Molecular orbital theory of the hydrogen bond. 25. Water–uracil complexes in excited n → π states

Hydrogen bonding of uracil with water in excited n → π* states has been investigated by means of ab initio SCF -CI calculations on uracil and water–uracil complexes. Two low-energy excited states arise from n → π* transitions in uracil. The first is due to excitation of the C₄? O group, while the second is associated with excitation of the C₂? O group. In the first n → π* state, hydrogen bonds at O₄ are broken, so that the open water–uracil dimer at O₄ dissociates. The “wobble” dimer, in which a water molecule is essentially free to move between its position in an open structure at N₃? H and a cyclic structure at N₃? H and O₄ in the ground state, collapses to a different “wobble” dimer at N₃? H and O₂ in the excited state. The third dimer, a “wobble” dimer at N₁? H and O₂, remains intact, but is destabilized relative to the ground state. Although hydrogen bonds at O₂ are broken in the second n → π* state, the three water–uracil dimers remain bound. The “wobble” dimer at N₁? H and O₂ changes to an excited open dimer at N₁? H. The “wobble” dimer at N₃? H and O₄ remains intact, and the open dimer at O₄ is further stabilized upon excitation. Dimer blue shifts of n → π* bands are nearly additive in 2:1 and 3:1 water:uracil structures. The fates of the three 2:1 water:uracil trimers and the 3:1 water:uracil tetramer in the first and second n → π* states are determined by the fates of the corresponding excited dimers in these states.     

Supramolecular hydrogen bonding of [5,10,15,20‐tetrakis(4‐carboxyphenyl)porphyrinato]palladium(II) in the presence of competing solvents

The title porphyrin compound forms hydrogen‐bonded adducts with methanol (1:1), [Pd(C₄₈H₂₈N₄O₈)]·CH₄O, (I), and with water and N,N‐dimethylformamide (1:4:4), [Pd(C₄₈H₂₈N₄O₈)]·4C₃H₇NO·4H₂O, (II). In (I), the metalloporphyrin unit lies across a mirror plane in Cmca, while in (II), this unit lies across an inversion center in P. Extended supramolecular hydrogen‐bonded arrays are formed in (I) by intermolecular interactions between the carboxylic acid functions, either directly or through the methanol species. These layers have a wavy topology and large interporphyrin pores, which are filled in the crystal structure by double interpenetration as well as enclathration of additional non‐interacting nitrobenzene solvent molecules. The supramolecular aggregation in (II) can be characterized by cascaded porphyrin layers, wherein adjacent porphyrin molecules are hydrogen bonded to one another through molecules of water that are incorporated into the hydrogen‐bonding scheme. Molecules of dimethylformamide partly solvate the carboxylic acid groups and fill the interporphyrin space in the crystal structure.     

Violuric acid monohydrate: a second polymorph with more extensive hydrogen bonding

Crystals of a second polymorph of violuric acid monohydrate [systematic name: pyrimidine‐2,4,5,6(1H,3H)‐tetrone monohydrate], C₄H₃N₃O₄·H₂O, have higher density and a more extensive hydrogen‐bonding arrangement than the previously reported polymorph. Violuric acid and water molecules form essentially planar hydrogen‐bonded sheets, which are stacked in an offset …ABCABC… repeat pattern involving no ring‐stacking interactions.     

Haloperoxidase‐like Compounds: Synthesis,Structure and Properties of Two New Oxidovanadium‐Poly(pyrazolyl)borate‐Carboxylate Complexes

Two new oxidovanadium (IV) complexes: TpVO(L₁) ( 1 ) and Tp*VO(pzH*)(L₂) ( 2 ) [Tp = hydrotris(pyrazolyl)borate, HL₁ = 5‐methyl‐1H‐pyrazole‐3‐carboxylic acid, Tp* = hydrotris(3,5‐dimethylpyrazolyl)borate, pzH* = 3,5‐dimethylpyrazole, HL₂ = 5‐phenyl‐1H‐pyrazole‐3‐carboxylic acid] have been synthesized and characterized by elemental analysis and IR spectroscopy. The single‐crystal structures of the complexes shows that the vanadium ion is in a distorted octahedral environment with a N₄O₂ donor set in each complex. Additionally, hydrogen bonding interaction exits in both complexes. Interestingly, the molecules of 1 are held together to form a 1D hydrogen bonded polymer along the b axis, whereas complex 2 is a hydrogen bonded dimer. In addition, the catalytic activities of complexes 1 and 2 in bromination reactions in phosphate buffer with phenol red as a trap were evaluated primary by UV/Vis spectroscopy. Furthermore, ab initio calculations of complexes 1 and 2 were performed.     

