Advertisement

Structural Chemistry

, Volume 29, Issue 3, pp 823–835 | Cite as

Structural analysis and probing the conformational space of dansylamide by means of gas-phase electron diffraction and quantum chemistry

  • Marwan Dakkouri
  • Georgiy Girichev
  • Nina Giricheva
  • Vjacheslav Petrov
  • Valentina Petrova
Original Research
  • 85 Downloads

Abstract

Dansylamide is perhaps the most ubiquitous fluorophore due to its donor-acceptor bifunctionality and its ability to form intra- and intermolecular hydrogen bonding. Among the diversity of its applications is the development of new generation of biosensors for the in vivo monitoring of traces of metals. The structure and conformational stability of dansylamide in the gas phase were investigated for the first time by a combined gas-phase electron diffraction-mass spectrometry (GED/MS), complemented by quantum chemical calculations. GED data indicate that different skewed conformers exist at T = 464 K, which are characterized by the deviation of two S–N bonds from the perpendicular orientation relative to the naphthalene plane. Maybe the most indicative structural parameters for electronic interactions between the donor-acceptor substituents and the aromatic naphthalene and the subsequent stabilization of the favorable skewed eclipsed-syn conformer are the dihedral angles C9–C1–S–N and C10–C5–N–C with the experimentally determined values of 66.8° (32) and 68.1° (72), respectively. The role of –SO2NH2 by forming intramolecular hydrogen bonds was scrutinized by employing the natural bond orbital approach (NBO), quantum theory atoms in molecules (QTAIM), and molecular electrostatic potential (MESP). The non-planarity of the naphthalene skeleton due to the electronic interactions with the substituents and its consequence for the fluorescence activity of dansylamide have been discussed.

Keywords

Structure conformation H-bond NBO QTAIM MESP Ring non-planarity 

Notes

Funding information

M. Dakkouri was supported by the state of Baden-Württemberg through bwHPC and the German Research Foundation (DFG) through grant no. INST 40/467-1 FUGG; G. Girichev is supported by Russian Ministry of Education and Science through grant no. 4.3232.2017/4.6.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11224_2018_1108_MOESM1_ESM.docx (100 kb)
ESM 1 (DOCX 100 kb)

