Hydrogen-Bonded Complexes of Diaminopyridines and Diaminotriazines: Opposite Effect of Acylation on Complex Stabilities

The association behavior of several 2,4-diamino-s-triazines, 2,6-diaminopyridines, and their acylated derivatives with uracil derivatives was studied. In solution (1)H-NMR and IR spectroscopy were used, and in the solid state as (co)crystals X-ray diffraction was used. Acylation of 2,6-diaminopyridine leads to an increase of the association constant in CDCl(3) of the complexes with N-propylthymine from 84 to 440-920 M(-)(1), whereas acylation of diamino-s-triazines leads to a dramatic fall in the association constant of the complexes with N-propylthymine from 890 to ca. 6 M(-)(1). This phenomenon is related to different conformational preferences of these compounds. The amide groups in bis(acylamino)pyridines prefer a trans conformation, with the carbonyl group anti with respect to the ring nitrogen and coplanar with the aromatic ring. The amides of bis(acylamino)triazines, however, reside predominantly in a cis conformation. Repulsive secondary electrostatic interactions between the cis-amide and uracil carbonyl groups are thought to be responsible for the low association constant of complexes of bis(acylamino)triazines with uracils. The relatively high dimerization constants of bis(acylamino)triazines have been rationalized by the strong tendency to dimerize via quadruple hydrogen bonding.     

Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study.

In order to study the differences of the structural properties of Aib-rich peptides in solution and in the crystalline state, molecular dynamics (MD) simulations of the Aib-containing peptide II (pBrBz-(Aib)5-Leu-(Aib)2-OMe) were performed in the crystalline state, starting from two different conformers obtained experimentally by X-ray diffraction. The structural properties as derived from X-ray crystallography (e.g., torsional angles and hydrogen bonds) are well-reproduced in both constant-volume and constant-pressure simulations, although the force-field parameters used result in a too-high density of the crystals. Through comparison with the results from previous MD and nuclear magnetic resonance (NMR) studies of the very similar peptide I (Z-(Aib)s-Leu-(Aib)2-OMe) in dimethylsulfoxide (DMSO) solution, it is found that, in the crystal simulation, the conformational distribution of peptide II is much narrower than that in the solution simulation of peptide. I. This leads to a significant difference in 3 [symbol: see text] (HN, HC alpha) coupling constant values, in agreement with experimental data, whereas the NOE intensities or proton-proton distance bounds appear insensitive to the difference in conformational distribution. For small peptides the differences between their conformational distribution in the crystalline form and in solution may be much larger than for proteins, a fact which should be kept in mind when interpreting molecular properties in the solution state by using X-ray crystallographic data.     

Syntheses and conformational structures of functionalized tetraoxacalix[2]arene[2]triazines

The syntheses and conformational structures of various functionalized tetraoxacalix[2]arene[2]triazines were studied. Applying the fragment coupling approach and the post-macrocyclization chemical manipulations, a number of tetraoxacalix[2]arene[2]triazines that contain, on the lower rim, one or two aldehyde, ester, carboxylic acid, hydroxymethyl, and aminomethyl functional groups were prepared in moderate to high chemical yields from cheap and commercially available materials. On the basis of X-ray crystallography and NMR spectroscopy, all tetraoxacalix[2]arene[2]triazines containing electron-withdrawing group(s) adopted 1,3-alternate conformation both in solution and in the solid state, while tetraoxacalix[2]arene[2]triazines bearing hydroxymethyl and aminomethyl substituent(s) existed as pinched or distorted partial cone conformers due to the formation of intramolecular hydrogen bond between hydroxyl or amino group and triazine ring.     

Conformational analysis of the structure of <Emphasis Type="Italic">p</Emphasis>-butoxybenzylidene-<Emphasis Type="Italic">p</Emphasis>′-propionyloxyaniline at temperatures of crystal → nematic and nematic → isotropic liquid phase transitions

The molecular structure and conformational properties of the p-butoxybenzylidene-p′-propionyloxyphenylaniline molecule in the crystalline state and at temperatures of the crystal → nematic and nematic → isotropic liquid phase transitions were examined by AM1 calculations. It was found that the nematic → isotropic liquid phase transition is accompanied by a change in the molecular conformation.     