Dimeric supramolecular motifs of two carboxylate–guanidinium compounds

The structures of N‐benzyl‐N′‐{6‐[(4‐carboxylatobenzyl)aminocarbonyl]‐2‐pyridylmethyl}guanidinium, C₂₃H₂₃N₅O₃, (I), and N‐[2‐(benzylaminocarbonyl)ethyl]‐N′‐{6‐[(4‐carboxylatobenzyl)aminocarbonyl]‐2‐pyridylmethyl}guanidinium monohydrate, C₂₆H₂₈N₆O₄·H₂O, (II), both form three‐dimensional supramolecular hydrogen‐bonded networks based on a dimeric primary synthon involving carboxylate–guanidinium linkages. The differences in the geometries and hydrogen‐bonding connectivities are driven by the additional methylpropionamide group and water of crystallization of (II).     

Frovatriptan salts of aliphatic carboxylic acids

The interaction of the antimigraine pharmaceutical agent frovatriptan with acetic acid and succinic acid yields the salts (±)‐6‐carbamoyl‐N‐methyl‐2,3,4,9‐tetrahydro‐1H‐carbazol‐3‐aminium acetate, C₁₄H₁₈N₃O⁺·C₂H₃O₂⁻, (I), (R)‐(+)‐6‐carbamoyl‐N‐methyl‐2,3,4,9‐tetrahydro‐1H‐carbazol‐3‐aminium 3‐carboxypropanoate monohydrate, C₁₄H₁₈N₃O⁺·C₄H₅O₄⁻·H₂O, (II), and bis[(R)‐(+)‐6‐carbamoyl‐N‐methyl‐2,3,4,9‐tetrahydro‐1H‐carbazol‐3‐aminium] succinate trihydrate, 2C₁₄H₁₈N₃O⁺·C₄H₄O₄²⁻·3H₂O, (III). The methylazaniumyl substitutent is oriented differently in all three structures. Additionally, the amide group in (I) is in a different orientation. All the salts form three‐dimensional hydrogen‐bonded structures. In (I), the cations form head‐to‐head hydrogen‐bonded amide–amide catemers through N—H...O interactions, while in (II) and (III) the cations form head‐to‐head amide–amide dimers. The cation catemers in (I) are extended into a three‐dimensional network through further interactions with acetate anion acceptors. The presence of succinate anions and water molecules in (II) and (III) primarily governs the three‐dimensional network through water‐bridged cation–anion associations via O—H...O and N—H...O hydrogen bonds. The structures reported here shed some light on the possible mode of noncovalent interactions in the aggregation and interaction patterns of drug molecule adducts.     

Molecular orbital theory of the hydrogen bond. 24. Ground-state water–uracil complexes

