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Exploring Potential Energy Surfaces for Chemical Reactions Prof. H. Bernhard Schlegel Department of Chemistry Wayne State University Current Research Group Dr. Jason SonnenbergDr. Peng Tao Barbara MunkJia Zhou Michael CatoJason Sonk Brian Psciuk Recent Group Members Dr. Xiaosong LiDr. Hrant Hratchian Dr. Stan SmithDr. Jie (Jessy) Li Dr. Smriti AnandDr. John Knox UC - Davis, March 14, 2007

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Research overview nWith molecular orbital calculations, it is possible to investigate details of chemical reactions and molecular properties that are often difficult to study experimentally nOur group is involved in both the development and the application of new methods in ab initio molecular orbital (MO) methods.

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Features of Potential Energy Surfaces

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Development of new algorithms nenergy derivatives for geometry optimization nsearching for transition states nfollowing reaction paths ncomputing classical trajectories for molecular dynamics directly from the MO calculations. nspin projection methods to obtain more accurate energetics for open shell systems (radicals) nsimultaneous optimization of the wavefunction and the geometry

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Applications Organic systems Inorganic systems Biochemistry Study of materials Dynamics uNickel catalyzed three component couplings uReactions involving nitric oxides uOrgano-metallic complexes uInteractions in the active site of enzymes uGuanine oxidation uAmber parameters for modified RNA and DNA bases uCVD studies on TiN and ZnO uOrganic LED materials uMolecules in a nanotube uBlue shifted hydrogen bonds uOne transition state serving two mechanisms uMolecules in intense laser fields uTwo and three body photo dissociation reactions

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Ni Catalyzed Three Component Coupling Montgomery, Acc. Chem. Res. 2000, 33, 467-473. Hratchian, Chowdhury, Gutierrez-Garcia, Amarasinghe, Heeg, Schlegel, Montgomery, Organomet. 2004, 23, 4636-4646, 5652. The mechanism for a family of nickel catalyzed three component coupling reactions has been studied experimentally by Prof. Montgomery (WSU). MO studies provide additional insight into the mechanism.

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Reaction Profile for L=H 2 NCH 2 CH 2 NH 2

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Ligand Exchange with ZnMe 2

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OXA-10 β-lactamase nX-ray structure shows carboxylated Lys70 nModified Lys70 has mechanistic role uRemoves proton from Ser67 uLeads to acylation of Ser67 by substrate nEnzyme shows biphasic kinetics during substrate turnover J. Li; J. B. Cross; T. Vreven; S. O. Meroueh; S. Mobashery; H. B. Schlegel; Proteins 2005, 61, 246-257

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ONIOM QM/MM Method nThe active site region is treated using high-level molecular orbital theory, while the most distant parts of the enzyme are treated using low-cost molecular mechanics.

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Carboxylation in Gas Phase and in Solution (B3LYP/6-31G(d,p)) ModelTS1PTS2DTS3P3TS4D4 Gas Phase38.75.439.617.70.732.5-6.1 Solution32.4-5.637.4-2.412.0-10.636.6-5.0 Rx1: CH 3 NH 2 +CO 2 Rx2: CH 3 NH 2 +HCO 3 - Rx3: CH 3 NH 2 +CO 2 +H 2 O Rx4: CH 3 NH 2 +HCO 3 - +H 2 O

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QM/MM Calculations of the Transition State for Lys-70 Carboxylation Trp-154 Lys-70 Ser-67 Trp-154 Lys-70 Ser-67 Stereoview of the TS showing a molecule of water catalyzing the addition of carbon dioxide to the side chain of Lys-70

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Carboxylation in the QM/MM model of the active site of OXA-10 ModelTS1PTS2DTS3P3TS4D4 Gas Phase38.75.439.617.70.732.5-6.1 Solution32.4-5.637.4-2.412.0-10.636.6-5.0 Enzyme37.9-12.025.6-36.113.8-12.742.8-51.8

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QM/MM Calculations of the Reactants, TS and Products for Lys-70 Carboxylation QM/MM values in normal text X-ray values in italics

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OXA-10 β-lactamase - Discussion n A water molecule in the active site can catalyze carboxylation of Lys70 with CO 2 n X-ray structure is most likely the deprotonated carboxylation product nCarboxylation is accompanied by deprotonation nRe-protonation of carbamate nitrogen results in barrierless loss of CO 2, accounting for biphasic kinetics of enzyme

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B. M. Munk, C. J. Burrows, H. B. Schlegel, Chem. Res. Toxicol. (accepted) Transformations of 8-hydroxy guanine radical B3LYP/6-31+G(d) gas phase optimization IEF-PCM B3LYP/aug-cc-pVTZ solution phase energies Oxidative Damage to DNA

