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Valenzuela SA, Cortés AJ, Tippins ZJE, Daly MH, Keel TE, Gherman BF, Spence JD. Effect of Extended Benzannelation Orientation on Bergman and Related Cyclizations of Isomeric Quinoxalenediynes. J Org Chem 2017; 82:13297-13312. [PMID: 29121468 DOI: 10.1021/acs.joc.7b02420] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A combined computational and experimental study was conducted to examine the effect of extended benzannelation orientation on C1-C5 and C1-C6 cyclization of acyclic quinoxalenediynes. Calculations (mPW1PW91/cc-pVTZ//mPW1PW91/6-31G(d,p)) on terminal and phenylethynyl-substituted 5,6-diethynylquinoxaline and 6,7-diethynylquinoxaline showed C1-C6 Bergman cyclization as the favored thermodynamic reaction pathway, with larger C1-C6 preference for the angular quinoxalenediynes due to gain of a new aromatic sextet. Kinetic studies, as a function of 1,4-cyclohexadiene concentration, revealed retro-Bergman ring opening predominates over hydrogen atom abstraction (k-1 > k2) for 6,7-diethynylquinoxaline while 5,6-diethynylquinoxaline undergoes irreversible Bergman cyclization indicative of a large retro-Bergman ring opening barrier (k2 > k-1). The effect of extended linear versus angular benzannelation on reaction pathway shows in the contrasting photocyclizations of phenylethynyl derivatives. While angular 5,6-diethynylquinoxalines gave exclusive C1-C6 photocyclization, linear 6,7-diethynylquinoxaline afforded C1-C5 fulvene products. Computed singlet-triplet gaps and biradical stabilization energies indicated weak interaction between the nitrogen lone pair and proximal radical center in angular 5,6-diethynylquinoxalines. The overall data indicates extended angular benzannelation effectively renders Bergman cyclization irreversible due to favorable aromatic stabilization energy, while extended linear benzannelation results in increased retro-Bergman ring opening, allowing C1-C5 cyclization to become a competitive reaction channel.
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Affiliation(s)
- Stephanie A Valenzuela
- Department of Chemistry, California State University, Sacramento , 6000 J Street, Sacramento, California 95819, United States
| | - Alondra J Cortés
- Department of Chemistry, California State University, Sacramento , 6000 J Street, Sacramento, California 95819, United States
| | - Zakery J E Tippins
- Department of Chemistry, California State University, Sacramento , 6000 J Street, Sacramento, California 95819, United States
| | - Morgan H Daly
- Department of Chemistry, California State University, Sacramento , 6000 J Street, Sacramento, California 95819, United States
| | - Terell E Keel
- Department of Chemistry, California State University, Sacramento , 6000 J Street, Sacramento, California 95819, United States
| | - Benjamin F Gherman
- Department of Chemistry, California State University, Sacramento , 6000 J Street, Sacramento, California 95819, United States
| | - John D Spence
- Department of Chemistry, California State University, Sacramento , 6000 J Street, Sacramento, California 95819, United States
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Fell JS, Steele DM, Hatcher TC, Gherman BF. Electronic effects on the reaction mechanism of the metalloenzyme peptide deformylase. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1674-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Spence JD, Rios AC, Frost MA, McCutcheon CM, Cox CD, Chavez S, Fernandez R, Gherman BF. Syntheses, thermal reactivities, and computational studies of aryl-fused quinoxalenediynes: effect of extended benzannelation on Bergman cyclization energetics. J Org Chem 2012; 77:10329-39. [PMID: 23067009 DOI: 10.1021/jo302009c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A series of [b]-fused 6,7-diethynylquinoxaline derivatives have been synthesized through an imine condensation strategy to examine the effect of extended benzannelation on the thermal reactivity of enediynes. Absorption and emission spectra of the highly conjugated quinoxalenediynes were red-shifted approximately 100-200 nm relative to those of 1,2-diethynylbenzene. Strong exotherms indicative of enediyne cyclization were observed by differential scanning calorimetry, while solution cyclizations in the presence of 1,4-cyclohexadiene confirmed C(1)-C(6) Bergman cyclization. To provide further insight into Bergman cyclization energetics, computational studies were performed to compare changes in the cyclization enthalpy barrier, reaction enthalpy, and barrier of retro-Bergman ring-opening. Extension of benzannelation from 1,2-diethynylbenzene to either 2,3-diethynylnaphthalene or the 6,7-diethynylquinoxalines had a minimal effect on the cyclization barrier. In comparison, the enthalpies of cyclization were increased upon linearly extended benzannelation, which resulted in reduced barriers to retro-Bergman ring-opening. In addition, the orientation of extended benzannelation was found to have a significant effect on the cyclization endothermicity. In particular, 5,6-diethynylquinoxaline exhibited a 6.9 kcal/mol decrease in cyclization enthalpy compared to 6,7-diethynylquinoxaline due to increased aromatic stabilization energy in the respective angularly versus linearly fused azaacene cyclized products.
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Affiliation(s)
- John D Spence
- Department of Chemistry, California State University, Sacramento, Sacramento, California 95819, USA.
