Synthesis of Oligonucleotides Containing Trans Mitomycin C DNA Adducts at N6 of Adenine and N2 of Guanine.

Mitomycin C, (MC), an antitumor drug, is a DNA alkylating agent currently used in the clinics. Inert in its native form, MC is reduced to reactive mitosenes, which undergo nucleophilic attack by guanine or adenine bases in DNA to form monoadducts as well as interstrand crosslinks (ICLs). Although ICLs are considered the most cytotoxic lesions, the role of each individual adduct in the drug's cytotoxicity is still not fully understood. Synthetic routes have been developed to access modified oligonucleotides containing dG MC-monoadducts and dG-MC-dG ICL at a single position of their base sequences to investigate the biological effects of these adducts. However, until now, oligonucleotides containing monoadducts formed by MC at the adenine base had not been available, thus preventing the examination of the role played by these lesions in the toxicity of MC. Here, we present a route to access these substrates. Structural proof of the adducted oligonucleotides were provided by enzymatic digestion to nucleosides and high-resolution mass spectral analysis. Additionally, parent oligonucleotides containing a dG monoadduct and a dG-MC-dG ICL were also produced. The stability and physical properties of all substrates were compared via CD spectroscopy and UV melting temperature studies. Finally, virtual models were created to explore the conformational space and structural features of these MC-DNA complexes.

Absolute configuration of seco-eudesmanolide inuloxin D from experimental and predicted chiroptical studies of its 4-O-acetyl derivative.

Sesquitepenoids inuloxins A-D, belonging to different subgroups, were isolated from Dittrichia viscosa and showed potential biocontrol of some parasitic plants as Pelipanche, Orobanche, and Cuscuta species. The absolute configurations of the first three inuloxins A-C were previously determined by using experimental and computational chiroptical spectroscopic methods. The absolute configuration of inuloxin D remains to be established. The bioactive inuloxin E, closely related to inuloxin D, was recently isolated from the same plant organic extract. The same relative configuration of inuloxin D was assigned to inuloxin E by comparison of their NMR spectroscopic data. The absolute configurations of inuloxin D and inuloxin E are suggested in this work by analysis of the experimental and predicted chiroptical properties of the 4-O-acetyl derivative of inuloxin D.

Synthesis of Oligonucleotides containing the cis-Interstrand Crosslink Produced by Mitomycins in their Reaction with DNA.

Mitomycin C (MC) an antitumor drug and decarbamoylmitomycin C (DMC), a derivative of MC lacking the carbamoyl moiety, are DNA alkylating agents which can form DNA interstrand crosslinks (ICLs) between deoxyguanosine residues located on opposing DNA strands. MC forms primarily deoxyguanosine adducts with a 1"-R stereochemistry at the guanine-mitosene bond (1"-α, trans) whereas DMC forms mainly adducts with a 1"-S stereochemistry (1"-ß, cis). The crosslinking reaction is diastereospecific: trans-crosslinks are formed exclusively at CpG sequences, while cis-crosslinks are formed only at GpC sequences. Until now, oligonucleotides containing 1"-ß-deoxyguanosine adducts or ICL at a specific site could not be synthesized, thus limiting the investigation of the role played by the stereochemical configuration at C1'' in the toxicity of these compounds. Here, a novel biomimetic synthesis to access these substrates is presented. Structural proof of the adducted oligonucleotides and ICL were provided by enzymatic digestion to nucleosides, high resolution mass spectral analysis, CD spectroscopy and UV melting temperature studies. Finally, a virtual model of the 25-mer 1"-ß ICL synthesized was created to explore the conformational space and structural features of the crosslinked duplex.

Absolute Configuration and Conformation of (-)-R-t-Butylphenylphosphinoamidate: Chiroptical Spectroscopy and X-ray Analysis.

The absolute configuration and conformations of (-)-tert-butylphenylphosphinoamidate were determined using three different chiroptical spectroscopic methods, namely vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and optical rotatory dispersion (ORD). In each of the spectroscopic methods used, experimental data for the (-)-enantiomer of tert-butylphenylphosphinoamidate were measured in the solution phase. Using the concentration-dependent experimental infrared spectra, the existence of dimers in the solution was investigated, and the monomer-dimer equilibrium constant was determined. Concomitant quantum mechanical predictions of the VCD, ECD, and ORD for monomeric tert-butylphenylphosphinoamidate were carried out using density functional theory (DFT) calculations using the B3LYP functional and the 6-31G(d), 6-311G(2d,2p) and aug-cc-pVDZ basis sets. Similar predictions for dimeric tert-butylphenylphosphinoamidate were also obtained using the B3LYP/6-31G(d) method. A comparison of theoretically predicted data with the corresponding experimental data led to the elucidation of the absolute configuration as (-)-(R)-tert-butylphenylphosphinoamidate with one predominant conformation in the solution. This conclusion was independently supported by X-ray analysis of the complex with (+)-R-2,2'-dihydroxy-1,1'-binaphthol ((+)-R- BINOL).

