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.

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.

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.

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.

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.

(m.n)-Homorubins. Syntheses and Structures.

Five new homorubin analogs of bilirubin with their two dipyrrinone components conjoined to (CH2)2, (CH2)3, and (CH2)4 units were synthesized with propionic acid chains shortened to acetic and elongated to butyric, and examined by spectroscopy and molecular mechanics computations for an ability to form conformation-determining hydrogen bonds. With m designating the number of conjoining CH2 units and n indicating the number of CH2 units of the alkanoic acid chains of (m.n)-homorubins, (2.1), (3.2), (4.2), and (4.3) homorubins were prepared and compared with previously synthesized (2.2) and (2.3), which adopt intramolecularly hydrogen bonded conformations in CHCl3.

Homorubins and Homoverdins.

The syntheses are described for centrally expanded bilirubin analogs: b -homorubins with propionic and butyric acid groups in the positions corresponding to the propionic acids of bilirubin. Their syntheses were accomplished by coupling two equivalents of a reactive monopyrrole (5-(bromomethylene)pyrrolin-2-one) to a dipyrrylethane. The corresponding b -homoverdins and dehydro- b -homoverdins were prepared by dehydrogenating the rubins or their dimethyl esters using DDQ. As supported by NMR measurements and molecular mechanics calculations, the homorubins are found to engage in conformation-determining intramolecular hydrogen bonding between the dipyrrinone and carboxylic acid moieties. Likewise, the homoverdins are believed to favor intramolecularly hydrogen-bonded conformations.

Intramolecular Hydrogen Bonding and Linear Pentapyrrole Conformation.

Three new linear pentapyrrole rubinoid analogs: 2,3,7,8,17,18,22,23-octamethyl-12,13-bis-(2-carboxyethyl)-1,10,15,24,25,27,28,29-octahydro-27H-pentapyrrin-1,24-dione and 2,3,8,12,13,17,22,23-octamethyl-7,18-bis-(2-carboxyethyl)-1,10,15,24,25,26,27,28,29-octahydro-27H-pentapyrrin-1,24-dione, and its 7,18-dihexanoic acid analog were synthesized, respectively, from 2,3,7,8-tetramethyl-(10H)-dipyrrin-2-one, from 2,3,8-trimethyl-7-[2-(methoxycarbonyl)ethyl]-(10H)-dipyrrinone, and 2,3,8-trimethyl-7-[5-(methoxycarbonyl)pentyl]-(10H)-dipyrrinone. 13C NMR and 1H NMR measurements in (CD3)2SO confirmed the pentapyrrole structures, while 1H NMR data indicate intramolecular hydrogen bonding between the CO2H and dipyrrinone groups. Molecular mechanics modeling studies suggest stable U-shape conformations capable of encapsulating small planar aromatic molecules.

Hydrogen Bonding: HOC=O· · ·H-N vs. HOC=O· · ·H-C.

A chloroform-soluble dipyrrinone, 8,9-bis-(5-carboxypentyl)-2,3-bis-(2-methoxyethoxy)-10H-dipyrrin-1-one, with solubilizing 2-methoxyethoxy ß-substituents on the lactam ring and two hexanoic acid groups (one at C(9), the other at C(8) of the pyrrole ring) was synthesized for its ability to form intramolecular hydrogen bonds to the lactam unit from either carboxylic acid, whether in the syn-(Z) or anti-(Z) conformation. In the syn-(Z) conformation, such intramolecular hydrogen bonds can also include the pyrrole N-H. In the anti-(Z), intramolecular hydrogen bonds can include the pyrrole C(7)-H. Evidence for both monomer conformations in equilibrium is provided by 1H NMR analyses, which indicate that the syn-(Z) is favored over the anti-(Z) and predict an interconversion barrier of approximately 40 kJ mol-1.

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.

Raman and ROA spectra of (-)- and (+)-2-Br-hexahelicene: experimental and DFT studies of a π-conjugated chiral system.

The Raman optical activity (ROA) spectra of both enantiomers of 2-Br-hexahelicene in chloroform solution have been measured in the range 1700-300 cm(-1). Density functional theory (DFT) calculations accurately reproduce the observed features. The most intense ROA features are also the most intense Raman features, in the region 1350-1400 cm(-1), and correspond to the so-called D-modes, which play a major role in coronene and other PAHs (polycyclic aromatic hydrocarbons). Together with a detailed analysis of the normal mode structure, the polarizability tensors for the intense Raman features are investigated and related to the principal characteristics of helicene systems, namely, chirality and π-conjugation. Through electron-phonon coupling analysis, we propose a mechanism that justifies the intense ROA signals.

Vibrational and electronic circular dichroism of dimethyl mesobilirubins-XIIIα.

The vibrational circular dichroism (VCD) spectra of (αR,α'R)-, (αS,α'S)-, (ßR,ß'R)-, and (ßS,ß'S)-dimethylmesobilirubin-XIIIα have been recorded in the range of 1800-900 cm(-1) in CDCl3 solution and in mixed DMSO-d6/CDCl3 solutions. Ab initio density functional theory (DFT) calculations predict IR vibrational absorption (VA) and VCD spectra in excellent to good correspondence with observed data. The same calculations confirmed the ridge-tile conformation that has been known for a long time. Assignment of vibrational normal modes (NMs) sheds light on the relative importance of local moieties and groups in determining conformational properties of the molecules, as well as their interaction with solvent molecules. Time-dependent DFT (TDDFT) calculations were also performed to provide an understanding of electronic circular dichroism (ECD) spectra and confirm the well-known interpretation based on the exciton model.

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.

Toward an amphiphilic bilirubin: the crystal structure of a bilirubin e-isomer.

A new bilirubinoid analog (1) with two methoxy beta-substituents on the lactam ring of each dipyrrinone was synthesized and examined spectroscopically. It is more soluble in CH3OH and CHCl3 than bilirubin, which is insoluble in CH3OH but soluble in CHCl3. The solubility of 1 is approximately 10 microg/mL in CH3OH (vs < or =1 microg/mL for bilirubin) and approximately 3 mg/mL in CHCl3 (vs approximately 0.6 mg/mL for bilirubin). Vapor pressure osmometry indicates that 1, like bilirubin, is monomeric in CHCl3, and NMR studies show that the most stable structure has the syn-4Z,syn-15Z configuration, with the pigment's dipyrrinones engaged in intramolecular hydrogen bonding to the propionic acid carboxyl groups. And, like bilirubin, Z,Z-1 adopts a conformation that is bent in the middle into a ridge-tile shape. For the first time, a crystal structure of a bilirubin E-isomer has been obtained. Crystallization of 1 under dim room lighting gave an X-ray quality crystal of the anti-4E,syn-15Z-(photo) isomer, in which only the Z-dipyrrinone half is engaged in intramolecular hydrogen bonding to a propionic acid. Hydrogen bonding is nearly completely disengaged in the E-dipyrrinone half; yet, the ridge-tile conformation persists.