Ab initio molecular dynamics simulation study of dissociative electron attachment to dialanine conformers.

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Ab Initio Molecular Dynamics Simulation Study of Dissociative Electron Attachment to Dialanine Conformers Wen-Ling Feng, and Shan Xi Tian J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/jp512173z • Publication Date (Web): 13 Feb 2015 Downloaded from http://pubs.acs.org on February 18, 2015

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The Journal of Physical Chemistry

Ab Initio Molecular Dynamics Simulation Study of Dissociative Electron Attachment to Dialanine Conformers

Wen-Ling Fenga and Shan Xi Tiana,b,*

a

Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China

b

Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China * Corresponding author. E-mail: [email protected]

1

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Abstract

Dissociative electron attachment (DEA) processes of six low-lying conformers (1- 6) of dialanine in gas phase are investigated by using ab initio molecular dynamics simulations. The incoming electron is captured and primarily occupied at the virtual molecular orbital π*, which is followed with the different dissociation processes. The electron attachments to the conformers 1 and 2 having the stronger N-H…N and O-H…O intramolecular hydrogen bonds do not lead to fragmentations; but two different backbone bonds are broken in the DEAs to conformers 3 (or 4) and 6, respectively. It is interesting that the hydrogen abstraction of -NH from the terminal methyl group -CH3 is found in the roaming dissociation of the temporary anion of conformer 3. The present simulations enable us to have more insights into the peptide backbone bond breaks in the DEA process, and demonstrate a promising way toward understanding of the radiation damages of complicated biological system.

Keywords: dissociative electron attachment; ab initio molecular dynamics simulation; dialanine; roaming dissociation

2


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1. Introduction Free secondary low-energy electrons (less than 20 eV) produced in the ionizing radiation can induce single- and double-strand breaks in DNA,1 which stimulated extensive examinations of the interactions between the low-energy electrons and biological molecules.2-5 In the dissociative electron attachment (DEA) to protein, the low-energy electron is captured and occupies at the amide π* or disulfide σ* virtual orbital of peptide, and then the N−Cα or SS backbone bond may be broken.3-6 The essential roles of Rydberg orbitals in charge transfer,3,4 the bond-cleavage selection of electron-molecule resonant states,6 and the vibrational effects7 were emphasized, but the dynamics of DEA to the large organic molecule is much more complicated than what we have understood, for examples, existence of many resonant states in the narrow energy range; spatial effects on the electron attachment arising from the various conformers or isomers; internal energy redistributions in the multiple freedoms before dissociations.

Recently, the DEA to dialanine (C6H12N2O3), as a peptide model of protein, was investigated.8-13 In the mass spectrometry experiments, various anionic fragments were observed, but their production mechanisms, in particular, for isobaric or nearly mass-equivalent fragments, were not well confirmed.8-13 As shown in the molecular scheme (the upper panel) of Figure 1, it was believed that the Cα-N3 bond cleavage was preferred after the electron attachment to the local virtual orbital of the neighboring carbonyl group π*(C=O).3,4,8-11 The corresponding 2Π* resonant state around 2~3 eV was frequently observed in the vertical electron attachment to organic molecules containing the C=O group.12 The fragments with masses of 87 (C3H7N2O) and 73 (C3H5O2) would be produced by the Cα-N3 bond cleavage. In the DEA to dialanine, the anionic 3



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fragments, m/z = 72, 87, and 88 with an intensity ratio about 80: 8: 1, were observed around 2 eV by Alizadeh et al.;9 while the additional fragment with m/z 73 was also observed, and the intensity ratio of the species with m/z of 72, 73, 87, and 88 was about 160: 5: 5: 1 determined by Muftakhov and Shchukin.8 These anionic fragments were assigned as: C3H4O2¯ (m/z=72), the isotopic ion of C3H4O2¯ or C3H5O2¯ (m/z=73), C3H7N2O¯ (m/z=87), and C3H6NO2¯ (m/z=88).8,9 The anion with m/z 88 was attributed to the amide bond N3-C4 cleavage and the anions with m/z 72 and 87 were indicative of the Cα-N3 bond being broken; while the anions with m/z 88 appeared at 1.7 eV might be from the unknown impurity.9,13 To date, no dynamic information about these dissociation processes is known. To the best of our knowledge, under their experimental conditions,8-11,13 several conformers of dialanine should co-exist in the gas phase. It is unclear whether there is conformational effect on the DEA processes.

