1 3
Top Curr Chem (Z) (2018) 376:24
42. Zimmermann T, Vanicek J (2014) Efficient on-the-fly ab initio semiclassical method for computing
time-resolved nonadiabatic electronic spectra with surface hopping or Ehrenfest dynamics. J Chem
Phys 141(13):134102
43. Tempelaar R, van der Vegte CP, Knoester J, Jansen TLC (2013) Surface hopping modeling of twodimensional spectra. J Chem Phys 138(16):164106
44. Richter M, Fingerhut BP (2016) Simulation of multi-dimensional signals in the optical
domain: quantum-classical feedback in nonlinear exciton propagation. J Chem Theory Comput
12(7):3284–3294
45. Petit AS, Subotnik JE (2014) Calculating time-resolved differential absorbance spectra for ultrafast
pump-probe experiments with surface hopping trajectories. J Chem Phys 141(15):154108
46. Mukamel S (1983) Non-impact unified theory of 4-wave mixing and 2-photon processes. Phys Rev
A 28(6):3480–3492
47. Abramavicius D, Valkunas L, Mukamel S (2007) Transport and correlated fluctuations in the nonlinear optical response of excitons. Epl 80(1):17005
48. Jiang J, Mukamel S (2010) Two-dimensional ultraviolet (2DUV) spectroscopic tools for identifying fibrillation propensity of protein residue sequences. Angew Chem Int Ed 49(50):9666–9669
49. Stuhldreier MC, Temps F (2013) Ultrafast photo-initiated molecular quantum dynamics in the
DNA dinucleotide d(apg) revealed by broadband transient absorption spectroscopy. Faraday Discuss 163:173–188; discussion 243–175
50. Ostroumov EE, Mulvaney RM, Cogdell RJ, Scholes GD (2013) Broadband 2D electronic spectroscopy reveals a carotenoid dark state in purple bacteria. Science 340(6128):52–56
51. Dean JC, Rafiq S, Oblinsky DG, Cassette E, Jumper CC, Scholes GD (2015) Broadband transient absorption and two-dimensional electronic spectroscopy of methylene blue. J Phys Chem A
119(34):9098–9108
52. Rivalta I, Nenov A, Cerullo G, Mukamel S, Garavelli M (2014) Ab initio simulations of twodimensional electronic spectra: The SOS//QM/MM approach. Int J Quantum Chem 114(2):85–93
53. Nenov A, Rivalta I, Mukamel S, Garavelli M (2014) Bidimensional electronic spectroscopy on
indole in gas phase and in water from first principles. Comput Theor Chem 1040:295–303
54. Nenov A, Beccara SA, Rivalta I, Cerullo G, Mukamel S, Garavelli M (2014) Tracking conformational dynamics of polypeptides by nonlinear electronic spectroscopy of aromatic residues: a firstprinciples simulation study. ChemPhysChem 15(15):3282–3290
55. Nenov A, Segarra-Marti J, Giussani A, Conti A, Rivalta I, Dumont E, Jaiswal VK, Altavilla SF,
Mukamel S, Garavelli M (2015) Probing deactivation pathways of DNA nucleobases by twodimensional electronic spectroscopy: First principles simulations. Faraday Discuss 177:345–362
56. Rivalta I, Nenov A, Weingart O, Cerullo G, Garavelli M, Mukamel S (2014) Modelling timeresolved two-dimensional electronic spectroscopy of the primary photoisomerization event in rhodopsin. J Phys Chem B 118(28):8396–8405
57. Nenov A, Giussani A, Segarra-Martí J, Jaiswal VK, Rivalta I, Cerullo G, Mukamel S, Garavelli
M (2015) Modeling the high-energy electronic state manifold of adenine: calibration for nonlinear
electronic spectroscopy. J Chem Phys 142(21):212443
58. Nenov A, Mukamel S, Garavelli M, Rivalta I (2015) Two-dimensional electronic spectroscopy of
benzene, phenol, and their dimer: an efficient first-principles simulation protocol. J Chem Theory
Comput 11(8):3755–3771
59. Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Tolomelli A, Mukamel S, Garavelli M (2016)
Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra. Theor Chem Acc 135(5):1–18
60. Li Q, Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Voityuk AA, Mukamel S, Roca-Sanjuán D, Garavelli M, Blancafort L (2016) Multiple decay mechanisms and 2D-UV spectroscopic fingerprints of singlet excited solvated adenine-uracil monophosphate. Chem—A Eur J
22(22):7497–7507
61. Segarra-Marti J, Jaiswal VK, Pepino AJ, Giussani A, Nenov A, Mukamel S, Garavelli M, Rivalta I
(2018) Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in
DNA/RNA aggregates. Faraday Discuss 207:233–250
62. Kim J, Mukamel S, Scholes GD (2009) Two-dimensional electronic double-quantum coherence
spectroscopy. Acc Chem Res 42(9):1375–1384
63. Li Z, Abrarnavicius D, Mukamel S (2008) Probing electron correlations in molecules by twodimensional coherent optical spectroscopy. J Am Chem Soc 130(11):3509–3515
109
Reprinted from the journal
Top Curr Chem (Z) (2018) 376:24