Ab initio SCF calculations with the STO -3G basis set have been performed to investigate the structural, energetic, and electronic properties of mixed water–uracil dimers formed at the six hydrogen-bonding sites in the uracil molecular plane. Hydrogen-bond formation at three of the carbonyl oxygen sites leads to cyclic structures in which a water molecule bridges N₁? H and O₂, N₃? H and O₂, and N₃? H and O₄. Open structures form at O₄, N₁? H, and N₃? H. The two most stable structures, with energies of 9.9 and 9.7 kcal/mole, respectively, are the open structure at N₁? H and the cyclic one at N₁? H and O₂. These two are easily interconverted, and may be regarded as corresponding to just one “wobble” dimer. At 1 kcal/mole higher in energy is another “wobble” dimer consisting of an open structure at N₃? H and a cyclic structure at N₃? H and O₄. The third cyclic structure at N₃? H and O₂ collapses to the “wobble” dimer at N₃? H and O₄. The two “wobble” dimers are significantly more stable than the open dimer formed at O₄, which has a stabilization energy of 5.4 kcal/mole. Uracil is a stronger proton donor to water through N₁? H than N₃? H, owing to a more favorable molecular dipole moment alignment when association occurs through H₁. Hydration of uracil by additional water molecules has also been investigated. Dimer stabilization energies and hydrogen-bond energies are nearly additive in most 2:1 water:uracil structures. There are three stable “wobble” trimers, which have stabilization energies that vary from 7 to 9 kcal/mole per water molecule. Hydrogen-bond strengths are slightly enhanced in 3:1 water:uracil structures, but the cooperative effect in hydrogen bonding is still relatively small. The single stable water–uracil tetramer is a “wobble” tetramer, with two water molecules which are relatively free to move between adjacent hydrogen-bonding sites, and a stabilization energy of approximately 8 kcal/mole per water molecule. Within the rigid dimer approximation, successive hydration of uracil is limited to the addition of one, two, or three water molecules.     

The hydrogen‐bonding patterns of 3‐phenylpropylammonium benzoate and 3‐phenylpropylammonium 3‐iodobenzoate: generation of chiral crystals from achiral molecules

The crystal structures and hydrogen‐bonding patterns of 3‐phenylpropylammonium benzoate, C₉H₁₄N⁺·C₇H₅O₂⁻, (I), and 3‐phenylpropylammonium 3‐iodobenzoate, C₉H₁₄N⁺·C₇H₄IO₂⁻, (II), are reported and compared. The addition of the I atom on the anion in (II) produces a different hydrogen‐bonding pattern to that of (I). In addition, the supramolecular heterosynthon of (II) produces a chiral crystal packing not observed in (I). Compound (I) packs in a centrosymmetric fashion and forms achiral one‐dimensional hydrogen‐bonded columns through charge‐assisted N—H...O hydrogen bonds. Compound (II) packs in a chiral space group and forms helical one‐dimensional hydrogen‐bonded columns with 2₁ symmetry, consisting of repeating R₄³(10) hydrogen‐bonded rings that are commonly observed in ammonium carboxylate salts containing chiral molecules. This hydrogen‐bond pattern, which has been observed repeatedly in ammonium carboxylate salts, thus provides a means of producing chiral crystal structures from achiral molecules.     

Three‐dimensional hydrogen‐bonded structures in the 1:1 proton‐transfer compounds of l‐tartaric acid with the associative‐group monosubstituted pyridines 3‐aminopyridine, 3‐carboxypyridine (nicotinic acid) and 2‐carboxypyridine (picolinic acid)

The 1:1 proton‐transfer compounds of l ‐tartaric acid with 3‐aminopyridine [3‐aminopyridinium hydrogen (2R,3R)‐tartrate dihydrate, C₅H₇N₂⁺·C₄H₅O₆⁻·2H₂O, (I)], pyridine‐3‐carboxylic acid (nicotinic acid) [anhydrous 3‐carboxypyridinium hydrogen (2R,3R)‐tartrate, C₆H₆NO₂⁺·C₄H₅O₆⁻, (II)] and pyridine‐2‐carboxylic acid [2‐carboxypyridinium hydrogen (2R,3R)‐tartrate monohydrate, C₆H₆NO₂⁺·C₄H₅O₆⁻·H₂O, (III)] have been determined. In (I) and (II), there is a direct pyridinium–carboxyl N⁺—H...O hydrogen‐bonding interaction, four‐centred in (II), giving conjoint cyclic R₁²(5) associations. In contrast, the N—H...O association in (III) is with a water O‐atom acceptor, which provides links to separate tartrate anions through O_hydroxy acceptors. All three compounds have the head‐to‐tail C(7) hydrogen‐bonded chain substructures commonly associated with 1:1 proton‐transfer hydrogen tartrate salts. These chains are extended into two‐dimensional sheets which, in hydrates (I) and (III) additionally involve the solvent water molecules. Three‐dimensional hydrogen‐bonded structures are generated via crosslinking through the associative functional groups of the substituted pyridinium cations. In the sheet struture of (I), both water molecules act as donors and acceptors in interactions with separate carboxyl and hydroxy O‐atom acceptors of the primary tartrate chains, closing conjoint cyclic R₄⁴(8), R₃⁴(11) and R₃³(12) associations. Also, in (II) and (III) there are strong cation carboxyl–carboxyl O—H...O hydrogen bonds [O...O = 2.5387 (17) Å in (II) and 2.441 (3) Å in (III)], which in (II) form part of a cyclic R₂²(6) inter‐sheet association. This series of heteroaromatic Lewis base–hydrogen l ‐tartrate salts provides further examples of molecular assembly facilitated by the presence of the classical two‐dimensional hydrogen‐bonded hydrogen tartrate or hydrogen tartrate–water sheet substructures which are expanded into three‐dimensional frameworks via peripheral cation bifunctional substituent‐group crosslinking interactions.     

