Syntheses, Crystal Structures, and Conformations of 10,10-Spiro-Bilirubins

Summary. Crystal structure determinations of two novel bilirubin analogs with spirocyclohexyl and spirofluorenyl groups at C(10) are reported. Conformation-determining torsion angles and key hydrogen bond distances and angles are compared to those from molecular dynamics calculations, and to the corresponding data from X-ray determinations and molecular dynamics calculations of bilirubin. Like bilirubin, the component dipyrrinones of spirocyclohexyl and spirofluorenyl rubins are present in the bis-lactam form with (Z)-configuration double bonds at C(4) and C(15). Their crystal structures show considerable similarity to that of bilirubin: both pigments adopt a folded, intramolecularly hydrogen-bonded ridge-tile conformation stabilized by six hydrogen bonds. The interplanar angle of the spirocyclohexyl ridge-tile is nearly the same (94°) as that of bilirubin (95°), but the interplanar angle of the spirofluorenyl ridge-tile is noticeably smaller (84°). The hydrogen bond distances of both spiro-rubin crystal structures are generally longer by 0.1–0.2Å than those in bilirubin. Both new pigments exhibit excellent lipophilicity and, unlike bilirubin, are soluble in methanol.     

Crystal Structure and Conformation of a 10-Thiabilirubin

Summary.  A crystal structure determination of a bilirubin analog with a sulfur instead of a C(10)–CH₂ linking the two dipyrrinones is reported. Conformation-determining torsion angles and key hydrogen bond distances and angles are compared to those obtained from molecular dynamics calculations as well as to the corresponding data from X-ray determinations and molecular dynamics calculations of bilirubin. Like other bilirubins, the component dipyrrinones of the analog are present in the bis-lactam form with (Z)-configurated double bonds at C(4) and C(15). Despite the large differences in bond lengths and angles at –S–vs.–CH₂–, the crystal structure shows considerable similarity to bilirubin: both pigments adopt a folded, intramolecularly hydrogen-bonded ridge-tile conformation stabilized by six hydrogen bonds – although the interplanar angle of the ridge-tile conformation of the title compound is smaller (∼ 86°) than that of bilirubin (∼ 98°). The collective data indicate that even with long C–S bond lengths and a smaller C–S–C bond angle at the pivot point on the ridge-tile seam, intramolecular hydrogen bonding persists. Received August 16, 2001. Accepted September 12, 2001     

Synthesis,Conformation, and Metabolism of a Selenium Bilirubin

Summary. A symmetrical C(10)-selena-bilirubin analog, 8,12-bis(2-carboxyethyl)-7,13-dimethyl-2,3,17,18-tetraethyl-10-selenabiladiene-ac-1,19(21H,24H)-dione was synthesized from 8-(2-carboxyethyl)-2,3-diethyl-7-methyl-(10H)-dipyrrin-1-one in one step by reaction with diselenyl dichloride. The selena-rubin exhibited UV-vis and NMR spectroscopic properties similar to those of the parent mesobilirubin, and like bilirubin and mesobilirubin, it adopts an intramolecularly hydrogen-bonded conformation, shaped like a ridge-tile but with a steeper pitch. The longer C–Se bond lengths (2.2Å) and smaller bond angles at C–Se–C (88°), as compared to C–CH₂–C (1.5Å, 106°), lead to an interplanar angle between the two dipyrrinones of only 72°, which is considerably less than that of bilirubin (100°) and close to that (74°) of its 10-thia-rubin analog. Despite the conformational distortion, the sensitivity of Se toward oxidation and the typically weak C–Se bond, the selena-rubin is metabolized in normal rats, like bilirubin, to acyl glucuronides, which are secreted into bile. In mutant (Gunn) rats lacking bilirubin glucuronosyl transferase (UGT1A1), glucuronide or other metabolites of the selena-rubin were not detected in bile, demonstrating the importance of hepatic glucuronidation for its biliary excretion.     

Crystal Structure and Conformation of a 10-Thiabilirubin

 A crystal structure determination of a bilirubin analog with a sulfur instead of a C(10)–CH₂ linking the two dipyrrinones is reported. Conformation-determining torsion angles and key hydrogen bond distances and angles are compared to those obtained from molecular dynamics calculations as well as to the corresponding data from X-ray determinations and molecular dynamics calculations of bilirubin. Like other bilirubins, the component dipyrrinones of the analog are present in the bis-lactam form with (Z)-configurated double bonds at C(4) and C(15). Despite the large differences in bond lengths and angles at –S–vs.–CH₂–, the crystal structure shows considerable similarity to bilirubin: both pigments adopt a folded, intramolecularly hydrogen-bonded ridge-tile conformation stabilized by six hydrogen bonds – although the interplanar angle of the ridge-tile conformation of the title compound is smaller (∼ 86°) than that of bilirubin (∼ 98°). The collective data indicate that even with long C–S bond lengths and a smaller C–S–C bond angle at the pivot point on the ridge-tile seam, intramolecular hydrogen bonding persists.     