Chiroptical Sensing: A Conceptual Introduction.

Chiroptical responses have been an essential tool over the last decades for chemical structural elucidation due to their exceptional sensitivity to geometry and intermolecular interactions. In recent times, there has been an increasing interest in the search for more efficient sensing by the rational design of tailored chiroptical systems. In this review article, advances made in chiroptical systems towards their implementation in sensing applications are summarized. Strategies to generate chiroptical responses are illustrated. Theoretical approaches to assist in the design of these systems are discussed. The development of efficient chiroptical reporters in different states of matter, essential for the implementation in sensing devises, is reviewed. In the last part, remarkable examples of chiroptical sensing applications are highlighted.

Complexation of Chiral Zinc(II) Porphyrin Tweezer with Achiral Aliphatic Diamines Revisited: Molecular Dynamics, Electronic CD, and 1H NMR Analysis.

We have reported here the complexation and chiroptical behavior of the host-guest complexes using a new chiral Zn(II) bisporphyrin tweezer host and a series of achiral aliphatic diamine guests varying the chain length. (1R,2R)-Cyclohexanediamine covalently links two Zn(II) porphyrin moieties, which thereby produces a strong chiral field around the bisporphyrin tweezer framework. The chiral tweezer upon complexation with achiral guest exhibited large changes in the UV-vis spectra and CD exciton couplets due to a sudden change in the porphyrin disposition, which is controlled by the host-guest stoichiometry as well as the chain lengths of the diamine guest. Addition of smaller diamines (n: 2-5) to the host resulted in the formation of 1:1 sandwich and 1:2 open complexes, respectively, at the low and high guest concentration, which eventually display two-step inversions of the CD couplet. With longer diamines (n: 6-8), however, only 1:1 sandwich complexes are formed with retention of the CD sign. Similar observations were also reported by us recently using another chiral bisporphyrin tweezer having (1R,2R)-diphenylethylenediamine as the spacer. In an effort to obtain deeper insights into the sudden changes of interporphyrin disposition just by changing the length of the achiral diamines, we have extended a series of computational studies and correlated closely with the results obtained from the experiment. While the previously published study has relied on commonly applied Monte Carlo (MC) sampling of the potential energy surface in addition to being guided by porphyrin effective transition moment approximation, the present study uses a considerably more robust molecular modeling protocol, namely Molecular Dynamics (MD) simulations followed by full ab initio geometry optimization and TD-DFT CD prediction. The experimental data corroborate with the results obtained from the theoretical conformational analysis. The latter are also supported by experimental 1H NMR data empowered by the porphyrin ring-current effect. The NMR spectral patterns of pyrrolic protons of the free host and the 1:1 sandwich complexes appear very diagnostic and reflect the changes in the mutual porphyrin disposition on moving from the free host to the complexed ones with short and long diamines. Overall, the experimental NMR data underscore the sensitivity of pyrrolic protons chemical shifts to subtle alterations of the geometrical features, and as such, they come in agreement with the theoretically derived models.

A Versatile Bis-Allylboron Reagent for the Stereoselective Synthesis of Chiral Diols.

Allylboron reagents are popular in synthesis owing to their versatility and the predictable stereochemical outcomes of their reactions with carbonyl compounds. Herein, we describe the synthesis of (Z,Z)-hexadienyl bis-boronate 1, a configurationally stable, crystalline, and easy to handle compound, which represents a class of bis-allylic boron reagents with heretofore untapped synthetic potential. In combination with a chiral phosphoric acid catalyst, the reagent can be employed for the enantioselective allyl transfer reaction to a variety of one-pot transformations, enabling swift access to functionalized 1,n-diols. The in situ conversion of the reagent into the corresponding bis-borinic ester allows for the direct and diastereoselective two-fold allyl transfer to aldehydes. This affords C2 - or Ci -symmetric stereotetrads containing a 1,4-diol moiety for natural product synthesis. The usefulness of our method was demonstrated with a short synthesis of the lignan (±)-neo-olivil.

Diverse Chiral Scaffolds from Diethynylspiranes: All-Carbon Double Helices and Flexible Shape-Persistent Macrocycles.

