Manuscript submitted to the Journal of the American Society for Mass Spectrometry, September 2011.

The Early Life of a Peptide Cation-Radical. Ground and Excited-State Trajectories of Electron-Based Peptide Dissociations During the First 330 Femtoseconds Christopher L. Moss, Wenkel Liang, Xiaosong Li,* František Tureček* Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA 98195-1700 Manuscript submitted to the Journal of the American Society for Mass Spectrometry, September 2011. Figures S1-S6, and Tables S1-S9 of optimized ion structures with total and zero-point energies. S1

Figure S1. Top panel (a) RRKM rate constants for C δ N ε (circles) and N ε H ε (triangles) dissociations in 3. Filled symbols: B3-PMP2/6-311++G(2d,p) transition state energies; open symbols: M06-2X/6-311++G(3df,2p) transition state energies. Bottom panel (b): Calculated ratios (log) of rate constants for loss of H and guanidine from 3 at the indicated levels of theory. S2

Figure S2. RRKM rate constant for N C α bond cleavage in 2 on the effective CCSD(T)/6-311++G(3df,2p) potential energy surface of the ground doublet state. The vertical line indicates that ion internal energy after resonant electron transfer to (AR + 2H) 2+ from a Cs atom and isomerization to intermediate 2. S3

Figure S3. Time dependence of the H 3 N---C α bond length from Ehrenfest dynamics calculations of the SOMO state of (AR + 2H) + calculated with CAM-B3LYP/4-31G*. S4

Figure S4. Geometries at the indicated times from CAM-B3LYP/4-31G(d) Ehrenfest dynamics calculations of the LUMO state of (AR + 2H) +. θ is the N,C,N,N dihedral angle of the guanidine group. S5

Figure S5. Geometries at the indicated times from CAM-B3LYP/4-31G(d) Ehrenfest dynamics calculations of the LUMO+1 state of (AR + 2H) +. θ is the N,C,N,N dihedral angle of the guanidine group. S6

Figure S6. Time dependence of the guanidinium H ε N ε bond lengths from Ehrenfest dynamics calculations of the LUMO+2 state of (AR + 2H) + calculated with CAM-B3LYP/4-31G*. Black circles: H ε N ε bond; blue circles: H 11 N 1 bond; pink circles: H 12 N 1 bond; green circles: H 21 N 2 bond; turquoise circles: H 22 N 2 bond. S7

Table S1. B3LYP/6-31+G(d,p) optimized geometry of (AR + 2H) 2+ ion 1 +.. 1 7 0 4.546252-2.470751-0.308685 2 6 0 4.219140-1.167340 0.401135 3 6 0 2.792768-0.831289-0.123531 4 8 0 2.251431-1.633778-0.897118 5 7 0 2.233492 0.302578 0.306713 6 1 0 4.777421-3.235790 0.329906 7 1 0 3.657721-2.688224-0.836982 8 6 0 0.959162 0.814598-0.208981 9 1 0 2.752536 0.967459 0.876519 10 6 0 1.027541 2.331731 0.003382 11 8 0 1.888999 2.866255 0.667366 12 8 0 0.034037 2.981590-0.615665 13 6 0-0.259410 0.150107 0.490271 14 6 0-1.596524 0.378187-0.236377 15 6 0-2.758560-0.312517 0.489112 16 1 0 4.162770-1.391049 1.470598 17 6 0 5.284450-0.105090 0.126325 18 1 0 0.911512 0.608574-1.284175 19 1 0 0.139893 3.938697-0.458143 20 1 0-0.314286 0.505595 1.526387 21 1 0-0.047922-0.923756 0.525479 22 1 0-1.803961 1.450900-0.309466 23 1 0-1.528848-0.013426-1.258887 24 1 0-2.830345 0.061209 1.519179 25 1 0-2.600520-1.396376 0.519741 26 1 0 5.316690-2.368087-0.976033 27 7 0-4.022350-0.048537-0.223987 28 6 0-5.184787-0.677429-0.010802 29 7 0-6.219931-0.471080-0.838271 30 7 0-5.318839-1.528928 1.014299 31 1 0-6.102103-0.008350-1.728388 32 1 0-7.154410-0.771630-0.598481 33 1 0-4.658629-1.545041 1.777025 34 1 0-6.136329-2.116398 1.102333 35 1 0-4.033543 0.730717-0.870208 36 1 0 5.341791 0.140036-0.939260 37 1 0 6.266048-0.441413 0.472834 38 1 0 5.055732 0.815105 0.669666 Rotational constants (GHZ): 0.7341925 0.1564286 0.1349062 E(B3LYP)/6-31+G(d,p) = -854.646293092 a.u. Zero point energy = 873.763 kj mol -1 S8

