Display options
Cite
Macchiagodena M, Del Frate G, Brancato G, et al. Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations. Phys Chem Chem Phys. 2017;19(45):30590-30602doi: 10.1039/c7cp04688j.
Macchiagodena, M., Del Frate, G., Brancato, G., Chandramouli, B., Mancini, G., & Barone, V. (2017). Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations. Physical chemistry chemical physics : PCCP, 19(45), 30590-30602. https://doi.org/10.1039/c7cp04688j
Macchiagodena, Marina, et al. "Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations." Physical chemistry chemical physics : PCCP vol. 19,45 (2017): 30590-30602. doi: https://doi.org/10.1039/c7cp04688j
Macchiagodena M, Del Frate G, Brancato G, Chandramouli B, Mancini G, Barone V. Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations. Phys Chem Chem Phys. 2017 Nov 22;19(45):30590-30602. doi: 10.1039/c7cp04688j. PMID: 29115317; PMCID: PMC5886372.
Copy Download .nbib Format: NLM
Share it on

Phys Chem Chem Phys. 2017 Nov 22;19(45):30590-30602. doi: 10.1039/c7cp04688j.

Computational study of the DPAP molecular rotor in various environments: from force field development to molecular dynamics simulations and spectroscopic calculations.

Physical chemistry chemical physics : PCCP

Marina Macchiagodena, Gianluca Del Frate, Giuseppe Brancato, Balasubramanian Chandramouli, Giordano Mancini, Vincenzo Barone

Affiliations

  1. Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. [email protected] [email protected].

PMID: 29115317 PMCID: PMC5886372 DOI: 10.1039/c7cp04688j

Abstract

Fluorescent molecular rotors (FMRs) belong to an important class of environment-sensitive dyes capable of acting as nanoprobes in the measurement of viscosity and polarity of their micro-environment. FMRs have found widespread applications in various research fields, ranging from analytical to biochemical sciences, for example in intracellular imaging studies or in volatile organic compound detection. Here, a computational investigation of a recently proposed FMR, namely 4-(diphenylamino)phthalonitrile (DPAP), in various chemical environments is presented. A purposely developed molecular mechanics force field is proposed and then applied to simulate the rotor in a high- and low-polar solvent (i.e., acetonitrile, tetrahydrofuran, o-xylene and cyclohexane), a polymer matrix and a lipid membrane. Subtle effects of the molecular interactions with the embedding medium, the structural fluctuations of the rotor and its rotational dynamics are analyzed in some detail. The results correlate with a previous work, thus supporting the reliability of the model, and provide further insights into the environment-specific properties of the dye. In particular, it is shown how molecular diffusion and rotational correlation times of the FMR are affected by the surrounding medium and how the molecular orientation of the dye becomes anisotropic once immersed in the lipid bilayer. Moreover, a qualitative correlation between the FMR rotational dynamics and the fluorescence lifetime is detected, a result in line with the observed viscosity dependence of its emission. Finally, optical absorption spectra are computed and successfully compared with their experimental counterparts.

References

  1. Phys Chem Chem Phys. 2013 Mar 21;15(11):3736-51 - PubMed
  2. Biophys J. 2001 Aug;81(2):643-58 - PubMed
  3. Biochemistry. 1989 Aug 8;28(16):6678-86 - PubMed
  4. J Am Chem Soc. 2010 Feb 3;132(4):1276-88 - PubMed
  5. J Chem Phys. 2008 Feb 7;128(5):054504 - PubMed
  6. Bioinformatics. 2013 Apr 1;29(7):845-54 - PubMed
  7. J Comput Chem. 2004 Jul 15;25(9):1157-74 - PubMed
  8. J Chem Theory Comput. 2012 Feb 14;8(2):527-41 - PubMed
  9. Chem Rev. 2009 Jan;109(1):190-212 - PubMed
  10. J Comput Chem. 2010 Mar;31(4):671-90 - PubMed
  11. Chem Rev. 2010 Nov 10;110(11):6595-663 - PubMed
  12. Biophys Chem. 2016 Jan;208:17-25 - PubMed
  13. J Phys Chem B. 2011 Aug 25;115(33):9980-9 - PubMed
  14. Phys Chem Chem Phys. 2012 Oct 5;14(37):12671-86 - PubMed
  15. J Chem Phys. 2007 Jan 7;126(1):014101 - PubMed
  16. J Phys Chem B. 2005 Nov 24;109(46):21954-62 - PubMed
  17. Chemphyschem. 2006 Jan 16;7(1):148-56 - PubMed
  18. Bioorg Chem. 2005 Dec;33(6):415-25 - PubMed
  19. Chem Commun (Camb). 2014 Nov 4;50(85):12955-8 - PubMed
  20. Phys Chem Chem Phys. 2016 Apr 14;18(14 ):9724-33 - PubMed
  21. Am J Physiol Heart Circ Physiol. 2002 May;282(5):H1609-14 - PubMed
  22. Phys Chem Chem Phys. 2013 Sep 28;15(36):14986-93 - PubMed
  23. J Fluoresc. 2015 Nov;25(6):1671-9 - PubMed
  24. Chem Rev. 2010 May 12;110(5):2579-619 - PubMed
  25. J Phys Chem B. 2015 May 21;119(20):6144-54 - PubMed
  26. J Chem Inf Model. 2011 Aug 22;51(8):2007-23 - PubMed
  27. Chemphyschem. 2016 Jul 4;17 (13):2043-55 - PubMed
  28. J Comput Chem. 2003 Apr 30;24(6):669-81 - PubMed
  29. J Chem Theory Comput. 2011 Aug 9;7(8):2498-506 - PubMed
  30. J Biol Eng. 2010 Sep 15;4:11 - PubMed
  31. Int Rev Cytol. 2000;192:189-221 - PubMed
  32. J Chem Theory Comput. 2009 Jan 13;5(1):192-9 - PubMed
  33. J Chem Theory Comput. 2008 May;4(5):751-64 - PubMed
  34. Biophys J. 2009 Jul 8;97(1):50-8 - PubMed
  35. Biochim Biophys Acta. 2011 Oct;1808(10):2608-17 - PubMed

Publication Types

Grant support