Valence Isomerization Research Articles

Let′s Play with Valence Isomers: The Influence of Different Main Group Elements on Their Relative Stability

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

1,2,5,6-Tetrasilabenzobenzvalene: A Valence Isomer of 1,2,3,4-Tetrasilanaphthalene

Abstract 1,2,5,6-Tetrasilabenzobenzvalene, a valence isomer of 1,2,3,4-tetrasilanaphthalene, was synthesized and structurally characterized by the coupling reaction of the dipotassium salt of the tetrasilacyclobutadiene dianion with o-dibromobenzene. The 1,2,5,6-tetrasilabenzobenzvalene was presumably obtained by the isomerization of the initially formed 1,2,3,4-tetrasilabenzo-1,4-Dewar benzene.

Thermal Valence Isomerization of 2,3‐Diborata‐1,4‐diphosphoniabuta‐1,3‐dienes to Bicyclo[1.1.0]butanes and Cyclobutane‐1,3‐diyls

Mind your Ps and Bs: Valence isomerizations of PBBP 1,3-butadienes are investigated and compared to those of PCCP and all-carbon systems. The 2,3-diborata-1,4-diphosphoniabuta-1,3-dienes thermally isomerize to bicyclo[1.1.0]butanes or cyclobutane-1,3-diyls. Under photolytic activation, the bicyclo[1.1.0]butanes rearrange into cyclobutenes. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z701578_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Let’s Play with Valence Isomers: The Influence of Different Main Group Elements on Their Relative Stability

Abstract Valence isomers are compounds featuring the same fragments connected in different ways. In this personal account, we describe how we first met by serendipity this kind of isomerism, and how later on we used the specific properties of phosphorus and boron to prepare two types of valence isomers that are not accessible with elements exclusively from the first long row. In the carbon series, benzene is calculated to be 608 kJ mol−1 lower in energy than its singlet diradical valence isomer, the anti-tricyclohexylene, but a tetraphosphorus analogue of the latter has been isolated. According to calculations, the parent amidinium salt is 541 kJ mol−1 more stable than its three-membered heterocyclic valence isomer, but in the phosphorus series, the difference in energy between the open and closed forms is only a few kJ mol−1; provided the right substituents are used, the cyclic form can be isolated. Lastly, among butadiene valence isomers, singlet cyclobutane-1,3-diyls were predicted only as transition states for the inversion of bicyclo[1.1.0]butane. In marked contrast, 1,3-dibora-2,4-diphosphacyclobutane-1,3-diyls can be prepared by valence isomerization of the corresponding butadiene derivatives and isolated under conventional experimental conditions.

Cell surface expression of melanocortin-1 receptor on HaCaT keratinocytes and α-melanocortin stimulation do not affect the formation and repair of UVB-induced DNA photoproducts

Ultraviolet (UV) exposure induces an up-regulation of melanocortin-1 receptor (MC1R) expression in human skin and the alpha-melanocyte-stimulating hormone (alpha-MSH) may reduce UVB-induced DNA damage in normal human melanocytes. Using high-performance liquid chromatography coupled to tandem mass spectrometry, we investigated the formation and repair of DNA lesions in UVB-irradiated HaCaT cells stably transfected with the wild type MC1R gene (HaCaT-MC1R). Similar levels of 8 bipyrimidine photoproducts including cyclobutane pyrimidine dimers (CPDs) (T<>T, T<>C, C<>T), (6-4) photoproducts ((6-4)PPs) (TT-(6-4)PPs, TC-(6-4)PPs) and their Dewar valence isomers together with 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) were found to be generated in both non-transfected and HaCaT-MC1R cells after UVB exposure. Time-course studies of DNA photoproduct yields indicated that the DNA repair ability depended upon radiation doses. It was shown that (6-4)PPs were removed from the DNA of UVB-irradiated cells much more efficiently than CPDs. The repair efficiency of 8-oxodGuo, CPDs and (6-4)PPs was relatively similar in both cell lines and was not modified by stimulation with alpha-MSH before UVB-exposure. In conclusion, cell surface-enforced expression of MC1Rs on HaCaT keratinocytes and alpha-MSH stimulation do not affect the formation of UVB-induced DNA photoproducts and their subsequent repair.

