vidossich ShilovReaction ESI · 2011. 12. 12. · 1 PtII as proton shuttle during C – H bond activation in the Shilov process Pietro Vidossich,* a Gregori Ujaque, Agustí Lledós

1

PtII as proton shuttle during C – H bond activation in the Shilov process

Pietro Vidossich,* a Gregori Ujaque, a Agustí Lledós a a Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Fax: (+)34 935812920; Tel: (+)34 935812857; E-mail: [email protected]

Supplementary Information

Electronic Supplementary Material (ESI) for Chemical CommunicationsThis journal is © The Royal Society of Chemistry 2012

2

Computional details

Ab initio molecular dynamics (AIMD) simulations were performed according to the Car-Parrinello

approach1 with the CPMD program.2 The trans-PtCl2(H2O)(CH4) and cis-PtCl2(H2O)(CH4) optimized

structures were solvated with 32 water molecules in a cubic box of ~10.18 Å edge and treated under

periodic boundary conditions. Models of similar sizes were successfully used to model the hydrolysis

of cisplatin,3 the Wacker process4 and to characterize the PtII aqua complex.5 The models initially

underwent 500 ps classical MD equilibration (fixing the coordinates of the complex) and the final

conformations were used to start the AIMD simulations. A time step of 5 au and a fictitious electron

mass of 900 au were used to solve the equations of motion. Simulations were performed at constant

temperature coupling the system to a Nose-Hoover thermostat.6, 7 The reference temperature was set to

350 K in order to guarantee the liquid state of the solvent.8, 9 AIMD simulations were based on the

Becke10 and Lee-Yang-Parr11 density functionals (BLYP). This functional has been successfully used to

model the hydrolysis of cisplatin.3, 12 Kohn-Sham13 valence orbitals were expanded in plane waves with

kinetic energy < 70 Ry. Martins-Troullier pseudopotentials were used to describe the core-valence shell

electrons interactions.14 For Cl, C, O and H only valence electrons were described explicitly, whereas

for Pt a semicore pseudopotential was used.

Metadynamics15, 16 was performed for the cis-PtCl2(H2O)(CH4) isomer in order to promote the C-H

bond cleavage within the timescale accessible to simulations. The coordination number (see ref 16 for

the mathematical formula, p=8, q=14, distance cutoff=1.7 Å) between the methane carbon atom and its

four bonded protons was used to activate the process. Metadynamics was performed in the extended

lagrangian formalism,16 coupling the collective variable to a fictitious particle of mass 100 amu by a

harmonic potential with force constant 1.5 au. A time dependent biasing potential was built adding

gaussian-shaped potential energy functions of width 0.015 and 0.19 kcal/mol height every 200

molecular dynamics steps.

Geometry optimizations were performed for the isolated complexes using the GDIIS17 method until the

largest component of the nuclear gradient was lower than 5 x 10-4 a.u. The models were placed in a

supercell and treated as isolated.18

pKa Calculation. As an alternative means of estimating the acidity of the Pt – H bond, its pKa was

computed according to standard methods.19, 20 The pKa is related to the free energy change of the


3

dissociation reaction by: pKa = ΔGaq/RTln10, where ΔGaq is calculated from the thermodynamic cycle

depicted in Scheme 1S. Geometries of trans-PtCl2(H2O)(CH4) and trans-PtHCl2(H2O)2(CH3) were

optimized with basis sets def2-TZVPP21 with the ORCA code.22 Scalar relativistic effects were

accounted for by the ZORA approximation.23, 24 Free energies of solvation were calculated using the

COSMO25 solvation model using a dielectric constant of ε=80 and atomic radii Pt = 2.01, O = 1.72, Cl

= 2.05, C = 2.00, H = 1.30 Å to define the solute cavity. The gas phase deprotonation energy included

zero point correction. Ggas(H+) was set to -6.28 kcal/mol,20 Gsol(H+) to -265.9 kcal/mol.26 The pKa

turned out to be negative (-5.2) pointing to a highly acidic proton.


