolecular desolvation of backbone hydrogen bonds in monomeric structures.
Abstract: The prediction of binding sites and the understanding of interfaces associated with protein complexation remains an open problem in molecular biophysics. This work shows that a crucial factor in predicting and rationalizing protein-protein interfaces can be inferred by assessing the extent of intramolecular desolvation of backbone hydrogen bonds in monomeric structures. Our statistical analysis of native structures shows that, in the majority of soluble proteins, most backbone hydrogen bonds are thoroughly wrapped intramolecularly by nonpolar groups except for a few ones. These latter underwrapped hydrogen bonds may be dramatically stabilized by removal of water. This fact implies that packing defects are "sticky" in a way that decisively contributes to determining the binding sites for proteins, as an examination of numerous complexes demonstrates.
TL;DR: The hydrogen bond interaction of pyridine with the silanol groups of the inner surfaces of MCM-41 and SBA-15 ordered mesoporous silica has been studied by a combination of solid-state NMR techniques as discussed by the authors.
Abstract: The hydrogen bond interaction of pyridine with the silanol groups of the inner surfaces of MCM-41 and SBA-15 ordered mesoporous silica has been studied by a combination of solid-state NMR techniques. The pore diameters were varied between 3 and 4 nm for MCM-41 and between 7 and 9 nm for SBA-15. 1 H MAS experiments performed under magic angle spinning (MAS) conditions in the absence and the presence of pyridine-d 5 reveal that the large majority of silanol groups are located in the inner surfaces, isolated from each other but able to form hydrogen bonds with pyridine. On the other hand, low- and room-temperature 1 5 N CPMAS and MAS experiments (CP ≡ cross-polarization) performed on pyridine- 1 5 N show that at low concentrations all pyridine molecules are involved in hydrogen bonds with the surface silanol groups. In the presence of an excess of pyridine, a non-hydrogen-bonded pyridine phase is observed at 120 K in the slow hydrogen bond exchange regime and associates with an inner core phase. From these measurements, the number of pyridine molecules bound to the inner surfaces corresponding to the number of silanol groups could be determined to be n O H 3 nm - 2 for MCM-41 and 3.7 nm - 2 for SBA-15. At room temperature and low concentrations, the pyridine molecules jump rapidly between the hydrogen-bonded sites. In the presence of an excess of pyridine, the hydrogen-bonded binding sites are depleted as compared to low temperatures, leading to smaller apparent numbers n O H . Using a correlation established previously between the 1 5 N and 1 H chemical shifts and the NHO hydrogen bond geometries, as well as with the acidity of the proton donors, the distances in the pyridine-hydroxyl pairs were found to be about r H N = 1.68 A, r O H = 1.01 A, and r O N = 2.69 A. This geometry corresponds in the organic solid state to acids exhibiting in water a pK a of about 4. Roomtemperature 1 5 N experiments on static samples of pyridine- 1 5 N in MCM-41 at low coverage show a residual 1 5 N chemical shift anisotropy, indicating that the jumps of pyridine between different different silanol hydrogen bond sites is accompanied by an anisotropic reorientational diffusion. A quantitative analysis reveals that in this regime the rotation of pyridine around the molecular C 2 axis is suppressed even at room temperature, and that the angle between the Si-O axes and the OH axes of the isolated silanol groups is about 47°. These results are corroborated by 2 H NMR experiments performed on pyridine-4-d 1 . In contrast, in the case of SBA-15 with the larger pore diameters, the hydrogen bond jumps of pyridine are associated with an isotropic rotational diffusion, indicating a high degree of roughness of the inner surfaces. This finding is correlated with the finding by 2 9 Si CPMAS of a substantial amount of Si(OH) 2 groups in SBA-15. in contrast to the MCM-41 materials. The Si(OH) 2 groups are associated with surface defects, exhibiting not only silanol groups pointing into the pore center but also silanol groups pointing into other directions of space including the pore axes, leading to the isotropic surface diffusion. All results are used to develop molecular models for the inner surface structure of mesoporous silica which may be a basis for future simulations of the surfaces of mesoporous silica.