Table S2. B3LYP/6-31+G(d,p) optimized geometry of (AR + 2H) 2+ cation-radical 1. 1 7 0 4.293982-2.617213-0.518692 2 1 0 2.300823-2.568220-0.702085 3 1 0 4.902233-3.269503-0.032994 4 1 0 4.727513-2.390631-1.411822 5 6 0 4.062152-1.397081 0.281063 6 1 0 3.899677-1.744477 1.317983 7 6 0 5.227118-0.399220 0.277506 8 1 0 5.402258-0.006775-0.730721 9 1 0 5.045311 0.447032 0.950218 10 1 0 6.143060-0.889351 0.621589 11 6 0 2.757048-0.818595-0.234140 12 8 0 1.782996-1.767038-0.467640 13 6 0 0.999168 2.427083-0.074358 14 8 0-0.010489 3.101426-0.082012 15 8 0 2.234181 2.970998-0.039225 16 1 0 2.136083 3.939171-0.019872 17 7 0 2.253245 0.339268 0.388410 18 1 0 2.974739 1.041227 0.494778 19 6 0 1.013801 0.901432-0.148350 20 1 0 0.940071 0.669579-1.226774 21 6 0-0.221406 0.301178 0.563968 22 1 0 0.002430-0.757009 0.718046 23 1 0-0.323108 0.767119 1.551177 24 6 0-1.526092 0.444500-0.231347 25 1 0-1.749084 1.506819-0.378743 26 1 0-1.407361-0.020491-1.218832 27 6 0-2.690716-0.227713 0.496455 28 1 0-2.516277-1.306423 0.579530 29 1 0-2.799522 0.194115 1.504117 30 7 0-3.945146-0.015867-0.257373 31 1 0-3.938951 0.731105-0.941227 32 6 0-5.094138-0.653770-0.050270 33 7 0-6.129399-0.483273-0.893243 34 1 0-6.016394 0.005341-1.769038 35 1 0-7.061674-0.781211-0.647287 36 7 0-5.232919-1.485007 0.993255 37 1 0-4.532516-1.533878 1.717470 38 1 0-6.022773-2.108875 1.065836 Rotational constants (GHZ): 0.6957073 0.1641327 0.1378257 E[B3LYP/6-31+G(d,p)] = -854.875598213 a.u. Zero point energy = 863.9237 kj mol -1 E[PMP2/6-311++G(3df,2p)] = -853.2087449 a.u. E[CCSD(T)/6-31+G(d,p)] = -852.6021431 a.u. E[CCSD(T)/6-311++G(3df,2p)] = -853.4239334 a.u. S9