4

On the assignment of the Pt oxidation state. The concept of oxidation state is certainly a fundamental

one in chemistry. For a transition metal atom it reflects the dn electron configuration and it would thus

appear accessible from quantum chemical calculations which determine the electron distribution within

the complex. It turns out that it is not straightforward to assign a formal integer oxidation state to a

metal atom from the outcome of electronic structure calculations.27 Methods based on population

analysis schemes27, 28 as well as methods based on the partitioning of the electron density29 fail to

reproduce integer variations which are expected from one electron reduction/oxidation (actually, this

observation was interpreted as a compensation mechanism in the metal-ligand orbital mixing29).

Furthermore, the observed variations in the metal charge are dependent on the ligands involved.28

An electron counting technique is generally used to assign formal oxidation states. Given the Lewis

structure of the compound, we assign electrons to atom X going through its X-Y bonds according to the

following rules: we count 1 if the bond is covalent, O if the bond is ionic and electronegativity(X) <

electronegativity(Y), 2 if the bond is ionic and electronegativity(X) > electronegativity(Y). A lone pair

counts 2. Comparison of the number of electrons assigned to X and the number of its valence electrons

gives the oxidation state of X.

In order to apply the above technique to the outcome of an electronic structure calculation, we have to

decide on the nature of each molecular orbital (MO). We will now show that this MO analysis is

facilitated by transforming the standard Kohn-Sham orbitals into a set of maximally localized Wannier

functions, as suggested by Sit et al.30 We illustrate the difference for PtHCl2(H2O)(CH3) in the gas

phase. Electrons “belonging” to Pt are those in orbitals with predominant Pt character. The assignment

may be done by visual inspection. However, to put the analysis on more quantitative grounds, we did

the following. We used Bader's Atoms in Molecules theory31 to determine the Pt atomic basin. We

have then integrated the density of each orbital within this basin. The resulting values are listed in

Table S1 for both KS and Wannier orbitals (please note orbital numbers cannot be put in

correspondence). It may be appreciated that a number of KS orbitals have sizable contributions on Pt.

To be noted that four KS orbitals (1, 12, 15 and 18) have Pt populations of about 1. On the contrary,

Wannier orbitals 1-4, 18, 23 and 24 are clearly centered on Pt, and we find only two orbitals (12 and

14) with a population of about 1. Of the remaining orbitals, 13, 19 and 22 are the only ones with Pt

density > 0.1. This is exactly the bonding situation we would expect in PtHCl2(H2O)(CH3): 7 non-

bonding orbitals on Pt, 2 covalent bonds and 3 ionic bonds.


5

Please note electron counting would assign 16 electrons to Pt for both KS and Wannier obitals (and the

total orbital population on Pt is identical for the two sets of obitals).

We close this section emphasizing that the procedure we have followed to assign oxidation states to Pt,

recently proposed by Sit et al.,30 is a MO analysis in which the orbitals have been conveniently

transformed. We believe this procedure facilitates the analysis, especially for condensed phase systems

(as in the present work).

Table S1. Integrated orbitals density on Pt for Kohn-Sham molecular orbitals (MO) and Wannier functions. Please note psuedopotentials were used in the calculations (of semicore type for Pt) resulting in 48 electrons in 24 orbitals.

