Synthesis and Regioselective Functionalization of Tetrafluorobenzo-[α]-Fused BOPYPY Dyes.

The synthesis of a new bis-BF2 tetrafluorobenzo-[α]-fused BOPYPY dye from 4,5,6,7-tetrafluoroisoindole and 2-hydrazinopyrazine is reported. The regioselectivity of nucleophilic substitution reactions at the periphery of the tetrafluorinated BOPYPY and its α-bromo derivative were investigated using N-, O-, S-, and C-based nucleophiles. Among the aromatic fluorine atoms, the F2 atom is consistently regioselectively substituted, except when the α-position contains a thiophenol group; in this case, F4 is substituted instead due to stabilizing π-π-stacking between the two aromatic groups. The α-bromo BOPYPY derivative also reacts under Stille cross-coupling reaction conditions to produce the corresponding α-substituted product. The spectroscopic properties of these new fluorinated BOPYPYs were investigated and compared with nonfluorinated analogs.

8(meso)-Pyridyl-BODIPYs: Effects of 2,6-Substitution with Electron-Withdrawing Nitro, Chloro, and Methoxycarbonyl Groups.

The introduction of electron-withdrawing groups on 8(meso)-pyridyl-BODIPYs tends to increase the fluorescence quantum yields of this type of compound due to the decrease in electronic charge density on the BODIPY core. A new series of 8(meso)-pyridyl-BODIPYs bearing a 2-, 3-, or 4-pyridyl group was synthesized and functionalized with nitro and chlorine groups at the 2,6-positions. The 2,6-methoxycarbonyl-8-pyridyl-BODIPYs analogs were also synthesized by condensation of 2,4-dimethyl-3-methoxycarbonyl-pyrrole with 2-, 3-, or 4-formylpyridine followed by oxidation and boron complexation. The structures and spectroscopic properties of the new series of 8(meso)-pyridyl-BODIPYs were investigated both experimentally and computationally. The BODIPYs bearing 2,6-methoxycarbonyl groups showed enhanced relative fluorescence quantum yields in polar organic solvents due to their electron-withdrawing effect. However, the introduction of a single nitro group significantly quenched the fluorescence of the BODIPYs and caused hypsochromic shifts in the absorption and emission bands. The introduction of a chloro substituent partially restored the fluorescence of the mono-nitro-BODIPYs and induced significant bathochromic shifts.

A Comparison of the Photophysical, Electrochemical and Cytotoxic Properties of meso-(2-, 3- and 4-Pyridyl)-BODIPYs and Their Derivatives.

Boron dipyrromethene (BODIPY) dyes bearing a pyridyl moiety have been used as metal ion sensors, pH sensors, fluorescence probes, and as sensitizers for phototherapy. A comparative study of the properties of the three structural isomers of meso-pyridyl-BODIPYs, their 2,6-dichloro derivatives, and their corresponding methylated cationic pyridinium-BODIPYs was conducted using spectroscopic and electrochemical methods, X-ray analyses, and TD-DFT calculations. Among the neutral derivatives, the 3Py and 4Py isomers showed the highest relative fluorescence quantum yields in organic solvents, which were further enhanced 2-4-fold via the introduction of two chlorines at the 2,6-positions. Among the cationic derivatives, the 2catPy showed the highest relative fluorescence quantum yield in organic solvents, which was further enhanced by the use of a bulky counter anion (PF6-). In water, the quantum yields were greatly reduced for all three isomers but were shown to be enhanced upon introduction of 2,6-dichloro groups. Our results indicate that 2,6-dichloro-meso-(2- and 3-pyridinium)-BODIPYs are the most promising for sensing applications. Furthermore, all pyridinium BODIPYs are highly water-soluble and display low cytotoxicity towards human HEp2 cells.

Synthesis and Optical Characterization of a Rhodamine B Spirolactam Dimer.

