Urszula Rychlewska

Factors Affecting Conformation of (R,R)-Tartaric Acid Ester, Amide and Nitrile Derivatives. X-Ray Diffraction, Circular Dichroism, Nuclear Magnetic Resonance and Ab Initio Studies

Abstract Derivatives 2a–15a of (R,R)-tartaric acid (1a) with all combinations of methyl ester, amide, N-methylamide and N,N-dimethylamide groups, as well as the corresponding O,O′-dibenzoyl derivatives 1b–15b and nitriles 16–18 have been synthesized. Their conformations have been studied by the NMR and CD methods in solution as well as by X-ray diffraction in the crystalline state. The preference for planar. T conformation of the four carbon chain is observed under conditions restricting the α-hydroxyacid, ester or amide group to be nearly planar, this conformation being stabilized by intramolecular hydrogen bonds of the S(5) motif and the electrostatic CO/C(β)H and CN/C(β)H coplanar bond interactions. The C=O/C(α)-O bond system tends to be either synplanar (ester, acid), or antiplanar (ester, primary and secondary amide). Ab initio calculations allowed to demonstrate that for the isolated molecules of diamides 10a and 15a there is strong preference for gauche G+(a,a) conformers, the driving force being the formation of the hydrogen bonded six-membered cycles of the S(6) motif joining the OH and C=O groups from two different halves of the molecule. The results compare favourably with the experimental values derived from NMR spectra of 15a in nonpolar solvent. In the absence of intramolecular hydrogen bonding the N,N-dimethylamide group is better accomodated in a gauche G− conformer. This releases the nonbonded interaction due to the amide methyl group anti to the carbonyl group.

Supramolecular organisation via hydrogen bonding in trimethoprim sulfonate salts

The present study deals with the crystal structures of four organic salts, namely, trimethoprim benzene sulfonate monohydrate 1, trimethoprim sulfanilate monohydrate 2, trimethoprim p-toluene sulfonate 3 and trimethoprim 3-carboxy-4-hydroxybenzene sulfonate dihydrate 4. Trimethoprim (TMP) is protonated at one of the ring nitrogens of the pyrimidine ring. Generally, in the TMP carboxylate complexes, the protonated pyrimidine ring is hydrogen-bonded to the carboxylate group forming a cyclic fork-like hydrogen-bonded bimolecular motif. In structures 1–3, the sulfonate group plays the role of the carboxylate anion. In compounds 1 and 2, there is no pairing of the pyrimidine rings because the pairing sites are blocked by water molecules donating hydrogen to the unprotonated ring nitrogen. Two of the cyclic motifs are bridged by the water molecule donating two hydrogen atoms, leading to a hydrogen-bonded supramolecular chain. This chain pairs with another chain running in the opposite direction. These two chains are cross-linked by O–H⋯O hydrogen bonds. In compound 2, two of the hydrogen atoms of the amino group of the sulfanilate bridge two methoxy oxygen of the two TMP cations via N–H⋯O hydrogen bonds resulting in a supramolecular zig-zag chain. In compound 3, two inversion related cyclic motifs are paired through a pair of N–H⋯N hydrogen bonds involving the 4-amino group and the N3 atom of the pyrimidine ring. In addition to the pairing, one of the sulfonate oxygen atoms bridges the 2-amino and 4-amino groups on either side of the paired bases, resulting in a self-complementary DADA (D represents the hydrogen bond donor and A represents hydrogen bond acceptor) array of quadruple hydrogen bonding patterns. In compound 4, one of the water molecules forms a hydrogen-bonded dimer with the inversion-related water molecule. The 3-carboxy-4-hydroxybenzene sulfonate moiety self-assembles into a supramolecular chain along the c axis through O–H⋯O hydrogen bonds. Two such oppositely running supramolecular chains are connected by dimeric and monomeric water molecules. The variation of supramolecular organization via hydrogen bonding in the four different trimethoprim sulfonate salts has been discussed.