State-of-the-art chiroptical spectroscopies are valuable tools for structural elucidation. However, the potential of these spectroscopies for everyday applications has not been exploited to date partially due to the lack of sufficiently stable and efficient chiroptical systems. To this end, the development of suitable chiroptical structures is essential. Herein, we present the synthesis of spiro-compounds (P2 )-1 and (P4 )-2 as well as (M2 )-1 and (M4 )-2 exhibiting remarkable chiroptical responses. Theoretical simulations show that (P2 )-1, constituted by two (P)-configured spiranic chiral axes, presents an all-carbon double helix structure with (M)-helicity. On the other hand, molecular dynamic simulations reveal (P4 )-2 to have a single path for geometry-modification along its flat conformational space, certifying it as a chiral flexible shape-persistent macrocycle. Geometric quantification of chirality has been used to compare the spiranic derivatives presented herein.

Complexation of Chiral Zinc-Porphyrin Tweezer with Achiral Diamines: Induction and Two-Step Inversion of Interporphyrin Helicity Monitored by ECD.

We report here the synthesis of a new chiral Zn(II) bisporphyrin tweezer in which two achiral Zn(II) porphyrin moieties are covalently linked by (1R,2R)-diphenylethylenediamine, which produces a strong chiral field around the porphyrin moieties. The chiral tweezer exhibits not only intensity modulation in UV-vis and CD exciton couplets but also a dramatic change, namely, the inversion in the sign of the interporphyrin helicity upon binding of achiral diamines of varying lengths. The stoichiometry-controlled formation of a 1:1 sandwich complex followed by a 1:2 open complex was realized with smaller achiral diamines (n: 2-5) at their low and high concentration regions, respectively, leading to two-step inversion of chirality. With longer achiral diamines (n: 6-8), however, only 1:1 sandwich complexes are formed with no change of sign in the CD couplet. As compared to a 1:2 open complex, a 1:1 sandwich complex shows an enhanced CD response as two porphyrin units come closer in space. Structural insights of the host-guest complexes have been obtained spectroscopically along with molecular mechanics minimizations with the newly implemented OPLS-3 force field followed by geometry optimization using density functional theory of the most stable conformer. The amide bridge in the Zn(II) bisporphyrin has a low rotational barrier, which provides conformational flexibility to change interporphyrin helicity between 1:1 and 1:2 binding depending on the size of the achiral guests in order to minimize host-guest steric interactions.

Structural Studies on Porphyrin-PNA Conjugates in Parallel PNA:PNA Duplexes: Effect of Stacking Interactions on Helicity.

Parallel PNA:PNA duplexes were synthesized and conjugated with meso-tris(pyridyl)phenylporphyrin carboxylic acid at the N-terminus. The introduction of one porphyrin unit was shown to affect slightly the stability of the PNA:PNA parallel duplex, whereas the presence of two porphyrin units at the same end resulted in a dramatic increase of the melting temperature, accompanied by hysteresis between melting and cooling curves. The circular dichroism (CD) profile of the Soret band and fluorescence quenching strongly support the occurrence of a face-to-face interaction between the two porphyrin units. Introduction of a L-lysine residue at the C-terminal of one strand of the parallel duplex induced a left-handed helical structure in the PNA:PNA duplex if the latter contains only one or no porphyrin moiety. The left-handed helicity was revealed by nucleobase CD profile at 240-280 nm and by the induced-CD observed in the presence of the DiSC2 (5) cyanine dye at ~500-550 nm. Surprisingly, the presence of two porphyrin units led to the disappearance of the nucleobase CD signal and the absence of CD exciton coupling within the Soret band region. In addition, a dramatic decrease of induced CD of DiSC2 (5) was observed. These results are in agreement with a model where the porphyrin-porphyrin interactions cause partial loss of chirality of the PNA:PNA parallel duplex, forcing it to adopt a ladder-like conformation.

Absolute stereochemistry of a 4 a-hydroxyriboflavin analogue of the key intermediate of the FAD-monooxygenase cycle.

The biological action of flavoenzymes, such as flavin adenine dinucleotide (FAD)-containing monooxygenase, involves the formation of oxygenated flavin derivatives, such as 4 a-hydroperoxyflavin and 4 a-hydroxyflavin, in which a new center of chirality is created at the 4 a position during the enzymatic reactions. So far, the absolute configuration of this center of chirality in natural 4 a-oxygenated flavins has remained unknown in spite of its key importance for the diverse functions of flavoenzymes. Herein, we report the 4 a-hydroxy adduct 3 of 3-benzyl-5-ethyl-10-(tetraacetyl-D-ribityl)flavinium (1), one of the key intermediates involved in the enantioselective organocatalytic oxidation of sulfides to sulfoxides. The 4 a-hydroxyflavin diastereomers (+)-3 and (-)-3, separated by HPLC, were characterized by electronic circular dichroism (CD) spectroscopy. Their absolute configurations at the 4 a position were, for the first time, determined by comparing experimental CD spectra with those calculated by means of time-dependent density functional theory (TDDFT) on DFT-optimized structures obtained after an extensive conformation analysis.