Amide derivatives of xanthene dyes such as rhodamine B are useful in a variety of sensing applications due to their colorimetric responses to stimuli such as acidity changes and UV light. The optical properties of these molecules can be influenced by intermolecular associations into dimeric structures, but the exact impact can be hard to predict. We have designed a covalently linked intramolecular dimer of the dye rhodamine B utilizing p-phenylenediamine to link the two dyes via amide bonds. The doubly closed spirolactam version of this dimer, RSL2, is isolated as a colorless solid. Under acidic conditions or UV exposure, RSL2 solutions develop a pink color that is expected for the ring-opened form of the molecule. However, nuclear magnetic resonance (NMR) and single-crystal diffraction data show that the equilibrium still prefers the closed dimer state. Interestingly, the emission profile of RSL2 shows solvatochromic blue fluorescence. Control studies of model compounds with similar structural motifs do not display similar blue fluorescence, indicating that this optical behavior is unique to the dimeric form. This behavior may lend itself to applications of such xanthene dimers to more sophisticated sensors beyond those with traditional binary on/off fluorescence profiles.

Investigations on the Synthesis, Reactivity, and Properties of Perfluoro-α-Benzo-Fused BOPHY Fluorophores.

The synthesis and reactivity of 3,8-dibromo-dodecafluoro-benzo-fused BOPHY 2 are reported, via SN Ar with O-, N- S- and C-nucleophiles, and in Pd(0)-catalyzed cross-coupling reactions (Suzuki and Stille). The resulting perfluoro-BOPHY derivatives were investigated for their reactivity in the presence of various nucleophiles. BOPHY 3 displays reversible color change and fluorescence quenching in the presence of bases (Et3 N, DBU), whereas BOPHY 7 reacts preferentially at the α-pyrrolic positions, and BOPHY 8 undergoes regioselective fluorine substitution in the presence of thiols. The structural and electronic features of the fluorinated BOPHYs were studied by TD-DFT computations. In addition, their spectroscopic and cellular properties were investigated; BOPHY 10 shows the most red-shifted absorption/emission (λmax 659/699 nm) and 7 the highest fluorescence (Φf =0.95), while all compounds studied showed low cytotoxicity toward human HEp2 cells and were efficiently internalized.

Syntheses and Investigations of Conformationally Restricted, Linker-Free α-Amino Acid-BODIPYs via Boron Functionalization.

A series of α-amino acid-BODIPY derivatives were synthesized using commercially available N-Boc-l-amino acids, via boron functionalization under mild conditions. The mono-linear, mono-spiro, and di-amino acid-BODIPY derivatives were obtained using an excess of basic (histidine, lysine, and arginine), acidic (aspartic acid), polar (tyrosine, serine), and nonpolar (methionine) amino acid residues, in yields that ranged from 37 to 66%. The conformationally restricted mono-spiro- and di-amino acid-BODIPYs display strong absorptions in the visible spectral region with high molar extinction coefficients and significantly enhanced fluorescence quantum yields compared with the parent BF2-BODIPY. Cellular uptake and cytotoxicity studies using the human HEp2 cell line show that both the presence of an N,O-bidentate spiro-ring and basic amino acids (His and Arg) increase cytotoxicity and enhance cellular uptake. Among the series of BODIPYs tested, the spiro-Arg- and spiro-His-BODIPYs were found to be the most cytotoxic (IC50 ∼ 22 µM), while the spiro-His-BODIPY was the most efficiently internalized, localizing preferentially in the cell lysosomes, ER, and mitochondria.

Synthesis and Investigation of Linker-Free BODIPY-Gly Conjugates Substituted at the Boron Atom.

An efficient synthesis of boron-functionalized cyclic BODIPY-Gly conjugates, using commercially available N-protected glycine amino acids and a BF2-BODIPY moiety as starting materials, is reported. The existence of two conformers (up and down) is revealed through comprehensive DFT calculations and 1H and 11B NMR analyses. The experimental and computational results indicate that all BODIPYs are stable in aqueous solutions at neutral pH and that Fmoc-BODIPY (4) is more stable than Ac-BODIPY (6) in the presence of trifluoroacetic acid (TFA). In part due to their enhanced rigidity, all BODIPY-Gly conjugates display increased fluorescence quantum yields (0.6 < Φ < 0.9) relative to the corresponding BF2-BODIPY, making them excellent candidates for fluorescence imaging applications.

Syntheses, Spectroscopic Properties, and Computational Study of ( E, Z)-Ethenyl and Ethynyl-Linked BODIPYs.