Crystal Structure and Conformation of a Dipyrrylmethane. The gem-Dimethyl Effect

Summary.  A crystal structure determination of the new dipyrrylmethane diethyl-2,3,5,5,7,8-hexamethyl-5,10-dihydrodipyrrin-1,9-dicarboxylate (1) is only the third reported for a dipyrrylmethane and the first with a gem-dimethyl group at the bridging carbon atom. Conformation determining torsion angles are compared to those from molecular mechanics calculations and to the corresponding data for an analogous dipyrrylmethane (2) with no gem-dimethyl moiety. The crystal structures of 1 and 2 differ significantly: 1 adopts the +ac,+ac or −ac,−ac conformation, whereas 2 exists in the −ac,+sc conformation in an intermolecularly hydrogen bonded dimer. There is no evidence for hydrogen bonding in crystals of 1, and its ac conformation is unlike that found about the central core of bilirubin (sc,sc). Taken collectively, the data indicate that the presence of a sterically demanding and potentially conformation distorting gem-dimethyl group located at the bridging carbon of a dipyrrylmethane (i) stabilizes a conformation that brings the pyrrole NH groups syn to the gem-dimethyls and (ii) would destabilize the ridge-title conformation of 10,10-dimethylbilirubin. Received December 3, 1999. Accepted December 15, 1999     

Synthesis, Conformation, and Metabolism of a Selenium Bilirubin

A symmetrical C(10)-selena-bilirubin analog, 8,12-bis(2-carboxyethyl)-7,13-dimethyl-2,3,17,18-tetraethyl-10-selenabiladiene-ac-1,19(21H,24H)-dione was synthesized from 8-(2-carboxyethyl)-2,3-diethyl-7-methyl-(10H)-dipyrrin-1-one in one step by reaction with diselenyl dichloride. The selena-rubin exhibited UV-vis and NMR spectroscopic properties similar to those of the parent mesobilirubin, and like bilirubin and mesobilirubin, it adopts an intramolecularly hydrogen-bonded conformation, shaped like a ridge-tile but with a steeper pitch. The longer C–Se bond lengths (2.2Å) and smaller bond angles at C–Se–C (88°), as compared to C–CH₂–C (1.5Å, 106°), lead to an interplanar angle between the two dipyrrinones of only 72°, which is considerably less than that of bilirubin (100°) and close to that (74°) of its 10-thia-rubin analog. Despite the conformational distortion, the sensitivity of Se toward oxidation and the typically weak C–Se bond, the selena-rubin is metabolized in normal rats, like bilirubin, to acyl glucuronides, which are secreted into bile. In mutant (Gunn) rats lacking bilirubin glucuronosyl transferase (UGT1A1), glucuronide or other metabolites of the selena-rubin were not detected in bile, demonstrating the importance of hepatic glucuronidation for its biliary excretion.     

Crystal Structure and Conformation of a Dipyrrylmethane. The gem -Dimethyl Effect

 A crystal structure determination of the new dipyrrylmethane diethyl-2,3,5,5,7,8-hexamethyl-5,10-dihydrodipyrrin-1,9-dicarboxylate (1) is only the third reported for a dipyrrylmethane and the first with a gem-dimethyl group at the bridging carbon atom. Conformation determining torsion angles are compared to those from molecular mechanics calculations and to the corresponding data for an analogous dipyrrylmethane (2) with no gem-dimethyl moiety. The crystal structures of 1 and 2 differ significantly: 1 adopts the +ac,+ac or −ac,−ac conformation, whereas 2 exists in the −ac,+sc conformation in an intermolecularly hydrogen bonded dimer. There is no evidence for hydrogen bonding in crystals of 1, and its ac conformation is unlike that found about the central core of bilirubin (sc,sc). Taken collectively, the data indicate that the presence of a sterically demanding and potentially conformation distorting gem-dimethyl group located at the bridging carbon of a dipyrrylmethane (i) stabilizes a conformation that brings the pyrrole NH groups syn to the gem-dimethyls and (ii) would destabilize the ridge-title conformation of 10,10-dimethylbilirubin.     