MO.1: 1.12 WANNIER.1: 1.93

MO.2: 1.66 WANNIER.2: 1.93

MO.3: 1.77 WANNIER.3: 1.95

MO.4: 1.79 WANNIER.4: 1.92

MO.5: 0.06 WANNIER.5: 0.01

MO.6: 0.50 WANNIER.6: 0.03

MO.7: 0.31 WANNIER.7: 0.04

MO.8: 0.20 WANNIER.8: 0.03

MO.9: 0.06 WANNIER.9: 0.01

MO.10: 0.19 WANNIER.10: 0.03

MO.11: 0.32 WANNIER.11: 0.03

MO.12: 1.25 WANNIER.12: 1.25

MO.13: 0.11 WANNIER.13: 0.15

MO.14: 0.35 WANNIER.14: 1.11

MO.15: 0.87 WANNIER.15: 0.04

MO.16: 0.32 WANNIER.16: 0.02

MO.17: 0.20 WANNIER.17: 0.06

MO.18: 0.91 WANNIER.18: 1.94

MO.19: 0.30 WANNIER.19: 0.51

MO.20: 0.12 WANNIER.20: 0.06

MO.21: 0.31 WANNIER.21: 0.04

MO.22: 1.40 WANNIER.22: 0.51

MO.23: 1.61 WANNIER.23: 1.92

MO.24: 1.74 WANNIER.24: 1.94


6

Figure S1. The graph shows the evolution of selected distances during five independent ab initio

molecular dynamics runs (a to e) of trans-PtCl2(H2O)(CH4). Each run was started from a conformation

obtained from a simulation in which all C-H bonds were restrained around the methane C-H bond

equilibrium distance (shown schematically on top of the graph). The chemical scheme on the left is

used to color code the lines in the graph: Pt-C black line, C-H red, Pt-H green, Owater-H blue.

time restrained MD

unrestrained MD

a b c d e

b

c

d

a

e


7

Figure S2. Selected structures were extracted from the AIMD simulation labeled a in Figure S1

(marked with stars on the time bar of the top graph). Solvent molecules were removed and only

reactive partners were maintained (shown in the middle panel). The bottom graph shows the energy of

each geometry at different levels of theory: PBE32 (black line), BLYP10, 11 (red), B3LYP11, 33 (green)

and MP2 (blue line). All electrons calculations were performed with the ORCA program22 using a

TZVP basis set on all atoms and accounting for scalar relativistic effects by the ZORA23, 24

approximation.

;

time (ps) 2 1 0.

5 1.5

2

4

0

dist.

(Å)


8

Figure S3. The graph shows the evolution of selected distances during the ab initio molecular

dynamics simulation of cis-PtCl2(H2O)(CH4): Pt-C black line, C-H red, Pt-H green, Owater-H blue. The

orange line shows the evolution of the collective variable used in the metadynamics part of the

simulation to activate the C-H bond. The collective variable used was the coordination number of the

methane carbon atom with its four bonded hydrogen: its value is ~4 for methane and ~3 for the methyl

complex. The vertical bar on the time axis represents the moment at which the addition of new terms in

the biasing potential was suspended. Please note the biasing potential acts only on the carbon

coordination number and not on other degrees of freedom.


9

Figure S4. Gas-phase optimized structures of trans-PtCl2(H2O)(CH4) (left) and cis-PtCl2(H2O)(CH4)

(right). Selected distances are given in Å.


10

Figure S5. The nuclear rearrangements taking place during the C – H bond cleavage are shown

superimposed to the evolution of the relevant Wannier centers (green dots, each representing two

valence electrons, with those corresponding to initial and final states shown larger in green and blue,

respectively). The figure nicely shows the C–H bond transforming into the Pt–C bond and a metal

orbital progressively moving its centre of gravity towards the proton as the C–H bond breaks and the

proton is transferred to the Pt.


11

Table S2. Atomic charges on Pt according to Bader’s31 / Hirsfeld’s34 partitioning of the electron density

of gas-phase optimized structures.

cis trans PtCl2(OH2)2 0.575 / 0.773 0.658 / 0.786 PtCl2(OH2)(CH4) 0.518 / 0.934 0.624 / 1.012 HPtCl2(OH2)(CH3) 0.518 / 1.240 0.557 / 1.252 PtCl4(OH2)2 1.243 / 1.149 1.197 / 1.157


12

References. 1. R. Car and M. Parrinello, Phys. Rev. Lett., 1985, 55, 2471-2474. 2. CPMD. www.cpmd.org 3. P. Carloni, M. Sprik and W. Andreoni, J. Phys. Chem. B, 2000, 104, 823-835. 4. A. Comas-Vives, A. Stirling, A. Lledos and G. Ujaque, Chemistry-a European Journal, 2010,

