Crystal Structure and Conformation of a Bilirubin Ester

Summary. Crystal structures determined for three bilirubin analogs with gem-dimethyl groups at C(10) are reported, including the first X-ray structure of a bilirubin dimethyl ester. Conformation-determining torsion angles and key hydrogen bond distances and angles were compared to those from molecular dynamics calculations. Like other rubins, the component dipyrrinones of the three compounds were found to adopt the syn conformation, with Z-configuration double bonds at C(4) and C(15) and bis-lactam tautomeric structures of the end rings. No large differences in bond lengths and bond angles at C(10) were found, and the crystal structures of the two 10,10-dimethyl rubin acids showed considerable similarity to that of bilirubin: both pigments adopt a folded, intramolecularly hydrogen bonded ridge-tile conformation stabilized by six hydrogen bonds, with an interplanar angle in ridge-tile of 98° and 86°. In contrast, the dimethyl ester is intermolecularly hydrogen bonded in the crystal. Each molecule of the ester has its two syn-Z-dipyrrinones rotated into a conformation syn to the gem-dimethyl group, whereas in the acids they are anti.     

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     

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.     

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.     

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.     

Molecular Structure of Diphenylphosphine As Determined by Gas-Phase Electron Diffraction and Quantum-Chemical Calculations

Gas-phase electron diffraction was used to show the title molecule has an asymmetric structure with torsion angles around P-C bonds of 65° and 154(7)°. The principal geometric parameters are as follows: interatomic distances, Å: P-C 1.829 and 1.833(4), C-Cav 1.401(1); bond angles, deg: CPC 101.0(20), PCC 120.4 and 119.4(16). Quantum-chemical calculations of chlorodiphenylphosphine were performed.     

Synthesis and metabolism of the first thia-bilirubin

A symmetrical C(10)-thiabilirubin analogue, 8,12-bis(2-carboxyethyl)-2,3,17,18-tetraethyl-7,13-dimethyl-10-thia-(21H,23H,24H)-bilin-1,19-dione (1), was synthesized from 8-(2-carboxyethyl)-2,3-diethyl-7-methyl-10H-dipyrrin-1-one in one step by reaction with sulfur dichloride. The thia-rubin exhibited the expected IR, UV-vis, and NMR spectroscopic properties, which are rather similar to those of mesobilirubin-XIIIalpha. Like bilirubin and mesobilirubin, 1 adopts an intramolecularly hydrogen-bonded conformation, shaped like a ridge-tile but with a steeper pitch. The longer C-S bond lengths and smaller bond angles at C-S-C, as compared to C-CH(2)-C, lead to an interplanar angle between the two dipyrrinones of only 74 degrees -or considerably less than that of bilirubin (approximately 100 degrees). On normal- and reversed-phase chromatography, 1 is substantially less polar than bilirubin. Despite this conformational distortion, 1 is metabolized in normal rats to acyl glucuronides, which are secreted into bile. In mutant (Gunn) rats lacking bilirubin glucuronosyl transferase, 1 (like bilirubin) was not excreted in bile.     

Crystallographic studies on sterically affected chemical species

The crystal and molecular structure of 2-carboxy-2-methoxybiphenyl has been determined to R=0.035. Crystals are tetragonal, of space group I4₁cd, witha=b=15.181(2)c=19.874(2) Å. Mean esd values for bond lengths and bond angles are 0.005 Å and 0.3°, respectively. The angle between phenyl rings is 54.5(1)°. The C(1) (carboxy) and O (methoxy) distance is 3.02 Å. Dimers of the title compound are hydrogen bonded with O·O distances of 2.68 Å and 2.58 Å. Due to the symmetry of the space group, the hydrogen atoms are necessarily located in the center of the O·O distance. Parameters of repulsive deformations for bond angles have been defined. Due to overcrowding in the region ofo,o-substitution, significant deformations of exocyclic bond angles have been observed. The magnitudes of these deformations depend roughly on the spatial requirements of the sterically interacting substituents, expressed by Charton's [1] parameter.     

Molecular conformation of bilirubin from semiempirical molecular orbital calculations

Semiempirical methods were utilized in the computation of a fully optimized structure of bilirubin. Bond lengths and bond angles obtained using either AM1 or PM3 calculations showed excellent agreement with those obtained by X-ray diffraction. This indicated that molecular orbital methods satisfactory reproduced the complex conjugation found in bilirubin. Dihedral angles of the crucial “hinge” and the dihedral angles of the propionic acid side chains agreed well with those found by X-ray diffraction. Calculated hydrogen- bond parameters (distance and angles) showed substantial differences from experimental values, probably due to inherent weakness in the parameterization of the molecular orbital techniques. Conformational studies were carried out using AM1 by rotating the C9? C10 bond in 5° increments showed that the most stable structure exhibited a minimum at about 125° and exhibited a structure similar to those postulated from X-ray and NMR experiments. The hydrogen bonds showed remarkable tenacity during rotation of the C9? C10 bond and resisted breaking until the molecule was under extreme strain. © 1992 John Wiley & Sons, Inc.     

