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Hydrogen-bond Donors (hydrogen-bond + donor)
Selected AbstractsStructure,activity relationships for gene activation oestrogenicity: Evaluation of a diverse set of aromatic chemicalsENVIRONMENTAL TOXICOLOGY, Issue 1 2002T. Wayne Schultz Abstract Structure,activity relationships for oestrogenicity were developed based on 120 aromatic chemicals evaluated in the Saccharomyces cerevisiae -based Lac -Z reporter assay. Relative gene activation was compared to 17,-estradiol and varied over eight orders of magnitude. Analysis of the data compared to 17,-estradiol identified three structural criteria that were related to xenoestrogen activity and potency: (1) the hydrogen-bonding ability of the phenolic ring mimicking the A-ring, (2) a hydrophobic centre similar in size and shape to the B- and C-rings, and (3) a hydrogen-bond donor mimicking the 17,-hydroxyl moiety of the D-ring, especially with an oxygen-to-oxygen distance similar to that between the 3- and 17,-hydroxyl groups of 17,-estradiol. Binding data were segregated into activity clusters including strong, moderate, weak, and detectable gene expression, and those compounds that were inactive. The hydrogen-bonding ability of hydroxy group in the 3-position on 17,-estradiol was observed to be essential for gene activation. Compounds with a 4-hydroxyl substituted benzene ring and a hydrophobic moiety of size and shape equivalent to the B-ring of 17,-estradiol were generally observed to be weakly active compounds. Moderately active compounds have a 4-hydroxyl substituted benzene ring with a hydrophobic moiety equivalent in size and shape to the B- and C-ring of 17,-estradiol, or have a high hydrogen-bond donor capacity owing to the presence of halogens on a nonphenolic ring. Strongly active compounds, similar to 4,4,-diethylethylene bisphenol (DES), possess the same hydrophobic ring structure as described for moderately active compounds and an additional hydroxyl group with an oxygen-to-oxygen distance close to that exhibited by the 3- and 17-hydroxyl groups of 17,-estradiol. © 2002 by Wiley Periodicals, Inc. Environ Toxicol 17: 14,23, 2002 [source] Ferrocene compounds: methyl 1,-aminoferrocene-1-carboxylateACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2010Christoph Förster The title compund, [Fe(C5H6N)(C7H7O2)], features one strong intermolecular hydrogen bond of the type N,H...O=C [N...O = 3.028,(2),Å] between the amine group and the carbonyl group of a neighbouring molecule, and vice versa, to form a centrosymmetric dimer. Furthermore, the carbonyl group acts as a double H-atom acceptor in the formation of a second, weaker, hydrogen bond of the type C,H...O=C [C...O = 3.283,(2),Å] with the methyl group of the ester group of a second neighbouring molecule at (x, ,y , , z , ). The methyl group also acts as a weak hydrogen-bond donor, symmetry-related to the latter described C,H...O=C interaction, to a third molecule at (x, ,y , , z + ) to form a two-dimensional network. The cyclopentadienyl rings of the ferrocene unit are parallel to each other within 0.33,(3)° and show an almost eclipsed 1,1,-conformation, with a relative twist angle of 9.32,(12)°. The ester group is twisted slightly [11.33,(8)°] relative to the cylopentadienyl plane due to the above-mentioned intermolecular hydrogen bonds of the carbonyl group. The N atom shows pyramidal coordination geometry, with the sum of the X,N,Y angles being 340,(3)°. [source] Form I of desloratadine, a tricyclic antihistamineACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2006Prashant M. Bhatt The title compound [systematic name: 8-chloro-11-(piperidin-4-ylidene)-6,11-dihydro-5H -benzo[4,5]cyclohepta[2,1- b]pyridine], C19H19ClN2, was crystallized from ethyl acetate. The interesting feature of the reported structure is that it does not contain any strong hydrogen bonds, although the molecule contains a secondary NH group, which is a good hydrogen-bond donor. [source] A Dual-Response [2]Rotaxane Based on a 1,2,3-Triazole Ring as a Novel Recognition StationCHEMISTRY - A EUROPEAN JOURNAL, Issue 47 2009Haiyan Zheng Abstract Two novel multilevel switchable [2]rotaxanes containing an ammonium and a triazole station have been constructed by a CuI -catalyzed azide,alkyne cycloaddition reaction. The macrocycle of [2]rotaxane containing a C6-chain bridge between the two hydrogen bonding stations exhibits high selectivity for the ammonium cation in the protonated form. Interestingly, the macrocycle is able to interact with the two recognition stations when the bridge between them is shortened. Upon deprotonation of both [2]rotaxanes, the macrocycle moves towards the triazole recognition site due to the hydrogen-bond interaction between the triazole nitrogen atoms and the amide groups in the macrocycle. Upon addition of chloride anion, the conformation of [2]rotaxane is changed because of the cooperative recognition of the chloride anion by a favorable hydrogen-bond donor from both the macrocycle isophthalamide and thread triazole CH proton. [source] Bonding in Tropolone, 2-Aminotropone, and Aminotroponimine: No Evidence of Resonance-Assisted Hydrogen-Bond EffectsCHEMISTRY - A EUROPEAN JOURNAL, Issue 14 2008Pablo Sanz Dr. Abstract The properties of the intramolecular hydrogen bond (IMHB) in tropolone, aminotropone, and aminotroponimine have been compared with those in the corresponding saturated analogues at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. In general, all those compounds in which the seven-membered ring is unsaturated exhibit a stronger IMHB than their saturated counterparts. Nevertheless, this enhanced strength is not primarily due to resonance-assisted hydrogen-bond effects, but to the much higher intrinsic basicity and acidity of the hydrogen-bond acceptor and donor groups, respectively, in the unsaturated compounds. These acidity and basicity enhancements have a double origin: 1),the unsaturated nature of the moiety to which the hydrogen-bond donor and acceptor are attached and 2),the cyclic nature of the compounds under scrutiny. As has been found for hydroxymethylene and aminomethylene cyclobutanones, and cyclobutenones and their nitrogen-containing analogues, the IMHB strength follows the [donor, acceptor] trend: [OH, CNH]>[OH, CO]>[NH2, CNH]>[NH2, CO] and fulfills a Steiner,Limbach correlation similar to that followed by intermolecular hydrogen bonds. [source] Simple Bisthiocarbonohydrazones as Sensitive, Selective, Colorimetric, and Switch-On Fluorescent Chemosensors for Fluoride AnionsCHEMISTRY - A EUROPEAN JOURNAL, Issue 10 2007Feng Han Abstract Bisthiocarbonohydrazones are found to be a class of sensitive, selective, ratiometric, and colorimetric chemosensors for anions such as fluoride (F,) or acetate (Ac,). The sensitivities, or the binding constants of the sensors with anions, were found to be strongly dependent on the substituents appended on the ,-conjugation framework, the delocalization bridge CHN, the aromatic moiety, and the hetero atom in the CX group (X=O, S) of the sensors. Single-crystal structures and 1H,NMR titration analysis shows that the CHN moiety is a hydrogen-bond donor, and it is proposed that an additional CH,,,F hydrogen bond is formed for the sensors in the presence F,. A sensor bearing anthracenyl groups is demonstrated as a switch-on fluorescent chemosensor for F, and Ac,. The recognition of F, in acetonitrile (MeCN) by a sensor with nitrophenyl substituents is tolerant to MeOH (MeCN/MeOH=10:1, v/v) and water (MeCN/H2O=30:1, v/v); at these solvent ratios the absorption intensity of the sensor,F, complex solution at maximal absorption wavelength was attenuated to half of the original value in pure MeCN. [source] Organocatalyzed Highly Enantioselective Direct Aldol Reactions of Aldehydes with Hydroxyacetone and Fluoroacetone in Aqueous Media: The Use of Water To Control RegioselectivityCHEMISTRY - A EUROPEAN JOURNAL, Issue 2 2007Xiao-Hua Chen Abstract An organocatalyst prepared from (2R,3R)-diethyl 2-amino-3-hydroxysuccinate and L -proline exhibited high regio- and enantioselectivities for the direct aldol reactions of hydroxyacetone and fluoroacetone with aldehydes in aqueous media. It was found that water could be used to control the regioselectivity. The presence of 20,30 mol,% of the catalyst