Since the dissociation doorway is closely related to the formation of electron-molecule resonance, quantum scattering theories, such as the complex Kohn variational, the Schwinger variational, and R-matrix methods, can treat the electron attachments strictly in physics.2 The following multichannel dissociations of the DEA to polyatomic molecule are still the challenge to these theories. As shown in one of our recent studies,6 with the chemical bond elongations the coupling between the discrete states and electron continuum background becomes weak, thereby, ab initio quantum chemistry methods are applicable at least in approaching the dissociative limit. The dissociation dynamic processes of the complicated polyatomic molecules induced by ionization14 and electron attachment7,15 can be mimicked well by ab initio molecular dynamics simulations. In this work, ab initio molecular dynamics simulations are performed to elucidate the 4


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dynamic processes to the fragments with masses of 72, 73, 87, and 88 in the DEA to alanine.

2. Computational Method As shown in Figure 1, six low-lying conformers (1 - 6) of the neutral dialanine were optimized at B3LYP/6-311++G(2d,2p) level and the single point energies were calculated at MP2/6-311++G(2d,2p) level. No imaginary frequencies were found for these stable conformers. Their lowest unoccupied molecular orbitals showed the predominant character π* of the acyl groups (C1=O and C4=O), and thus the low-energy incoming electron would occupy these local orbitals in the vertical attachment. As proposed before, the potential energy curve cross between 2

Π* and 2Σ* states led to weakening a covalent bond (the excess electron transferred to the local

antibond orbital σ*), and finally this bond was broken.3,4,12 Therefore, in the following molecular dynamics simulations, the structural and energetic evolvements would start with the 2Π* resonant state, and then undergo at the lower 2Σ* state. This non-adiabatic state-state transition was not explicitly described but should be presented in our dynamics simulations.

Ab initio molecular dynamics simulations for the dissociation trajectories of the dialanine temporary anion were carried out with the atom-centered density matrix propagation method16-18 [ADMP-B3LYP/6-31G(d)]. The structural propagation was initiated in the Franck-Condon region for the vertical electron attachment to the neutral target. Quasiclassical trajectories were sampled with the initial internal energy 2.0 eV, which mimicked the DEA processes at the attachment energy around 2.0 eV. The time step was 0.2 femtosecond (fs), and the time scale of simulations was about 4 or 6 picoseconds. In our ADMP calculations, no dissociation pathways were 5



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constrained, but all possible processes involved in the DEA could not be presented in the finite number (6 - 10) of trajectories.

To evaluate the negative charge distributions of fragments, we calculated the total charge of each fragment, on the basis of both the natural bond orbital and Mulliken atomic population analysis using the wavefunctions at the B3LYP/6-31G(d) level. All quantum chemistry calculations were performed with GAUSSIAN 09 program,19 and the natural bond orbital analysis were done with NBO 5.0.20

3. Results and Discussion

3.1. Structures and the Relative Stabilities of Conformers In contrast to the dipeptide structure in solution which is defined with two dihedral angles in Ramachandran plot, the structure of neutral dialanine is described by four dihedral angles along the backbone including the N- and C-terminals: C1-Cα-N3-C4, Cm-Cα-N3-C4, Cm’-Cα’-C4-N3, and N6-Cα’-C4-N3 (see Figure 1). The interactions between the peptide bond and the side or terminal groups, in particular, the intermolecular hydrogen bonds (N-H…N or O, O-H… O or N, etc.), affect the overall structure of the peptide. With references of the protonated dialanine,21-23 six low-lying conformers are adopted here although more conformers are found as the local minima on the potential energy surface. The structure 3 in ref. (9) and the conformer in ref. (10) show the much higher energies; while the structures 1 and 2 in ref. (9) correspond to 4 and 5, respectively.

