Insights into the Structures of Bilirubin and Biliverdin from Vibrational and Electronic Circular Dichroism: History and Perspectives.

In this work we review research activities on a few of the most relevant structural aspects of bilirubin (BR) and biliverdin (BV). Special attention is paid to the exocyclic C=C bonds being in mostly Z rather than E configurations, and to the overall conformation being essentially different for BR and BV due to the presence or absence of the double C=C bond at C-10. In both cases, racemic mixtures of each compound of either M or P configuration are present in achiral solutions; however, imbalance between the two configurations may be easily achieved. In particular, results based on chiroptical spectroscopies, both electronic and vibrational circular dichroism (ECD and VCD) methods, are presented for chirally derivatized BR and BV molecules. Finally, we review deracemization experiments monitored with ECD data from our lab for BR in the presence of serum albumin and anesthetic compounds.

Biliverdin chiral derivatives as chiroptical switches for pH and metal cation sensing.

A series of six optically active derivatives of the bile pigment biliverdin, namely (ßS,ß'S)-dimethylmesobiliverdin-XIIIα, cyclic esters of linear diols [HO(CH2)nOH] where n = 1-6, have been investigated by vibrational circular dichroism (VCD) and density functional theory (DFT) calculations. The results were correlated with the length (n) of the diester belt, the verdin helicity and an M ⇄ P conformational equilibrium - as previously shown by electronic circular dichroism (ECD). Furthermore, ECD spectra have been found to be quite sensitive to solvent nature and pH. TD-DFT calculations of the protonated/deprotonated verdins with n = 1 and 2 diester belts respectively have allowed one, moreover, to explain the spectroscopic data in terms of a change in the M ⇄ P equilibrium. Finally, the set of investigated compounds, together with other chirally functionalized "non-belted" biliverdin analogs, has also been found to be sensitive to the presence of metal ions, with which the verdins chelate. On the basis of ECD and VCD data, we propose that the spectroscopic changes observed are consistent with self-association (dimerization) of the verdin molecules promoted by the metal cations, as bolstered by DFT calculations, and for which a dimerization constant of 73 000 M-1 is evaluated. We envision the use of current chiroptical spectroscopies in connection with chiral biliverdin derivatives as natural sensors or probes of the micro-environmental conditions, such as pH or the presence of metal ions.

On the aggregation of bilirubinoids in solution as evidenced by VCD and ECD spectroscopy and DFT calculations.

Vibrational and electronic circular dichroism (VCD and ECD) spectra of 3 optically active bilirubin analogs with propionic acid groups replaced by (1) 1-(S)-methylpropyl groups, (2) 3-acetoxy-1-(S)-methylpropyl groups, and (3) 1-(S)-2-(R)-dimethyl-2-(methoxycarbonyl)ethyl groups have been recorded at different concentrations in chloroform. The aliphatic chains attached to C-8 and C-12 of the 3 chosen mesobilirubins were modified so as to possess no OH group. The variation of the VCD spectra with concentration is consistent with the formation of dimers at high concentration. Density functional theory and time-dependent density functional theory calculations on monomeric and dimeric forms support such a conclusion. Comparing with previous VCD (ECD) and IR (UV) studies of other mesobilirubin molecules, it is concluded that here, the key feature for aggregation is the missing OH groups on the propionic acid chains. The latter, in synergy with the polar groups of lactam moieties, appear to be involved in intramolecular phenomena and thus favor monomeric forms. Investigation of ECD and UV spectra of the same compounds in mixed DMSO/chloroform solutions provide further clues to the proposed picture.

Bicamphor: a prototypic molecular system to investigate vibrational excitons.

Vibrational circular dichroism (VCD) and IR spectra have been recorded in the fingerprint and carbonyl stretching regions for endo,endo-bicamphor (1), exo,exo-bicamphor (2), endo,exo-bicamphor (3), 3,3'-bicamphorylidene (4), and exo,exo-bis-thiocamphor (5). The C2 symmetry possessed by these molecular systems (except in one case), as well as their limited conformational mobility associated with well-defined degrees of freedom, allow for optimal test of the vibrational circular dichroism exciton chirality (VCDEC) rule introduced by Taniguchi and Monde. Density functional theory calculations are employed not only to predict the entire aspect of the VCD and IR spectra but also to study how the VCDEC rule may be impacted by the coupling between C═O stretchings and from C═O stretchings with other vibrational modes and by the rotation about the C-C bond connecting the two camphors. Comments are provided about the limitations and potentialities of the VCDEC method and about the manifestation of different vibrational excitons in other regions of the VCD spectra, either in the mid-IR or in the CH-stretching regions.