Table S3. B3LYP/6-31+G(d,p) optimized geometry of (AR + 2H) 2+ cation-radical 2. 1 7 0 5.359491-0.117260-0.005476 2 1 0 4.262570 1.347165 0.885911 3 1 0 6.210030-0.056780-0.556756 4 1 0 5.447285-0.908197 0.629247 5 6 0 4.163679-0.243543-0.859286 6 1 0 4.331267 0.442602-1.709883 7 6 0 3.919041-1.653514-1.414992 8 1 0 3.724359-2.364797-0.604236 9 1 0 3.074228-1.684586-2.114069 10 1 0 4.799096-1.994046-1.968426 11 6 0 3.018591 0.298650-0.029723 12 8 0 3.301640 1.417547 0.701060 13 6 0 0.091653-0.534217 1.029069 14 8 0-0.905642-1.199461 0.713336 15 8 0 0.918832-0.931583 1.999000 16 1 0 0.608791-1.785049 2.350800 17 7 0 1.726957 0.314596-0.555683 18 1 0 1.527642-0.469428-1.165703 19 6 0 0.593797 0.706257 0.301490 20 1 0 0.997556 1.401218 1.041797 21 6 0-0.489306 1.390776-0.542108 22 1 0 0.007935 2.194361-1.090704 23 1 0-0.843175 0.681020-1.300670 24 6 0-1.678818 1.956420 0.278290 25 1 0-1.610088 1.655897 1.331126 26 1 0-1.647270 3.049722 0.277642 27 6 0-3.056691 1.538215-0.249572 28 1 0-3.843850 2.024684 0.338941 29 1 0-3.166788 1.844405-1.298849 30 7 0-3.198068 0.078499-0.140380 31 1 0-2.342547-0.445158 0.112750 32 6 0-4.314350-0.613823-0.297882 33 7 0-4.325031-1.930767-0.006256 34 1 0-3.485008-2.373068 0.340884 35 1 0-5.065977-2.532505-0.332150 36 7 0-5.448580-0.031941-0.728981 37 1 0-5.462115 0.935963-1.009788 38 1 0-6.331521-0.518658-0.699313 Rotational constants (GHZ): 1.0060280 0.1792060 0.1699305 E[B3LYP/6-31+G(d,p)] = -854.887053805 a.u. Zero point energy = 863.872 kj mol -1 E[PMP2/6-311++G(3df,2p)] = -853.2191653 a.u. E[CCSD(T)/6-31+G(d,p)] = -852.6120901 a.u. E[CCSD(T)/6-311++G(3df,2p)] = -853.4344674 a.u. S10

Table S4. B3LYP/6-31+G(d,p) optimized geometry of (AR + 2H) 2+ cation-radical 3. 1 7 0 4.183217-2.694553-0.173306 2 6 0 4.059788-1.297926 0.405791 3 6 0 2.684753-0.832259-0.158005 4 8 0 2.111831-1.597888-0.952745 5 7 0 2.221978 0.344277 0.245476 6 1 0 4.152696-3.433618 0.531890 7 1 0 3.304762-2.736417-0.787639 8 6 0 0.962083 0.934292-0.233174 9 1 0 2.759348 0.946554 0.865681 10 6 0 1.125649 2.436193-0.007676 11 8 0 1.989352 2.907436 0.707606 12 8 0 0.215909 3.158535-0.665590 13 6 0-0.263333 0.336955 0.507991 14 6 0-1.616903 0.629134-0.154196 15 6 0-2.758883-0.095293 0.569654 16 1 0 4.006752-1.391614 1.493729 17 6 0 5.239692-0.419333-0.011304 18 1 0 0.868540 0.734863-1.305432 19 1 0 0.358509 4.100965-0.462493 20 1 0-0.251881 0.681600 1.549873 21 1 0-0.108858-0.747714 0.527014 22 1 0-1.808881 1.707896-0.169735 23 1 0-1.599931 0.295412-1.198624 24 1 0-2.781972 0.215411 1.631368 25 1 0-2.589861-1.175192 0.555734 26 1 0 5.024890-2.818546-0.740543 27 7 0-4.024758 0.146744-0.107484 28 6 0-5.156868-0.668790 0.207410 29 7 0-6.158742-0.600061-0.795128 30 7 0-4.855894-1.995566 0.633888 31 1 0-5.956752 0.054041-1.543213 32 1 0-7.104268-0.491533-0.448402 33 1 0-4.892789-2.127527 1.638269 34 1 0-5.457507-2.668931 0.168956 35 1 0-4.283641 1.128465-0.076400 36 1 0 5.299697-0.325285-1.100571 37 1 0 6.182096-0.822844 0.370889 38 1 0 5.125829 0.585624 0.402419 Rotational constants (GHZ): 0.6581455 0.1657598 0.1379489 E[B3LYP/6-31+G(d,p)] = -854.855669588 a.u. Zero point energy = 865.5521 kj mol -1 E[PMP2/6-311++G(3df,2p)] = -853.1900606 a.u. E[CCSD(T)/6-31+G(d,p)] = -852.5837665 a.u. E[CCSD(T)/6-311++G(3df,2p)] = -853.4041086 a.u. S11

