Dynamics of H-atom loss in adenine: Supplementary information

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1 Dynamics of H-atom loss in adenine: Supplementary information M. Zierhut, W. Roth, and I. Fischer Institute of Physical Chemistry, University of Würzburg, Am Hubland, D Würzburg; 1 Computational Details 1.1 Choice of methods We calculated the dissociation energies of adenine into a hydrogen atom and all possible adeninyl radicals to get more information about competing fragmentation channels. At energies available in our experiments the products will be in their electronic ground state and only those have been considered: The adenine molecule is (most likely) excited into to 1 A' (ππ * ) state. Subsequently a rapid conversion into the N-H dissociative 1 A" (πσ * ) [1] occurs when an electron switches from a π * into the σ * orbital of the corresponding bond. In the fragmentation process, the hydrogen atom takes away one of the three electrons from the σ and σ * orbitals while the other two remain with the (in plane) non-bonding/lone pair orbital of the nitrogen atom. Consequently, the adeninyl radical which is thus formed will be a π-radical, known to be more stable than σ-radicals. Zhao et al. recently proposed a new density functional named BB1K optimised for the calculation of thermochemical kinetics against a dataset of reaction energies, forward and reverse barriers [2]. We tested this functional together with some standard double and triple-ζ basis sets for the photochemical hydrogen abstraction in the tert.-butyl radical we

2 investigated recently [3]. The dissociation energy of 152±3 kj/mol is reproduced within the experimental error bar by this functional when the aug-cc-pvdz or cc-pvtz basis sets are used. These results are much better (see [4]) than for other density functionals like B3LYP, B97-2, PBE which have been considered in the literature [5], [6], [7], [8], [9]. 1.2 Program details Unrestricted SCF calculations have been carried out using GAUSSIAN [10]. The density functional BB1K has been implemented using the IOp (see [11]) specified by Zhao et al. [2] together with the aug-cc-pvdz basis set from the program library. All structures have been fully optimised with as SCF convergence criterion and /bohr and /degree, respectively, as convergence criterion for the gradient optimisation of the structure, e.g. the tight convergence criterion. Vibrational frequencies were calculated in the harmonic approximation to verify the minimum energy structure and to get the zero point vibrational energy (ZPE) contribution from the stabilisation energy. The molecular energy is calculated as the sum of the electronic (E el. ) and zero point energy (ZPE). The dissociation energy D 0 of adenine (9-methyladenine) as given below is taken as the difference of the results for adenine (9-MA) and the fragments hydrogen plus adeninyl (9-methyl(en)adeninyl), respectively. In the calculations on the 9-methyladenine fragments, convergence of the molecular geometry was slow. From the normal mode analysis it was obvious that the the barrier for the rotation of the methyl group is quite low thus making it difficult to locate the global minimum energy structure. However, we believe that the calculated dissociation energies are reliable within an numerical error bar of 1 kj/mol. 2/6

3 2 Results 2.1 Adenin adeninyl + H In adenine, there are five hydrogen atoms which have to be considered: two amino -H s ( NH a,b 2 ), one azine H (N 9 H) and two hydrogens that are bound to carbon atoms (C 2,8 H). The small difference for the dissociation of the two amino H atoms (approx. 3 kj/mol, the same result can be found in 9-MA) might be explained by lone pair repulsion between the amino group N and the neighbouring nitrogen atom N 3. Table I. Calculated energy values (BB1K/aug-cc-pVDZ) for the dissociation of adenine into a hydrogen atom and an adeninyl radical. (adenine: E el. = -467,188097, ZPE = 0,115149, hydrogen: E el. = -0, ) E el. ZPE D 0 radical: kj/mol N 9 H -466, , C 8 H -466, , C 2 H -466, , NH 2 (a) -466, , NH 2 (b) -466, , Methyladenin methyl-/methyleneadeninyl + H For 9-methyladenine, the azine-h atom is replaced by a methyl group, thus introducing more hydrogen atoms. Assuming an almost free, e.g. unhindered rotation of the methyl group, all three can be treated considering only one of them. Abstraction of a H atom will lead in any case to a methylene group (MeH). 3/6

4 Table I. Calculated energy values (BB1K/aug-cc-pVDZ) for the dissociation of 9-methyladenine into a hydrogen atom and an methyl- or methyleneadeninyl radical. (9-methyladenine: E el. = -506,476731, ZPE = 0,143189, hydrogen: E el. = -0, ) E el. ZPE D 0 radical: kj/mol MeH -505, , C 8 H -505, , C 2 H -505, , NH 2 (a) -505, , NH 2 (b) -505, , Geometry files Results of our computational study are provided as optimised molecular geometries of all structures mentioned in.xyz file format which can be read by programs such as Molden, WebLabViewer, GaussView, or XMol. Included files are (A = adenine, 9MA = 9-methyladenine): A.BB1K.av2z.xyz A.N9H.BB1K.av2z.xyz A.C2H.BB1K.av2z.xyz A.C8H.BB1K.av2z.xyz A.NHa.BB1K.av2z.xyz A.NHb.BB1K.av2z.xyz 9MA.BB1K.av2z.xyz 9MA.MeH.BB1K.av2z.xyz 9MA.C2H.BB1K.av2z.xyz 9MA.C8H.BB1K.av2z.xyz 9MA.NHa.BB1K.av2z.xyz 9MA.NHb.BB1K.av2z.xyz 4/6