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Transformations of 8-hydroxy guanine radical Path 1: reduction followed by tautomerization and ring opening

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Transformations of 8-hydroxy guanine radical Path 2: tautomerization followed by ring opening and reduction

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Transformations of 8-hydroxy guanine radical Path 3: ring opening followed by reduction and tautomerization

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Transformations of 8-hydroxy guanine radical Path 4: ring opening followed by tautomerization and reduction

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Transformations of 8-hydroxy guanine radical (a) Pathways 2 and 4 are preferred (b) Barriers for ring opening and tautomerization are lower for the radical than for the closed shell molecule

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AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA R. Aduri, B. T. Psciuk, P. Saro, H. B. Schlegel, J. SantaLucia Jr. J. Chem. Theor. Comp. (submitted) N2-methylguanosine 1-methylpseudouridine 5-carboxymethylamino methyluridine 4-demethylwyosine galactosyl-queuosine queuosine

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Protocol for Determining Atom-centered Partial Charges

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Modular approach to fitting RESP charges The C3’ endo sugar charge was obtained by multi equivalencing the four natural nucleosides Two stage RESP was used to fit the ESP of the modified bases and sugars Atom types and parameters available in GAFF were sufficient for almost all 103 modifications The “prepin” and “frcmod” files generated for all 103 modifications Parameters can be downloaded from http://ozone3.chem.wayne.edu:8080/Modifieds/index.jsp

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Test Application of the Parameters for Modified RNA Bases H. Shi and P. B. Moore RNA (2000) 6 1091-2000 5MC MRG MRC 5MC 7MG WBG 2MG M2G PSU 2MG DHU 5MUPSU tRNA Phe with and without modified bases (1EHZ)

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Ab Initio Molecular Dynamics (AIMD) nAIMD – electronic structure calculations combined with classical trajectory calculations nEvery time the forces on the atoms in a molecule are needed, do an electronic structure calculation nBorn – Oppenheimer (BO) method: converge the wavefunction at each step in the trajectory nExtended Lagrangian methods: propagate the wavefunction along with the geometry uCar-Parrinello – plane-wave basis, propagate MO’s uADMP – atom centered basis, propagate density matrix

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Ab Initio Classical Trajectory on the Born-Oppenheimer Surface Using Hessians Calculate the energy, gradient and Hessian Solve the classical equations of motion on a local 5 th order polynomial surface Millam, J. M.; Bakken, V.; Chen, W.; Hase, W. L.; Schlegel, H. B.; J. Chem. Phys. 1999, 111, 3800-5.

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A Reaction with Branching after the Transition State Previous work with S. Shaik (JACS 1997, 119, 9237 and JACS 2001, 123, 130): Common TS for inner sphere ET and SUB(C) reactions. Long C-C bond in TS (ca. > 2.45 Å ) favors ET; shorter favors SUB( C ). A less electronegative halide switches the mechanism from SUB( C ) to ET. Poorer electron donors of radical anions favor SUB( C ). More bulkier alkyl halide or more strained TS favor ET.

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Sub(C) OCH 2 CH 3 + Cl - ET CH 2 O + CH 3 + Cl - SUB(C) and ET Reaction Paths for CH 2 O.- + CH 3 Cl TS (C-C) (bohr) (C-Cl) (bohr)

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Energetics at the UHF/6-31G(d) level of theory

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Temperature dependence of the branching ratio Li, J.; Li, X.; Shaik, S.; Schlegel, H. B. J. Phys. Chem. A 2004, 108, 8526-8532.

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Energetics at the G3 level of theory

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Improved Potential Energy Surfaces using Bond Additivity Corrections (BAC) nThe most important correction needed for this reaction are C-C and C-Cl bond stretching potentials. nBAC (bond additivity correction) uadd simple corrections to get better energetics for the reaction u E = E′+ ∆E u ∆E = A C-C Exp{-α C-C R C-C } + A C-Cl Exp{- α C-Cl R C-Cl } uadd the corresponding corrections to gradient and hessian u G = G′+ ∂(∆E)/∂x u H = H′+ ∂ 2 (∆E)/∂x 2 uA and α are parameters obtained by fitting to G3 energies

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BAC-UHF Dynamics Results SUB(C)SUB(C)-ETDirect ETSUB(O)NR UHF/6-31G(d)42.4%53.2%1.0%0.5%3.0% BHandHLYP/6-31G(d)48.8%24.1%15.3%0.0%10.3% BAC-UHF/6-31G(d)56.2%35.5%6.9%0.0%1.5% Table 2. Branching ratios at different levels of theory. Li, J.; Shaik, S.; Schlegel, H. B.; J. Phys. Chem. A 2006, 110, 2801-2806..