afforded the direct aldol reactions of a wide range of aldehydes with hydroxyacetone to give the otherwise disfavored products with excellent enantioselectivities, ranging from 91 to 99,%,ee, and high regioselectivities. Aldolizations of fluoroacetone with aldehydes mediated by 30 mol,% of the organocatalyst in aqueous media preferentially occurred at the methyl group, yielding products with high enantioselectivities (up to 91,%,ee); however, these additions took place dominantly at the fluoromethyl group in THF. Optically active 3,5-disubstituted tetrahydrofurans and (2S,4R)-dihydroxy-4-biphenylbutyric acid were prepared by starting from the aldol reaction of hydroxyacetone. Theoretical studies on the role of water in controlling the regioselectivity revealed that the hydrogen bonds formed between the amide oxygen of proline amide, the hydroxy of hydroxyacetone, and water are responsible for the regioselectivity by microsolvation with explicit one water molecule as a hydrogen-bond donor and/or an acceptor. [source] Hydrogen-Bonding Cooperativity: Using an Intramolecular Hydrogen Bond To Design a Carbohydrate Derivative with a Cooperative Hydrogen-Bond Donor CentreCHEMISTRY - A EUROPEAN JOURNAL, Issue 17 2004Virginie Vicente Dr. Abstract Neighbouring groups can be strategically located to polarise HO,,,OH intramolecular hydrogen bonds in an intended direction. A group with a unique hydrogen-bond donor or acceptor character, located at hydrogen-bonding distance to a particular OH group, has been used to initiate the hydrogen-bond network and to polarise a HO,,,OH hydrogen bond in a predicted direction. This enhanced the donor character of a particular OH group and made it a cooperative hydrogen-bond centre. We have proved that a five-membered-ring intramolecular hydrogen bond established between an amide NH group and a hydroxy group (1,2-e,a), which is additionally located in a 1,3 -cis- diaxial relationship to a second hydroxy group, can be used to select a unique direction on the six-membered-ring intramolecular hydrogen bond between the two axial OH groups, so that one of them behaves as an efficient cooperative donor. Talose derivative 3 was designed and synthesised to prove this hydrogen-bonding network by NMR spectroscopy, and the mannopyranoside derivatives 1 and 2 were used as models to demonstrate the presence in solution of the 1,2-(e,a)/five-membered-ring intramolecular hydrogen bond. Once a well-defined hydrogen-bond is formed between the OH and the amido groups of a pyranose ring, these hydrogen-bonding groups no longer act as independent hydrogen-bonding centres, but as hydrogen-bonding arrays. This introduces a new perspective on the properties of carbohydrate OH groups and it is important for the de novo design of molecular recognition processes, at least in nonpolar media. Carbohydrates 1,3 have shown to be efficient phosphate binders in nonpolar solvents owing to the presence of cooperative hydroxy centres in the molecule. [source] Synthesis and Modulation of Bis(triazine) Hydrogen-Bonding ReceptorsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 6 2006Pamela V. Mason Abstract The synthesis of bis(triazine) molecules capable of acting as synthetic receptors for barbiturate guest molecules is described. The binding properties are also reported illustrating the modulation of the binding properties of these species by the modification of the hydrogen-bonding patterns of the receptor molecule, namely 1,3- N,N, -bis[4-(dibenzylamino)-6-(butylamino)-1,3,5-triazin-2-yl]xylylenediamine (1). Thus 1,3- O,O, -bis[4-(dibenzylamino)-6-(butylamino)-1,3,5-triazin-2-yl]benzenedimethanol (3) and 1,3- O,O, -bis[4-(dibenzylamino)-6-(diethylamino)-1,3,5-triazin-2-yl]benzenedimethanol (5) have been prepared, and their binding constants compared to those observed for 1. In the case of compounds 3 and 5 the hydrogen-bonding secondary amines at the apex of the receptor 1 are substituted by non-hydrogen-bonding ether links. The hydrogen-bonding ability is further modified in the case of 5 by the removal of all hydrogen-bond donors from the receptor site, replacing secondary amines by tertiary amines. NMR binding studies illustrate how these simple modifications of the hydrogen-bonding patterns of these receptors influences the overall strength of binding demonstrating a simple mechanism for controlling host-guest complex formation. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Main-chain, thermotropic, liquid-crystalline, hydrogen-bonded polymers of 4,4,-bipyridyl with aliphatic dicarboxylic acidsJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 9 2003Pradip K. Bhowmik Abstract A series of main-chain, thermotropic, liquid-crystalline (LC), hydrogen-bonded polymers or self-assembled structures based on 4,4,-bipyridyl as a hydrogen-bond acceptor and aliphatic dicarboxylic acids, such as adipic and sebacic acids, as hydrogen-bond donors were prepared by a slow evaporation technique from a pyridine solution and were characterized for their thermotropic, LC properties with a number of experimental techniques. The homopolymer of 4,4,-bipyridyl with adipic acid exhibited high-order and low-order smectic phases, and that with sebacic acid exhibited only a high-order smectic phase. Like the homopolymer with adipic acid, the two copolymers of 4,4,-bipyridyl with adipic and sebacic acids (75/25 and 25/75) also exhibited two types of smectic phases. In contrast, the copolymer of 4,4,-bipyridyl with adipic and sebacic acids (50/50), like the homopolymer with sebacic acid, exhibited only one high-order smectic phase. Each of them, including the copolymers, had a broad temperature range of LC phases (36,51 °C). The effect of copolymerization for these hydrogen-bonded polymers on the thermotropic properties was examined. Generally, copolymerization increased the temperature range of LC phases for these polymers, as expected, with a larger decrease in the crystal-to-LC transition than in the LC-to-isotropic transition. Additionally, it neither suppressed the formation of smectic phases nor promoted the formation of a nematic phase in these hydrogen-bonded polymers, as usually observed in many thermotropic LC polymers. The thermal transitions for all of them, measured by differential scanning calorimetry, were well below their decomposition temperatures, as measured by thermogravimetric analysis, which were in the temperature range of 193,210 °C. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1282,1295, 2003 [source] Selecting the right compounds for screening: use of surface-area parametersPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 3 2002Colin M Tice Abstract Polar surface area, total surface area and percentage surface area have been calculated from three-dimensional structures of 88 post-emergence herbicides, 93 pre-emergence herbicides and 237 insecticides. Preferred ranges of values of these parameters were identified. Since the compounds in the training sets are used on a wide variety of species and target sites with various application modes, the parameter ranges are necessarily broad. The utility of the surface-area parameter ranges in selection of compounds for agrochemical screening was compared with the use of ranges of the Lipinski Rule of 5 parameters: molecular mass, calculated log P, number of hydrogen-bond donors and number of hydrogen-bond acceptors. The more computationally intensive surface-area parameters did not offer any obvious advantage over the Lipinski Rule of 5 parameters. © 2002 Society of Chemical Industry [source] Engineering hydrogen-bonded duplexesPOLYMER INTERNATIONAL, Issue 4 2007Bing Gong Abstract Based on several simple, readily available building blocks, oligoamide strands carrying various arrays of hydrogen-bond donors and acceptors, i.e. hydrogen-bonding sequences, have been designed and synthesized. Detailed characterization indicates that these oligoamide strands associate via their hydrogen-bonding edges into doubled stranded pairs (duplexes), which are characterized by programmable sequence specificity and adjustable stability. Using these hydrogen-bonded duplexes as association units, supramolecular structures, such as ,-sheets and non-covalent block copolymers, are obtained by simply mixing the corresponding components. Recently, by incorporating reversible