Simple synthetic method and structural characteristics of (1,3-propanediaminetetraacetato)cobalt(II) complexes: uniform crystal packing in a series of metal(II) complexes with 1,3-propanediaminetetraacetate ligand

Abstract Starting from Ba[Ba(1,3-pdta)]·2H2O three new hexadentate cobalt(II) complexes [MII(H2O)6][CoII(1,3-pdta)]·2H2O (MII=Ba (1), Co (2) and Mg (3)) (where 1,3-pdta represents the 1,3-propanediaminetetraacetate ion) have been prepared and characterized. Presented in this paper, the crystal structures of the complexes containing CoII and MgII counter cations are isomorphic, as are the other crystal structures of metal(II) complexes with 1,3-pdta ligand, so far reported in the literature. The complexes crystallize in the space group Pnna of the orthorhombic crystal system. The structural unit consists of discrete [CoII(1,3-pdta)]2− and [MII(H2O)6]2+ octahedra, and two water solvent molecules all of which lie on a twofold axis of symmetry. The complex cations and anions alternate in the crystal lattice each being octahedrally surrounded by the counter ions. Electronic absorption spectra of [CoII(1,3-pdta)]2− complexes are presented and discussed in terms of octahedral distortion in edta-type CoII complexes.

Synthesis and X-ray structural study of magnesium (1,3-propanediaminetetraacetato)cuprate(II) octahydrate, Mg[Cu(1,3-pdta)]·8H2O.: Stereochemistry of hexadentate copper(II)–edta-type complexes in relation to the structure of the ligand

Abstract The hexadentate complex Mg[Cu(1,3-pdta)]·8H2O (1) (where 1,3-pdta represents the 1,3-propanediaminetetraacetate ion) has been prepared and isolated and its structure established by X-ray crystallography. The structure converged to R=0.030 for 1537 observed reflections. The Cu(II) ion is surrounded by two nitrogen atoms and four oxygen atoms of the ligand, making a tetragonally elongated octahedron (T=0.868). The Mg cation is bonded octahedrally to six water molecules. Both complex ions utilize a two-fold symmetry axis that is present in the crystal. The conformations of the chelate rings were found to be envelope for the glycinates and skew-boat for the six-membered diamine (T) ring. Comparison of the structures of the hexadentate copper(II)–edta-type complexes shows an expected variation in their stereochemistry, depending on the structure of the ligand. Infrared (carboxylate region) and electronic absorption spectra are also given.

Conformational disparity of (R,R)-tartaric acid esters and amides

Abstract Exciton chirality method is used to determine anti and gauche conformations, respectively, of ester and dialkylamide derivatives of (R,R) - tartaric acid. Gauche conformation of (R,R)-N,N,N′-tetramethyltartamide and its O,O-dibenzoyl derivative is found in the solid state by X-ray analysis.

Circular Dichroism of 9,10‐Dihydrophenanthrene Derivatives Reveals both the Absolute Configuration and Conformation: A Novel Approach to Mislow's Helicity Rule

The absolute configuration and the conformation of 9,10-trans-disubstituted 9,10-dihydrophenanthrenes, known chiral metabolites of phenanthrene-9,10-oxide, have been determined by circular dichroism. The absolute configuration assignment is based on the sign of the long-wavelength Cotton effect (A-band), which is conformation invariant and originates from benzylic chirality. This provides a new interpretation of the Mislow biphenyl-helicity rule for the case of the 9,10-dihydrophenanthrene chromophore. The sign of the B-band Cotton effect reflects the conformation of the biphenyl chromophore in 9,10-dihydrophenanthrenes. It is shown that the origin of chiroptical properties of 9,10-dihydrophenanthrenes is closely related to those of 5,6-trans-disubstituted 1,3-cyclohexadienes.