Conformation-changing aggregation in hydroxyacetone: a combined low-temperature FTIR, jet, and crystallographic study

Aggregation in hydroxyacetone (HA) is studied using low-temperature FTIR, supersonic jet expansion, and X-ray crystallographic (in situ cryocrystallization) techniques. Along with quantum chemical methods (MP2 and DFT), the experiments unravel the conformational preferences of HA upon aggregation to dimers and oligomers. The O-H···O═C intramolecular hydrogen bond present in the gas-phase monomer partially opens upon aggregation in supersonic expansions, giving rise to intermolecular cooperatively enhanced O-H···O-H hydrogen bonds in competition with isolated O-H···O═C hydrogen bonds. On the other hand, low-temperature IR studies on the neat solid and X-ray crystallographic data reveal that HA undergoes profound conformational changes upon crystallization, with the HOCC dihedral angle changing from ~0° in the gas phase to ~180° in the crystalline phase, hence giving rise to a completely new conformation. These conclusions are supported by theoretical calculations performed on the geometry derived from the crystalline phase.     

The Distinct Conformational Landscapes of 4S-Substituted Prolines That Promote an endo Ring Pucker

4-Substitution on proline directly impacts protein main chain conformational preferences. The structural effects of N-acyl substitution and of 4-substitution were examined by NMR spectroscopy and X-ray crystallography on minimal molecules with a proline 4S-nitrobenzoate. The effects of N-acyl substitution on conformation were attenuated in the 4S-nitrobenzoate context, due to the minimal role of the n→π* interaction in stabilizing extended conformations. By X-ray crystallography, an extended conformation was observed for most molecules. The formyl derivative adopted a δ conformation that is observed at the i+2 position of β-turns. Computational analysis indicated that the structures observed crystallographically represent the inherent conformational preferences of 4S-substituted prolines with electron-withdrawing 4-position substituents. The divergent conformational preferences of 4R- and 4S-substituted prolines suggest their wider structure-specific application in molecular design. In particular, the proline endo ring pucker favored by 4S-substituted prolines uniquely promotes the δ conformation [(ϕ, ψ) ≈(−80°, 0°)] found in β-turns. In contrast to other acyl capping groups, the pivaloyl group strongly promoted trans amide bond and polyproline II helix conformation, with a close n→π* interaction in the crystalline state, despite the endo ring pucker, suggesting its special capabilities in promoting compact conformations in ϕ due to its strongly electron-donating character.     

Spectroscopic, crystallographic and computational studies of the formation and isomerization of cyclic acetals and ketals of pentonolactones

The different reactivities of D-ribonolactone, L-arabinonolactone, D-xylonolactone, D-lyxonolactone 2-deoxy-D-ribonolactone toward benzaldehyde and acetone in acidic media, were examined. The reactions involved complex equilibria and were investigated with extensive ¹³C NMR studies as well as X-ray crystallographic analysis of selected products. Molecular mechanics (MM2) and semiempirical (PM3 and AM1) calculations of some derivatives were carried out in order to facilitate structural and conformational assignments. The differences in reactivity observed for the reactions of D-pentono-1,4-lactones with benzaldehyde and acetone are rationalized in terms of their structural and conformational features.     

Theoretical Study of the Formation of Benzofurotriazines by Reaction of 3-Substituted 1,2,4-Triazines and Fused Azolo[1,2,4]triazines with Resorcinol

3-Methylthio- and 3-amino-1,2,4-triazines react with resorcinol to give benzofurotetrahydrotriazine derivatives, while reactions of [1,2,4]triazolo[4,3-b]- and tetrazolo[1,5-b][1,2,4]triazines with resorcinol stop at the stage of resorcinol addition. According to the results of quantum-chemical calculations, the possibility for further cyclization of the resorcinol addition products is determined by the following factors: tautomeric and conformational states of the compounds, which ensure spatial proximity of the hydroxy group to the cyclization center (C⁶); charges on the C⁶ atom of the triazine ring and oxygen atom of the resorcinol fragment in the conformation most favorable for cyclization; and energies of the highest occupied and lowest unoccupied molecular orbitals of the resorcinol addition products.     