covalent interactions into these hydrogen-bonded duplexes, sequence-specific formation of covalently linked structures has been realized under thermodynamic conditions, which has opened an entirely new avenue to the development of previously unknown dynamic covalent structures such as various block copolymers. Copyright © 2007 Society of Chemical Industry [source] Comparison of the effects of pressure on three layered hydrates: a partially successful attempt to predict a high-pressure phase transitionACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2009Russell D. L. Johnstone We report the effect of pressure on the crystal structures of betaine monohydrate (BTM), l -cysteic acid monohydrate (CAM) and S -4-sulfo- l -phenylalanine monohydrate (SPM). All three structures are composed of layers of zwitterionic molecules separated by layers of water molecules. In BTM the water molecules make donor interactions with the same layer of betaine molecules, and the structure remains in a compressed form of its ambient-pressure phase up to 7.8,GPa. CAM contains bi-layers of l -cysteic acid molecules separated by water molecules which form donor interactions to the bi-layers above and below. This phase is stable up to 6.8,GPa. SPM also contains layers of zwitterionic molecules with the waters acting as hydrogen-bond donors to the layers above and below. SPM undergoes a single-crystal to single-crystal phase transition above 1,GPa in which half the water molecules reorient so as to form one donor interaction with another water molecule within the same layer. In addition, half of the S -4-sulfo- l -phenylalanine molecules change their conformation. The high-pressure phase is stable up to 6.9,GPa, although modest rearrangements in hydrogen bonding and molecular conformation occur at 6.4,GPa. The three hydrates had been selected on the basis of their topological similarity (CAM and SPM) or dissimilarity (BTM) with serine hydrate, which undergoes a phase transition at 5,GPa in which the water molecules change orientation. The phase transition in SPM shows some common features with that in serine hydrate. The principal directions of compression in all three structures were found to correlate with directions of hydrogen bonds and distributions of interstitial voids. [source] Predictable close-packing similarities between cis - and trans -2-hydroxy-1-cyclooctanecarboxylic acids and trans -2-hydroxy-1-cyclooctanecarboxamideACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2002Alajos Kálmán In order to extend the experimental data already available on the close packing of cyclopentanes substituted with vicinal COX (X,=,OH, NH2) and OH groups to the analogous cyclohexanes, cycloheptanes and cyclooctanes, (1R*,2S*) -cis- 2-hydroxy-1-cyclooctanecarboxylic acid (8C), (1R*,2R*)- trans -2-hydroxy-1-cyclooctanecarboxylic acid (8T) and (1R*,2R*)- trans -2-hydroxy-1-cyclooctanecarboxamide (8T*) were subjected to X-ray crystal structure analysis. In 8T and 8T*, the hydrogen bonds form infinite ribbons of dimers joined by (12) rings with Ci symmetry. Two types of dimer alternate along each ribbon. The dimers differ in the donor and acceptor roles of the functional groups. This pattern was previously deduced topologically among the possible forms of association for heterochiral dimers [Kálmán et al. (2002). Acta Cryst. B58, 494,501]. As they have the same pattern of hydrogen bonds, 8T and 8T* are isostructural. The additional donor (i.e. the second hydrogen of the NH2 group) present in 8T* links the adjacent ribbons so as to form smaller (8) rings between them. The crystals of the cis stereoisomer 8C are built up from antiparallel hydrogen-bonded helices. The topology and symmetry of this structure are the same as for the close packing of (1R*,2R*,4S*)-4- tert -butyl-2-hydroxy-1-cyclopentanecarboxamide [Kálmán et al. (2001). Acta Cryst. B57, 539,550]; only the hydrogen-bond donors and acceptors are interchanged, in the same way as in the two dimer types of 8T and 8T* ribbons. This analogy suggests that helices may originate as homochiral dimers with C2 symmetry and polymerize into helices during crystal formation. The