Table S5. B3LYP/6-31+G(d,p) optimized geometry of TS(1 2) for side-chain rotation 1 7 0 4.835648-2.101518-0.380516 2 1 0 2.895094-2.403766-0.789282 3 1 0 5.498104-2.661586 0.147426 4 1 0 5.312366-1.749833-1.208699 5 6 0 4.296819-0.991994 0.431550 6 1 0 4.090460-1.422260 1.428779 7 6 0 5.249215 0.198477 0.601356 8 1 0 5.461120 0.670204-0.364991 9 1 0 4.838257 0.959837 1.274665 10 1 0 6.195681-0.135764 1.037344 11 6 0 2.969551-0.629670-0.209562 12 8 0 2.218127-1.721482-0.586722 13 6 0 0.599930 2.205610-0.104564 14 8 0-0.524891 2.667673-0.103473 15 8 0 1.699437 2.981207-0.016793 16 1 0 1.412095 3.909197 0.043062 17 7 0 2.196240 0.381876 0.395174 18 1 0 2.758025 1.203965 0.578102 19 6 0 0.924924 0.719057-0.246614 20 1 0 1.003518 0.548551-1.336669 21 6 0-0.231545-0.144908 0.303348 22 1 0 0.173338-1.145022 0.472064 23 1 0-0.540636 0.257838 1.275433 24 6 0-1.436542-0.219670-0.645632 25 1 0-1.728878 0.797220-0.925175 26 1 0-1.149300-0.728344-1.571703 27 6 0-2.645021-0.944558-0.014247 28 1 0-2.856530-1.885115-0.533104 29 1 0-2.445718-1.168055 1.041629 30 7 0-3.853606-0.095631-0.098997 31 1 0-3.695159 0.892915-0.254278 32 6 0-5.102104-0.493589 0.129017 33 7 0-6.134400 0.337543-0.106548 34 1 0-5.999877 1.215329-0.586190 35 1 0-7.056209 0.145478 0.256297 36 7 0-5.352738-1.732348 0.579561 37 1 0-4.607746-2.332459 0.899166 38 1 0-6.288762-2.109493 0.583395 Rotational constants (GHZ): 0.8286183 0.1594812 0.1371188 E[B3LYP/6-31+G(d,p)] = -854.871829122 a.u. Zero point energy = 863.9157 kj mol -1. S12

Table S6. B3LYP/6-31+G(d,p) optimized geometry of TS(N ε H ε ) for loss of H ε. 1 7 0 4.482324-2.482437-0.232957 2 6 0 4.190545-1.152195 0.433552 3 6 0 2.800983-0.785445-0.169175 4 8 0 2.329620-1.568824-1.013299 5 7 0 2.222258 0.328935 0.255452 6 1 0 4.535399-3.265721 0.420888 7 1 0 3.617937-2.579975-0.864617 8 6 0 0.937114 0.833771-0.254120 9 1 0 2.679990 0.950013 0.919789 10 6 0 0.977276 2.336877 0.020678 11 8 0 1.754868 2.840533 0.810061 12 8 0 0.069811 3.012546-0.683293 13 6 0-0.263874 0.127365 0.428089 14 6 0-1.615899 0.399757-0.239988 15 6 0-2.758985-0.381353 0.419315 16 1 0 4.092076-1.334061 1.507201 17 6 0 5.293642-0.132133 0.151501 18 1 0 0.896141 0.659103-1.333647 19 1 0 0.110079 3.953793-0.434113 20 1 0-0.286333 0.416002 1.487023 21 1 0-0.047836-0.947080 0.391373 22 1 0-1.869662 1.462495-0.198604 23 1 0-1.572960 0.125362-1.301081 24 1 0-2.771235-0.150887 1.499035 25 1 0-2.585062-1.464025 0.320709 26 1 0 5.336115-2.467396-0.795376 27 7 0-4.008697-0.004069-0.221988 28 6 0-5.077978-0.719869-0.021789 29 7 0-6.195335-0.488353-0.798280 30 7 0-5.195936-1.731199 0.909061 31 1 0-6.075334 0.282413-1.443110 32 1 0-7.092266-0.488042-0.327920 33 1 0-4.642821-1.679146 1.750426 34 1 0-6.069349-2.231063 0.986214 35 1 0-4.227202 1.558369 0.255149 36 1 0 5.398625 0.054475-0.922346 37 1 0 6.252117-0.470291 0.556353 38 1 0 5.057947 0.820841 0.631503 Rotational constants (GHZ): 0.7216884 0.1590369 0.1364322 E[B3LYP/6-31+G(d,p)] = -854.815152966 a.u. Zero point energy = 841.4689 kj mol -1 E[PMP2/6-311++G(3df,2p)] = -853.1546656 a.u. E[CCSD(T)/6-31+G(d,p)] = -852.539181 a.u. E[CCSD(T)/6-311++G(3df,2p)] = -853.3626076 a.u. S13