In this work, we do not exhaust all possible stable conformers of dialanine, only six 6


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representative ones are depicted in Figure 1 by inspecting the stabilization effect of the intramolecular hydrogen bonding interactions24,25 and the steric effect of two terminal methyl groups (-CmH3 and -Cm’H3). The dihedral angles and the intramolecular hydrogen bond lengths shown in Figure 1 are predicted at the B3LYP/6-311++G(2d,2p) level. As listed in Table 1, the B3LYP and MP2 calculations predict the similar stability order: 1 > 2 > 3 > 4 > 5 (or 5 > 4) > 6. The dipole moments µ are also predicted, and all of them show the values larger than 2.8 Debye. Since the large dipole moment can support the existence of dipole-bound anion,26 these strong electrostatic dipole fields could be responsible for the initial capture of the incoming electron. In the molecular dynamics simulations, the small basis set 6-31G(d) is utilized to eliminate the interferences of dipole-bound interaction, and we find that the incoming electron occupies the π* orbital (see Figure S3-S8 of Supporting Information), thus the all dynamics trajectories start with the valence-bound anion.

3.2. Intramolecular Hydrogen Transfer In conformers 1 and 2, there are two strong intramolecular hydrogen bonds, O-H…O and N-H… N, as well as a weak one C-H…O. The stronger hydrogen bonding interactions and weaker steric repulsions between two terminal methyl groups result in their highest stabilities. As shown in Figures 2 and S1 (Supporting Information), the dipeptide anions retain the intact structures within the evolvement time of 6.0 ps. The intramolecular hydrogen transfers are found to occur around 1 ps between the OH of the carboxyl group and C4=O group via the O-H…O hydrogen bond. A similar process was found previously for the dehydrogenated dialanine.10 Moreover, one can find that the rotations of the terminal -Cm’H3 and -N6H2 groups with respect to Cα’-C4 bond axis. Both 7



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the group rotations and the hydrogen transfer should be two dominant processes of the internal energy dissipation. It is noted that the present 6-ps simulations do not suggest the existence of the parent anion. No parent anions were observed in the experiments,8-11,13 implying that the excess electron of the parent anion could be autodetached due to the molecular internal motions.

3.3. Peptide Bond (Cα-N3) Cleavage As shown in Figures 3 and 4, in the DEA to conformer 3 the peptide bond (Cα-N3) cleavage happens at 1.1 ps, and then the orientations between two fragments, C3H7N2O (left) and C3H5O2 (right), are rearranged until 2.4 ps when a hydrogen bond N3… H-Cm is formed. Around 2.8 ps, the hydrogen (of the terminal -CmH3 group) involved in this hydrogen bond is abstracted to form an amino group (-N3H2). During this roaming dissociation, as shown in Figure 4, the bond lengths oscillate remarkably, in particular, from 1.0 to 3.0 ps. After the bond (Cα-N3) cleavage, two fragments are bound weakly by some hydrogen bonds, such as N…H-C, O…H-C, N-H…O, see Figure 3.

The fragment charge distributions at the final simulation time are analyzed within the natural bond orbital (Table 2) and Mulliken atomic charge (Table S1, see Supporting Information) schemes. The charge values are similar to each other for a given fragment. For the DEA to conformer 3, at 2.4 ps, the most negative charge is on the fragment C3H7N2O; while with the hydrogen transfer, the negative charge is transferred simultaneously, and then negatively charged fragment C3H4O2¯ (m/z = 72) is formed. However, the present simulations do not indicate that the C3H4O2¯ (m/z = 72) is the only anionic product, perhaps, another charged fragment C3H7N2O¯ 8


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(m/z = 87) may also be produced. In fact, both of them were detected in the mass spectrometry experiments.8,9 In contrast to the previous studies,4,8-13 the indirect production mechanism, i.e., by the hydrogen and charge transfers in the roaming dissociation, of a certain anionic fragment is proposed here for the first time.