Substituent steric effects and molecular structure of anionic σ-complexes of 5,7-dinitroquinoline

Molecular structure and conformational flexibility of Meisenheimer complexes of 5,7-dinitroquinoline derivatives are studied experimentally using X-ray diffraction and theoretically by semi-empirical AM1 calculations. The dihydrocycle is found to possess high conformational flexibility in all anionic σ-complexes considered. Substituent steric effects at the saturated carbon atom of the anion significantly influence the equilibrium conformation and deformability of the partially hydrogenated ring. An increase of the bending strain does not cause considerable changes of the conformational characteristics of ring. In the crystal phase, the geometry of the anion depends essentially on the crystal structure and on the cation coordination.     

sym-Triazine Derivatives. 2. Synthesis, Properties, and Structure of 2-Oxo-1,2-dihydro-sym-triazines

Previously unreported 2-oxo-1,2-dihydro-sym-triazines have been prepared and their alkylation reactions have been studied. It was found that, independently of the structure and nature of the substituent in positions 4 and 6 of the triazine ring or the structure of the alkyl halide used, the reaction occurs regioselectively at the oxygen atom. The stereostructure of the 2-oxo-1,2-dihydro-sym-triazines was investigated by X-ray analysis and it was shown that they exist as dimers in the crystalline state.     

Molecular modeling studies of novel heteroarotinoids

The molecular structure and conformational properties of structurally related oxo and thio heteroarotinoids have been calculated by employing AM1 molecular orbital and both MM2P and Chem-X “optimize” molecular mechanics methods, and the results have been compared with crystal structure data. For the cis and trans oxo heteroarotinoids, MM2P gives values of the bridge torsion angles ?₁ and ?₂ in closest agreement with the crystal structure, and all three computational methods yield values of ?₁ and ?₂ within about 10° of that found in the crystal structures. All three computational methods locate a minimum-energy conformation for the trans isomer corresponding to the two bridged aryl rings being mutually perpendicular, in agreement with the crystal structure and similar to that found for the structurally analogous trans-stilbene. The calculated heteroring geometries also reproduce the twist-sofa conformation observed for the crystal structure. Calculated conformational energies versus ?₁ and ?₂ indicate broad energy wells about the minimum-energy conformation with barriers to rotation at the planar and perpendicular conformations, and with higher barriers found for the more sterically congested cis isomer. The corresponding cis and trans thio heteroarotinoids exhibit conformational properties similar to their oxo analogues. Both AM1 and MM2P fare poorly in reproducing the crystal structure values of the sulfur-containing bond lengths and bond angles. The C-S bonds found in these thio heteroarotinoids may possess more double-bond character than accounted for in the calculations. Also, the results suggest that the MM2P sulfur-related force-field parameters adopted for these calculations may require further refinement.     

Synthesis,Thermal, and Optical Properties of Tris(5-aryl-1,3,4-oxadiazol-2-yl)-1,3,5-triazines,New Star-Shaped Fluorescent Discotic Liquid Crystals

The synthesis of tris(aryloxadiazolyl)triazines (TOTs), C₃-symmetrical star-shaped mesogenes with a 1,3,5-triazine center, 5-phenyl-1,3,4-oxadiazole arms, and various peripheral alkoxy side chains is reported. Threefold Huisgen reaction on a central triazine tricarboxylic acid and suitable aryltetrazoles yields the title compounds. Selected analogues with a benzene center are included in this study and allow for an evaluation of the impact of the central unit on the physical properties. Thermal (differential scanning calorimetry, DSC; polarization optical microscopy, POM), optical (UV/Vis, fluorescence), electric (time of flight, TOF), and structural (single crystal; wide-angle X-ray scattering, WAXS) properties of these compounds were investigated. The modification of alkoxy chain length and substitution pattern allows for a tuning of the physical properties. TOTs emit blue to yellow light, depending on conjugation length, donor–acceptor substitution, and solvent polarity, whereas concentration quenches and aggregation enhances the emission. The width of the mesophases is typically around ΔT=100–150 K but can even exceed 220 K. Polarization optical microscopy and X-ray diffraction on oriented filaments reveal that TOTs are highly ordered liquid crystals (LCs) with long-range hexagonal columnar structure.     