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Electronic Response of Molecules Short, Intense Laser Pulses nFor intensities of 10 14 W/cm 2, the electric field of the laser pulse is comparable to Coulombic attraction felt by the valence electrons – strong field chemistry nNeed to simulate the response of the electrons to short, intense pulses nTime dependent Schrodinger equations in terms of ground and excited states = C i (t) i i ħ dC i (t)/dt = H ij (t) C i (t) nRequires the energies of the field free states and the transition dipoles between them nNeed to limit the expansion to a subset of the excitations – TD-CIS, TD-CISD nTime dependent Hartree-Fock equations in terms of the density matrix i ħ dP(t)/dt = [F(t), P(t)] nFor constant F, can use a unitary transformation to integrate analytically P(t i+1 ) = V P(t i ) V † V = exp{ i t F } nFock matrix is time dependent because of the applied field and because of the time dependence of the density (requires small integration step size – 0.05 au)

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Test Case H 2 in an intense laser field TD-HF/6-311++G(d,p) E max = 0.10 au (3.5 10 14 W/cm 2 ) = 0.06 au (760 nm)

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Test Case (a) (b) (c) H 2 in an intense laser field TD-HF/6-311++G(d,p) E max = 0.12 au (5.0 10 14 W/cm 2 ) = 0.06 au (760 nm) Laser pulse Instantaneous dipole response Fourier transform of the residual dipole response

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Hydrogen Molecule aug-pVTZ basis plus 3 sets of diffuse sp shells E max = 0.07 au (1.7 10 14 W/cm 2 ), = 0.06 au (760 nm) (a) (b) (c) (b) (c) (d) (e) (f) TD-CIS TD-CISD TD-HF

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Butadiene in an intense laser field (8.75 x 10 13 W/cm 2 760 nm) HF/6-31G(d,p) t = 0.0012 fs

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The Charge Response of Neutral Butadiene

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Butadiene in an intense laser field TD-CIS/6-31G(d,p), 160 singly excited states = 0.06 au (760 nm) Fourier transform of the residual dipole Excited state weights in the final wavefunction

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Polyacenes in Intense Laser Pulse (Levis et al. Phys. Rev. A 69, 013401 (2004)) 1 10 14 W·cm -2 Time-of-flight, s Ion Signal, normalized

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TDHF Simulations for Polyacenes Polyacenes ionize and fragment at much lower intensities than polyenes Polyacene experimental data shows the formation of molecular +1 cations prior to fragmentation with 60 fs FWHM pulses Time-dependent Hartree-Fock simulations with 6-31G(d,p) basis, t = 0.0012 fs, ω=1.55 eV and 5 fs FWHM pulse Intensities chosen to be ca 75% of the experimental single ionization intensities Intensities of 8.75 x 10 13, 3.08 x 10 13, 2.1 x 10 13 and 4.5 x10 12 for benzene, naphthalene, anthracene and tetracene Nonadiabatic multi-electron excitation model was used to check that these intensities are non-ionizing

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Tetracene: Dipole Response I = 3.38 x 10 12 W/cm 2 ω = 1.55eV, 760 nm

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Naphthalene +1 : Dependence on the Field Strength ω = 1.55eV, 760 nm

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Energy (eV) 1.1 eV 4.5 eV 7.1 eV Transition Amplitude 1.1 eV 3.1 eV (2x1.55 eV) 4.5 eV 7.1 eV Energy (eV) E = 0.0155 au E = 0.029 auE = 0.034 au 8.95 eV Naphthalene +1 : Dependence on the Field Strength ω = 1.55eV, 760 nm

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Anthracene +1 : Dependence on the Field Frequency E max = 0.0183 au

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ω = 1.00 eV 1.95 eV 3.63 eV 4.95 eV 6.32 eV 7.79 eV 9.57 eV 5 10 15 20 25 Transition Amplitude ω = 2.00 eV 1.95 eV 3.63 eV 6.32 eV 7.97 eV 40 30 20 10 ω = 3.00 eV 2.79 eV 3.63 eV 4.61 eV 5.58 eV 7.97 eV 10.23 eV 10 20 30 40 50 Anthracene +1 : Dependence on the Field Frequency Energy Energy Energy

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n Non-adiabatic behavior increases with length n Non-adiabatic behavior is greater for monocation n Increasing the field strength increases the non-resonant excitation of the states with the largest transition dipoles n Increasing the field frequency increases the non-resonant excitation of higher states Smith, S. M.; Li, X.; Alexei N. Markevitch, A. N.; Romanov, D. A.; Robert J. Levis, R. J.; Schlegel, H. B.; Numerical Simulation of Nonadiabatic Electron Excitation in the Strong Field Regime: 3. Polyacene Neutrals and Cations. (JPCA submitted) Polyacenes: Summary