A series of ( E, Z)-ethenyl- and ethynyl-linked boron dipyrromethene (BODIPY) dimers were synthesized in 23-34% yields by condensation of pyrroles with the corresponding bis-benzaldehydes, followed by oxidation and boron complexation. The BODIPY dimers were characterized by 1H, 13C, and 11B NMR spectroscopy, high-resolution mass spectrometry, and, in the cases of 1b, 2, and 3, by X-ray crystallography. The spectroscopic properties for this series of dimers were investigated in tetrahydrofuran solutions, and very similar absorption and emission profiles were observed for all dimers. Density functional theory calculations show minimal conjugation between the two BODIPY units in the dimers, as a result of the large dihedral angle between the BODIPYs and the linker. The ( E)-ethenyl-linked dimer 1a showed the highest fluorescence quantum yield of all dimers investigated in this study.

Stability of a Series of BODIPYs in Acidic Conditions: An Experimental and Computational Study into the Role of the Substituents at Boron.

Boron-dipyrromethene (BODIPY) dyes have been extensively investigated in recent years for a variety of bioanalytical and bioimaging applications. The success of these applications relies on the stability of BODIPYs, particularly under acidic conditions. In this work, the stability of a series of 4,4'-disubstituted BODIPYs (-F, -CN, -Ph, -Me, -OMe) toward addition of excess trifluoroacetic acid (TFA) was studied systematically and comprehensively through 11B and 1H NMR, UV-vis, fluorescence, thin layer chromatography, mass spectrometry, and infrared. The results indicate that 4,4'-dicyano-BODIPY 2 is the most stable among this series and remains unchanged even 3 days after addition of excess TFA. On the other hand, 4,4'-dimethyl-BODIPY 3 and 4,4'-dimethoxy-BODIPY 5 are the least stable, toward addition of TFA, and the 4,4'-diphenyl and 4,4'-difluoro-BODIPYs 1 and 4 were found to have intermediate stability. The experimental analysis and comparison with theoretical calculations indicate that the 4,4'-dicyano-BODIPY 2 has the greater aromaticity of the series, as evaluated by the BLA parameter, decreased charge on boron, and upon TFA addition it forms an unusually stable BODIPY 2···TFA complex. On the other hand, all other BODIPYs decompose within hours after TFA addition. Computational modeling demonstrates that 4,4'-dicyano substitution increases aromaticity and stabilizes the B-N bond, resulting in the most stable compound from the series studied.

Synthesis, Crystal Structure, and the Deep Near-Infrared Absorption/Emission of Bright AzaBODIPY-Based Organic Fluorophores.

Annularly fused azaBODIPY-based organic fluorophores (HBPs 2) containing up to 13 aromatic ring fusions were synthesized by a Suzuki coupling reaction with bromoazadipyrromethenes and a subsequent regioselective oxidative ring-fusion reaction. X-ray analysis indicates almost planar dipyrrin cores for all crystals but overall curved or "wave" conformations for those HBP dyes. These molecules exhibit unique structural and physical properties including excellent spectral selectivity (negligible absorption between 300 and 700 nm), sharp near-infrared (NIR) absorption (up to 878 nm) and emission (up to 907 nm), large extinction coefficient (up to 4.5 × 105 M-1 cm-1), and excellent photostabilities.

Synthesis, Structure, and Properties of Near-Infrared [b]Phenanthrene-Fused BF2 Azadipyrromethenes.

A new class of phenanthrene-fused BF2 azadipyrromethene (azaBODIPY) dyes have been synthesized through a tandem Suzuki reaction and oxidative ring-fusion reaction, or a palladium-catalyzed intramolecular C-H activation reaction. These phenanthrene-fused azaBODIPY dyes are highly photostable and display markedly redshifted absorption (up to λ=771 nm) and emission bands (λ≈800 nm) in the near-infrared region. DFT calculations and cyclic voltammetry studies indicate that, upon annulation, more pronounced stabilization of the LUMO is the origin of the bathochromic shift of the absorption and high photostability.

Synthesis and reactivity of 4,4-Dialkoxy-BODIPYs: an experimental and computational study.