TL;DR: The crystal structure analysis of (l)-2 and (d)-2 reveals that the alanine molecules pack to form two-dimensional bilayers running parallel to (001), implying the retention of the hydrogen bonded structure in water despite the accommodation of hydrophobic methanol groups within the supramolecular (H(2)O)(15)(CH(3)OH)(3) framework.
Abstract: Phosphorus functionalized trimeric alanine compounds (l)- and (d)-P(CH2NHCH(CH3)COOH)3 2 are prepared in 90% yields by the Mannich reaction of Tris(hydroxymethyl)phosphine 1 with (l)- or (d)- Alanine in aqueous media. The hydration properties of (l)-2 and (d)-2 in water and water−methanol mixtures are described. The crystal structure analysis of (l)-2·4H2O, reveals that the alanine molecules pack to form two-dimensional bilayers running parallel to (001). The layered structural motif depicts two closely packed monolayers of 2 each oriented with its phosphorus atoms projected at the center of the bilayer and adjacent monolayers are held together by hydrogen bonds between amine and carboxylate groups. The water bilayers are juxtaposed with the H-bonded alanine trimers leading to 18-membered (H2O)18 water rings. Exposure of aqueous solution of (l)-2 and (d)-2 to methanol vapors resulted in closely packed (l)-2 and (d)-2 solvated with mixed water−methanol (H2O)15(CH3OH)3 clusters. The O−O distances in the mix...
TL;DR: Novel diacetylene derivatives allowing various hydrogen-bonding states were synthesized by coupling carboxy-substituted (ortho-, meta-, and para-) anilide groups with a typical single-chain diacetaldehyde lipid, resulting in unprecedented colorimetric reversibility under both thermal and pH stimuli.
Abstract: To investigate the role of hydrogen-bonding on colorimetric transition of polydiacetylene supramolecules, novel diacetylene derivatives allowing various hydrogen-bonding states were synthesized by coupling carboxy-substituted (ortho-, meta-, and para-) anilide groups with a typical single-chain diacetylene lipid. One with a terminal carboxyl group at the meta position provided the resulting supramolecular Langmuir−Schaefer films with enhanced hydrogen-bonding, and hence resulted in unprecedented colorimetric reversibility under both thermal and pH stimuli.
TL;DR: A theoretical framework for rationalizing the excess proton mobility, based on computer simulations, theory of proton transfer in condensed media, and analysis of classical proton conductivity experiments over broad temperature ranges is discussed in this paper.
Abstract: The excess proton mobility in water has attracted scientific attention for more than a century. Detailed theoretical concepts and models are also presently in strong focus in efforts toward understanding this ubiquitous phenomenon. In the present report, we discuss a theoretical framework for rationalizing the excess proton mobility, based on computer simulations, theory of proton transfer (PT) in condensed media, and analysis of classical proton conductivity experiments over broad temperature ranges. The mechanistic options involved are (i) classical hydrodynamic motion of the hydronium ion (H3O+), (ii) proton transfer from hydronium to a neighboring water molecule, and (iii) structural diffusion of the Zundel complex (H5O2+), the processes all controlled by orientational fluctuations or hydrogen bond breaking in neighboring hydration shells. Spontaneous conversion of excess proton states between Zundel and hydrated hydronium states and between hydrated and bare hydronium states are the crucial parts of ...
TL;DR: The interplay between strong and weak interactions in ligand binding possibly leads to a satisfactory enthalpy–entropy balance in macromolecular structures, and the implications to crystallographic refinement and molecular dynamics software are discussed.