Interplay of EnE‘3-nC Valence Isomers (E, E‘ = Si, Ge): Bicyclo[1.1.0]butanes with Very Short Bridging Bonds and Their Isomerization to Alkyl-Substituted Cyclopropenes

1,2,3-Trisila- and 1,3-disila-2-germabicyclo[1.1.0]butane derivatives 7a,b were synthesized in high yields by the reduction of the appropriate precursors, 1,3-dichloro[1,2,3]trisiletane and 1,3-dichloro[1,3,2]disilagermetane, with KC8. The X-ray analysis of 7a revealed an exceedingly short Si−Si bridging bond of 2.2664(9) A, which is much shorter than the normal Si−Si single bond of 2.34 A. The nature of such an unusual bridging bond is discussed in terms of both electronic and steric effects of the methylene bridge. The thermolysis of bicyclo[1.1.0]butanes 7a,b unexpectedly resulted in the formation of their valence isomers, alkyl-substituted 1H-trisilirene 8a and 1H-disilagermirene 8b, representing a new type of E4 valence isomer (E = group 14 element). The germanium versions, 1H-siladigermirene 8c and 1H-trigermirene 8d, were also prepared.

A model for triplet mutation formation based on error-prone translesional DNA synthesis opposite UV photolesions

A triplet mutation is defined as multiple base substitutions or frameshifts within a three-nucleotide sequence which includes a dipyrimidine sequence. Triplet mutations have recently been identified as a new type of UV-specific mutation, although the mechanism of their formation is unknown. A total of 163 triplet mutations were identified through an extensive search of previously published data on UV-induced mutations, including mutations from skin, skin cancer, and cultured mammalian cells. Seven common patterns of sequence changes were found: Type I, NTC → TTT; Type IIa, NCC → PyTT or PyCT (Py, pyrimidine); Type IIb, TCC → PuTT or PuCT (Pu, purine); Type III, NCC → NAT or NTA; Type IV, NTT → AAT; Type Va, NCT → NTX; and Type Vb, PuCT → XTT (N and X, independent anonymous bases). Furthermore, it is suggested that the type of UV lesion responsible for each of these triplet mutation classes are (a) pyrimidine(6-4)pyrimidone photoproducts for Types I, IIb, III, IV and Vb, (b) cyclobutane pyrimidine dimers for Type Va, and (c) Dewar valence isomers for Types IIa and IIb. These estimations are based primarily on results from previous studies using photolyases specific for each type of UV lesion. A model is proposed to explain the formation of each type of triplet mutation, based on error-prone translesional DNA synthesis opposite UV-specific photolesions. The model is largely consistent with the ‘A-rule’, and predicts error-prone insertions not only opposite photolesions but also opposite the undamaged template base one-nucleotide downstream from the lesions.

High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications

A high-resolution crystal structure is reported for d(TpA)*, the intramolecular thymine–adenine photoadduct that is produced by direct ultraviolet excitation of the dinucleoside monophosphate d(TpA). It confirms the presence of a central 1,3-diazacyclooctatriene ring linking the remnants of the T and A bases, as previously deduced from heteronuclear NMR measurements by Zhao et al. (The structure of d(TpA)*, the major photoproduct of thymidylyl-(3′-5′)-deoxyadenosine. Nucleic Acids Res., 1996, 24, 1554–1560). Within the crystal, the d(TpA)* molecules exist as zwitterions with a protonated amidine fragment of the eight-membered ring neutralizing the charge of the internucleotide phosphate monoanion. The absolute configuration at the original thymine C5 and C6 atoms is determined as 5S,6R. This is consistent with d(TpA)* arising by valence isomerization of a precursor cyclobutane photoproduct with cis–syn stereochemistry that is generated by [2 + 2] photoaddition of the thymine 5,6-double bond across the C6 and C5 positions of adenine. This mode of photoaddition should be favoured by the stacked conformation of adjacent T and A bases in B-form DNA. It is probable that the primary photoreaction is mechanistically analogous to pyrimidine dimerization despite having a much lower quantum yield.