Absolute configurations of fungal and plant metabolites by chiroptical methods. ORD, ECD, and VCD studies on phyllostin, scytolide, and oxysporone.

The absolute configuration (AC) of the bioactive metabolites phyllostin (1) and scytolide (2), two hexahydro-1,4-benzodioxines produced by Phyllosticta cirsii, and oxysporone (3), a dihydrofuropyranone recently isolated from a strain of Diplodia africana, has been assigned by computational analysis of their optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) spectra. Computational prediction of ORD, ECD, and VCD allowed us to assign (3S,4aR,8S,8aR) AC to naturally occurring (-)-1, while (4aR,8S,8aR) AC was assigned to (-)-2 employing only ECD and VCD, because in this case ORD analysis turned out to be unsuitable for AC assignment. Theoretical prediction of both ORD and ECD spectra of 3 led to assignment of (4S,5R,6R) AC to (+)-3. In this case a satisfactory agreement between experimental and calculated VCD spectra was obtained only after taking into account solvent effects. This study shows that in the case of flexible and complex natural products only a concerted application of more than a single chiroptical technique permits unambiguous assignment of absolute configuration.

Epiafzelechin from the root bark of Cassia sieberiana: detection by DART mass spectrometry, spectroscopic characterization, and antioxidant properties.

The root bark of Cassia sieberiana was analyzed using direct analysis in real time mass spectrometry, and a main flavonoid component with an [M + H](+) mass of 275 was identified. The flavonoid, epiafzelechin, was isolated and fully characterized with the concerted use of NMR spectroscopy, circular dichroism, and optical rotation. Electronic circular dichroism and optical rotation TDDFT calculations were also performed, and their agreement with the experimental results confirmed the enantiomeric identity of the isolated natural product. The antioxidant activity of the compound was also investigated.

Bulky melamine-based Zn-porphyrin tweezer as a CD probe of molecular chirality.

The transfer of chirality from a guest molecule to an achiral host is the subject of significant interest especially when, upon chiral induction, the chiroptical response of the host/guest complex can effectively report the absolute configuration (AC) of the guest. For more than a decade, dimeric metalloporphyrin hosts (tweezers) have been successfully applied as chirality probes for determination of the AC for a wide variety of chiral synthetic compounds and natural products. The objective of this study is to investigate the utility of a new class of melamine-bridged Zn-porphyrin tweezers as sensitive AC reporters. A combined approach based on an experimental CD analysis and a theoretical prediction of the prevailing interporphyrin helicity demonstrates that these tweezers display favorable properties for chiral recognition. Herein, we discuss the application of the melamine-bridged tweezer to the chiral recognition of a diverse set of chiral guests, such as 1,2-diamines, α-amino-esters and amides, secondary alcohols, and 1,2-amino-alcohols. The bulky periphery and the presence of a rigid porphyrin linkage lead, in some cases, to a more enhanced CD sensitivity than that reported earlier with other tweezers.

Enantiomerically pure alleno-acetylenic macrocycles: synthesis, solid-state structures, chiroptical properties, and electron localization function analysis.

New enantiomerically pure alleno-acetylenic macrocycles were prepared by oxidative homocoupling of optically active 1,3-diethynylallenes. Enantiomer separation resulted from a combined strategy of synthesis and chiral HPLC techniques. Two other achiral stereoisomers were also isolated and fully characterized. In addition, the X-ray structures of the chiral D(4)- and C(2)-symmetric macrocycles are reported. The chiroptical properties of these macrocycles are discussed on the basis of quantum chemical calculations, by using the CAM-B3LYP functional. Studies were carried out to investigate the vibronic fine structure observed experimentally in the UV/Vis and CD spectra. The origin of the intense chiroptical response of the chiral alleno-acetylenic macrocycles is explained by considering the topology of the molecular orbitals involved, thus relating electronic properties to structural features. Further analysis of the canonical molecular orbitals and the electron localization function (ELF) shows that these macrocycles belong to a relatively rare class of highly stable and formally anti-aromatic Hückel compounds.

CD-sensitive Zn-porphyrin tweezer host-guest complexes, part 1: MC/OPLS-2005 computational approach for predicting preferred interporphyrin helicity.