Abstract: The characteristics of N-H...O, O-H...O, and C-H...O hydrogen bonds are examined in a group of 28 high-resolution crystal structures of protein-ligand complexes from the Protein Data Bank and compared with interactions found in small-molecule crystal structures from the Cambridge Structural Database. It is found that both strong and weak hydrogen bonds are involved in ligand binding. Because of the prevalence of multifurcation, the restrictive geometrical criteria set up for hydrogen bonds in small-molecule crystal structures may need to be relaxed in macromolecular structures. For example, there are definite deviations from linearity for the hydrogen bonds in protein-ligand complexes. The formation of C-H...O hydrogen bonds is influenced by the activation of the C(alpha)-H atoms and by the flexibility of the side-chain atoms. In contrast to small-molecule structures, anticooperative geometries are common in the macromolecular structures studied here, and there is a gradual lengthening as the extent of furcation increases. C-H...O bonds formed by Gly, Phe, and Tyr residues are noteworthy. The numbers of hydrogen bond donors and acceptors agree with Lipinski's "rule of five" that predicts drug-like properties. Hydrogen bonds formed by water are also seen to be relevant in ligand binding. Ligand C-H...O(w) interactions are abundant when compared to N-H...O(w) and O-H...O(w). This suggests that ligands prefer to use their stronger hydrogen bond capabilities for use with the protein residues, leaving the weaker interactions to bind with water. In summary, the interplay between strong and weak interactions in ligand binding possibly leads to a satisfactory enthalpy-entropy balance. The implications of these results to crystallographic refinement and molecular dynamics software are discussed.
TL;DR: In this paper, a 1,3,5-Cyclohexanetricarboxylic acid (H3CTA) is crystallized with bipyridine bases 1,2-bis(4-pyridyl)ethane (bipy-eta), 1,4-bis (4pyrinyl-2-ethyl)benzene (bippy-etabz), and 1, 2-bi(2-(4-polygonal)ethenyl)enzene to afford molecular complexes.
Abstract: cis,cis-1,3,5-Cyclohexanetricarboxylic acid (H3CTA) is crystallized with bipyridine bases 1,2-bis(4-pyridyl)ethane (bipy-eta), 1,4-bis(4-pyridyl-2-ethyl)benzene (bipy-etabz), 1,2-bis(4-pyridyl)ethylene (bipy-ete), and 1,4-bis(2-(4-pyridyl)ethenyl)benzene (bipy-etebz) to afford molecular complexes (H3CTA)·(bipy-eta)1.5 1, (H3CTA)·(bipy-etabz) 2, (H2CTA-)·(bipy-ete2H+)0.5 3, and (H2CTA-)·(bipy-etebz2H+)0.5 4. Cocrystal 1 has a super honeycomb hydrogen bond network stabilized by carboxylic acid-bipyridine O−H···N synthon Va. The hexagonal cavity of 34.1 × 36.7 A is filled by parallel triple interpenetration of independent networks. 2 has zigzag chains of synthon Va connected via O−H···O hydrogen bonds. Carboxylic acid to pyridine proton transfer occurs in 3 and 4. These structures have undulated and flat 2D layers of O−H···O- and O−H···O hydrogen bonds that are connected to bipyridinium via N+−H···O- hydrogen bond Vb. H2CTA- anions in 4 form a porous parquet grid of 14.5 × 7.5 A with the channels accommodati...
TL;DR: In this paper, molecular dynamics simulations of a polyalanine model were performed, which is an -helix in its native state and observed a metastable -hairpin intermediate.
Abstract: The aggregation of -helix-rich proteins into -sheet-rich amyloid fibrils is associ- ated with fatal diseases, such as Alzheimer's disease and prion disease. During an aggregation process, protein secondary structure elements—-helices— undergo conformational changes to -sheets. The fact that proteins with different sequences and structures undergo a similar transition on aggrega- tion suggests that the sequence nonspecific hydro- gen bond interaction among protein backbones is an important factor. We perform molecular dynam- ics simulations of a polyalanine model, which is an -helix in its native state and observe a metastable -hairpin intermediate. Although a -hairpin has larger potential energy than an -helix, the entropy of a -hairpin is larger because of fewer constraints imposed by the hydrogen bonds. In the vicinity of the transition temperature, we observe the intercon- version of the -helix and -sheet states via a ran- dom coil state. We also study the effect of the environment by varying the relative strength of side-chain interactions for a designed peptide—an -helix in its native state. For a certain range of side-chain interaction strengths, we find that the intermediate-hairpin state is destabilized and even disappears, suggesting an important role of the environment in the aggregation propensity of a peptide. Proteins 2003;53:220 -228.