5 3 References and Annotations [1] According to theoretical and experimental results, the lowest 1 A" state is of nπ * character, see AL Sobolewski, W Domcke: On the mechanism of nonradiative decay of DNA bases: ab initio and TDDFT results for the excited states of 9H-adenine. Eur. J. Phys. D 20 (2002) 369 NJ Kim, G Jeong, YS Kim, J Sung, SK Kim, YD Park: Resonant two-photon ionization and laser induced fluorescence spectroscopy of jet-cooled adenine. J. Chem. Phys. 113 (2000) [2] Y Zhao, BJ Lynch, DG Truhlar: Development and Assessment of a New Hybrid Density Functional Model for Thermochemical Kinetics. J. Phys. Chem. A 108 (2004) 2715 [3] M Zierhut, W Roth, I Fischer: Photodissociation of the tert-butyl Radical, C 4 H 9. J. Phys. Chem. A 108 (2004) ASAP [4] Dissociation energy D 0 of the tert.-butyl radical into methylpropene and hydrogen calculate at the following levels of theory (full optimisation): BPW91/cc-pVTZ 149 kj/mol, B1B95/cc-pVTZ 147 kj/mol, B97-2/cc-pVTZ 149 kj/mol, PBE/aug-cc-pVdZ 151 kj/mol, HCTH-120/cc-pVTZ 154 kj/mol, BB1K/cc-pVDZ 155 kj/mol, BB1K/aug-cc-pVDZ 154 kj/mol, BB1K/cc-pVTZ 153 kj/mol, B3LYP/aug-cc-pVDZ 155 kj/mol, B3LYP/6-31+G(d,p) 164 kj/mol [5] Y Zhao, J Pu, BJ Lynch, DG Truhlar: Tests of second-generation and third-generation density functionals for thermochemical kinetics. Phys. Chem. Chem. Phys. 6 (2004) 673 [6] VA Guner, KS Khuong, KN Houk, A Chuma, P Pulay: The Performance of the Handy/Cohen Functionals, OLYP and O3LYP, for the Computation of Hydrocarbon Pericyclic Reaction Activation Barriers. J. Phys. Chem. A 108 (2004) 2959 [7] Y Zhao, BJ Lynch, DG Truhlar: Doubly Hybrid Meta DFT: New Multi-Coefficient Correlation and Density Functional Methods for Thermochemistry and Thermochemical Kinetics. J. Phys. Chem. A 108 (2004) /6

6 [8] VA Guner, KS Khuong, AG Leac, PS Lee, MD Bartberger, KN Houk: A Standard Set of Pericyclic Reactions of Hydrocarbons for the Benchmarking of Computational Methods: The Performance of ab Initio, Density Functional, CASSCF, CASPT2, and CBS-QB3 Methods for the Prediction of Activation Barriers, Reaction Energetics, and Transition State Geometries. J. Phys. Chem. A 107 (2003) [9] BJ Lynch, DG Truhlar: How Well Can Hybrid Density Functional Methods Predict Transition State Geometries and Barrier Heights? J. Phys. Chem. A 105 (2001) 2936 [10] MJ Frisch, GW Trucks, HB Schlegel, GE Scuseria, MA Robb, JR Cheeseman, JA Montgomery, T Vreven, KN Kudin, JC Burant, JM Millam, SS Iyengar, J Tomasi, V Barone, B Mennucci, M Cossi, G Scalmani, N Rega, GA Petersson, H Nakatsuji, M Hada, M Ehara, K Toyota, R Fukuda, J Hasegawa, M Ishida, T Nakajima, Y Honda, O Kitao, H Nakai, M Klene, X Li, JE Knox, HP Hratchian, JB Cross, C Adamo, J Jaramillo, R Gomperts, RE Stratmann, O Yazyev, AJ Austin, R Cammi, C Pomelli, JW Ochterski, PY Ayala, K Morokuma, GA Voth, P Salvador, JJ Dannenberg, VG Zakrzewski, S Dapprich, AD Daniels, MC Strain, O Farkas, DK Malick, AD Rabuck, K Raghavachari, JB Foresman, JV Ortiz, Q Cui, AG Baboul, S Clifford, J Cioslowski, BB Stefanov, G Liu, A Liashenko, P Piskorz, I Komaromi, RL Martin, DJ Fox, T Keith, MA Al-Laham, CY Peng, A Nanayakkara, M Challacombe, PMW Gill, B Johnson, W Chen, MW Wong, C Gonzalez, JA Pople, Gaussian 03. Gaussian, Inc., Pittsburgh PA, 2003 [11] The BB1K density functional can be implemented in Gaussian 03 using the following combination of keyword and IOp: UBB95 IOp(3/76= ) see also the authors ([2]) webpage 6/6