The peptide bond (Cα-N3) cleavage in the DEA to conformer 4 is much faster. In Figure 5, the bond break happens at 0.3 ps, without the hydrogen and negative charge transfers between two departing fragments. As shown in Tables 1 and S1, the fragment C3H7N2O should be negatively charged, contributing to the C3H7N2O¯ (m/z = 87) ions detected in the mass spectrometry experiments.8,9 Alternatively, this fragment may be the neutral, but the optimization at the B3LYP/6-311++G(2d,2p) level for the geometrical parameters of this neutral further leads to the Cα'-C4 bond cleavage (decomposition to CH3CHNH2 and OCNH radicals).

As shown in Figures S5 and S6, the initial capture of excess electron shows the occupation at the π* orbital of the neutral, indicating the dynamics evolvement beginning with the 2Π* state. At 1.1 ps (for conformer 3 in Figure S5) and 0.3 ps (for conformer 4 in Figure S6), the peptide bond (Cα-N3) is broken; meanwhile, the orbital map shows the typical Cα-N3 anti-bond character, σ*. Therefore, the state-state transition from 2Π* to 2Σ* is included in the present simulations, because the ADMP calculations always mimic the dynamics evolvements at the lowest state (in the Franck-Condon region, 2Σ* lies at the higher energy than 2Π*). In Figure S5, the concerted hydrogen- and charge-transfers are also observed around 2.4 ~ 2.8 ps after the electron attachment to conformer 3. 9



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3.4. Amide Bond (N3-C4) Cleavage The DEA to conformer 5 does not lead to the cleavages of the peptide backbone bonds. In Figure S2, the neutral hydrogen atom of carboxyl group is predicted to be released about 0.85 ps, and thus the deprotonated anion C6H11N2O3¯ (m/z = 159).8-11 The relative orientations of the terminal methyl and carboxyl groups in conformer 5 are different from conformer 6, see Figure 1, which surprisingly leads to the significant different dissociative processes. As depicted in Figures 6 and 7, at 0.152 ps, a hydrogen transfer to the -N3H from the -C1OOH group; then the amide bond N3-C4 breaks at 0.2 ps. Due to the hydrogen bonding interactions of N6-H… N3 and N6-H… O=C1, two fragments are loosely combined until 3.0 ps (see Figure 7b). At 4.4 ps, the carbon monoxide (C4O) is released from the nearly neutral fragment C3H6NO (mass = 72). As listed in Tables 1 and S1, during this roaming dissociation, there are no hydrogen or charge transfers between two fragments before 4.0 ps, and the negative charge locates at the larger fragment C3H6NO2¯ (m/z = 88). Figures S6 and S8 show again the typical π* → σ* charge transfer (before 0.2 and 0.3 ps) which induces the N3-C4 bond cleavage.

3.5. Appearance Energies of the Anionic Fragments Appearance energy (AE) of an anionic fragment produced in the vertical electron attachment is defined as, AE = E(fragments)- E(neutral), where E denotes the total energy of the free anionic and neutral fragments or the neutral parent. As listed in Table 3, all values of AE are positive and less than 2 eV, indicating that the dissociations are endothermic. With the zero-point vibrational energy correction, the results obtained at the B3LYP/6-311++G(2d,2p) level are in good 10


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agreement with the experimental observations, i.e., the AE values of the ions with m/z = 72, 73, 87, and 88 are less than 1 eV. 8,9 The energies for the Cα-N3 bond cleavage are nearly equivalent to those for the N3-C4 bond breaks, indicating no differences in thermal chemistry. However, the dissociation dynamic processes are in the varied forms as revealed above. Moreover, in our AE calculations, the structures of the same fragment may be different. See Figure S3, for example, the geometry of C3H7N2O¯ (m/z = 87) for conformer 3 is slightly different from that conformer 4.