Table S7. B3LYP/6-31+G(d,p) optimized geometry of TS(N C α ).for N C α bond cleavage. 1 7 0 5.173930-0.242340 0.354299 2 1 0 4.266507 1.334953 0.807250 3 1 0 6.124199-0.329019 0.008849 4 1 0 5.034222-0.937920 1.083785 5 6 0 4.172718-0.363197-0.721437 6 1 0 4.647218 0.043042-1.626382 7 6 0 3.710906-1.796034-1.014993 8 1 0 3.208380-2.231596-0.145291 9 1 0 3.025406-1.840134-1.867908 10 1 0 4.575845-2.415623-1.266828 11 6 0 3.036753 0.596927-0.358963 12 8 0 3.356211 1.572448 0.491514 13 6 0 0.090856-0.559405 0.739619 14 8 0-0.864643-1.247377 0.272827 15 8 0 0.967271-1.129587 1.617735 16 1 0 0.647329-2.027058 1.803394 17 7 0 1.797180 0.570267-0.803017 18 1 0 1.603749-0.204819-1.430606 19 6 0 0.480144 0.773987 0.315695 20 1 0 1.006125 1.324778 1.093648 21 6 0-0.540279 1.606991-0.445368 22 1 0-0.011670 2.481328-0.832932 23 1 0-0.874232 1.043694-1.325394 24 6 0-1.765941 2.065191 0.398942 25 1 0-1.659187 1.744868 1.441813 26 1 0-1.815002 3.158206 0.418810 27 6 0-3.117155 1.564062-0.130267 28 1 0-3.923835 1.944007 0.508406 29 1 0-3.282030 1.936692-1.150722 30 7 0-3.136645 0.097972-0.126814 31 1 0-2.215620-0.395260-0.029040 32 6 0-4.200211-0.680469-0.192911 33 7 0-4.050440-2.008283 0.011331 34 1 0-3.118922-2.364789 0.188392 35 1 0-4.742376-2.661733-0.322787 36 7 0-5.433292-0.194494-0.439346 37 1 0-5.574089 0.783207-0.638621 38 1 0-6.254610-0.760869-0.291524 Rotational constants (GHZ): 1.0078633 0.1891761 0.1719082 E[B3LYP/6-31+G(d,p)] = -854.883468193 a.u. Zero point energy = 859.1245 kj mol -1 E[PMP2/6-311++G(3df,2p)] = -853.2145332 a.u. E[CCSD(T)/6-31+G(d,p)] = -852.6006225 a.u. E[CCSD(T)/6-311++G(3df,2p)] = -853.4233274 a.u. S14