TL;DR: The aqua adducts of the anticancer complexes (X=biphenyl (Bip) 1, X=5,8,9,10-tetrahydroanthracene (THA) 2, X-DHA and THA 3; en=ethylenediamime) were separated by HPLC and characterised by mass spectrometry as the products of hydrolysis in water.
Abstract: The aqua adducts of the anticancer complexes [(eta(6)-X)Ru(en)Cl][PF(6)] (X=biphenyl (Bip) 1, X=5,8,9,10-tetrahydroanthracene (THA) 2, X=9,10-dihydroanthracene (DHA) 3; en=ethylenediamime) were separated by HPLC and characterised by mass spectrometry as the products of hydrolysis in water. The X-ray structures of the aqua complexes [(eta(6)-X)Ru(en)Y][PF(6)](n), X=Bip, Y=0.5 H(2)O/0.5 OH, n=1.5 (4), X=THA, Y=0.5 H(2)O/0.5 OH, n=1.5 (5 A), X=THA, Y=H(2)O, n=2 (5 B), and X=DHA, Y=H(2)O, n=2 (6), are reported. In complex 4 there is a large propeller twist of 45 degrees of the pendant phenyl ring with respect to the coordinated phenyl ring. Although the THA ligand in 5 A and 5 B is relatively flat, the DHA ring system in 6 is markedly bent (hinge bend ca. 35 degrees ) as in the chloro complex 3 (41 degrees ). The rates of aquation of 1-3 determined by UV/Vis spectroscopy at various ionic strengths and temperatures (1.23-2.59x10(-3) s(-1) at 298 K, I=0.1 M) are >20x faster than that of cisplatin. The reverse, anation reactions were very rapid on addition of 100 mM NaCl (a similar concentration to that in blood plasma). The aquation and anation reactions were about two times faster for the DHA and THA complexes compared to the biphenyl complex. The hydrolysis reactions appear to occur by an associative pathway. The pK(a) values of the aqua adducts were determined by (1)H NMR spectroscopy as 7.71 for 4, 8.01 for 5 and 7.89 for 6. At physiologically-relevant concentrations (0.5-5 microM) and temperature (310 K), the complexes will exist in blood plasma as >89 % chloro complex, whereas in the cell nucleus significant amounts (45-65 %) of the more reactive aqua adducts would be formed together with smaller amounts of the hydroxo complexes (9-25 %, pH 7.4, [Cl(-)]=4 mM).
TL;DR: The experimental determination of solute descriptors offers an alternative approach for estimating logP, and other biopartitioning properties, which is suitable for the rapid, high throughput determination of logP for neutral, weakly acidic, and weakly basic compounds.
TL;DR: A single crystal of 1-butyl-3methylimidazolium chloride [bmim]Cl, a prototype ionic liquid, has successfully been prepared and an X-ray crystallographic analysis has been performed as mentioned in this paper.
Abstract: A single crystal of 1-butyl-3-methylimidazolium chloride [bmim]Cl, a prototype ionic liquid, has successfully been prepared and an X-ray crystallographic analysis has been performed It reveals the presence of a hydrogen bonding network involving the chloride anion and the ring as well as the n-butyl hydrogen atoms, a strong hydrophobic interaction between the two n-butyl groups of the [bmim] cations, and a unique corrugated sheets structure of the imidazolium rings Considering the similarity of the Raman spectra of crystalline and liquid states, we suspect that the three dimensional structure determined in the present study also exist, at least partially, in the ionic liquid state