4. Conclusive Remarks

The DEAs to conformers 1- 6 of dialanine at 2.0 eV are investigated with ab initio molecular dynamics simulations. The dissociation pathways show the strong conformational dependences, in which we pay more attention to the cleavages of dipeptide backbone bonds. Some remarks are summarized: (1) Within 6 ps of the simulation time scale, the most stable conformers 1 and 2 show the intact parent anions after the electron attachment, although there are the intramolecular hydrogen transfers from the carboxyl group (-C1OOH) to the carbonyl (-C4=O). (2) We find the direct release of the hydrogen atom from the carboxyl group (conformer 5), while the hydrogen transfer from the carboxyl to the –N3H group before the N3-C4 cleavage (conformer 6) or that from the end methyl to the –N3H group after the backbone bond Cα-N3 cleavage (conformer 3). (3) The peptide bond Cα-N3 cleavages are observed in the DEA processes of conformers 3 and 4, moreover, both the hydrogen and charge transfers between two fragments are found in the roaming dissociation27 for conformer 3. (4) Besides the amide bond N3-C4 cleavage, small fragments, CO and C2H6N, may be produced via the cascade process in the DEA to conformer 6. At last, we have to confess that it is a challenge to reproduce the relative intensities of different 11



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anionic fragments observed in the experiments. The relative contributions of the thermal conformers in gas phase are dependent on the vaporizing temperatures in the experiments, moreover, the DEA to the vibrational exited-state molecule is different from that to the ground-state target. The dissociations to the other fragments observed in the experiments,8-11,13 in particular, those produced at the higher electron energies, are beyond the present investigation.

Acknowledgements This work is partially supported by NSFC (Grant No. 21273213) and MOST (Grant No. 2011CB921401).

Supporting Information Full information of references (9) and (19), fragment charges for the selected dialanine conformers obtained with Mulliken atomic charge analysis, snapshots after the vertical electron attachment to conformers 2 and 5, evolvements of the highest single-occupied molecular orbital of the parent anion, fragment structures and geometrical parameters for the DEA to conformers 3-6. These materials are available free of charge via the Internet at http://pubs.acs.org.

References and Notes (1) Boudaiffa, B.; Cloutier, P.; Hunting, D.; Huels, M. A.; Sanche, L. Resonant Formation of DNA Strand Breaks by Low-Energy (3 to 20 eV) Electrons. Science 2000, 287, 1658-1660. (2) Baccarelli, I.; Bald, I.; Gianturco, F. A.; Illenberger, E.; Kopyra, J. Electron-Induced Damage of DNA and Its Components: Experiments and Theoretical Models. Phys. Rep. 2011, 508, 1-44. 12


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Limão-Vieira, P.; Denifl, S. Electron Attachment to the Dipeptide Dialanine: Influence of Methylation on Site Selective Dissociation Reactions. Phys. Chem. Chem. Phys. 2013, 15, 3834-3840. (12) Sobczyk, M.; Anusiewicz, I.; Berdys-Kochanska, J.; Sawicka, A.; Skurski, P.; Simons, J. Coulomb-Assisted Dissociative Electron Attachment: Application to a Model Peptide. J. Phys. Chem. A 2005, 109, 250-258. (13) Vasil’ev, Y. V.; Figard, B. J.; Morré, J.; Deinzer, M. L. Fragmentation of Peptide Negative Molecular Ions Induced by Resonance Electron Capture. J. Chem. Phys. 2009, 131, 044317 1-11. (14) Tian, S. X.; Yang, J. L. Communication: Ab Initio Photoionization Dynamics of β-Alanine. J. Chem. Phys. 2007, 126, 141103 1-4. (15) Xia, L.; Wu, B.; Li, H.-K.; Zeng, X.-J.; Tian, S. X. Communication: Imaging the Indirect Dissociation Dynamics of Temporary Negative Ion: N2O¯→ N2 + O¯. J. Chem. Phys. 2012, 137, 151102 1-4. (16) Iyengar, S. S.; Schlegel, H. B.; Millam, J. M.; Voth, G. A.; Scuseria, G. E.; Frisch, M. J. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. II. Generalizations Based on Mass-Weighting, Idempotency, Energy Conservation and Choice of Initial Conditions. J. Chem. Phys. 2001, 115, 10291-10302. (17) Schlegel, H. B.; Millam, J. M.; Iyengar, S. S.; Voth, G. A.; Scuseria, G. E.; Daniels, A. D.; Frisch, M. J. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. J. Chem. Phys. 2001, 114, 9758-9763. (18) Schlegel, H. B.; Iyengar, S. S.; Li, X.; Millam, J. M.; Voth, G. A.; Scuseria, G. E.; Frisch, M. J. Ab initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. III. 14