Experimental and calculated CPL spectra and related spectroscopic data of camphor and other simple chiral bicyclic ketones.

UV, circular dichroism (CD), fluorescence and circularly polarized luminescence (CPL) spectra were recorded for a set of four related [2.2.1] bicyclic compounds ((1S,4S)-and (1R,4R)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-one, namely (1S)- and (1R)-camphor (), (1S,4R)-4,7,7-trimethylbicyclo[2.2.1]hept-5-en-2-one, (1S)-dehydro-epicamphor (), (1S,4S)-1,7,7-trimethylbicyclo[2.2.1]heptane-2,5-dione, (1S)-5-oxocamphor (), (1S,4R)- and (1R,4S)-1,7,7-trimethylbicyclo[2.2.1]heptane-2,3-dione, (1S)- and (1R)-camphorquinone ()) and a set of three related [2.2.2] bicyclic compounds (1S,4S)-bicyclo[2.2.2]octan-2,5-dione (saturated diketone ()), (1R,4R)-bicyclo[2.2.2]oct-7-en-2,5-dione (unsaturated diketone ()), ((1S,4S)-bicyclo[2.2.2]oct-7-en-5(S)-ol-2-one (which we refer to as unsaturated hydroxy-ketone ()). For the latter three compounds also mid-IR vibrational circular dichroism (VCD) spectra were recorded and are presented. Time-Dependent Density Functional (TD-DFT) calculations provide a satisfactory interpretation of both absorption and emission chiroptical spectra and permit insight into ground and excited state electronic properties. We discuss the applicability of the octant rule or of other approximated models to rationalize the observed sign of the CPL.

Thermal motion of tert-butyl groups III. tert-Butyl substituents in aromatic hydrocarbons, the view from the bottom of the well.

The rigidity of the tert-butyl group (TBG) as a substituent in aromatic hydrocarbons is investigated, with a modified Hirshfeld test of anisotropic displacement parameters (ADPs) as a primary criterion. Four new structures are analyzed, along with low-temperature studies of a previously published crowded supermesityl dimer; three of the five structures meet the primary test. Most of the TBGs meet the Hirshfeld test at 100 K, and the ADPs are improved by omitting low-order data in the final refinement. The three most precise structures yield a wide variation in libration amplitudes (and in estimated rotation barriers) for 13 unique TBGs. A similar range of values is found in analyses of structures in the Cambridge Crystallographic Database. The libration amplitudes are calculated with the program THMA14C, with each TBG as an attached rigid group (ARG). Packing analysis suggests that large ADPs, especially for some individual TBG methyl groups, correspond to voids in the crystal. Published barriers to TBG reorientation, determined by solid-state NMR spin-lattice relaxation methods, for six related crystalline compounds are compared with barriers calculated from their crystal structure data.

Experimental and calculated vibrational and electronic circular dichroism spectra of 2-Br-hexahelicene.

The vibrational circular dichroism (VCD) and IR absorption spectra of the (-)-enantiomer of 2-Br-hexahelicene have been measured and interpreted by use of density functional theory (DFT) calculations. From time dependent DFT calculations we also interpret the electronic circular dichroism (ECD) spectra of 2-Br-hexahelicene. We compare the calculated IR, VCD and ECD spectra to the corresponding calculated data of hexahelicene and 2-aza-hexahelicene; for the last compound we also recorded the ECD spectra. Comparison with current literature allows an insight to be gained on the meaning and usefulness of some VCD features.

Comparative analysis of IR and vibrational circular dichroism spectra for a series of camphor-related molecules.

The absorption spectra and vibrational circular dichroism (VCD) spectra in the mid-IR range 1600-950 cm(-1) of 10 camphor-related compounds have been recorded and compared to DFT calculated spectra at the B3PW91/TZ2P level and have been examined together with the corresponding data of the parent molecules. The rigidity of the bridged structure common to all compounds investigated permits (a) identification of three spectroscopic regions in the mid-IR range that can be "used" separately by the interested stereochemist for structural diagnosis and assignment of some major characteristics of the VCD spectra in these regions to what we call "skeletal chiral sense" and (b) recognition of possible conformers for flexible substituent groups, when present. VCD spectra of the 10 molecules have been recorded and analyzed also in the CH-stretching region, 3100-2800 cm(-1). Here, we have been able to identify and characterize features of vibrational excitons by comparison of data within the 10-molecule class. To find a theoretical justification of result (a), we have examined the potential energy distribution of the normal modes in the mid-IR range, the partitioning of the calculated rotational strengths in terms of contributions from all couples of internal coordinates, the angle formed by the two vectors, the electric dipole transition moment and the magnetic dipole transition moment, and finally the overlap of normal modes of different molecules. A discussion is provided as to the usability of the introduced algorithms.