Ammonium violurate: a compact structure with extensive hydrogen bonding in three dimensions

The title compound [systematic name: ammonium pyrimidine‐2,4‐5,6(1H,3H)‐tetrone 5‐oximate], NH₄⁺·C₄H₂N₃O₄⁻, crystallizes from water in the triclinic space group P and is ismorphous with a known rubidium complex [Gillier (1965). Bull. Soc. Chim. Fr. pp. 2373–2384]. The principal feature of the structure is hydrogen bonding; each ammonium H atom acts as a bifurcated donor and three of the four violurate O atoms are bifurcated acceptors, with the fourth acting as a trifurcated acceptor. The pattern of hydrogen bonding around the cation is very similar to the rubidium coordination environment in the related structure. The violurate anions pack as hydrogen‐bonded crinkled tapes, which are linked and separated by the ammonium cations to give a compact three‐dimensional structure.     

Multicomponent crystals of erlotinib

Erlotinib [systematic name: N‐(3‐ethynylphenyl)‐6,7‐bis(2‐methoxyethoxy)quinazolin‐4‐amine], a small‐molecule epidermal growth factor receptor inhibitor, useful for the treatment of non‐small‐cell lung cancer, has been crystallized as erlotinib monohydrate, C₂₂H₂₃N₃O₄·H₂O, (I), the erlotinib hemioxalate salt [systematic name: 4‐amino‐N‐(3‐ethynylphenyl)‐6,7‐bis(2‐methoxyethoxy)quinazolin‐1‐ium hemioxalate], C₂₂H₂₄N₃O₄⁺·0.5C₂O₄²⁻, (II), and the cocrystal erlotinib fumaric acid hemisolvate dihydrate, C₂₂H₂₃N₃O₄·0.5C₄H₄O₄·2H₂O, (III). In (II) and (III), the oxalate anion and the fumaric acid molecule are located across inversion centres. The water molecules in (I) and (III) play an active role in hydrogen‐bonding interactions which lead to the formation of tetrameric and hexameric hydrogen‐bonded networks, while in (II) the cations and anions form a tetrameric hydrogen‐bonded network in the crystal packing. The title multicomponent crystals of erlotinib have been elucidated to study the assembly of molecules through intermolecular interactions, such as hydrogen bonds and aromatic π–π stacking.     

Charge‐assisted hydrogen bonding in salts of 2‐amino‐1H‐benzimidazole with 3‐phenylpropynoic acid and oct‐2‐ynoic acid

The 100 K structures of two salts, namely 2‐amino‐1H‐benzimidazolium 3‐phenylpropynoate, C₇H₈N₃⁺·C₉H₅O₂⁻, (I), and 2‐amino‐1H‐benzimidazolium oct‐2‐ynoate, C₇H₈N₃⁺·C₈H₁₁O₂⁻, (II), both have monoclinic symmetry (space group P2₁/c) and display N—H...O hydrogen bonding. Both structures show packing with corrugated sheets of hydrogen‐bonded molecules lying parallel to the [001] direction. Two hydrogen‐bonded ring motifs can be identified and described with graph sets R²₂(8) and R⁴₄(16), respectively, in both (I) and (II). Computational chemistry calculations performed on both compounds show that the hydrogen‐bonded ion pairs are more energetically favourable in the crystal structure than their hydrogen–bonded neutral molecule counterparts.     