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Comparison with Born-Oppenheimer Dynamics. J. Chem. Phys. 2002, 117, 8694-8704. (19) Gaussian 09, Revision D.01, Frisch, M. J.; et al. Gaussian, Inc., Wallingford CT, 2009. (20) Glendening, E. D.; Badenhoop, J. K.; Reed, A. E.; Carpenter, J. E.; Bohmann, J. A.; Morales, C. M.; Weinhold, F. NBO 5.0; Theoretical Chemistry Institute: University of Wisconsin, Madison, 2001. (21) Lucas, B.; Grégoire, G.; Lemaire, J.; Maître, P.; Ortega, J.-M.; Rupenyan, A.; Reimann, B.; Schermann, J. P.; Desfrançois, C. Investigation of the Protonation Site in the Dialanine Peptide by Infrared Multiphoton Dissociation Spectroscopy. Phys. Chem. Chem. Phys. 2004, 6, 2659-2663. (22) Marinica, D. C.; Grégoire, G.; Desfrançois, C.; Schermann, J. P.; Borgis, D.; Gaigeot, M. P. Ab Initio Molecular Dynamics of Protonated Dialanine and Comparison to Infrared Multiphoton Dissociation Experiments. J. Phys. Chem. A 2006, 110, 8802-8810. (23) Sohn, W. Y.; Lee, J. S. Structure and Conformational Stability of Protonated Dialanine. J. Phys. Chem. A 2010, 114, 7537–7543. (24) Tian, S. X.; Yang, J. L. Effects of Intramolecular Hydrogen Bonding on the Ionization Energies of Proline. Angew. Chem. Int. Ed. 2006, 45, 2069-2072. (25) Tian, S. X. Hydrogen Bonding Effects on Conformational Stabilities and Dissociative Ionization Dynamics of Amino Acids. Prog. Chem. 2009, 21, 600-605. (26) Simons, J.; Skurski, P. In Theoretical Prospect of Negative Ions; Kalcher, J., Eds.; Research Signpost: Kerale, India, 2002. (27) Hause, M.; Herath, N.; Zhu, R.; Lin, M. C.; Suits, A. G. Roaming-Mediated Isomerization in the Photodissociation of Nitrobenzene. Nature Chem. 2011, 3, 932-937.

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Table 1. Total energy (in au), relative energy (∆E in kcal/mol), and dipole moment (µ in Debye) for the stable dialanine conformer conformer

Total energya

∆Ea

Total energy

µ

B3LYP/ 6-311++G(2d,2p)

a

1

-571.087918

2

-571.085284

3

-571.085400

4

-571.084363

5

-571.082450

6

-571.081088

0.00 1.43 2.02 2.60 3.72 4.54

∆E

µ

MP2/6-311++G(2d,2p) 7.15

-569.851816

0.00

7.84

7.41

-569.849566

1.41

8.10

3.05

-569.848289

2.21

2.84

4.66

-569.847054

2.99

5.16

4.96

-569.847798

2.52

5.53

6.73

-569.844391

4.66

7.40

Including the zero-point vibrational energy correction.

Table 2. Fragment charges for the selected dialanine conformers obtained with natural bond orbital analysis conformer 3

conformer 4

fragment charge C3H7N2O(mass =87)

C3H5O2(mass=7 3)

1.1 ps

-0.703

-0.297

1.6 ps

-0.920

2.0 ps

-0.827

2.4 ps

fragment charge C3H7N2O( mass=87)

C3H5O2(mass= 73)

0.3 ps

-0.756

-0.244

-0.080

1.0 ps

-0.725

-0.275

-0.173

2.0 ps

-0.729

-0.271

-0.799

-0.201

3.0 ps

-0.690

-0.310

C3H8N2O(mass =88)

C3H4O2(mass=7 2)