References

  1. 1.
    Liu CY, Guo CW, Chang YF, Wang JT, Shih HW, Hsu YF, Chen CW, Chen SK, Wang YC, Cheng TJ, Ma C, Wong CH, Fang JM, Cheng WC (2010) Synthesis and evaluation of a new fluorescent transglycosylase substrate: lipid II-based molecule possessing a dansyl-C20 Polyprenyl moiety. Org Lett 12:1608–1611CrossRefGoogle Scholar
  2. 2.
    Nyland JF, Bai JJ, Katz HE, Silbergeld EK (2009) In vitro interactions between splenocytes and dansylamide dye-embedded nanoparticles detected by flow cytometry. Nanomedicine 5:298–304CrossRefGoogle Scholar
  3. 3.
    Cao J, Ding L, Hu W, Chen X, Chen X, Yu F (2014) Ternary system based on fluorophore–surfactant assemblies—Cu2+ for highly sensitive and selective detection of arginine in aqueous solution. Langmuir 30:15364–15372CrossRefGoogle Scholar
  4. 4.
    Antolini L, Menabue L, Sola M, Battaglia LP, Corradi AB (1986) The effect of a dansyl group on the co-ordinative ability of N-protected amino acids. Part 2. Binary copper(II) complexes and their pyridine and 2,2′-bipyridine adducts. Crystal and molecular structure of the complexes aquabis(N-dansylglycinato-O)bis(pyridine)copper(II) and (2,2′-bipyridine)(N-dansylglycinato-NO)(methanol)copper(II), and neutral N-dansylglycine. J Chem Soc Dalton Trans 1367-1373Google Scholar
  5. 5.
    Bachechi F, Flieger M, Sinibaldi M (2002) Molecular complexes for the study of enantiodiscriminative processes. Struct Chem 13:41–51CrossRefGoogle Scholar
  6. 6.
    Teng L, Zhang Y, Zhang Sl QY, Xyo X (2009) 5-(1H-Imidazol-1-ylsulfon­yl)-N,N-di­methyl­naphthalen-1-amine. Acta Cryst E65:o55Google Scholar
  7. 7.
    Bhatt P, Govender T, Kruger HG, Maguire GEM (2011) N-Benzyl-5-(di­methyl­amino)­naphthalene-1-sulfonamide. Acta Cryst E67:o2458–o2459Google Scholar
  8. 8.
    Kavallieratos K, Rosenberg JM, Chen WZ, Ren T (2005) Fluorescent sensing and selective Pb(II) extraction by a dansylamide ion-exchanger. J Am Chem Soc 127:6514–6515CrossRefGoogle Scholar
  9. 9.
    Wong WY, Choi KH, Lin Z (2002) Syntheses, structures, and photophysical properties of metal carbonyl clusters with dansyl and acridone luminophores. Eur J Inorg Chem 8:2112–2120CrossRefGoogle Scholar
  10. 10.
    Giricheva NI, Lapykina EA, Fedorov MS, Petrova DA (2015) Fluorescent tags. Dansyl amide (CH3)2N–С10Н6–SO2NH2: reflection of the conformational properties of a free molecule in crystal structures. J Struct Chem 56:619–627CrossRefGoogle Scholar
  11. 11.
    Girichev GV, Utkin AN, Revichev YF (1984) Upgrading the EMR-100 electron diffraction camera for use with gases. Instrum Exp Tech 27:457–461Google Scholar
  12. 12.
    Girichev GV, Shlykov SA, Revichev YF (1986) Apparatus for study of molecular structure of valence-unsaturated compounds. Instrum Exp Tech 29:939–942Google Scholar
  13. 13.
    Girichev EG, Zakharov AV, Girichev GV, Bazanov MI (2000) Physicochemical experiment automatisation: photometry and voltammetry Izv Vys Uch Zav Tekstiln Prom 2:142–146Google Scholar
  14. 14.
    SDBSWeb (2017) http://sdbs.db.aist.go.jp (National Institute of Advanced Industrial Science and Technology
  15. 15.
    Petrov VM, Giricheva NI, Ivanov SN, Petrova VN, Girichev GV (2017) Molecule 1,5-C10H6(SO2Cl)2 as prototype of conformational properties of naphthalene sulfonyl derivatives. J Mol Struct 1132:56–62CrossRefGoogle Scholar
  16. 16.
    Miehlich B, Savin A, Stoll H, Preuss H (1989) Results obtained with the correlation energy density functionals of Becke and Lee, Yang and Parr. Chem Phys Lett 157:200–206CrossRefGoogle Scholar
  17. 17.
    Woon DE, Dunning TH (1993) Gaussian basis set for use in correlated molecular calculations. III The atoms aluminum through argon. J Chem Phys 98:1358–1371CrossRefGoogle Scholar
  18. 18.
    Frisch MJ, Head-Gordon M, Pople JA (1990) A direct MP2 gradient method. Chem Phys Lett 166:275–280CrossRefGoogle Scholar
  19. 19.
    Grimme S (2006) Semiempirical hybrid density functional with perturbative second-order correlation. J Chem Phys 24:034108–034116CrossRefGoogle Scholar
  20. 20.
    Grimme S, Schwabe T (2006) Towards chemical accuracy for the thermodynamics of large molecules: new hybrid density functionals including non-local correlation effects. Phys Chem Chem Phys 8:4398–4401CrossRefGoogle Scholar
  21. 21.
    Glendening ED, Badenhoop JK, Reed AE, Carpenter JE, Bohmann JA, Morales CM, Weinhold F (2001) (Theoretical Chemistry Institute, University of Wisconsin, Madison, WI, http://www.chem.wisc.edu/~nbo5
  22. 22.
    Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected density functional theory. J Comput Chem 32:1456–1465CrossRefGoogle Scholar
  23. 23.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery Jr JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2013) Gaussian 09, Revision D.01. Gaussian, Inc., WallingfordGoogle Scholar
  24. 24.
    Zhurko GA, Zhurko D Chemcraft Program, version 1.6: http://www.chemcraftprog.com
  25. 25.
    Sipachev VA (2001) Local centrifugal distortions caused by internal motions of molecules. J Mol Struct 567-568:67–72CrossRefGoogle Scholar