A series of boron-disubstituted O-BODIPYs were synthesized, and their structures and spectroscopic properties were investigated using both computational and experimental methods. Three methods were investigated for the preparation of 4,4-dimethoxy-BODIPYs bearing electron-donating or electron-withdrawing 8-aryl groups: method A employs refluxing in the presence of NaOMe/MeOH, method B uses AlCl3 in refluxing dichloromethane followed by addition of methanol as nucleophile, and method C involves activation of the BODIPYs using TMSOTf in refluxing toluene followed by addition of methanol. The yields obtained depend on the method used and the structure of the starting BODIPYs; for example, 1a and 3a were most efficiently prepared using method C (98 and 70%, respectively), while 2a was best prepared by method A (50%). Methods B and C were employed for the synthesis of seven new 4,4-dialkoxy-BODIPYs. 4,4-Dipropargyloxy-BODIPY 1e reacted under Cu(I)-catalyzed alkyne-azide Huisgen cycloaddition conditions to produce 4,4-bis(1,2,3-triazole)-BODIPY 4 in 78% yield. The substitution of the fluorides for alkoxy groups on the BODIPYs had no significant effect on the absorption and emission wavelengths but altered their fluorescence quantum yields. Among this series of dialkoxy-BODIPYs, the 4,4-dipropargyloxy 1e and its corresponding bis(1,2,3-triazole) 4 show the largest quantum yields in toluene and THF, respectively.

Spectroscopic, computational modeling and cytotoxicity of a series of meso-phenyl and meso-thienyl-BODIPYs.

A series of twenty-two BODIPY compounds were synthesized, containing various meso-phenyl and meso-thienyl groups, and their spectroscopic and structural properties were investigated using both experimental and computational methods. Further functionalization of the BODIPY framework via iodination at the 2,6-pyrrolic positions was explored in order to determine the effect of these heavy atoms on the photophysical and cytotoxicity of the meso-aryl-BODIPYs. BODIPYs bearing meso-thienyl substituents showed the largest red-shifted absorptions and emissions and reduced fluorescence quantum yields. The phototoxicity of the BODIPYs in human carcinoma HEp2 cells depends on both the presence of iodines and the nature of the meso-aryl groups. Six of the eleven 2,6-diiodo-BODIPYs investigated showed at least a sevenfold enhancement in phototoxicity (IC50 = 3.5-28 µM at 1.5 J/cm(2)) compared with the non-iodinated BODIPYs, while the others showed no cytotoxicity, while their singlet oxygen quantum yields ranged from 0.02 to 0.76. Among the series investigated, BODIPYs 2a and 4a bearing electron-donating meso-dimethoxyphenyl substituents showed the highest phototoxicity and dark/phototoxicity ratio, and are therefore the most promising for application in PDT.

Synthesis, computational modeling, and properties of benzo-appended BODIPYs.

A series of new functionalized mono- and dibenzo-appended BODIPY dyes were synthesized from a common tetrahydroisoindole precursor following two different synthetic routes. Route A involved the assembly of the BODIPY core prior to aromatization, while in Route B the aromatization step was performed first. In general, Route A gave higher yields of the target dibenzo-BODIPYs, due to the ease of aromatization of the BODIPYs compared with the corresponding dipyrromethenes, probably due to their higher stability under the oxidative conditions (2,3-dichloro-5,6-dicyano-1,4-benzoquinone in refluxing toluene). However, due to the slow oxidation of highly electron-deficient BODIPY 3 c bearing a meso-C(6)F(5) group, dibenzo-BODIPY 4 c was obtained, in 35 % overall from dipyrromethane, only by Route B. Computational calculations performed at the 6-31G(d,p) level are in agreement with the experimental results, showing similar relative energies for all reaction intermediates in both routes. In addition, BODIPY 3 c had the highest molecular electrostatic potential (MEPN), confirming its high electron deficiency and consequent resistance toward oxidation. X-ray analyses of eight BODIPYs and several intermediates show that benzannulation further enhances the planarity of these systems. The π-extended BODIPYs show strong red-shifted absorptions and emissions, about 50-60 nm per benzoannulated ring, at 589-658 and 596-680 nm, respectively. In particular, db-BODIPY 4 c bearing a meso-C(6)F(5) group showed the longest λ(max) of absorption and emission, along with the lowest fluorescence quantum yield (0.31 in CH(2)Cl(2)); on the other hand monobenzo-BODIPY 8 showed the highest quantum yield (0.99) of this series. Cellular investigations using human carcinoma HEp2 cells revealed high plasma membrane permeability for all dibenzo-BODIPYs, low dark- and photo-cytotoxicities and intracellular localization in the cell endoplasmic reticulum, in addition to other organelles. Our studies indicate that benzo-appended BODIPYs, in particular the highly stable meso-substituted BODIPYs, are promising fluorophores for bioimaging applications.