Inducing Geometrical Changes of Biliverdin Chromophores by 23<Emphasis Type="Italic">N</Emphasis>-Methylation

Summary. Transfer of sterical hindrance from the periphery to the center of biliverdins by placing a methyl group at N23 and hydrogens at the -carbons in position 12 and 13 changes the conformation of the chromophore from (10syn,14syn) to (10anti,14anti). Additional reduction of sterical hindrance by placing a further hydrogen at the -carbon in position 8 induces a change in configuration from (9Z) to (9E).     

Novel Linear Tetrapyrroles: Hydrogen Bonding in Diacetylenic Bilirubins

Summary. Bilirubin congeners with dipyrrinones conjoined to a diaceteylene unit (–CC–CC–) rather than to –CH₂– were synthesized and examined spectroscopically. This new class of rubrified linear tetrapyrroles cannot easily fold or bend in the middle, but the dipyrrinones can rotate independently about the diacetylene unit. Thus, unlike bilirubin, which is bent in the middle and has a ridge-tile shape, the diacetylene unit orients the attached dipyrrinones along a linear path, and intramolecular hydrogen bonding between the dipyrrinones and opposing carboxylic acids preserves a twisted linear molecular shape when the usual propionic acids are replaced by hexanoic. In a bis-hexanoic acid rubin, the extended planes of the dipyrrinones intersect along the –(CC)₂– axis at an angle of 102° for the conformation stabilized by intramolecular hydrogen bonding. With propionic acid chains, however, neither CO₂H can engage an opposing dipyrrinone in intramolecular hydrogen bonding, and the energy-minimum conformation of this linear pigment, shows nearly co-planar dipyrrinones, with an intersection of an angle of 180° of the extended planes of the dipyrrinones. Spectroscopic evidence for such linearized and twisted (bis-hexanoic) and planar (bis-propionic) structures comes from the pigments NMR spectral data and their exciton UV-Vis and induced circular dichroism spectra.     

On the Molecularity of Bilirubins and their Esters and Anions in Chloroform Solution

Summary.  Bilirubins with propionic acids at C-8 and C-12 engage in intramolecular hydrogen bonding and are thought to be monomeric in solution, although the latter is unproven. In contrast, their dimethyl esters and etiobilirubin analogs (with the C-8 and C-12 propionic acids replaced by alkyl residues) favor intermolecular hydrogen bonding and are thought to be dimeric in nonpolar solvents. There is little information on the molecularity of the bilirubin dianion in solution. In this work, vapor pressure osmometry studies of chloroform solutions of bilirubins, their dimethyl esters, and etio-analogs clearly indicate that the diacids and dianions are monomeric, whereas the diesters and dialkyls are dimeric. However, the presence of a C-10 gem-dimethyl group causes the ester and the etiobilirubin to become monomeric. Received May 9, 2000. Accepted May 19, 2000     

Quantum Mechanical Study of the Syn and Anti Conformations of Solvated Cyclic GMP

Self-consistent Reaction Field (SCRF) computational methods have been applied to guanosine 3:5-cyclic monophosphate (cGMP) to determine the geometries and energetics of the syn and anti conformations of this cyclic nucleotide in aqueous solution. The syn conformation of cGMP has been predicted to be more stable in the gas phase due to an internal hydrogen bond. The syn conformation is observed in the crystal structure of the sodium tetrahydrate salt, although a bridging water molecule is present in lieu of the internal hydrogen bond. In the gas phase, we find from Hartree–Fock/6-31+G(d) optimizations that the syn conformation is more stable than the anti by about 4 kcal/mol. However, we report here that the anti conformation is more stable in aqueous solution, according to estimates based upon results from both the Onsager model and the Isodensity Polarized Continuum Method (IPCM). Our best estimate from single-point IPCM B3LYP/6-31+G(d) calculations has the anti conformation 19 kcal/mol lower in energy. For comparison purposes, we also present SCRF results for syn and anti adenosine 3:5-cyclic monophosphate (cAMP). For cAMP, we estimate the anti conformation to be more stable than the syn by about 6 kcal/mol. We suggest that the relative stability of the anti conformation of cGMP be considered in studies, such as, enzyme docking.     

Nitration of cubane-1,4-dicarboxylic acid dimethyl ester by dinitrogen tetraoxide

A first direct nitration of C—H bond of cubane-1,4-dicarboxylic acid dimethyl ester by dinitrogen tetraoxide at 20 °C has been carried out. During the nitration no rearrangement of cubane skeleton has been observed.     