conformational characteristics of the heterochiral dimers observed in the title compounds and in closely related structures are discussed. [source] Different hydrogen-bonding modes in two closely related oximesACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2010Grzegorz Dutkiewicz Two closely related oximes, namely 1-chloroacetyl-3-ethyl-2,6-diphenylpiperidin-4-one oxime, C21H23ClN2O2, (I), and 1-chloroacetyl-2,6-diphenyl-3-(propan-2-yl)piperidin-4-one oxime, C22H25ClN2O2, (II), despite their identical sets of hydrogen-bond donors and acceptors, display basically different hydrogen-bonding patterns in their crystal structures. While the molecules of (I) are organized into typical centrosymmetric dimers, created by oxime,oxime O,H...N hydrogen bonds, in the structure of (II) there are infinite chains of molecules connected by O,H...O hydrogen bonds, in which the carbonyl O atom from the chloroacetyl group acts as the hydrogen-bond acceptor. Despite the differences in the hydrogen-bond schemes, the ,OH groups are always in typical anti positions (C,N,O,H torsion angles of ca 180°). The oxime group in (I) is disordered, with the hydroxy groups occupying two distinct positions and C,C,N,O torsion angles of approximately 0 and 180° for the two alternatives. This disorder, even though the site-occupancy factor of the less occupied position is as low as ca 0.06, is also observed at lower temperatures, which seems to favour the statistical and not the dynamic nature of this phenomenon. [source] Unusual hydrate stabilization in the two-dimensional layered structure of quinacrinium bis(2-carboxy-4,5-dichlorobenzoate) tetrahydrate, a proton-transfer compound of the drug quinacrineACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2009Graham Smith The crystal structure of the hydrated proton-transfer compound of the drug quinacrine [rac- N,-(6-chloro-2-methoxyacridin-9-yl)- N,N -diethylpentane-1,4-diamine] with 4,5-dichlorophthalic acid, C23H32ClN3O2+·2C8H3Cl2O4,·4H2O, has been determined at 200,K. The four labile water molecules of solvation in the structure form discrete ...O,H...O,H... hydrogen-bonded chains parallel to the quinacrine side chain, the two N,H groups of which act as hydrogen-bond donors for two of the water acceptor molecules. The other water molecules, as well as the acridinium H atom, also form hydrogen bonds with the two anion species and extend the structure into two-dimensional sheets. Between these sheets there are also weak cation,anion and anion,anion ,,, aromatic ring interactions. This structure represents the third example of a simple quinacrine derivative for which structural data are available but differs from the other two in that it is unstable in the X-ray beam due to efflorescence, probably associated with the destruction of the unusual four-membered water chain structures. [source] (1,3-Dimethylimidazolidine-2-selone-,Se)bis(1,10-phenanthroline-,2N,N,)copper(II) bis(perchlorate) and bis(2,2,-bipyridyl-,2N,N,)(imidazolidine-2-thione-,S)copper(II) bis(perchlorate)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2007Alexander J. Blake In the first title salt, [Cu(C12H8N2)2(C5H10N2Se)](ClO4)2, the CuII centre occupies a distorted trigonal,bipyramidal environment defined by four N donors from two 1,10-phenanthroline (phen) ligands and by the Se donor of a 1,3-dimethylimidazolidine-2-selone ligand, with the equatorial plane defined by the Se and by two N donors from different phen ligands and the axial sites occupied by the two remaining N donors, one from each phen ligand. The Cu,N distances span the range 1.980,(10),2.114,(11),Å and the Cu,Se distance is 2.491,(3),Å. Intermolecular ,,, contacts between imidazolidine rings and the central rings of phen ligands generate chains of cations. In the second salt, [Cu(C10H8N2)2(C3H6N2S)](ClO4)2, the CuII centre occupies a similar distorted trigonal,bipyramidal environment comprising four N donors from two 2,2,-bipyridyl (bipy) ligands and an S donor from an imidazolidine-2-thione ligand. The equatorial plane is defined by the S donor and two N donors from different bipy ligands. The Cu,N distances span the range 1.984,(6),2.069,(7),Å