Amide hydrogen bonding: control of the molecular and extended structures of two symmetrical pyridine‐2‐carboxamide derivatives

The crystal structures of two symmetrical pyridine‐2‐carboxamides, namely N,N′‐(propane‐1,3‐diyl)bis(pyridine‐2‐carboxamide), C₁₅H₁₆N₄O₂, (I), and N,N′‐(butane‐1,4‐diyl)bis(pyridine‐2‐carboxamide), C₁₆H₁₈N₄O₂, (II), exhibit extended hydrogen‐bonded sequences involving their amide groups. In (I), conventional bifurcated amide–carbonyl (N—H)...O hydrogen bonding favours the formation of one‐dimensional chains, the axes of which run parallel to [001]. Unconventional bifurcated pyridine–carbonyl C—H...O hydrogen bonding links adjacent one‐dimensional chains to form a `porous' three‐dimensional lattice with interconnected, yet unfilled, voids of 60.6 (2) ų which combine into channels that run parallel to, and include, [001]. 4% of the unit‐cell volume of (I) is vacant. Compound (II) adopts a Z‐shaped conformation with inversion symmetry, and exhibits an extended structure comprising one‐dimensional hydrogen‐bonded chains along [100] in which individual molecules are linked by complementary pairs of amide N—H...O hydrogen bonds. These hydrogen‐bonded chains interlock viaπ–π interactions between pyridine rings of neighbouring molecules to form sheets parallel with (010); each sheet is one Z‐shaped molecule thick and separated from the next sheet by the b‐axis dimension [7.2734 (4) Å].     

Copper(II) and zinc(II) complexes of pyridine‐2,6‐di­carboxyl­ic acid

The title compounds, bis­(pyridine‐2,6‐di­carboxyl­ato‐N,O,O′)copper(II) monohydrate, [Cu(C₇H₄NO₄)₂]·H₂O, andbis(pyridine‐2,6‐dicarboxylato‐N,O,O′)zinc(II) trihydrate, [Zn(C₇H₄NO₄)₂]·3H₂O, have distorted octahedral geometries about the metal centres. Both metal ions are bonded to four O atoms and two pyridyl‐N atoms from the two terdentate ligand mol­ecules, which are nearly perpendicular to each other. The copper(II) complex has twofold crystallographic symmetry and contains two different ligand mol­ecules, one of which is neutral and another doubly ionized. In contrast, the zinc(II) complex contains two identical singly ionized ligand mol­ecules. Both crystal structures are stabilized by O—H?O intermolecular hydrogen bonds between the complex and the water mol­ecules.     

Proton‐transfer and non‐transfer in compounds of quinoline and quinaldic acid with l‐tartaric acid

The structures of two compounds of l ‐tartaric acid with quinoline, viz. the proton‐transfer compound quinolinium hydrogen (2R,3R)‐tartrate monohydrate, C₉H₈N⁺·C₄H₅O₆⁻·H₂O, (I), and the anhydrous non‐proton‐transfer adduct with quinaldic acid, bis­(quinolinium‐2‐carboxyl­ate) (2R,3R)‐tar­taric acid, 2C₁₀H₇NO₂·C₄H₆O₆, (II), have been determined at 130 K. Compound (I) has a three‐dimensional honeycomb substructure formed from head‐to‐tail hydrogen‐bonded hydrogen tartrate anions and water mol­ecules. The stacks of π‐bonded quinolinium cations are accommodated within the channels and are hydrogen bonded to it peripherally. Compound (II) has a two‐dimensional network structure based on pseudo‐centrosymmetric head‐to‐tail hydrogen‐bonded cyclic dimers comprising zwitterionic quinaldic acid species which are inter­linked by tartaric acid mol­ecules.     