Carboxylic Acid to Thioamide Hydrogen Bonding.

The lactam groups of dipyrrinones avidly engage in amide-amide hydrogen bonding to form dimeric association complexes in nonpolar solvents (in CHCl(3), K(D) ~25,000 M(-1) at 22 degrees C). The corresponding thioamides (dipyrrinthiones), prepared from dipyrrinones by reaction with Lawesson's reagent, also form intermolecularly hydrogen-bonded dimers in nonpolar solvents, albeit with much weaker association constants (in CHCl(3), K(D) ~200 M(-1) at 22 degrees C). When a carboxylic acid group is tethered to C(9) of the dipyrrinone, as in the hexanoic acid of [6]-semirubin, tight intramolecular hydrogen bonding between the carboxylic acid group and the lactam moiety (intramolecular K(assoc) >>25,000) is found in CHCl(3) with no evidence of dimers. In contrast, the analogous dipyrrinthione, [6]-thiosemirubin, eschews intramolecular hydrogen bonds, as determined using NMR spectroscopy and vapor pressure osmometry, preferring to form intermolecularly hydrogen-bonded dimers of the thioamide-thioamide type.

Amphiphilic Dipyrrinones. Methoxylated [6]-Semirubins.

Replacing the typical beta-alkyl substituents of [6]-semirubin and [6]-oxosemirubin, two intramolecularly hydrogen-bonded bilirubin analogs, with methoxy groups produces amphiphilic dipyrrinones. Synthesized from the respective 9H-dipyrrinones prepared by base-catalyzed condensation of 3,4-dimethoxypyrrolin-2-one with the appropriate pyrrole alpha-aldehyde, the 2,3-dimethoxy and 2,3,7,8-tetramethoxy analogs of [6]-semirubin are yellow-colored dipyrrinones that form intramolecularly hydrogen-bonded monomers in CDCl(3), as deduced from (1)H-NMR NH chemical shifts. They are monomeric in CHCl(3), as determined by vapor pressure osmometry. In contrast, in the solid, X-ray crystallography reveals supramolecular ribbons of intermolecularly hydrogen-bonded (dipyrrinone to dipyrrinone and acid to acid) 2,3,7,8-tetramethoxy-[6]-semirubin. The latter is approximately 20 times more soluble in water than the parent [6]-semirubin with four beta-methyl groups.

Slipping past UGT1A1 and multidrug resistance-associated protein 2 in the liver: effects of steric compression and hydrogen bonding on the hepatobiliary elimination of synthetic bilirubins.

The hepatobiliary metabolism and excretion of three isomeric bilirubin analogs with propanoic replaced by benzoic acid side-chains were studied in the rat. Despite their isomeric relationship and similar constitutions, the three analogs were metabolized quite differently from each other and from bilirubin. In the di-o-benzoic compound, steric hindrance involving the phenyl groups reinforces intramolecular hydrogen bonding of the two carboxyl groups. This compound is considerably less polar than bilirubin on reverse-phase high-performance liquid chromatography and, like bilirubin, was not excreted in bile in UGT1-deficient (Gunn) rats. But, quite unlike bilirubin, it was not glucuronidated or excreted in bile in normal rats. In contrast to both bilirubin and the di-o-benzoic isomer, the more polar m- and p-isomers, in which intramolecular hydrogen bonding of carboxyl groups is sterically difficult, were excreted rapidly in bile in unchanged form in both normal and Gunn rats. However, only one of them, the di-m-isomer, was excreted rapidly and unchanged in bile in rats (TR(-) rats) congenitally deficient in the canalicular ATP-binding cassette transporter Mrp2. The marked differences in hepatobiliary metabolism of the three isomers studied can be rationalized on the basis of their computed three-dimensional structures and minimum-energy conformations and the remote effects of steric compression on intramolecular hydrogen bonding.

l-Stercobilin-HCl and d-Urobilin-HCl. Analysis of Their Chiroptical and Conformational Properties by VCD, ECD, and CPL Experiments and MD and DFT Calculations.

Vibrational circular dichroism (CD) and IR spectra of dichloromethane solutions of l-stercobilin and d-urobilin hydrochlorides have been recorded in the mid-IR region. The spectra are best interpreted by combining molecular dynamics calculations and density functional theory (DFT) calculations within the quantum mechanics/molecular mechanics ONIOM-type framework, and the combined predicted results are better and more informative than the more standard analysis provided by DFT calculations. The same approach also sheds light on the Cotton effect sign inversion of room temperature versus low-temperature electronic CD spectra of the same compounds in methanol-glycerol solution. Finally, circularly polarized luminescence spectra for l-stercobilin in chloroform solution provide information on the excited-state geometry of this molecule.