and the Cu,S distance is 2.366,(3),Å. Intermolecular ,,, contacts between imidazolidine and pyridyl rings form chains of cations. A major difference between the two structures is due to the presence in the second complex of two N,H...O hydrogen bonds linking the imidazolidine N,H hydrogen-bond donors to perchlorate O-atom acceptors. [source] A new ,hydrogen-bond rule' applied to the structure of l -seryl- l -alanine and pairs of dipeptide retroanaloguesACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2000Carl Henrik Görbitz A new `rule' for the association of hydrogen-bond donors and acceptors in crystal structures is presented. It implies that ranks are assigned to each donor and each acceptor (1 is best, 2 is next best etc.), and that hydrogen bonds should be formed between donors and acceptors in rank order. l -Ser- l -Ala, C6H12N2O4, is used together with its retroanalogue, l -Ala- l -Ser, and three other pairs of dipeptide retroanalogues to illustrate this rule and the reasons why it may not always be followed. [source] Modulation of Stacking Interactions by Transition-Metal Coordination: Ab Initio Benchmark StudiesCHEMISTRY - A EUROPEAN JOURNAL, Issue 18 2010Shaun Abstract A series of ab initio calculations are used to determine the CH,,,, and ,,,,,-stacking interactions of aromatic rings coordinated to transition-metal centres. Two model complexes have been employed, namely, ferrocene and chromium benzene tricarbonyl. Benchmark data obtained from extrapolation of MP2 energies to the basis set limit, coupled with CCSD(T) correction, indicate that coordinated aromatic rings are slightly weaker hydrogen-bond acceptors but are significantly stronger hydrogen-bond donors than uncomplexed rings. It is found that ,,,,, stacking to a second benzene is stronger than in the free benzene dimer, especially in the chromium case. This is assigned, by use of energy partitioning in the local correlation method, to dispersion interactions between metal d and benzene , orbitals. The benchmark data is also used to test the performance of more efficient theoretical methods, indicating that spin-component scaling of MP2 energies performs well in all cases, whereas various density functionals describe some complexes well, but others with errors of more than 1,kcal,mol,1. [source] Chiral Encapsulation by Directional InteractionsCHEMISTRY - A EUROPEAN JOURNAL, Issue 45 2009Agnieszka Szumna Abstract The complexation of chiral guests in the cavity of dimeric self-assembled chiral capsule 12 was studied by using NMR spectroscopy and X-ray crystallography. Capsule 12 has walls composed of amino acid backbones forming numerous directional binding sites that are arranged in a chiral manner. The polar character of the interior dictates the encapsulation preferences towards hydrophilic guests and the ability of the capsule to extract guests from water into an organic phase. Chiral discrimination towards hydroxy acids was evaluated by using association constants and competition experiments, and moderate de values were observed (up to 59,%). Complexes with one or two guest molecules in the cavity were formed. For 1:1 complexes, solvent molecules are coencapsulated; this influences guest dynamics and makes the chiral recognition solvent dependent. Reversal of the preferences can be induced by coencapsulation of a nonchiral solvent in the chiral internal environment. For complexes with two guests, filling of the capsule's internal space can be very effective and packing coefficients of up to 70,% can be reached. The X-ray crystal structure of complex 12,((S) -6)2 with well-resolved guest molecules reveals a recognition motif that is based on an extensive system of hydrogen bonds. The optimal arrangement of interactions with the alternating positively and negatively charged groups of the capsule's walls is fulfilled by the guest carboxylic groups acting simultaneously as hydrogen-bond donors and acceptors. An additional guest molecule interacting externally with the capsule reveals a possible entrance mechanism involving a polar gate. In solution, the structural features and dynamic behavior of the D4 -symmetric homochiral