Multifunctional Supramolecular Dendrimers with an s‐Triazine Ring as the Central Core: Liquid Crystalline,Fluorescence and Photoconductive Properties

Novel liquid crystal (LC) dendrimers have been synthesised by hydrogen bonding between an s‐triazine as the central core and three peripheral dendrons derived from bis(hydroxymethyl)propionic acid. Symmetric acid dendrons bearing achiral promesogenic units have been synthesised to obtain 3:1 complexes with triazine that exhibit LC properties. Asymmetric dendrons that combine the achiral promesogenic unit and an active moiety derived from coumarin or pyrene structures have been synthesised in order to obtain dendrimers with photophysical and electrochemical properties. The formation of the complexes was confirmed by IR and NMR spectroscopy data. The liquid crystalline properties were investigated by differential scanning calorimetry, polarising optical microscopy and X‐ray diffractometry. All complexes displayed mesogenic properties, which were smectic in the case of symmetric dendrons and their complexes and nematic in the case of asymmetric dendrons and their dendrimers. A supramolecular model for the lamellar mesophase, based mainly on X‐ray diffraction studies, is proposed. The electrochemical behaviour of dendritic complexes was investigated by cyclic voltammetry. The UV/Vis absorption and emission properties of the compounds and the photoconductive properties of the dendrons and dendrimers were also investigated     

The Crystal Structure of 5,5′,7,7′-tetramethyl-3,3′,9-triethyl thiacarbocyanine perchlorate

The crystal structure of the title compound has been determined by X-ray crystallographic analysis from diffractometer data. The compound is found to exist in the crystalline state as the mono-cis isomer (a). The conjugated chain is in a folded configuration and the two sulfur atoms are on opposing sides. It is the first time such a mono-cis isomer has been analysed by X-ray crystallography.     

Carbene Complexes of Pnictogen Pentafluorides and Boron Trifluoride

 Synthesis, characterization, and solid state X-ray crystallographic structures for 12-Pn-6 complexes derived from carbene 4,5-dichloro-1,3-dimesitylimidazol-2-ylidene and phosphorus, arsenic, or antimony pentafluoride are reported. The adducts show octahedral geometries at the pnictogen centers with C-Pn bond distances of 189.8 (P), 199.9 (As), and 217.5 (Sb) pm. The structures are those of internal zwitterions with imidazolium ion character in the heterocyclic ring and a pentafluoropnictanide anion bonded to C². Adducts of BF₃ with 1,3-dimesitylimidazol-2-ylidene and 4,5-dichloro-1,3-dimesitylimidazol-2-ylidene are also reported for comparison. Although the reactivity of chlorinated and non-chlorinated carbenes varies considerably, the spectroscopic and structural properties of analogous adducts are remarkably similar.     

New supramolecular liquid crystals induced by hydrogen bonding between pyridyl‐1,2,4‐oxadiazole derivatives and 2,5‐thiophene dicarboxylic acid

Supramolecular liquid crystalline complexes were obtained from binary mixtures of 3‐(4‐pyridyl)‐5‐(4‐n‐alkoxy)phenyl‐1,2,4‐oxadiazoles and 2,5‐thiophene dicarboxylic acid. Although the oxadiazole derivatives and the dicarboxylic acid are non‐mesomorphic, the H‐bonded complexes exhibit mesomorphism. Their liquid crystalline properties were investigated by differential scanning calorimetry and polarizing optical microscopy. The complexes exhibit enantiotropic nematic phases. A structural study involving AM1 semi‐empirical calculations is also described.     