This article describes a computational study on dimeric zinc porphyrin tweezer complexes with primary/secondary amines and secondary alcohols that validates the use of Optimized Potential for Liquid Simulations (OPLS-2005) as the lead computational choice for assisting the tweezer methodology in the absolute configurational assignment of organic compounds. A supramolecular, microscale approach known as the tweezer method has been widely applied in the past decade for determining the absolute configuration of chiral substrates that are difficult to study by other readily available methods. The method relies on a host/guest complexation mechanism between a porphyrin tweezer moiety and a substrate, after its conversion into a bidentate conjugate. The formation of 1:1 complexes is a stereodifferentiating process: upon complexation, the originally achiral tweezer adopts a preferential interporphyrin helicity, dictated by the absolute configuration of the chiral substrate. By correctly predicting the sign of the interporphyrin helicity in the complex, OPLS-2005 provides a correlation between the observed circular dichroism (CD) signal and the absolute configuration of the substrate. It also offers a great degree of insight into the structural factors responsible for chiral recognition and the amplitude of exciton couplets. Moreover, the preferential binding sites between the Zn-tweezer and secondary amine conjugates were revealed by using the new computational approach.

CD-sensitive Zn-porphyrin tweezer host-guest complexes, part 2: cis- and trans-3-hydroxy-4-aryl/alkyl-beta-lactams. A case study.

This article describes an application of the host-guest chiral recognition approach called tweezer methodology for the determination of the absolute configuration of 3-hydroxy-beta-lactams. These substrates represent challenging cases due to their chemical reactivity, the presence of multiple stereogenic centers and several functional groups which offer various possibilities of binding to the Zn-porphyrin host. OPLS-2005, the force field used in this work to predict the interporphyrin twist, modeled correctly the host-guest complexation mechanism and revealed conformational details of the bound substrates. The computational study also suggested that in cases where an increase in the magnitude of the stereodifferentiation and an intense experimental CD are observed, the bound conformation of the conjugates are hydrogen bonded. The present investigation provides evidence that when the tweezer method is assisted by the OPLS-2005 based computational approach, it can be successfully applied to the configurational and conformational elucidation of multi-functional compounds with multiple stereogenic centers.

Role of environmental factors on the structure and spectroscopic response of 5'-DNA-porphyrin conjugates caused by changes in the porphyrin-porphyrin interactions.

We have explored the utility, strength, and limitation of through-space exciton-coupled circular dichroism in determination of the secondary structure of optically active chromophoric nanoarrays using the example of end-capped porphyrin- and metalloporphyrin-oligodeoxynucleotide conjugates. We put special emphasis on the explanation of the origin and significance of the distinctive multiple bands in the CD spectra (trisignate and tetrasignate CD bands). Such CD profiles are often observed in chiral aggregates or multichromophoric arrays but have never before been studied in detail. We found that variation of temperature and ionic strength has a profound effect on the geometry of the porphyrin-DNA conjugates and thus the nature of electronic interactions. At lower temperatures and in the absence of NaCl all three 5'-DNA-porphyrin conjugates display negative bisignate CD exciton couplets of variable intensity in the Soret region resulting from through-space interaction between the electric transition dipole moments of the two end-capped porphyrins. As the temperature is raised these exciton couplets are transformed into single positive bands originating from the porphyrin-single-strand DNA interactions. At higher ionic strengths and low temperatures, multisignate CD bands are observed in the porphyrin Soret region. These CD signature bands originate from a combination of intermolecular, end-to-end porphyrin-porphyrin stacking between duplexes and porphyrin-DNA interactions. The intermolecular aggregation was confirmed by fluorescence and absorption spectroscopy and resonance light scattering. DeVoe theoretical CD calculations, in conjunction with molecular dynamics simulations and Monte Carlo conformational searches, were used to mimic the observed bisignate exciton-coupled CD spectra as well as multiple CD bands. Calculations correctly predicted the sign and shape of the experimentally observed CD spectra. These studies reveal that the exciton-coupled circular dichroism is a very useful technique for the determination of the structure of optically active arrays.

Absolute configuration of 3,3'-diphenyl-[2,2'-binaphthalene]-1,1'-diol revisited.

The experimental vibrational circular dichroism, electronic circular dichroism, and optical rotatory dispersion spectra and corresponding quantum chemical predictions of 3,3'-diphenyl-[2,2'-binaphthalene]-1,1'-diol (VANOL) are used to confirm its absolute configuration as (+)(589)-(aR) or (-)(589)-(aS). A discrepancy in the literature crystal structure has been resolved by determining the X-ray crystal structure of the brucine binaphtholphosphate salt of the (aS)-enantiomer of VANOL.