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Recent Group Members

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Current Group Members

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Current Research Group Dr. Jason SonnenbergDr. Peng Tao Barbara MunkMichael Cato Jia ZhouJason Sonk Brian Psciuk Recent Group Members Prof. Xiaosong Li, U of Washington Prof. Smriti Anand, Christopher-Newport U. Dr. Hrant Hratchian, Indiana U. (Raghavachari grp) Dr. Jie Li, U. California, Davis (Duan group) Dr. Stan Smith, Temple U. (Levis group) Dr. John Knox (Novartis) Funding and Resources: National Science Foundation Office of Naval Research NIH Gaussian, Inc. Wayne State U. Acknowledgements Collaborators : Dr. T. Vreven, Gaussian Inc. Dr. M. J. Frisch, Gaussian Inc. Prof. John SantaLucia, Jr., WSU Raviprasad Aduri (SantaLucia group) Prof. G. Voth, U. of Utah Prof. David Case, Scripps Prof. Bill Miller, UC Berkeley Prof. Thom Cheatham, U. of Utah Prof. S.O. Mobashery, Notre Dame U. Prof. R.J. Levis, Temple U. Prof. C.H. Winter, WSU Prof. C. Verani, WSU Prof. E. M. Goldfield, WSU Prof. D. B. Rorabacher, WSU Prof. J. F. Endicott, WSU Prof. J. W. Montgomery, U. of Michigan Prof. Sason Shaik, Hebrew University Prof. P.G. Wang, Ohio State U. Prof. Ted Goodson, U. of Michigan Prof. G. Scuseria, Rice Univ. Prof. Srini Iyengar, Indiana U Prof. O. Farkas, ELTE Prof. M. A. Robb, Imperial, London

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Molecular geometries and orientation of the field

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Effect of Charge and Geometry on the Dipole Moment Response: Butadiene I = 8.75 x 10 13 W/cm 2 ω = 1.55eV, 760 nm

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Butadiene +1 : Fourier Analysis of Residual Oscillations 4.10 eV 5.69 eV Main Transition (TDHF Coefficient) Energy (eV) Transition Dipole (au) Oscil. Stren. Neutral Geometry HOMO → SOMO (1.00) 2.531.700.12 SOMO → LUMO (0.92) 4.871.750.38 Ion Geometry HOMO → SOMO (0.95) 4.031.940.39 HOMO → LUMO (0.83) 5.690.230.01 Ion Geometry Transition Amplitude 2.32 eV Neutral Geometry 2.57 eV 4.90 eV

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n The monocations have lower energy excited states and show greater non-adiabatic behavior than the dications n Relaxing the geometry increases the energy of the lowest excited states and decreases the non-adiabatic behavior n Fourier transform of the residual oscillations in the dipole moment shows that the non-adiabatic excitation involves the lowest excited states Smith, S. M.; Li, X.; Alexei N. Markevitch, A. N.; Romanov, D. A.; Robert J. Levis, R. J.; Schlegel, H. B.; Numerical Simulation of Nonadiabatic Electron Excitation in the Strong Field Regime: 2. Linear Polyene Cations. J. Phys. Chem. A 2005, 109, 10527-10534. Polyene Cations: Summary

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Ionization Probability using NME Molecule Excited State Energy (Δ) Transition Dipole Moment (au) Ionization Probability Benzene Neutral8.001.87000.0022 +1 Neutral Geometry5.591.02940.0052 +1 Ion Geometry5.601.11650.0054 +2 Neutral Geometry7.531.37390.00034 +2 Ion Geometry7.411.25110.00023 Naphthalene Neutral6.943.01040.0001 +1 Neutral Geometry6.991.70970.011 +1 Ion Geometry7.262.33530.00018 +2 Neutral Geometry6.632.35040.00025 +2 Ion Geometry6.352.37330.00026 Anthracene Neutral6.213.99170.00015 +1 Neutral Geometry6.372.74560.00047 +2 Neutral Geometry5.943.16930.00056 Tetracene Neutral5.704.88400.00006 +1 Neutral Geometry6.283.39350.0011 +2 Neutral Geometry5.443.89640.00095

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n Time-dependent HF or DFT propagation of the electron density n Classical propagation of the nuclear degrees of freedom n Novel integration method using three different time scales Li, X.; Tully, J. C.; Schlegel, H. B.; Frisch, M. J.; Ab Initio Ehrenfest Dynamics. J. Chem. Phys. 2005, 123, 084106 Ehrenfest Dynamics

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Potential energy curves for H 2 C=NH 2 + torsion

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Torsional dynamics for H 2 C=NH 2 +

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Exploring Potential Energy Surfaces Using Ab Initio Molecular Dynamics Prof. H. Bernhard Schlegel Department of Chemistry Wayne State University Current.

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