Methyl 4‐O‐benzoyl‐2,3‐O‐isopropyl­idene‐α‐l‐rhamnopyran­oside

The title compound, C₁₇H₂₂O₆, has an exocyclic ester group at the hexopyranosyl sugar residue. The carbonyl group shows a conformation that is eclipsed with respect to the adjacent ring C—H bond. The two ester torsion angles are denoted by syn and cis conformations. One of these torsion angles is indicated to have a similar conformation in solution, as analyzed by NMR spectroscopy and a Karplus‐type relationship.     

Kerr constants and dipole moments of aminobenzoic acids in dioxane

Aminobenzoic acids in dioxane have been investigated by dipole moment and Kerr effect methods.m-Aminobenzoic acid exists in a solution mainly (60 %) in thesyn-form. Inp-aminobenzoic acid, conjugation flattens the pyramidal configuration of the nitrogen atom, which is even more flattened ino-aminobenzoic acid owing to an intramolecular hydrogen bond.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 859–861, May, 1994.     

Study of conformations and hydrogen bonds in the configurational isomers of pyrrole‐2‐carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis

The ¹H, ¹³C and ¹⁵N NMR studies have shown that the E and Z isomers of pyrrole‐2‐carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole‐2‐carbaldehyde oxime is stabilized by the N? H···N and N? H···O intramolecular hydrogen bonds, respectively. The N? H···N hydrogen bond in the E isomer causes the high‐frequency shift of the bridge proton signal by about 1 ppm and increase the ¹J(N, H) coupling by ～3 Hz. The bridge proton shows further deshielding and higher increase of the ¹J(N, H) coupling constant due to the strengthening of the N? H···O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by ～3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of ¹H shielding and ¹J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N? H···N and N? H···O hydrogen bondings to be estimated. The NBO analysis suggests that the N? H···N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N? H bond through the N? H···O hydrogen bond occurs in the Z isomer. Copyright © 2010 John Wiley & Sons, Ltd.     

Ferrocene compounds: methyl 1′‐aminoferrocene‐1‐carboxylate

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)°.     

Inducing Geometrical Changes of Biliverdin Chromophores by 23N-Methylation

Transfer of sterical hindrance from the periphery to the center of biliverdins by placing a methyl group at N23 and hydrogens at the -carbons in position 12 and 13 changes the conformation of the chromophore from (10syn,14syn) to (10anti,14anti). Additional reduction of sterical hindrance by placing a further hydrogen at the -carbon in position 8 induces a change in configuration from (9Z) to (9E).     

Neue τ-Boride

The following -borides have been synthesized: Cr₁₃Ir₁₀B₆, Mn₁₆Ir₇B₆, Fe_10–15.4Ir_13–7.6B₆, Co₁₅Ir₈B₆.

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Herrn Prof. Dr.A. Knappwost in Freundschaft gewidmet.     

The gem-dimethyl effect: amphiphilic bilirubins

New bilirubin congeners (1a-1d) with the central C(10) CH₂ replaced by C(CH₃)₂ were smoothly synthesized by coupling two identical dipyrrinones with 2,2-dimethoxypropane under acid catalysis. The new yellow pigments, with acid chains varying from acetic (n=1) to propionic (n=2) to butyric (n=3) to hexanoic (n=5), exhibit unusual amphiphilicity relative to the parent mesobilirubins without the gem-dimethyls and have highly favorable solubility in organic solvents ranging from nonpolar (benzene) to polar (CH₃OH). Like the parent rubins, 1a-1d can easily bend about the middle but unlike the parents they cannot form mesobiliverdin analogs. NMR spectroscopic analysis and molecular dynamics calculations indicate that, like the parents, 1a-1d adopt ridge-tile shapes that are stabilized by intramolecular hydrogen bonding. Confirmation of the conformation in 1b comes from its X-ray crystallographic structure.     

<Superscript>1</Superscript>H and <Superscript>13</Superscript>C NMR Study of Bifurcated Intramolecular Hydrogen Bonds in 2,6-Bis(2-pyrrolyl)pyridine and 2,6-Bis(1-vinyl-2-pyrrolyl)pyridine

According to the ¹H and ¹³C NMR data, bifurcated intramolecular hydrogen bond NH?N?HN in 2,6-bis(2-pyrrolyl)pyridine fixes its molecule in a conformation with syn orientation of the pyrrole rings. An analogous bifurcated hydrogen bond CH?N?HC is formed in 2,6-bis(1-vinyl-2-pyrrolyl)pyridine. 2-(1-Vinyl-2-pyrrolyl)-6-(2-pyrrolyl)pyridine is characterized by unsymmetrical bifurcated hydrogen bond NH? N?HC.