Synthesis,structure and bonding of 2-aminopyridinium heptamolybdate trihydrate

Summary 2-aminopyridinium heptamolybdate trihydrate crystallizes in the monoclinic system with space group P2₁/n and Z=4 (R=0.030). The unit cell dimensions area=14.8161(4) Å,b=17.5073(4) Å,c=20.8492(6) Å, =107.503(2)°, V=5157.7(2) ų. The [Mo₇O₂₄]^6– anions in the 2-aminopyridinium, ammonium⁽⁴⁾, guanidium⁽²⁾, propyl- and isopropyl-ammonium⁽¹⁾ molybdates, while similar, show slightly differences in several bond lengths and angles. The distinguishing features of 2-aminopyridinium heptamolybdate trihydrate structure is its extensive hydrogen bonding. The planar cations and the water molecules are positioned so as to be able to form hydrogen bonds with either molybdate oxygen atoms or water oxygen atoms. Four different types of hydrogen bonds have been found-: N-H... O (mono- and bifurcated), N-H... Ow (monofurcated), Ow-Hw... O (mono- and bi-furcated) and Ow-Hw...OW (monofurcated). The closest approach distances associated with 27 of these potential hydrogen bonds vary from 2.67 to 3.24 Å^(7,8)). The proposed strong hydrogen bonding interactions appear to stabilize the structure and explain the way of three water molecules are lost upon heating. Some of these hydrogen bonds can play an important role in the possible photochromism of this compound.     

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.     

Hydro­gen bonding and C—H⋯O interactions in 3‐(3‐amino­phthal­imido)phthalic acid dihydrate

The title compound, C₁₆H₁₀N₂O₆·2H₂O, crystallized in the centrosymmetric triclinic space group P with one organic mol­ecule and two water mol­ecules as the asymmetric unit. Eight intermolecular hydrogen bonds have donor?acceptor distances in the range 2.602 (2)–3.289 (2) Å, with angles in the range 137 (2)–177 (2)°. These generate a three‐dimensional hydrogen‐bond network. There is a single intramolecular hydrogen bond. There are six significant intermolecular C—H?O interactions with H?O distances in the range 2.39–2.74 Å, and C—H?O angles in the range 131–157°.     

Crystal Structure of the Complex of 1,2-Bis[2-(o-hydroxyphenoxy)ethoxy]ethane with Ammonium Thiocyanate

The complex of the podand 1'2-bis[2-(o-hydroxyphenoxy)ethoxy]ethane (L) with ammoniumthiocyanate, [NH₄(SCN)L], was prepared, studied by single crystal X-ray diffraction. This is a host-guestcomplex; in its molecule the podand L is wrapped around the NH ₄ ⁺ cation, which forms hydrogen bondswith all the six oxygen atoms of the podand and one hydrogen bond with the sulfur atom of the SCN^- anion. The geometric parameters (bond lengths, bond angles, torsion angles, etc.) of the molecule of [NH₄(SCN)L] and packing of the molecules in the crystal were determined. The molecules are linked into infinite polymeric chains by intermolecular hydrogen bonds O-H···NCS.     

Molecular Structure of an Isocytosine Analog: Combined X-ray Structural and Computational Study of 2-Diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone

The structure of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone has been studied by X-ray crystallography and quantum-chemical calculations. X-ray analysis established that 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone exists exclusively as the lactam tautomer protonated at the N3 ring nitrogen in the solid state. Crystals of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are monoclinic (space group P2₁/n); the unit-cell dimensions are: a = 11.0460(8) Å, b = 5.0064(4) Å, c = 22.8358(17) Å, = = 90°, = 90.521(1)°. In the crystal, molecules of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are assembled in planar centrosymmetric dimers by strong resonance-assisted N—H···O intermolecular hydrogen bonds from the NH group of one molecule to the C=O of the adjacent molecule (N—H···O distance 2.804 Å). Bond distances and angles are generally similar to those reported for the corresponding tautomer of isocytosine and derivatives. Quantum-chemical calculations on 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are also reported in order to estimate the relative energies of the possible tautomeric forms; ab initio and DFT results predict the coexistence of the N3 and AH tautomers in the gas phase. There is excellent correspondence between the crystal and the HF/6-311G** or B3LYP/6-31G* calculated structures of the N3 lactam form; the largest deviations between the experimental and computed structures are mostly the effects of strong intermolecular H bonds in the crystal.     

Crystal structure of 1,3-diphenyladamantane and trans-1,4-diphenylcyclohexane: torsion angles about C-Ph bonds in α,ω-diphenyl(alicyclic hydrocarbon)

The orientation of the two phenyl rings in α,ω-diphenylalkanes with rigid carbon skeletons is investigated through characterization of the crystal and molecular structures of 1,3-diphenyladamantane (1) and trans-1,4-diphenylcyclohexane (2). The two phenyl rings in 1 have different conformations about the C-Ph bonds, with torsion angles between the phenyl ring and the C1-C2-C3 plane of 0.65 and 71.7°. A hydrogen atom at the meta-position of one of the phenyl rings contact intermolecularly with a tertiary hydrogen atom at C5 of adamantane within the sum of van der Waals radii. Due to the helical conformation, the short CH?HC contacts (2.231 Å) construct supramolecular triple helical strands. In contrast to 1, the phenyl rings in 2 have identical configurations, with equatorial position and bisected conformation as expected from density functional calculations. The molecular packing of 2 exhibits a herringbone pattern of (aromatic)C-H?π contacts.     