Table S8. B3LYP/6-31+G(d,p) optimized geometry of TS(C δ N ε ) for loss of guanidine. 1 7 0 4.348379-2.627843-0.101902 2 6 0 4.137487-1.259672 0.515525 3 6 0 2.773354-0.840791-0.098072 4 8 0 2.195870-1.681711-0.820358 5 7 0 2.295978 0.361347 0.209393 6 1 0 4.468981-3.373472 0.586486 7 1 0 3.419762-2.737598-0.640490 8 6 0 1.015408 0.883724-0.274933 9 1 0 2.829736 1.018062 0.773832 10 6 0 1.146334 2.397954-0.170075 11 8 0 2.005432 2.948714 0.494364 12 8 0 0.210491 3.048215-0.870666 13 6 0-0.185319 0.316800 0.548997 14 6 0-1.565683 0.520728-0.108863 15 6 0-2.671400-0.158168 0.650760 16 1 0 4.016992-1.411771 1.594133 17 6 0 5.309032-0.320905 0.233897 18 1 0 0.889280 0.596032-1.323870 19 1 0 0.338679 4.005374-0.742290 20 1 0-0.162575 0.750158 1.555890 21 1 0-0.000767-0.757474 0.654420 22 1 0-1.775981 1.592396-0.202234 23 1 0-1.537166 0.119143-1.130882 24 1 0-2.940115 0.290532 1.608338 25 1 0-2.613050-1.243818 0.701928 26 1 0 5.136414-2.651468-0.753220 27 7 0-4.209302 0.058965-0.450508 28 6 0-5.272890-0.681420-0.139726 29 7 0-6.393347-0.261503 0.572832 30 7 0-5.201473-2.051958-0.356517 31 1 0-6.361974 0.685332 0.924403 32 1 0-6.772087-0.915084 1.252968 33 1 0-4.550442-2.298329-1.091458 34 1 0-6.093571-2.517837-0.470328 35 1 0-4.398169 1.046767-0.297077 36 1 0 5.442374-0.159507-0.840829 37 1 0 6.236879-0.715510 0.659271 38 1 0 5.132865 0.653763 0.696154 Rotational constants (GHZ): 0.6780148 0.1564884 0.1318351 E[B3LYP/6-31+G(d,p)] = -854.831242122 a.u. Zero point energy = 852.2488 kj mol -1 E[PMP2/6-311++G(3df,2p)] = -853.159875 a.u. E[CCSD(T)/6-31+G(d,p)] = a.u. E[CCSD(T)/6-311++G(3df,2p)] = a.u. S15

Table S9. B3LYP/6-31+G(d,p) optimized geometry of (AR + H) + by loss of H ε. 1 7 0 4.356936-2.552045-0.234601 2 6 0 4.110230-1.211946 0.430684 3 6 0 2.732119-0.801328-0.169679 4 8 0 2.235144-1.568555-1.013644 5 7 0 2.188065 0.329544 0.258003 6 1 0 4.382309-3.336131 0.419963 7 1 0 3.489824-2.620756-0.866576 8 6 0 0.915256 0.870030-0.246448 9 1 0 2.667453 0.936995 0.919377 10 6 0 1.001008 2.371911 0.020221 11 8 0 1.802161 2.858932 0.796395 12 8 0 0.102899 3.071158-0.674345 13 6 0-0.302876 0.200690 0.443491 14 6 0-1.647105 0.472788-0.241825 15 6 0-2.805245-0.282535 0.423521 16 1 0 4.008268-1.388949 1.504789 17 6 0 5.245206-0.228752 0.144457 18 1 0 0.863517 0.691761-1.324949 19 1 0 0.184019 4.012687-0.436594 20 1 0-0.327066 0.511162 1.496365 21 1 0-0.105194-0.877603 0.431579 22 1 0-1.884062 1.540348-0.238982 23 1 0-1.597346 0.166470-1.293902 24 1 0-2.864272 0.033769 1.482912 25 1 0-2.579188-1.364660 0.432525 26 1 0 5.211147-2.567091-0.796380 27 7 0-4.031818 0.004837-0.290523 28 6 0-5.085068-0.680906-0.011772 29 7 0-6.214310-0.567507-0.814471 30 7 0-5.189911-1.636356 0.985981 31 1 0-6.110786 0.153137-1.517377 32 1 0-7.108181-0.534446-0.340365 33 1 0-4.613183-1.538639 1.806482 34 1 0-6.071201-2.106932 1.125971 35 1 0 5.353106-0.046556-0.929841 36 1 0 6.193301-0.597674 0.546905 37 1 0 5.042006 0.731801 0.624238 Rotational constants (GHZ): 0.7063520 0.1615549 0.1379512 E[B3LYP/6-31+G(d,p)] = -854.313053573 a.u. Zero point energy = 836.2715 kj mol -1 E[PMP2/6-311++G(3df,2p)] = -852.661536 a.u. E[CCSD(T)/6-31+G(d,p)] = -852.0479059 a.u. E[CCSD(T)/6-311++G(3df,2p)] = -852.8680736 a.u. S16