Fluorinated Cyclobutanes and Their Derivatives

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Valence isomer of a β-diketiminate-supported phosphinidene: a case of C–H activation and ring contraction

A valence isomer of a beta-diketiminate-supported phosphinidene has been prepared by potassium metal reduction of the corresponding chlorophosphenium cation.

Structure and relative energies of regioisomers and valence isomers of C60 adducts. HF and DFT study

AbstractFullerene C60 and N‐bridged C60NH regioisomeres are investigated by HF and DFT methods with BLYP, B3LYP and PBE functionals at the 6‐31G**, 6‐311G** and TZ2P levels. Method DFT/PBE/TZ2P, providing the good compliance with experimental results, is chosen. Cross‐sections of potential energy surface of adducts at a variation of 5,6‐ or 6,6‐ bonds lengths are investigated. It is shown, that C60C2H4NH and C60H2 are characterized by local minima for [5,6]‐closed forms, whereas local minima for [5,6]‐open forms are absent. So absence of stable conformations of the [5,6]‐closed forms of methanofullerenes and aziridinofullerenes is a consequence of strain energy in three‐membered rings. It is shown that relative stability of the regioisomers depends from the lengths of single or double bonds of monoadducts, participating in reactions. The coordinated change of relative energies of the open and closed isomers N‐bridged mono‐(C60NR 1–7) and bis‐adducts (C60(NR)2 8–14) is revealed. The [6,6]‐closed form is more stable for compounds C60NR (2,3) and cis‐1‐C60 (NR)2 (9,10) (R = Me, Ph), while [5,6]‐open and cis‐1 [6,6]‐open forms are more stable for compounds C60NR (6,7) and cis‐1‐C60(NR)2 (13,14) (R = COOMe, R*‐the nitropyrimidine), what has been confirmed by experiment. The factors, defining relative isomers stability are investigated. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Description ofCarbo-oxocarbons and Assessment of Exchange-Correlation Functionals for the DFT Description ofCarbo-mers

Mono- and polycyclic valence isomers of carbo-[3]oxocarbon C(9)O(3) and carbo-[5]oxocarbon C(15)O(5) have been characterized on the singlet spin state potential energy surface. By contrast to their geometry, their relative stability is highly sensitive to the calculation level. The performance of LDA, GGA, meta-GGA, and hybrid functionals is compared to that of HF, post-HF, and multiconfigurational calculations. The results obtained for C(9)O(3) are compared to those obtained for hydrocarbon analogues such as &[3]pericyclyne C9(H2)3 and carbo-[3]radialene C9(CH2)3 and are analyzed on the basis of an energy decomposition scheme. The respective role of the exchange and correlation counterparts of the functional in the discrepancy of the results is discussed.

Differential sensing of protein influences by NO and CO vibrations in heme adducts.

Heme proteins bind the gaseous ligands XO (X = C, N, O) via backbonding from Fe d(pi) electrons. Backbonding is modulated by distal interactions of the bound ligand with the surrounding protein and by variations in the strength of the trans proximal ligand. Vibrational modes associated with FeX and XO bond stretching coordinates report on these interactions, but the interpretive framework developed for CO adducts, involving anticorrelations of nuFeC and nuCO, has seemed not to apply to NO adducts. We have now obtained an excellent anticorrelation of nuFeN and nuNO, via resonance Raman spectroscopy on (N-methylimidazole)Fe(II)TPP-Y(NO), where TPP-Y is tetraphenylporphine with electron-donating or -withdrawing substituents, Y, that modulate the backbonding; the problem of laser-induced dissociation of the axial base was circumvented by using frozen solutions. New data are also reported for CO adducts. The anticorrelations are supported by DFT calculations of structures and spectra. When protein data are examined, the NO adducts show large deviations from the modeled anticorrelation when there are distal H-bonds or positive charges. These deviations are proposed to result from closing of the FeNO angle due to a shift in the valence isomer equilibrium toward the Fe(III)(NO-) form, an effect that is absent in CO adducts. The differing vibrational patterns of CO and NO adducts provide complementary information with respect to protein interactions, which may help to elucidate the mechanisms of ligand discrimination and signaling in heme sensor proteins.