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.     

The geometry of intermolecular interactions in some crystalline fluorine-containing organic compounds

The propensity of C-F groups to form C-F H-C interactions with C-H groups on other molecules has been analyzed. Crystal structures of molecules containing only carbon, hydrogen, and fluorine, but no oxygen, nitrogen, or other hydrogen-bond-forming elements, were chosen for an initial study in which the intermolecular interactions in crystal-structure determinations of polycyclic aromatic hydrocarbons and their analogous fluoro derivatives were analyzed. It is found that C-F H-C interactions occur, but they are weak, as judged by the intermolecular distances and the angles involved. In a study of crystal structures of molecules containing other elements in addition to carbon, hydrogen, and fluorine, it was found that when an oxygen atom is in a neighboring position on an interacting molecule, a C-O group is more likely than a C-F group to form a linear interaction to the hydrogen atom of a C-H group. Thus, in spite of the high electronegativity of the fluorine atom, a C-F group competes unfavorably with a C-O^–, C-OH, or C=O group to form a hydrogen bond to an O-H, N-H, or C-H group. It is found, however, particularly for polycyclic aromatic hydrocarbons with substituted CF₃ groups that, in the absence of other functional groups that can form stronger interactions, C-F H-C interactions may serve to align molecules and give a different crystal packing from that in the pure hydrocarbon (where fluorine is replaced by hydrogen). Thus, C-F H-X (X = C, N, O) interactions are very weak, much weaker than C=O H-X interactions, but they cannot be ignored in predictions of modes of molecular packing in complexes and in crystals.     

Molecular Structure of 1-Germatrahol and its Complex With Chloroform

The crystal structures of anhydrous 1-germatranol and its complex with HCCl₃ are centrosymmetrical dimers because of their intermolecular hydrogen bonds. In the germatranol crystal, the axial and equatorial oxygen atoms of its two molecules are hydrogen bonded into an eight-membered coordination cycle. In the complex with HCCl₃, the two molecules of germatranol are likewise linked in dimers, and both axial oxygen atoms are H bonded with HCCl₃. In the investigated structures, the axial Ge—O bond is shorter than the equatorial ones. Depending on the number and strength of the hydrogen bonds, the interatomic Ge—O and Ge ← N distances change markedly. The quantitative estimates of the H bond energy are obtained from quantum chemical calculations of the model systems containing 1-germatranol and HCCl₃ molecules.     

Synthesis and Structures of the Novel Pyridoxal Oxime Derivatives

Novel pyridoxal oxime derivatives were prepared and characterized by means of IR, ¹H and ¹³C NMR spectroscopy. The crystal structures of the 3-hydroxy-4-hydroxyiminomethyl-5-hydroxymethyl-1,2-dimethylpyridinium iodide 1 and 3-hydroxy-4-hydroxyiminomethyl-5-hydroxymethyl-1,2-dimethylpyridinium chloride monohydrate 2 were determined by X-ray analysis. The both compounds crystallize in the triclinic crystal system, space group P . Crystal data: 1 a = 6.286(2) Å, b = 8.748(4) Å, c = 11.736(4) Å, = 104.02(3)°, = 94.70(3)°, = 107.44(6)°, V = 589.0(4) ų, Z = 2, R = 0.0526; 2 a = 6.8980(5) Å, b = 8.6409(6) Å, c = 11.1777(6) Å, = 111.138(5)°, = 93.114(6)°, = 105.158(5)°, V = 591.57(7) ų, Z = 2, R = 0.0492. The bond distances and angles in both structures agree very well. The main difference between these structures was observed in the orientation of the hydroxymethyl group with respect to the pyridinium ring. In the both structures intramolecular hydrogen bond forming six-membered ring were observed. The intermolecular OsI hydrogen bonds in the crystal structure of the compound 1 form dimers. In the crystal structure of compound 2, the water molecules and chlorines build eight-membered rings, which are also connected to pyridinium cations by OsCl and OsO intermolecular hydrogen bonds forming a three-dimensional network.     

The crystal structure of carbamoyl fluoride,NH<Subscript>2</Subscript>COF

Although first synthesized in 1940, the X-ray crystal structure of carbamoyl fluoride, NH₂COF, has until now remained unknown. [1] NH₂COF crystallizes in the orthorhombic space group Ibam, is planar, and exhibits a short C-N bond length, 1.3168(13) Å, implying a significant degree of donation from the nitrogen lone pair. The structure features one molecule in the asymmetric unit and eight molecules in the unit cell. There are four molecules in two planar layers that are connected by a network of NH·O hydrogen bonds with N·O distances of 2.987(2) Å and 2.945(2) Å. The compound was also studied by quantum chemical calculations at both the ab initio (MP2) and density functional theory (B3LYP) level.