4.0 ps

-0.653

-0.347

2.8 ps

-0.051

-0.949

4.0 ps

-0.053

-0.947

conformer 6

fragment charge C3H6NO(mass= 72)

C3H6NO2(mass =88)

0.2 ps

-0.298

-0.702

2.0 ps

-0.056

-0.944

4.0 ps

-0.088

-0.912

16


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Table 3. Appearance energies (eV) of the anionic fragment produced in the selected dissociation pathway.

a

B3LYP/6-31G(d)

B3LYP/6-311++G(2d,2p) MP2/6-311++G(2d,2p)

a

b

conformer 3

conformer 4

C3H7N2O¯ (m/z=87) + C3H5O2

C3H7N2O¯ (m/z=87)+ C3H5O2

1.41

1.43

0.58

0.58

1.57

1.58

C3H8N2O+ C3H4O2¯ (m/z=72) B3LYP/6-31G(d) a

1.37

B3LYP/6-311++G(2d,2p)

a

b

MP2/6-311++G(2d,2p)

B3LYP/6-31G(d)

1.40

a

B3LYP/6-311++G(2d,2p)

0.30

a

MP2/6-311++G(2d,2p) b

conformer 5

conformer 6

C6H11N2O3¯ (m/z = 159)+H

C3H6NO+C3H6NO2¯ (m/z = 88)

0.89

1.31

0.45

0.51

0.91

1.31 CO+C2H6N+C3H6NO2¯ (m/z = 88)

B3LYP/6-31G(d)

a

B3LYP/6-311++G(2d,2p)

1.52 a

0.56

MP2/6-311++G(2d,2p) b

1.53

a

Including the zero-point vibrational energy correction. b Obtained with the single-point energies over the geometries optimized at B3LYP/6-311++G(2d,2p) level.

17



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Figure 1. The dihedral angles and intramolecular hydrogen bonds of different dialanine conformers. Oxygen, hydrogen, nitrogen, and carbon atoms are in red, white, blue, and brown, respectively.

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Figure 2. Snapshots after the vertical electron attachment to conformer 1.

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Figure 4. Evolvements of the N3-Cα and N3 - H (Cm) atomic distances after the vertical electron attachment to conformer 3.

21



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Figure 5. Snapshots after the vertical electron attachment to conformer 4 (a). Evolvement of the N3-Cα atomic distance (b).

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Figure 7. Evolvements of the selected atom-atom distances after the vertical electron attachment to conformer 6.

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For Table of Contents Only

25


Ab initio molecular dynamics study of the aqueous HOO(-) ion.

Dissolution of NaCl nanocrystals: an ab initio molecular dynamics study.

Ab initio molecular dynamics study of small alkali metal clusters.

Molecular Mechanical Molecular Dynamics Simulation.

Hydrated Electron Transfer to Nucleobases in Aqueous Solutions Revealed by Ab Initio Molecular Dynamics Simulations.

Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo.

Ab initio molecular dynamics simulation of proton hopping in a model polymer membrane.

Acceleration of self-consistent field convergence in ab initio molecular dynamics simulation with multiconfigurational wave function.

Ab initio molecular dynamics simulation of low energy radiation responses of α-Al2O3.

An Efficient Local Molecular Dynamics Polymerization Simulation Combined with an Ab Initio MO Method.

Water-accelerated OH addition to sulfur dioxide SO₂: direct ab initio molecular dynamics (AIMD) study.

Multiple time step integrators in ab initio molecular dynamics.

Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO2-H2O systems.

Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization.

Ab initio molecular dynamics study of high-pressure melting of beryllium oxide.

Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study.

N2 dissociation on W(110): An ab initio molecular dynamics study on the effect of phonons.

Oxidation of ligand-protected aluminum clusters: an ab initio molecular dynamics study.

An ab initio molecular dynamics study of thermal decomposition of 3,6-di(azido)-1,2,4,5-tetrazine.

Dissociative electron attachment studies on acetone.

Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study.

An efficient approach to ab initio Monte Carlo simulation.

State selectivity and dynamics in dissociative electron attachment to CF₃I revealed through velocity slice imaging.

MM molecular dynamics study.