Why [(eta5-C5Me(n)H5-n)2Ti]2(micro2,eta2,eta2-N2) can not add a H2 molecule to the side-on-coordinated N2 while its Zr and Hf analogues can? insights from computational studies.

The potential energy surface of the reaction [(eta5-C5MenH5-n)2M]2(micro2,eta2,eta2-N2) + H2 --> [(eta5-C5MenH5-n)2M][(eta5-C5MenH5-n)2MH](micro2,eta2,eta2-NNH) at low-lying singlet and triplet electronic states of the reactants was investigated using density functional methods, for n = 0 and 4, and M = Ti, Zr, and Hf. Ground electronic states of the Ti complexes are found to be triplet states, while that for the corresponding Zr and Hf complexes are singlet states. In their singlet state, all these complexes satisfy known necessary conditions (they have a side-on-coordinated N2 molecule and appropriate frontier orbitals) for successful addition of an H2 molecule to the coordinated N2, and consequently, add of an H2 molecule with a reasonable energy barrier. Hf complexes show slightly higher reactivity than corresponding Zr complexes, and in turn, both are more reactive than their singlet-state Ti counterparts. The calculated trend in reactivity of Zr and Hf complexes is consistent with the latest experimental data (see refs 13 and 16). However, Ti complexes have the ground triplet state that lacks in appropriate frontier orbitals. As a result, H2 addition to the Ti complexes at their triplet ground states requires a larger activation barrier than the singlet state and is endothermic (lacks of driven force for reaction). On the basis of these results, we predict that the [(eta5-C5Me4H)2M]2(micro2,eta2,eta2-N2) and [(eta5-C5H5)2M]2(micro2,eta2,eta2-N2) complexes cannot react with an H2 molecule for M = Ti, while those for M = Zr and Hf can. It was shown that the difference in the B3LYP (hybrid) and PBE (nonhybrid) calculated energy gaps between the lowest closed-shell singlet and triplet states of the present complexes reduces via first- > second- > third-row transition metals; both hybrid and nonhybrid density functionals can be safely used to describe reactivity of the low-lying low-spin and high-spin states of second- and third-row transition metal complexes.

Parameter Calibration of Transition-Metal Elements for the Spin-Polarized Self-Consistent-Charge Density-Functional Tight-Binding (DFTB) Method: Sc, Ti, Fe, Co, and Ni.

Recently developed parameters for five first-row transition-metal elements (M = Sc, Ti, Fe, Co, and Ni) in combination with H, C, N, and O as well as the same metal (M-M) for the spin-polarized self-consistent-charge density-functional tight-binding (DFTB) method have been calibrated. To test their performance a couple sets of compounds have been selected to represent a variety of interactions and bonding schemes that occur frequently in transition-metal containing systems. The results show that the DFTB method with the present parameters in most cases reproduces structural properties very well, but the bond energies and the relative energies of different spin states only qualitatively compared to the B3LYP/SDD+6-31G(d) density functional (DFT) results. An application to the ONIOM(DFT:DFTB) indicates that DFTB works well as the low level method for the ONIOM calculation.

Does dinitrogen hydrogenation follow different mechanisms for [(eta5-C5Me4H)2Zr]2(mu2,eta2,eta2-N2) and {[PhP(CH2SiMe2NSiMe2CH2)PPh]Zr}2(mu2,eta2,eta2-N2) complexes? A computational study.

