title: Monitoring Non-Adiabatic Dynamics of the RNA Base Uracil by UV-Pump-IR-Probe Spectroscopy.
abstract: Resolving the excited state dynamics of DNA- and RNA- nucleobases has attracted considerably attention. UV irradiation of the isolated nucleobases leads to the population of an electronic excited state which is quenched by internal conversion mediated by conical intersections on an ultrafast timescale. We present non-adiabatic on-the-fly molecular dynamics simulations of the UV-pump-IR-probe signal of the pyrimidine nucleobase uracil using a novel semiclassical protocol which takes into account the path integral over the excited state vibrational dynamics and properly describes the joint temporal and spectral resolution of the technique. Simulations of vibrational motions of carbonyl fingerprint modes in the electronically excited states reveal clear signatures of different relaxation pathways on a timescale of hundreds of femtoseconds which arise from an ultrafast branching in the excited state. We show that the inherent temporal and spectral resolution of the technique is not purely instrumental but also depends on the vibrational fluctuation timescale.
authors.affiliation: Chemistry Department, University of California, Irvine, California 92697-2025, USA.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Fingerhut
authors.forename: Konstantin E
authors.initials: KE
authors.lastname: Dorfman
authors.forename: Shaul
authors.initials: S
authors.lastname: Mukamel
keywords: DNA; excited states; non-adiabatic on-the-fly dynamics; time-resolved IR spectroscopy
references.citation: J Am Chem Soc. 2010 Sep 1;132(34):11834-5
references.pmid: 20698570
references.citation: Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10196-10201
references.pmid: 16803961
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21453-8
references.pmid: 21115845
references.citation: Chem Phys. 2008 May 23;347(1-3):383-392
references.pmid: 19936322
references.citation: Annu Rev Phys Chem. 2007;58:461-88
references.pmid: 17105414
references.citation: Nature. 2006 Jun 8;441(7094):E7; discussion E8
references.pmid: 16760929
references.citation: Angew Chem Int Ed Engl. 2008;47(47):9044-8
references.pmid: 18932183
references.citation: Phys Chem Chem Phys. 2010 May 21;12(19):5007-15
references.pmid: 20407677
references.citation: Annu Rev Phys Chem. 2009;60:217-39
references.pmid: 19012538
references.citation: Opt Lett. 2010 Dec 15;35(24):4178-80
references.pmid: 21165129
references.citation: J Phys Chem A. 2008 Nov 27;112(47):11965-8
references.pmid: 18959396
references.citation: J Am Chem Soc. 2005 Dec 28;127(51):18100-6
references.pmid: 16366562
references.citation: Opt Express. 2013 Jan 28;21(2):2118-25
references.pmid: 23389192
references.citation: J Chem Phys. 2010 Jun 14;132(22):224501
references.pmid: 20550402
references.citation: J Am Chem Soc. 2004 Mar 3;126(8):2262-3
references.pmid: 14982403
references.citation: J Am Chem Soc. 2009 Apr 15;131(14):5038-9
references.pmid: 19309140
references.citation: Phys Rev Lett. 2010 Nov 19;105(21):217401
references.pmid: 21231351
references.citation: J Am Chem Soc. 2006 Jan 18;128(2):607-19
references.pmid: 16402849
references.citation: Nature. 1976 Apr 22;260(5553):679-83
references.pmid: 1264239
references.citation: J Chem Phys. 2005 Feb 15;122(7):074316
references.pmid: 15743241
references.citation: J Am Chem Soc. 2002 Jun 19;124(24):6818-9
references.pmid: 12059190
references.citation: Angew Chem Int Ed Engl. 2012 Jan 9;51(2):408-11
references.pmid: 22109845
references.citation: New J Phys. 2013 Feb 1;15:
references.pmid: 24223491
references.citation: Science. 2009 Dec 18;326(5960):1690-4
references.pmid: 19965381
references.citation: Opt Lett. 2004 Dec 1;29(23):2701-3
references.pmid: 15605477
references.citation: J Phys Chem Lett. 2012 Sep 20;3(18):2575-81
references.pmid: 26295877
references.citation: Phys Chem Chem Phys. 2013 Aug 7;15(29):12348-59
references.pmid: 23783120
references.citation: J Phys Chem A. 2009 Sep 24;113(38):10211-8
references.pmid: 19722485
references.citation: J Chem Phys. 2012 May 28;136(20):204307
references.pmid: 22667560
references.citation: J Chem Phys. 2011 Apr 28;134(16):161101
references.pmid: 21528943
references.citation: J Phys Chem A. 2012 Mar 22;116(11):2654-61
references.pmid: 22074393
references.citation: Science. 2005 Oct 7;310(5745):83-6
references.pmid: 16210532
references.citation: Science. 1995 Aug 18;269(5226):962-6
references.pmid: 7638619
references.citation: J Phys Chem A. 2007 Aug 30;111(34):8500-8
references.pmid: 17685594
references.citation: Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):435-40
references.pmid: 17197421
references.citation: Proc Natl Acad Sci U S A. 1989 Nov;86(21):8387-91
references.pmid: 2554314
references.citation: Science. 2007 Feb 2;315(5812):625-9
references.pmid: 17272716
references.citation: Chem Rev. 2004 Apr;104(4):1977-2019
references.pmid: 15080719
references.citation: J Am Chem Soc. 2005 May 4;127(17):6257-65
references.pmid: 15853331
references.citation: Nature. 2005 Aug 25;436(7054):1141-4
references.pmid: 16121177
references.citation: J Phys Chem A. 2011 Jun 2;115(21):5247-55
references.pmid: 21548626
references.citation: J Phys Chem B. 2009 Mar 19;113(11):3548-55
references.pmid: 19239209