Influence of conformation and intramolecular hydrogen bonding on the acyl glucuronidation and biliary excretion of acetylenic bis-dipyrrinones related to bilirubin.

Glucuronidation and transporter-mediated efflux into bile are important in the elimination of xeno- and endobiotics, including the natural biladienone pigment bilirubin. The mechanisms of these processes and the structural factors that dictate whether cholephilic compounds are excreted directly in bile or require prior glucuronidation are poorly understood. To investigate effects of molecular shape and intramolecular hydrogen bonding on the interplay between direct excretion and glucuronidation in the liver, we studied a series of novel synthetic exploded and homologated bilirubin analogues. These include dicarboxylic mono- and diacetylenic tetrapyrroles with linear shapes that are unable to adopt the folded ridge-tile conformations that are crucially important in bilirubin metabolism. Intramolecular hydrogen bonding was varied by adjusting the alkyl chain lengths of the pendent carboxyl groups, and preferred conformations were predicted by molecular dynamics calculations. Metabolism studies were done in rats, including Gunn rats, congenitally deficient in UGT1 glucuronosyl tranferases, and TR- rats, deficient in the canalicular transporter Mrp2 (Abcc2). The results show strikingly that minor, seemingly inconsequential, changes in constitution, amplified by their influence on hydrogen bonding and molecular conformation, can profoundly influence competing clearance pathways in the liver, an effect that is unlikely to be restricted to bis-dipyrrinone carboxylic acids. Exposed carboxyl groups seem to favor the direct route of elimination, whereas the potential for carboxyl infolding by hydrogen bonding seems to favor glucuronidation. The results also show that molecular shape is less important in the hepatic glucuronidation and biliary excretion of bilirubin and of this series of acids than the capacity for intramolecular hydrogen bonding.

Converting 9-Methyldipyrrinones to 9-H and 9-CHO Dipyrrinones.

Yellow 9-methyldipyrrinones can be converted readily and in high yields to symmetric linear tetrapyrroles, blue biliverdinoids, which are cleaved in half, smoothly at room temperature to afford yellow 9-H dipyrrinones, and 9-CHO dipyrrinones as their violet to orange colored adducts with the carbon acid used for the scission: thiobarbituric acid (TBA), N,N'-diethylthiobarbituric acid, barbituric acid, N,N'-dimethylbarbituric acid and Meldrum's acid. The adducts, usually only of passing interest, are formally Knövenagel condensation products of a 9-CHO dipyrrinone with TBA and other carbon acids of this work, and a reverse Knövenagel reaction of such adducts leads to 9-CHO dipyrrinones. Under a set of improved reaction conditions the sequence thus efficiently converts 9-CH(3) dipyrrinones to 9-H and 9-CHO dipyrrinones.

Intermolecularly Hydrogen-Bonded Dimeric Helices. Tripyrrindiones.

A rare and unusual class of tripyrrolic compounds, violet-colored tripyrrin-1,14-diones, can be prepared easily and in moderately high yields from base (piperidine)-catalyzed condensation of 3-pyrrolin-2-ones with 2,5-diformylpyrroles. Dipyrrinones adopt the all syn-Z conformation leading to helical, lock-washer like structures, which form dimers that are held together by intermolecular hydrogen bonds in nonpolar solvents and in the crystal. Strong bathochromic spectral shifts of the tripyrrindione approximately 480 nm long wavelength UV-visible absorption band are seen with added base: DBU, 615 nm; TFA, 573 nm; and Zn (OAc)(2), 586 nm.

pH Dependent Chiroptical Properties of (1R,2R)- and (1S,2S)-trans-Cyclohexane Diesters and Diamides from VCD, ECD, and CPL Spectroscopy.

Diesters of (1R,2R)- and (1S,2S)-cyclohexanediols and diamides of (1R,2R)- and (1S,2S)-diaminocyclohexane with p-hydroxycinnamic acid have been known for some time to exhibit intense bisignate electronic circular dichroism (ECD) spectra in CH3OH. It was also known that added NaOH causes a bathochromic shift of ∼50 nm in CH3OH, and an even higher one in DMSO. We have measured vibrational circular dichroism (VCD) spectra both for neutral compounds and in the presence of NaOH and other bases. The VCD and IR spectra in the mid-IR region for CD3OD and DMSO-d6 solution exhibit high sensitivity to the charged state for the diesters. They possess two strong bisignate features in the presence of bases in the mid-IR, which are interpreted in terms of vibrational exciton couplets, while this phenomenon is less evident in diamides. VCD allied to density functional theory (DFT) calculations allows one to shed some light on the spectral differences of diesters and diamides by studying their conformational properties. Optical rotatory dispersion (ORD) curves confirm the ECD data. Circularly polarized luminescence (CPL) data have been also acquired, which are rather intense in basified solution: the CPL spectra are monosignate and are as intense in the diester and in the diamide case.