The mechanisms of dinitrogen hydrogenation by two different complexes--[(eta(5)-C(5)Me(4)H)(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)), synthesized by Chirik and co-workers [Nature 2004, 427, 527], and {[P(2)N(2)]Zr}(2)(mu(2),eta(2),eta(2)-N(2)), where P(2)N(2) = PhP(CH(2)SiMe(2)NSiMe(2)CH(2))(2)PPh, synthesized by Fryzuk and co-workers [Science 1997, 275, 1445]--are compared with density functional theory calculations. The former complex is experimentally known to be capable of adding more than one H(2) molecule to the side-on coordinated N(2) molecule, while the latter does not add more than one H(2). We have shown that the observed difference in the reactivity of these dizirconium complexes is caused by the fact that the former ligand environment is more rigid than the latter. As a result, the addition of the first H(2) molecule leads to two different products: a non-H-bridged intermediate for the Chirik-type complex and a H-bridged intermediate for the Fryzuk-type complex. The non-H-bridged intermediate requires a smaller energy barrier for the second H(2) addition than the H-bridged intermediate. We have also examined the effect of different numbers of methyl substituents in [(eta(5)-C(5)Me(n)H(5)(-)(n))(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) for n = 0, 4, and 5 (n = 5 is hypothetical) and [(eta(5)-C(5)H(2)-1,2,4-Me(3))(eta(5)-C(5)Me(5))(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) and have shown that all complexes of this type would follow a similar H(2) addition mechanism. We have also performed an extensive analysis on the factors (side-on coordination of N(2) to two Zr centers, availability of the frontier orbitals with appropriate symmetry, and inflexibility of the catalyst ligand environment) that are required for successful hydrogenation of the coordinated dinitrogen.

The heat of formation of chlorine-isocyanate and the relative stability of isoelectronic molecules: an experimental and theoretical study.

Accurate thermochemical data of small molecules are invaluable to the progress of every aspect of chemistry, especially in the atmosphere, combustion and industry. In this work, photofragmentation translational spectroscopy and 1st principles electronic structure theory reveal the literature value of the heat of formation of chlorine-isocyanate to be in error by more than 40 kcalmol. We report a revised experimental value for D0(Cl-NCO) = 51+/-3 kcal/mol which leads to a Delta Hf (ClNCO) = 8.5+/-3 kcal/mol. High level ab initio (CCSD(T)) electronic structure calculations extrapolated to the complete basis set limit give D0(Cl-NCO) = 6.3 kcal/mol, in good agreement with experiment. In light of the present results, the destabilization of azides relative to isoelectronic isocyanates has been evaluated empirically for three pairs of related molecules. It is found to be 90-110 kcal/mol, and has been attributed mainly to the weakening of the N-NN bond relative to the N-CO bond. Electronic structure calculations employing decomposition analysis suggest that, compared to homopolar N2, the (+delta)CO(-delta) pi polarity provides better orbital interaction (charge transfer) and electrostatic attraction and results in a closer encounter and larger stabilization between the fragments and that this is the origin of isoelectronic destabilization of azides relative to the isocyanates.

Theoretical Study of the Structure and Properties of [(η(5)-C5Me4H)2Zr]2(µ(2),η(2),η(2)-N2).

Recently Pool et al. [Pool, J. A.; Lobkovsky, E.; Chirik, P. J. Nature 2004, 427, 527.] showed that the [(η(5)-Cp')2Zr]2(µ(2),η(2),η(2)-N2), Cp' = η(5)-C5Me4H, complex is promising for dinitrogen hydrogenation. In the present study we examine computationally the structure and relative energies of different possible positional isomers of this dimer complex as well as different isomers of the monomer complex (Cp'2Zr)(η(2)-N2). The relative stability of isomers of the monomer is determined by the electrostatic repulsion between the negatively charged N atoms of the N2 molecule and the negatively charged C atoms of the Cp' ring that are bound to H. Substitution of H atoms by methyl groups significantly changes the charge distribution in Cp rings, increases the negative charge of CH atom, and affects the relative stability of the isomers. On the other hand, competition between the electrostatic effects and the steric repulsion determines the relative energy of the positional isomers of the dimer (Cp'2Zr)2(µ(2),η(2),η(2)-N2).