capsule were analyzed by variable-temperature NMR spectroscopy and the results were compared with those for the S8 -symmetric heterochiral capsule. [source] Protonated Macrobicyclic Hosts Containing Pyridine Head Units for Anion RecognitionCHEMISTRY - A EUROPEAN JOURNAL, Issue 19 2008David Esteban-Gómez Dr. Abstract In this paper, we report two macrobicyclic receptors containing pyridine head units derived from 1,10-diaza-15-crown[5] (L1) or 4,13-diaza-18-crown[6] (L2) that can be protonated in MeCN and used for anion recognition. The interaction of these protonated lateral macrobicycles with different anions has been investigated by means of spectrophotometric titrations in MeCN. The association constants for the complexes of halide anions with the protonated macrobicycles follow the sequences Cl,>Br,>I,>F, (L1) and Cl,>F,>I,>Br, (L2), whereby an increase of more than two logarithmic units is observed from F, to Cl, for the binding constants of the receptor derived from L1. The association constants also indicate an important degree of selectivity of these macrobicyclic receptors for Cl, over Br, or I,. The X-ray crystal structure analyses of the chloride and bromide complexes confirms the formation of the envisaged supramolecular complexes. Moreover, the binding constants indicate that these receptors present a high sulfate-to-nitrate binding selectivity. The stability trend observed for the recognition of halide anions by the macrobicycles presented herein as well as the sulfate-to-nitrate binding selectivity have been rationalised by means of DFT calculations at the B3LYP/LanL2DZ level. These studies indicate that the especially high binding selectivity for Cl, is the result of the optimum fit between the protonated macrobicyclic cavity and the size of the anion, whereas the sulfate-to-nitrate selectivity results from shape complementarity between the hydrogen-binding acceptor sites on sulfate and the hydrogen-bond donors of the macrobicycle. [source] Anion Recognition by Neutral Macrocyclic AmidesCHEMISTRY - A EUROPEAN JOURNAL, Issue 20 2005J. Chmielewski Dr., Micha Abstract Although amides often serve as anchoring groups in natural and synthetic anion receptors, the structure,affinity relationship studies of amide-based macrocyclic receptors are still very limited. Therefore, we decided to investigate the influence of the size of the macroring on the strength and selectivity of anion binding by uncharged, amide-based receptors. With this aim, we synthesized a series of macrocyclic tetraamides derived from 2,6-pyridinedicarboxylic acid and aliphatic ,,,-diamines of different lengths. X-ray analysis shows that all ligands studied adopt expanded conformations in the solid state with the convergent arrangement of all four hydrogen-bond donors. 1H NMR titrations in DMSO solution revealed a significant effect of the ring size on the stability constants of anion complexes; the 20-membered macrocyclic tetraamide 2 is a better anion receptor than its both 18- and 24-membered analogues. This effect cannot be interpreted exclusively in terms of matching between anion diameter and the size of macrocyclic cavity, because 2 forms the most stable complexes with all anions studied, irrespective of their sizes. However, geometric complementarity manifests in extraordinarily high affinity of 2 towards the chloride anion. The results obtained for solutions were interpreted in the light of solid-state structural studies. Taken together, these data suggest that anion binding by this family of macrocycles is governed by competitive interplay between their ability to adjust to a guest, requiring longer aliphatic spacers, and preorganization, calling for shorter spacers. The 20-membered receptor 2 is a good compromise between these factors and, therefore, it was selected as a promising leading structure for further development of anion receptors. Furthermore, the study of an open chain analogue of 2 revealed a substantial macrocyclic effect. X-ray structure of the acyclic model 14 suggests that this may be due to its ill-preorganized conformation, stabilized by two intramolecular hydrogen bonds. [source] | |||||||||||||