Jaroslaw J. Szymczak

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 mechanisms, the calculations show a distinct grouping into purine and pyrimidine bases as concerns the complexity of the photodynamics. The purine bases adenine and guanine represent the most simple photodeactivation mechanism with the dynamics leading along a diabatic ππ* path directly and without barrier to the conical intersection seam with the ground state. In the case of the pyrimidine bases, the dynamics starts off in much flatter regions of the ππ* energy surface due to coupling of several states. This fact prohibits a clear formation of a single reaction path. Thus, the photodynamics of the pyrimidine bases is much richer and includes also nπ* states with varying importance, depending on the actual nucleobase considered. Trapping in local minima may occur and, therefore, the deactivation time to the ground state is also much longer in these cases. Implications of these findings are discussed (i) for identifying structural possibilities where singlet/triplet transitions can occur because of sufficient retention time during the singlet dynamics and (ii) concerning the flexibility of finding other deactivation pathways in substituted pyrimidines serving as candidates for alternative nucleobases.

Critical appraisal of excited state nonadiabatic dynamics simulations of 9H-adenine

In spite of the importance of nonadiabatic dynamics simulations for the understanding of ultrafast photo-induced phenomena, simulations based on different methodologies have often led to contradictory results. In this work, we proceed through a comprehensive investigation of on-the-fly surface-hopping simulations of 9H-adenine in the gas phase using different electronic structure theories (ab initio, semi-empirical, and density functional methods). Simulations that employ ab initio and semi-empirical multireference configuration interaction methods predict the experimentally observed ultrafast deactivation of 9H-adenine with similar time scales, however, through different internal conversion channels. Simulations based on time-dependent density functional theory with six different hybrid and range-corrected functionals fail to predict the ultrafast deactivation. The origin of these differences is analyzed by systematic calculations of the relevant reaction pathways, which show that these discrepancies can always be traced back to topographical features of the underlying potential energy surfaces.

Photodynamics Simulations of Thymine: Relaxation into the First Excited Singlet State†

Ab initio nonadiabatic dynamics simulations are reported for thymine with focus on the S(2) --> S(1) deactivation using the state-averaged CASSCF method. Supporting calculations have been performed on vertical excitations, S(1) and S(2) minima, and minima on the crossing seam using the MS-CASPT2, RI-CC2, MR-CIS, and MR-CISD methods. The photodynamical process starts with a fast (<100 fs) planar relaxation from the S(2) pipi* state into the pi(O)pi* minimum of the S(2) state. The calculations demonstrate that two pi-excited states (denoted pipi* and pi(O)pi*) are actually involved in this stage. The time in reaching the S(2)/S(1) intersections, through which thymine can deactivate to S(1), is delayed by both the change in character between the states as well as the flatness of the S(2) surface. This deactivation occurs in an average time of 2.6 ps at the lowest-energy region of the crossing seam. After that, thymine relaxes to the npi* minimum of the S(1) state, where it remains until the transfer to the ground state takes place. The present dynamics simulations show that not only the pi(O)pi* S(2) trapping but also the trapping in the npi* S(1) minimum contribute to the elongation of the excited-state lifetime of thymine.

Nonadiabatic dynamics of uracil: population split among different decay mechanisms.

Nonadiabatic dynamics simulations performed at the state-averaged CASSCF method are reported for uracil. Supporting calculations on stationary points and minima on the crossing seams have been performed at the MR-CISD and CASPT2 levels. The dominant mechanism is characterized by relaxation into the S(2) minimum of ππ* character followed by the relaxation to the S(1) minimum of nπ* character. This mechanism contributes to the slower relaxation with a decay constant larger than 1.5 ps, in good agreement with the long time constants experimentally observed. A minor fraction of trajectories decay to the ground state with a time constant of about 0.7 ps, which should be compared to the experimentally observed short constant. The major part of trajectories decaying with this time constant follows the ππ* channel and hops to the ground state via an ethylenic conical intersection. A contribution of the relaxation proceeding via a ring-opening conical intersection was also observed. The existence of these two latter channels together with a reduced long time constant is responsible for a significantly shorter lifetime of uracil compared to that of thymine.

The decay mechanism of photoexcited guanine − A nonadiabatic dynamics study

Ab initio surface hopping dynamics calculations were performed for the biologically relevant tautomer of guanine in gas phase excited into the first ππ∗ state. The results show that the complete population of UV-excited molecules returns to the ground state following an exponential decay within ∼220 fs. This value is in good agreement with the experimentally obtained decay times of 148 and 360 fs. No fraction of the population remains trapped in the excited states. The internal conversion occurs in the ππ∗ state at two related types of conical intersections strongly puckered at the C2 atom. Only a small population of about 5% following an alternative pathway via a nπ∗ state was found in the dynamics.

Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process?

Nonadiabatic photodynamical simulations are presented for the all-trans and 5-cis isomers of the hepta-3,5,7-trieniminium cation (PSB4) with the goal of characterizing the types of torsional modes occurring in the cis-trans isomerization processes in retinal protonated Schiff base (RPSB), the rhodopsin and bacteriorhodopsin chropomhore. Steric hindrance of these processes due to environmental effects have been modeled by imposing different sets of mechanical restrictions on PSB4 and studying its response in the photodynamics. Both the mechanism toward the conical intersection and the initial phase of the hot ground state dynamics has been studied in detail. A total of 600 trajectories have been computed using a complete active space self-consistent field wave function. Careful comparison with higher level methods has been made in order to verify the accuracy of the results. The most important mechanism driving restricted PSB4 isomerization in the excited state is characterized by two concerted twist motions (bipedal and closely related to it nonrigid bipedal) from which only one torsion tends to be continued during the relaxation into the ground state. The one-bond-flip is found to be important for the trans isomer as well. The main isomerization trend is a torsion around C(5)C(6) (equivalent to C(11)C(12) in RPSB) in the case of the cis isomer and around C(3)C(4) (C(13)C(14) in RPSB) in the case of the trans isomer. The simulations show an initial 70 fs relaxation into twisted regions and give an average internal conversion time of 130-140 fs, timings that are fully compatible with the general picture described by femtosecond transient absorption spectroscopic studies.

Mechanism of Ultrafast Photodecay in Restricted Motions in Protonated Schiff Bases: The Pentadieniminium Cation

Ab initio surface-hopping dynamics simulations for the trans-penta-3,5-dieniminium cation (PSB3) are presented imposing different sets of mechanical restrictions in order to investigate the response of the molecular system to certain environmental degrees of hindrance. A general scheme for classification of photoisomerization mechanisms in conjugated chains based on the analysis of torsional angles is proposed allowing direct characterization of the different isomerization mechanisms proposed previously. On the basis of a statistical analysis of 300 trajectories a new photoisomerization mechanism-the Folding Table-was found. This mechanism and the One-Bond-Flip are almost entirely responsible for the photoisomerization process in PSB3.

Molecular properties of protonated homogeneous and mixed carbon oxide and carbon dioxide clusters

The molecular structures and characteristics of CO and CO2 protonated homogeneous and mixed complexes were studied by theoretical, ab initio calculations. The thermodynamics, vibrational properties, charge distribution, and interaction energy decomposition components are investigated as a function of the increasing size of clusters. The study reveals the similarities and differences between homogeneous protonated carbon oxide and protonated carbon dioxide clusters. In the first-order approximation the structural differences between (CO)nH+ and (CO2)nH+ clusters are the consequence of the electronic charge distribution in the protonated OCH+ and OCOH+ core fragments. The symmetry of protonated dimers, constituting the cationic core of clusters is the second important factor in determining the overall structure of extended complexes. The OCH+ as well as the OCOH+ fragments are stabilized by cluster formation. The structures and energetics of complexes emerge as a balance between competing electrostatic, exc...

Model Systems for Dynamics of π-Conjugated Biomolecules in Excited States

Mixed-quantum classical dynamics simulations have recently become an important tool for investigations of time-dependent properties of electronically excited molecules, including non-adiabatic effects occurring during internal conversion processes. The high computational costs involved in such simulations have often led to simulation of model compounds instead of the full biochemical system. This chapter reviews recent dynamics results obtained for models of three classes of biologically relevant systems: protonated Schiff base chains as models for the chromophore of Rhodopsin proteins ; nucleobases and heteroaromatic rings as models for UV-excited nucleic acids ; and formamide as a model for photoexcited peptide bonds

Atomistic simulations of reactive processes in the gas- and condensed-phase

This review focuses on force-field-based approaches to investigate – through computer simulations – reactive processes in chemical and biological systems. Both, reactions in the gas-phase and in condensed-phase environments are discussed and opportunities and the potential for further developments are pointed out. Where available, results are compared with alternative methods and the advantages and drawbacks of the methods are compared. Particular applications include vibrationally and electronically induced (photo)dissociation of small molecules, proton transfer in the gas- and condensed phase and ligand un- and re-binding in proteins.