Reactions of Unsaturated Azides. Part 20. Experimental and Theoretical Characterization of the Valence Isomerization of Bi‐2H‐azirin‐2‐yls to Diazabenzenes.

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Synthesis of oligonucleotides containing the Dewar valence isomer of the (6–4) photoproduct and their application to (6–4) photolyase studies

The (6-4) photoproduct, which is a major UV light-induced lesion formed between adjacent pyrimidine bases, is isomerized to its Dewar valence isomer by exposure to longer wavelengths. We have synthesized a phosphoramidite building block of the Dewar photoproduct formed at the thymidylyl(3'-5')thymidine site, and incorporated it into oligonucleotides on a DNA synthesizer, aiming to use them for biological studies. An alternative activator, benzimidazolium triflate, gave better results, while by-products were detected at longer retention time in the ordinary synthesis. We characterized the synthetic oligonucleotides by UV conversion, nuclease digestion and mass spectrometry. Their use in the study of the (6-4) photolyase, a DNA repair enzyme, revealed its different recognition modes between the (6-4) photoproduct and the Dewar isomer.

Experimental and Theoretical Characterization of the Valence Isomerization of Bi‐2H‐azirin‐2‐yls to Diazabenzenes

3,4-diazidocyclobutenes 16 were prepared from the corresponding dihalides. Some of these diazides, such as parent compound 16 d and phenyl-substituted derivatives 16 c,f, underwent spontaneous stereoselective electrocyclic ring opening below room temperature, whereas the tetraalkyl derivatives of 16 had to be heated to force the same reaction. In most cases, the resulting 1,4-diazidobuta-1,3-dienes 8 were isolated to study their photochemical transformation into bi-2H-azirin-2-yls 9 via intermediate mono-azirines 17. Except for starting materials with a low number of substituents such as 9 d and 9 f, title compounds 9 underwent a thermal valence isomerization which led exclusively to pyridazines 18 at surprisingly low temperatures. Based on quantum-chemical calculations for the parent bi-2H-azirinyl-2-yl 9 d at the UB3LYP/6-31+G(d) and MR-MP2/TZV(2df,2p) levels, the valence isomerization process is best explained by simultaneous homolytic cleavage of both C--N single bonds of 9 to generate energetically favorable N,N' diradicals 26, which cyclize to 18. The theoretical studies indicate also that one stereoisomer of 9, namely, the rac compound, should undergo valence isomerization more easily than the other, which is in conformity with different rates of these rearrangement reactions found experimentally. For the tetramethyl-bi-2H-azirin-2-yls 9 g, which are better models for the experimentally studied compounds, simultaneous homolytic cleavage of both C--N single bonds is also predicted by the calculations, although the intermediate diradicals 26 g are significantly higher in energy than those of the parent system 9 d.

Chemical synthesis of oligodeoxyribonucleotides containing the Dewar valence isomer of the (6–4) photoproduct and their use in (6–4) photolyase studies