The Behaviour of Nitrilimines Towards Ethyl Isocyanoacetate

 Interactions between nitrilimines and the title isocyanide afford, through two competing pathways, 2,3-dihydro-1,2,4-triazines and 1,3-oxazoles. In situ cycloaddition of unreacted nitrilimine with the triazines gives rise to a third class of products, the bicyclic 1,5,6,8a-tetrahydro[1,2,4]triazolo[4,3-d][1,2,4]triazines. Acceptor-free representatives of the latter are prone to triazine ring cleavage, yielding triazolyl ketone hydrazones which served as a structure proof. Substituent effects became apparent upon employment of N-(4-methoxyphenyl)- and N-(4-nitrophenyl)nitrilimines: whereas the former afforded a quinoxaline as the fourth product, triazine formation was totally blocked with the latter, the corresponding oxazole being the sole product. The constitution of acceptor-substituted bicyclic compounds (which failed to give the structure-revealing hydrazones) was established by an X-ray diffraction analysis.     

Conformational energy penalties of protein-bound ligands

The conformational energies required for ligands to adopt their bioactive conformations were calculated for 33 ligand–protein complexes including 28 different ligands. In order to monitor the force field dependence of the results, two force fields, MM3 and AMBER, were employed for the calculations. Conformational analyses were performed in vacuo and in aqueous solution by using the generalized Born/solvent accessible surface (GB/SA) solvation model. The protein-bound conformations were relaxed by using flat-bottomed Cartesian constraints. For about 70% of the ligand–protein complexes studied, the conformational energies of the bioactive conformations were calculated to be 3 kcal/mol. It is demonstrated that the aqueous conformational ensemble for the unbound ligand must be used as a reference state in this type of calculations. The calculations for the ligand–protein complexes with conformational energy penalties of the ligand calculated to be larger than 3 kcal/mol suffer from uncertainties in the interpretation of the experimental data or limitations of the computational methods. For example, in the case of long-chain flexible ligands (e.g. fatty acids), it is demonstrated that several conformations may be found which are very similar to the conformation determined by X-ray crystallography and which display significantly lower conformational energy penalties for binding than obtained by using the experimental conformation. For strongly polar molecules, e.g. amino acids, the results indicate that further developments of the force fields and of the dielectric continuum solvation model are required for reliable calculations on the conformational properties of this type of compounds.     

Ruthenium complexes of easily accessible tridentate ligands based on the 2-aryl-4,6-bis(2-pyridyl)-s-triazine motif: absorption spectra, luminescence properties, and redox behavior

A family of tridendate ligands 1 a-e, based on the 2-aryl-4,6-di(2-pyridyl)-s-triazine motif, was prepared along with their hetero- and homoleptic Ru(II) complexes 2 a-e ([Ru(tpy)(1 a-e)](2+); tpy=2,2':6',2"-terpyridine) and 3 a-e ([(Ru(1 a-e)(2)](2+)), respectively. The ligands and their complexes were characterized by (1)H NMR spectroscopy, ES-MS, and elemental analysis. Single-crystal X-ray analysis of 2 a and 2 e demonstrated that the triazine core is nearly coplanar with the non-coordinating ring, with dihedral angles of 1.2 and 18.6 degrees, respectively. The redox behavior and electronic absorption and luminescence properties (both at room temperature in liquid acetonitrile and at 77 K in butyronitrile rigid matrix) were investigated. Each species undergoes one oxidation process centered on the metal ion, and several (three for 2 a-e and four for 3 a-e) reduction processes centered on the ligand orbitals. All compounds exhibit intense absorption bands in the UV region, assigned to spin-allowed ligand-centered (LC) transitions, and moderately intense spin-allowed metal-to-ligand charge-transfer (MLCT) absorption bands in the visible region. The compounds exhibit relatively intense emissions, originating from triplet MLCT levels, both at 77 K and at room temperature. The incorporation of triazine rings and the near planarity of the noncoordinating ring increase the luminescence lifetimes of the complexes by lowering the energy of the (3)MLCT state and creating a large energy gap to the dd state.