16, 8738-8747. 5. A. Stirling, I. Bako, L. Kocsis, L. Hajba and J. Mink, Int. J. Quantum Chem, 2009, 109, 2591-

2598. 6. W. G. Hoover, Phys. Rev. A, 1985, 31, 1695-1697. 7. S. Nose, Mol. Phys., 1984, 52, 255-268. 8. M. V. Fernandez-Serra and E. Artacho, J. Chem. Phys., 2004, 121, 11136-11144. 9. J. VandeVondele, F. Mohamed, M. Krack, J. Hutter, M. Sprik and M. Parrinello, J. Chem. Phys.,

2005, 122. 10. A. D. Becke, Phys. Rev. A, 1988, 38, 3098-3100. 11. C. T. Lee, W. T. Yang and R. G. Parr, Phys. Rev. B, 1988, 37, 785-789. 12. J. K.-C. Lau and B. Ensing, PCCP, 2010, 12, 10348-10355. 13. W. Kohn and L. J. Sham, Physical Review, 1965, 140, 1133-&. 14. N. Troullier and J. L. Martins, Phys. Rev. B, 1991, 43, 1993-2006. 15. A. Laio and M. Parrinello, Proceedings of the National Academy of Sciences of the United

States of America, 2002, 99, 12562-12566. 16. M. Iannuzzi, A. Laio and M. Parrinello, Phys. Rev. Lett., 2003, 90. 17. P. Csaszar and P. Pulay, J. Mol. Struct., 1984, 114, 31-34. 18. G. J. Martyna and M. E. Tuckerman, J. Chem. Phys., 1999, 110, 2810-2821. 19. J. J. Klicic, R. A. Friesner, S. Y. Liu and W. C. Guida, J. Phys. Chem. A, 2002, 106, 1327-1335. 20. G. M. Ullmann, L. Noodleman and D. A. Case, J. Biol. Inorg. Chem., 2002, 7, 632-639. 21. F. Weigend and R. Ahlrichs, PCCP, 2005, 7, 3297-3305. 22. ORCA. http://www.thch.uni-bonn.de/tc/orca 23. E. van Lenthe, A. Ehlers and E. J. Baerends, J. Chem. Phys., 1999, 110, 8943-8953. 24. C. van Wullen, J. Chem. Phys., 1998, 109, 392-399. 25. A. Klamt and G. Schuurmann, Journal of the Chemical Society-Perkin Transactions 2, 1993,

799-805. 26. M. Krol, M. Wrona, C. S. Page and P. A. Bates, J. Chem. Theory Comput., 2006, 2, 1520-1529. 27. P. H. L. Sit, R. Car, M. H. Cohen and A. Selloni, Inorg. Chem., 2011, 50, 10259-10267. 28. G. Aullon and S. Alvarez, Theoretical Chemistry Accounts, 2009, 123, 67-73. 29. H. Raebiger, S. Lany and A. Zunger, Nature, 2008, 453, 763-766. 30. P. H. L. Sit, F. Zipoli, J. Chen, R. Car, M. H. Cohen and A. Selloni, Chemistry – A European

Journal, 2011, 17, 12136-12143. 31. R. F. W. Bader, Chem. Rev., 1991, 91, 893-928. 32. J. P. Perdew, K. Burke and M. Ernzerhof, Phys. Rev. Lett., 1996, 77, 3865-3868. 33. A. D. Becke, J. Chem. Phys., 1993, 98, 5648-5652. 34. F. L. Hirshfeld, Theoretica Chimica Acta, 1977, 44, 129-138.


Documents

vidossich ShilovReaction ESI · 2011. 12. 12. · 1 PtII as proton shuttle during C – H bond activation in the Shilov process Pietro Vidossich,* a Gregori Ujaque, Agustí Lledós