42. Zimmermann T, Vanicek J (2014) Efficient on-the-fly ab initio semiclassical method for computing
time-resolved nonadiabatic electronic spectra with surface hopping or Ehrenfest dynamics. J Chem
Phys 141(13):134102
43. Tempelaar R, van der Vegte CP, Knoester J, Jansen TLC (2013) Surface hopping modeling of twodimensional spectra. J Chem Phys 138(16):164106
44. Richter M, Fingerhut BP (2016) Simulation of multi-dimensional signals in the optical
domain: quantum-classical feedback in nonlinear exciton propagation. J Chem Theory Comput
12(7):3284–3294
45. Petit AS, Subotnik JE (2014) Calculating time-resolved differential absorbance spectra for ultrafast
pump-probe experiments with surface hopping trajectories. J Chem Phys 141(15):154108
46. Mukamel S (1983) Non-impact unified theory of 4-wave mixing and 2-photon processes. Phys Rev
A 28(6):3480–3492
47. Abramavicius D, Valkunas L, Mukamel S (2007) Transport and correlated fluctuations in the nonlinear optical response of excitons. Epl 80(1):17005
48. Jiang J, Mukamel S (2010) Two-dimensional ultraviolet (2DUV) spectroscopic tools for identifying fibrillation propensity of protein residue sequences. Angew Chem Int Ed 49(50):9666–9669
49. Stuhldreier MC, Temps F (2013) Ultrafast photo-initiated molecular quantum dynamics in the
DNA dinucleotide d(apg) revealed by broadband transient absorption spectroscopy. Faraday Discuss 163:173–188; discussion 243–175
50. Ostroumov EE, Mulvaney RM, Cogdell RJ, Scholes GD (2013) Broadband 2D electronic spectroscopy reveals a carotenoid dark state in purple bacteria. Science 340(6128):52–56
51. Dean JC, Rafiq S, Oblinsky DG, Cassette E, Jumper CC, Scholes GD (2015) Broadband transient absorption and two-dimensional electronic spectroscopy of methylene blue. J Phys Chem A
119(34):9098–9108
52. Rivalta I, Nenov A, Cerullo G, Mukamel S, Garavelli M (2014) Ab initio simulations of twodimensional electronic spectra: The SOS//QM/MM approach. Int J Quantum Chem 114(2):85–93
53. Nenov A, Rivalta I, Mukamel S, Garavelli M (2014) Bidimensional electronic spectroscopy on
indole in gas phase and in water from first principles. Comput Theor Chem 1040:295–303
54. Nenov A, Beccara SA, Rivalta I, Cerullo G, Mukamel S, Garavelli M (2014) Tracking conformational dynamics of polypeptides by nonlinear electronic spectroscopy of aromatic residues: a firstprinciples simulation study. ChemPhysChem 15(15):3282–3290
55. Nenov A, Segarra-Marti J, Giussani A, Conti A, Rivalta I, Dumont E, Jaiswal VK, Altavilla SF,
Mukamel S, Garavelli M (2015) Probing deactivation pathways of DNA nucleobases by twodimensional electronic spectroscopy: First principles simulations. Faraday Discuss 177:345–362
56. Rivalta I, Nenov A, Weingart O, Cerullo G, Garavelli M, Mukamel S (2014) Modelling timeresolved two-dimensional electronic spectroscopy of the primary photoisomerization event in rhodopsin. J Phys Chem B 118(28):8396–8405
57. Nenov A, Giussani A, Segarra-Martí J, Jaiswal VK, Rivalta I, Cerullo G, Mukamel S, Garavelli
M (2015) Modeling the high-energy electronic state manifold of adenine: calibration for nonlinear
electronic spectroscopy. J Chem Phys 142(21):212443
58. Nenov A, Mukamel S, Garavelli M, Rivalta I (2015) Two-dimensional electronic spectroscopy of
benzene, phenol, and their dimer: an efficient first-principles simulation protocol. J Chem Theory
Comput 11(8):3755–3771
59. Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Tolomelli A, Mukamel S, Garavelli M (2016)
Spectroscopic fingerprints of DNA/RNA pyrimidine nucleobases in third-order nonlinear electronic spectra. Theor Chem Acc 135(5):1–18
60. Li Q, Giussani A, Segarra-Martí J, Nenov A, Rivalta I, Voityuk AA, Mukamel S, Roca-Sanjuán D, Garavelli M, Blancafort L (2016) Multiple decay mechanisms and 2D-UV spectroscopic fingerprints of singlet excited solvated adenine-uracil monophosphate. Chem—A Eur J
22(22):7497–7507
61. Segarra-Marti J, Jaiswal VK, Pepino AJ, Giussani A, Nenov A, Mukamel S, Garavelli M, Rivalta I
(2018) Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in
DNA/RNA aggregates. Faraday Discuss 207:233–250
62. Kim J, Mukamel S, Scholes GD (2009) Two-dimensional electronic double-quantum coherence
spectroscopy. Acc Chem Res 42(9):1375–1384
63. Li Z, Abrarnavicius D, Mukamel S (2008) Probing electron correlations in molecules by twodimensional coherent optical spectroscopy. J Am Chem Soc 130(11):3509–3515
109
Reprinted from the journal