Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations.

نویسندگان

  • Artur Nenov
  • Javier Segarra-Martí
  • Angelo Giussani
  • Irene Conti
  • Ivan Rivalta
  • Elise Dumont
  • Vishal K Jaiswal
  • Salvatore Flavio Altavilla
  • Shaul Mukamel
  • Marco Garavelli
چکیده

The SOS//QM/MM [Rivalta et al., Int. J. Quant. Chem., 2014, 114, 85] method consists of an arsenal of computational tools allowing accurate simulation of one-dimensional (1D) and bi-dimensional (2D) electronic spectra of monomeric and dimeric systems with unprecedented details and accuracy. Prominent features like doubly excited local and excimer states, accessible in multi-photon processes, as well as charge-transfer states arise naturally through the fully quantum-mechanical description of the aggregates. In this contribution the SOS//QM/MM approach is extended to simulate time-resolved 2D spectra that can be used to characterize ultrafast excited state relaxation dynamics with atomistic details. We demonstrate how critical structures on the excited state potential energy surface, obtained through state-of-the-art quantum chemical computations, can be used as snapshots of the excited state relaxation dynamics to generate spectral fingerprints for different de-excitation channels. The approach is based on high-level multi-configurational wavefunction methods combined with non-linear response theory and incorporates the effects of the solvent/environment through hybrid quantum mechanics/molecular mechanics (QM/MM) techniques. Specifically, the protocol makes use of the second-order Perturbation Theory (CASPT2) on top of Complete Active Space Self Consistent Field (CASSCF) strategy to compute the high-lying excited states that can be accessed in different 2D experimental setups. As an example, the photophysics of the stacked adenine-adenine dimer in a double-stranded DNA is modeled through 2D near-ultraviolet (NUV) spectroscopy.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Design of Biosensors Based Transition-Metal Dichalcogenide for DNA-base Detection: A First-Principles Density Functional Theory Study

The main function purpose of nanobiosensors is to sense a biologically specific material and the kind of sensing platform and doping engineering has been an emerging topic and plays an important role in monolayer molybdenum disulfide (mMoS2). In this paper, we theoretically reveal the electronic structures of mMoS2 doped by 3d transition metals. Furthermore, adsorption of nucleic acid [Adenine ...

متن کامل

Tracking conformational dynamics of polypeptides by nonlinear electronic spectroscopy of aromatic residues: a first-principles simulation study.

The ability of nonlinear electronic spectroscopy to track folding/unfolding processes of proteins in solution by monitoring aromatic interactions is investigated by first-principles simulations of two-dimensional (2D) electronic spectra of a model peptide. A dominant reaction pathway approach is employed to determine the unfolding pathway of a tetrapeptide, which connects the initial folded con...

متن کامل

Relaxation mechanisms of UV-photoexcited DNA and RNA nucleobases.

A comprehensive effort in photodynamical ab initio simulations of the ultrafast deactivation pathways for all five nucleobases adenine, guanine, cytosine, thymine, and uracil is reported. These simulations are based on a complete nonadiabatic surface-hopping approach using extended multiconfigurational wave functions. Even though all five nucleobases share the basic internal conversion mechanis...

متن کامل

Excited states dynamics of DNA and RNA bases: characterization of a stepwise deactivation pathway in the gas phase.

Radiationless deactivation pathways of excited gas phase nucleobases were investigated using mass-selected femtosecond resolved pump-probe resonant ionization. By comparison between nucleobases and methylated species, in which tautomerism cannot occur, we can access intrinsic mechanisms at a time resolution never reported so far (80 fs). At this time resolution, and using appropriate substituti...

متن کامل

Probing nucleobase photoprotection with soft x-rays

Nucleobases absorb strongly in the ultraviolet region, leading to molecular excitation into reactive states. The molecules avoid the photoreactions by funnelling the electronic energy into less reactive states on an ultrafast timescale via non-BornOppenheimer dynamics. Current theory on the nucleobase thymine discusses two conflicting pathways for the photoprotective dynamics. We present our fi...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • Faraday discussions

دوره 177  شماره 

صفحات  -

تاریخ انتشار 2015