  26. 26.
    Sipachev VA (1999) In: Advances in molecular structure research, Hargittai, I, Hargittai M (eds) JAI Greenwich, pp 323-371Google Scholar
  27. 27.
    Andersen B, Seip HM, Strand TG, Stolevik R (1969) Procedure and computer programs for the structure determination of gaseous molecules from electron diffraction data. Acta Chem Scand 23:3224–3234CrossRefGoogle Scholar
  28. 28.
    Giricheva NI, Petrov VM, Dakkouri M, Oberhammer H, Petrova VN, Shlykov SA, Ivanov SN, Girichev GV (2015) Structures and intriguing conformational behavior of 1- and 2-naphthalenesulfonamides as determined by gas-phase electron diffraction and computational methods. J Phys Chem A 119:1502–1509CrossRefGoogle Scholar
  29. 29.
    Giricheva NI, Girichev GV, Dakkouri M, Ivanov SN, Petrov VM, Petrova VN (2013) Molecular structure and barriers to internal rotation of α-naphthalenesulfonyl chloride: a study by gas-phase electron diffraction and quantum chemical calculations. Struct Chem 24:819–826CrossRefGoogle Scholar
  30. 30.
    Giricheva NI, Petrov VM, Dakkouri M, Oberhammer H, Petrova VN, Shlykov SA, Ivanov SN, Girichev GV (2013) Interrelation of nonequivalent C-C bonds of naphthalene frame and spatial orientation of substituents: beta-naphthalene sulfonyl fluoride and beta-naphthalene sulfonyl chloride. J Mol Struct 1042:66–72CrossRefGoogle Scholar
  31. 31.
    Campanelli AR, Domenicano A, Ramondo F, Hargittai I (2004) Group electronegativities from benzene ring deformations: a quantum chemical study. J Phys Chem A 108:4940–4948CrossRefGoogle Scholar
  32. 32.
    Campanelli AR, Domenicano A, Ramondo F (2003) Electronegativity, resonance, and steric effects and the structure of monosubstituted benzene rings: an ab initio MO study. J Phys Chem 107:6429–6440CrossRefGoogle Scholar
  33. 33.
    Bader RFW (1990) Atoms in molecules—a quantum theory. Oxford University Press, OxfordGoogle Scholar
  34. 34.
    Bader RFW (1998) In: Schleyer PVR (ed) Encyclopedia of computational chemistry. Wiley, New York Atoms in MoleculesGoogle Scholar
  35. 35.
    Bader RFW (1991) A quantum theory of molecular structure and its applications. Chem Rev 91:893–928CrossRefGoogle Scholar
  36. 36.
    Bader RFW, Essén H (1984) The characterization of atomic interactions. J Chem Phys 80:1943–1960CrossRefGoogle Scholar
  37. 37.
    Frisch Æ, Hratchian HP, Dennington II RD, Todd A, Keith TA, Millam J (2009) GaussView 5. Gaussian, Inc., WallingfordGoogle Scholar
  38. 38.
    Feliks M, Lafaye CL, Shu X, Royant A, Field M (2016) Structural determinants of improved fluorescence in a family of bacteriophytochrome-based infrared fluorescent proteins: insights from continuum electrostatic calculations and molecular dynamics simulations. Biochemist 55:4263–4274CrossRefGoogle Scholar
  39. 39.
    Nijegorodov N, Luhanga PVC, Nkoma JS, Winkoun DP (2006) The influence of planarity, rigidity and internal heavy atom upon fluorescence parameters and the intersystem crossing rate constant in molecules with the biphenyl basis. Spectrochimica Acta Part A 64:1–5CrossRefGoogle Scholar
  40. 40.
    Nijegorodov NI, Downey WS (1994) The influence of planarity and rigidity on the absorption and fluorescence parameters and intersystem crossing rate constant in aromatic molecules. J Phys Chem 98:5639–5643CrossRefGoogle Scholar
  41. 41.
    Aoki S, Tomiyama Y, Kegeyama Y, Yamada Y, Shiro M, Kimura E (2009) Photolysis of the sulfonamide bond of metal complexes of N-dansyl-1,4,7,10-tetraazacyclododecane in aqueous solution: a mechanistic study and application to the photorepair of cis,syn-cyclobutane thymine photodimer. Chem Asian J 4:561–573CrossRefGoogle Scholar
  42. 42.
    Balzani V, Bergamini G, Ceroni P, Vögtle F (2007) Electronic spectroscopy of metal complexes with dendritic ligands. Coord Chem Rev 251:525–535CrossRefGoogle Scholar
  43. 43.
    Lowe MP, Parker D (2001) pH switched sensitisation of europium(III) by a dansyl group. Inorg Chem Acta 317:163–173CrossRefGoogle Scholar
  44. 44.
    Chen QY, Chen CF (2005) A new Hg2+-selective fluorescent sensor based on a dansyl amide-armed calix[4]-aza-crown. Tetrahedron Lett 46:165–168CrossRefGoogle Scholar
  45. 45.
    Holmes-Farley SR, Whitesides GM (1986) Fluorescence properties of dansyl groups covalently bonded to the surface of oxidatively functionalized low-density polyethylene film. Langmuir 2:266–282CrossRefGoogle Scholar
  46. 46.
    Nair SK, Elbaum D, Christianso DW (1996) Unexpected binding mode of the sulfonamide fluorophore 5-dimethylamino-1-naphthalene sulfonamide to human carbonic anhydrase II. Implications for the development of a zinc biosensor. J Biol Chem 271:1003–1007CrossRefGoogle Scholar
  47. 47.
    Kimura E, Aoki S (2001) Chemistry of zinc(II) fluorophore sensors. Biometals 14:191–204CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of ElectrochemistryUniversity of UlmUlmGermany
  2. 2.Ivanovo State University of Chemistry and TechnologyIvanovoRussia
  3. 3.Ivanovo State UniversityIvanovoRussia

Personalised recommendations