Synthesis of the First Fluorinated Bilirubin.

A symmetrical difluorinated bilirubin analog, 8,12-bis(2-carboxy-2-fluoroethyl)-3,17-diethyl-2,7,13,18-tetramethyl-10H,21H,23H,24H-biline-1,19-dione (9), was synthesized from methyl 3-[2,4-dimethyl-5-(methoxycarbonyl)-1H-pyrrol-3-yl] propionate (1) in nine steps. Fluorine was introduced by reaction of an intermediate methyl 3-[1-(tert-butoxycarbonyl)-2,4-dimethyl-5-(methoxycarbonyl)-1H-pyrrol-3-yl]-2-hydroxypropionate (5), with (diethylamino)sulfur trifluoride (DAST). The fluorinated rubin exhibited the expected IR, UV-vis, and NMR spectroscopic properties, similar to those of the unfluorinated parent, mesobilirubin XIIIalpha. However, the solubility properties unexpectedly differed, with the fluorinated rubin being less soluble in organic solvents than its parent. While this phenomenon may be attributed to the much increased acidity of the carboxylic acid hydrogens in 9, it probably also arises from less effective intramolecular hydrogen bonding due to a decreased basicity of the propionic acid carbonyl groups.

Hemirubin: An Intramolecularly Hydrogen-Bonded Analogue for One-Half Bilirubin.

A model for one-half bilirubin, the neurotoxic yellow-orange pigment of jaundice, 9-[2-(2-carboxyethyl)benzyl]-2,3,7,8-tetramethyl-1,10-dihydrodipyrrin (1, hemirubin) was synthesized following SnCl(4)-catalyzed Friedel-Crafts acylation at C(9) of 2,3,7,8-1-oxo-1,10-dihydrodipyrrin (7) with methyl o-(chlorocarbonyl)hydrocinnamate. Unlike earlier bilirubin model compounds, hemirubin is predicted and found to engage in intramolecular hydrogen bonding. Like bilirubin, the propionic acid carboxyl group of hemirubin is linked to the opposing dipyrrinone by intramolecular hydrogen bonds, and thus, 1 shares in some of the solution properties of its parent bilirubin, e.g., an acid that is less polar than its methyl ester.

Altering the Acidity and Solution Properties of Bilirubin. Methoxy and Methylthio Substituents.

Substitution of electron-withdrawing groups at the alpha-position of an aliphatic carboxylic acid can be expected to increase the acidity of the acid. Methoxy and methylthio groups are especially effective; they increase the acidity of acetic acid by approximately 1.1 pK(a) units. Bilirubin, the water-insoluble pigment of jaundice, has two propionic acids, and an alpha-methoxy or alpha-methylthio substituent in each propionic acid can be expected to lower the pK(a) similarly and thus alter its solubility properties. (A previously synthesized analogue, alpha,alpha'-difluororubin (4), is soluble in water.) Two new analogues of bilirubin, alpha,alpha'-dimethoxyrubin (1) and alpha,alpha'-bis(methylthio)rubin (2), have been synthesized, separated into diastereomers, and analyzed. The isomers are shown by NMR to adopt intramolecularly hydrogen-bonded ridge-tile-shaped conformations. Like bilirubin, both 1 and 2 are insoluble in water. Unlike bilirubin, 1 is soluble in dilute aqueous bicarbonate, but 2 is insoluble, which would not be predicted from the expectation that 1 and 2 have the same pK(a). The data hint at a much larger steric size of SCH(3) relative to OCH(3).

NICHD Conference on Kernicterus: Research on Prevention of Bilirubin-Induced Brain Injury and Kernicterus: Bench-to-Bedside--Diagnostic Methods and Prevention and Treatment Strategies.

In July 2003, the National Institute of Child Health and Human Development (NICHD) organized a consensus conference, where a group of experts were invited to review and discuss the current state of knowledge regarding neonatal hyperbilirubinemia and identify areas in which where future research should be directed. This paper summarizes the presentations addressing the current methodologies for direct and noninvasive assessments of serum total bilirubin concentrations as well as prevention and treatment strategies for the management of neonatal hyperbilirubinemia.