Packing modes of (R,R)-tartaric acid esters and amides

The molecular packing modes of a series of mono- and diamides of (R, R)-tartaric acid are discussed on the basis of their crystal structures. Derivatives include combinations of methylester, amide, N-methylamide and N,N-dimethylamide groups, both symmetrically and asymmetrically substituted. The symmetrically substituted derivatives do not utilize their C(2) symmetry in the crystal. The packing of primary tartramides seems to be driven by NH.O=C hydrogen bonds and supplemented by strong OH.O=C and weak NH.OH bonds. On the other hand, in derivatives containing methylester and/or methylamide groups OH.OH.O=C hydrogen-bond patterns seem to dominate. Types of aggregates, characteristic for the investigated derivatives, include cyclic dimers and ring systems analogous to the dimers, but formed by two different although complementary functional groups, as well as sets of chains aligned in a manner resembling the helical arrangement of peptides. The helices are formed along the screw axis with an identity period of approximately 5 A. In tartramic acids, containing in one molecule both carboxyl and amide functions, in competition between the two groups to control the molecular arrangement, the latter dominates, unless it is N-substituted tartramide, in which case the carboxyl group predominates. Problems with packing, which occur in some of the structures owing to the steric bulk of the methyl groups, are overcome by changes in conformation (esters) or by co-crystallization with solvent water molecules (methylamides and dimethylamides). These derivatives are also more likely to crystallize with multiple asymmetric units.

(R,R)-Tartaric Acid Dimethyl Diester from X-Ray and Ab Initio Studies: Factors Influencing Its Conformation and Packing

The conformation of dimethyl (R,R)-tartrate has been analyzed on the basis of the single crystal X-ray diffraction method as well as by ab-initio quantum chemical studies. The results showed that the extended T conformation containing two planar hydroxyester moieties predominates in both ab-initio and X-ray studies. The lowest energy conformer in ab-initio calculations has C2 symmetry and hydrogen bonds between a hydroxyl group and the nearest carbonyl oxygen. The second in energetical sequence, with an energy difference of only 1.2 kcal/mol, is the asymmetrical conformer, which differs from the lowest energy form by the rotation of one of the ester groups by 180°. Intramolecular OH...O hydrogen bonds observed in this rotamer again involve only proximal functional groups. This conformer is present in the crystal structure of the studied compound, although its conformation in the solid state is no longer stabilized by intramolecular hydrogen bonds of the type mentioned above. In the crystal, hydroxyl groups are mostly involved in intermolecular hydrogen bonds and form only a weak intramolecular hydrogen bond with each other. The planar arrangement of the α-hydroxyester moieties combined with the extended conformation of the carbon chain seems to be stabilized by the intramolecular hydrogen bonds between neighboring functional groups and by the long range dipole-dipole interactions between two pairs of CO and (β)C-H bonds.

Absolute stereochemistry of the cadinenes from eupatorium trapezoideum

Abstract Chemical examination of Eupatorium trapezoideum has furnished five cadinenes 1 a, 2 a, 2 b, 4 a & 5 and a degraded cadinene 3 a whose stereostructures are presented in this paper. The absolute stereochemistry of the major component 1 a has been determined by application of Horeaus method as well as chemical correlation studies and has been confirmed by X-ray analysis of 1 f thus suggesting that it belongs to the amorphane group.

Novel chiral pyromellitdiimide (1,2,4,5-benzenetetracarboxydiimide) dimers and trimers: Exploring their structure, electronic transitions, and exciton coupling

The chiral but highly symmetrical acyclic and cyclic pyromellitic diimide dimers and trimers 2-5 have been obtained and characterized for the first time. The pyromellitdiimide chromophores in these molecules are linked by a rigid diequatorially 1,2-disubstituted cyclohexane skeleton. The structures of the compounds have been determined in detail by molecular modeling and, in the case of cyclic dimer 4 and trimer 5, by means of X-ray diffraction analysis. The electronically excited states of the pyromellitdiimide chromophore (1a) have been studied in these and other model compounds by means of linear dichroism (LD), magnetic circular dichroism (MCD), and circular dichroism (CD) spectroscopy. CD spectra of the rigid cyclic trimer 5 have provided the most detailed information on the excited states of the pyromellitdiimide chromophore. The low-energy tail (340-360 nm) of the absorption envelope can be assigned to out-of-plane polarized n-pi* transitions (I, II). The higher energy bands are due to contributions from up to six pi-pi* transitions, these being polarized either along the long (IV-VI, VIII) or short axis (III, VII). The results of ab initio CIS/cc-pVDZ and semiempirical INDO/S-CI calculations have been compared with the experimental data. CD Cotton effects in the region 200-260 nm, which result from exciton interactions between electric dipole allowed transitions of two pyromellitdiimide chromophores in compounds 2-5, provide reliable and useful information concerning the conformation and absolute configuration of these molecules, which may be extrapolated to other oligoimide systems.