The pyrimidine(6–4)pyrimidone photoproduct, a major UV lesion formed between adjacent pyrimidine bases, is transformed to its Dewar valence isomer upon exposure to UVA/UVB light. We have synthesized a phosphoramidite building block of the Dewar photoproduct formed at the thymidylyl(3′–5′)thymidine site and incorporated it into oligodeoxyribonucleotides. The diastereoisomers of the partially protected dinucleoside monophosphate bearing the (6–4) photoproduct, which were caused by the chirality of the phosphorus atom, were separated by reversed-phase chromatography, and the (6–4) photoproduct was converted to the Dewar photoproduct by irradiation of each isomer with Pyrex-filtered light from a high-pressure mercury lamp. The Dewar photoproduct was stable under both acidic and alkaline conditions at room temperature. After characterization of the isomerized base moiety by NMR spectroscopy, a phosphoramidite building block was synthesized in three steps. Although the ordinary method could be used for the oligonucleotide synthesis, benzimidazolium triflate as an alternative activator yielded better results. The oligonucleotides were used for the analysis of the reaction and the binding of Xenopus (6–4) photolyase. Although the affinity of this enzyme for the Dewar photoproduct-containing duplex was reportedly similar to that for the (6–4) photoproduct-containing substrate, the results suggested a difference in the binding mode.

Recent Advances in Metallabenzene Chemistry

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Super-Delocalized Valence Isomer of Coronene

Coronene (1) has been proposed to be "superaromatic", but energetic, geometric, and magnetic criteria of global and local aromaticity fail to support this proposal, and indeed, the calculated current-density map shows opposition of currents: diatropic on the 18-carbon rim and paratropic on the 6-carbon hub. However, [7,5,7,5,7,5]-isocoronene (2) ([7,5,7,5,7,5:6]-circulene, or isocoronene, for short), which is a valence isomer in which alternate pentagons and heptagons replace the hexagons surrounding the central ring, is predicted to have a single, unopposed, intense diatropic perimeter current arising from its four pi HOMO electrons, such as in the ipsocentric description of classically aromatic [4n + 2]-annulenes, hence, qualifying 2 as superaromatic on the magnetic criterion. This conclusion is in excellent agreement with anisotropy of magnetic susceptibility (359 cgs-ppm for isocoronene vs 247 cgs-ppm for coronene) and exaltation of magnetic susceptibility (isocoronene exceeds coronene by 51.4 cgs-ppm). Central and perimeter bond lengths suggest an increased aromaticity of isocoronene. In contrast, the energetic criterion shows that isocoronene is destabilized with respect to coronene by ca. 105 kcal/mol of which only ca. 30 kcal/mol can be attributed to differential strain.

Clar's Sextet Rule Is a Consequence of the σ-Electron Framework

A number of condensed PAHs are examined to identify the underlying reasons governing empirical Clar's rule taking benzene as a limiting case. It is found that the so-called Clar's structures are the only minima on the MP2(fc) potential energy hypersurfaces, meaning that other conceivable valence isomers are nonexistent. The influence of the electron correlation energies to the stability of Clar's structures is substantial with predominating influence of the sigma-electrons. However, the contributions arising from the sigma- and pi-electron correlation energies are approximately the same, if Clar's structures are compared with some artificial pi-electron localized or graphite-like delocalized planar systems. Analysis of the Hartree-Fock (HF) energies provides a compelling evidence that the origin of stability of Clar's structures lies in a decrease of the positive T, V(ee) and V(nn) energy terms relative to some characteristic virtual "delocalized" or "localized" model geometries. Partitioning of the mixed and terms in the sigma- and pi-type contributions, by using the stockholder (SHR), equipartitioning (EQP) and standard pi (SPI) schemes, unequivocally shows that the driving force leading to Clar's structures are more favorable sigma-type interactions. All these conclusions hold for the archetypal benzene too, which could be considered as a limiting Clar system. Finally, the boundaries of Clar's hypothesis and some common misconceptions are briefly discussed. Perusal of the geometric parameters and pi-bond orders reveals that there are no benzene rings completely "vacant" or "fully occupied" by the pi-electrons, envisaged by Clar in his picture of condensed benzenoid compounds. Instead, there are six-membered rings with higher and lower total pi-electron density. The bond length anisotropy of the former rings is smaller. It is concluded that Clar's proposition is a useful rule of thumb providing qualitative information on the stability of the PAH systems, which in turn should not be overinterpreted.