Substituted pyridine coordinated N,N-trans and N,N-cis cyclopalladated complexes of (S)-4-tert-butyl-2-phenyl-2-oxazoline: Crystal structures, spectral study and catalysis of the decomposition of PS pesticides

Three pyridine coordinated cyclopalladated complexes: (S)-chloro{2-[2-(4-tert-butyl)oxazolinyl]phenyl-C,N}(4-R-pyridine)palladium(II) (R = H, 2; R = CF₃, 3; R = NMe₂, 4), have been synthesized and structurally characterized. While the crystal structure shows that 2 has a normal N,N-trans-conformation in the coordination sphere of palladium(II), 3 and 4 exhibit uncommon N,N-cis-conformations. From ¹H NMR measurements, the major coordination isomer in deuterated chloroform solution is N,N-trans configuration for three palladacycles. It was found that the three complexes catalyze effectively the methanolysis of the PS pesticides including chiral thiophosphates but show different activity depending on the substituents of co-coordinated pyridine ring in 2–4.     

The antitumour drug 7‐ethyl‐10‐hydroxycamptothecin monohydrate and its solid‐state hydrolysis mechanism on heating

7‐Ethyl‐10‐hydroxycamptothecin [systematic name: (4S)‐4,11‐diethyl‐4,9‐dihydroxy‐1H‐pyrano[3′,4′:6,7]indolizino[1,2‐b]quinoline‐3,14(4H,12H)‐dione, SN‐38] is an antitumour drug which exerts activity through the inhibition of topoisomerase I. The crystal structure of SN‐38 as the monohydrate, C₂₂H₂₀N₂O₅·H₂O, reveals that it is a monoclinic crystal, with one SN‐38 molecule and one water molecule in the asymmetric unit. When the crystal is heated to 473 K, approximately 30% of SN‐38 is hydrolyzed at its lactone ring, resulting in the formation of the inactive carboxylate form. The molecular arrangement around the water molecule and the lactone ring of SN‐38 in the crystal structure suggests that SN‐38 is hydrolyzed by the water molecule at (x, y, z) nucleophilically attacking the carbonyl C atom of the lactone ring at (x − 1, y, z − 1). Hydrogen bonding around the water molecules and the lactone ring appears to promote this hydrolysis reaction: two carbonyl O atoms, which are hydrogen bonded as hydrogen‐bond acceptors to the water molecule at (x, y, z), might enhance the nucleophilicity of this water molecule, while the water molecule at (−x, y + , −z), which is hydrogen bonded as a hydrogen‐bond donor to the carbonyl O atom at (x − 1, y, z − 1), might enhance the electrophilicity of the carbonyl C atom.     

The twinned crystal structure of rac‐(R,R)‐N,N′‐oxalyl­divalinol

The title compound, rac‐(R,R)‐N,N′‐bis(1‐hydroxy‐3‐methyl‐2‐butyl)oxalamide, C₁₂H₂₄N₂O₄, crystallizes as a non‐merohedral twin in the triclinic space group . The twin is generated by a twofold rotation about c*. The terminal hydroxy groups of molecules related by an inversion center form hydrogen‐bonded dimers. This hydrogen‐bonding pattern is further extended into a one‐dimensional chain by N—H⋯O hydrogen bonds.     

2‐Acetamido‐N‐benz­yl‐2‐(methoxy­amino)acetamides: functionalized amino acid anticonvulsants

In the crystal structure of 2‐acetamido‐N‐benz­yl‐2‐(methoxy­amino)acetamide (3L), C₁₂H₁₇N₃O₃, the 2‐acetyl­amino­acetamide moiety has a linearly extended conformation, with an inter­planar angle between the two amide groups of 157.3 (1)°. In 2‐acetamido‐N‐benz­yl‐2‐[meth­oxy(meth­yl)­amino]­acetamide (3N), C₁₃H₁₉N₃O₃, the planes of the two amide groups inter­sect at an angle of 126.4 (4)°, resulting in a chain that is slightly more bent. The replacement of the methoxy­amino H atom of 3L with a methyl group to form 3N and concomitant loss of hydrogen bonding results in some positional/thermal disorder in the meth­oxy­(methyl)­amino group. In both structures, in addition to classical N—H⋯O hydrogen bonds, there are also weak non‐standard C—H⋯O hydrogen bonds. The hydrogen bonds and packing inter­actions result in planar hydro­philic and hydro­phobic areas perpendicular to the c axis in 3L and parallel to the ab plane in the N‐meth­yl derivative. Stereochemical comparisons with phenytoin have identified two O atoms and a phenyl group as mol­ecular features likely to be responsible for the anticon­vulsant activities of these compounds.