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Spiropulos NG, Standley EA, Shaw IR, Ingalls BL, Diebels B, Krawczyk SV, Gherman BF, Arif AM, Brown EC. Synthesis of zinc and cadmium O-alkyl thiocarbonate and dithiocarbonate complexes and a cationic zinc hydrosulfide complex. Inorganica Chim Acta 2012. [DOI: 10.1016/j.ica.2012.01.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Korovina NV, Chang ML, Nguyen TT, Fernandez R, Walker HJ, Olmstead MM, Gherman BF, Spence JD. Syntheses and Reactivity of Naphthalenyl-Substituted Arenediynes. Org Lett 2011; 13:3660-3. [DOI: 10.1021/ol201317w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nadezhda V. Korovina
- Department of Chemistry, California State University, Sacramento, 6000 J Street, Sacramento, California 95819, United States, and Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Michael L. Chang
- Department of Chemistry, California State University, Sacramento, 6000 J Street, Sacramento, California 95819, United States, and Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Trang T. Nguyen
- Department of Chemistry, California State University, Sacramento, 6000 J Street, Sacramento, California 95819, United States, and Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Ramiro Fernandez
- Department of Chemistry, California State University, Sacramento, 6000 J Street, Sacramento, California 95819, United States, and Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Heather J. Walker
- Department of Chemistry, California State University, Sacramento, 6000 J Street, Sacramento, California 95819, United States, and Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Marilyn M. Olmstead
- Department of Chemistry, California State University, Sacramento, 6000 J Street, Sacramento, California 95819, United States, and Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Benjamin F. Gherman
- Department of Chemistry, California State University, Sacramento, 6000 J Street, Sacramento, California 95819, United States, and Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - John D. Spence
- Department of Chemistry, California State University, Sacramento, 6000 J Street, Sacramento, California 95819, United States, and Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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Bateni SB, England KR, Galatti AT, Kaur H, Mendiola VA, Mitchell AR, Vu MH, Gherman BF, Miranda JA. Prediction of reduction potentials from calculated electron affinities for metal-salen compounds. Beilstein J Org Chem 2009; 5:82. [PMID: 20300473 PMCID: PMC2839914 DOI: 10.3762/bjoc.5.82] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2009] [Accepted: 12/07/2009] [Indexed: 11/23/2022] Open
Abstract
The electron affinities (EAs) of a training set of 19 metal-salen compounds were calculated using density functional theory. Concurrently, the experimental reduction potentials for the training set were measured using cyclic voltammetry. The EAs and reduction potentials were found to be linearly correlated by metal. The reduction potentials of a test set of 14 different metal-salens were then measured and compared to the predicted reduction potentials based upon the training set correlation. The method was found to work well, with a mean unsigned error of 99 mV for the entire test set. This method could be used to predict the reduction potentials of a variety of metal-salen compounds, an important class of coordination compounds used in synthetic organic electrochemistry as electrocatalysts.
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Affiliation(s)
- Sarah B Bateni
- Department of Chemistry, California State University, Sacramento, 6000 J Street, Sacramento, CA 95819-6057, USA
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Winter AH, Falvey DE, Cramer CJ, Gherman BF. Benzylic Cations with Triplet Ground States: Computational Studies of Aryl Carbenium Ions, Silylenium Ions, Nitrenium Ions, and Oxenium Ions Substituted with Meta π Donors. J Am Chem Soc 2007; 129:10113-9. [PMID: 17655230 DOI: 10.1021/ja070143m] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory (B3LYP/6-31G(d,p)) was used to predict the effect of meta substitution on aryl cationic (Ar-X+) species, including aryloxenium ions, arylsilylenium ions, arylnitrenium ions, and arylcarbenium ions. Multireference second-order perturbation theory (CASPT2) calculations were used to benchmark the quantitative accuracy of the DFT calculations for representative systems. Substituting the meta positions on these species with pi donors stabilizes a pi,pi* diradical state analogous to the well-known m-xylylene diradical. Notably, the 3,5-bis(N,N-dimethylamino)benzyl cation is predicted to have a triplet ground state by 1.9 kcal/mol by DFT and to have essentially degenerate singlet-triplet states at the CASPT2(10,9) level of theory. Adding electron-withdrawing CF3 groups to the exocyclic carbon of this meta-disubstituted benzyl cation further increases the predicted singlet-triplet gap in favor of the triplet. Other aryl cationic species substituted with strong pi electron-donating groups in the meta positions are predicted to have low-energy or ground-state triplet states. Systems analogous to the naphthaquinodimethane diradicals are also reported.
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Affiliation(s)
- Arthur H Winter
- Department of Chemistry & Biochemistry, University of Maryland, College Park Maryland 20742-2021, USA
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Gherman BF, Tolman WB, Cramer CJ. Characterization of the structure and reactivity of monocopper-oxygen complexes supported by β-diketiminate and anilido-imine ligands. J Comput Chem 2006; 27:1950-61. [PMID: 17019721 DOI: 10.1002/jcc.20502] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Copper-oxygen complexes supported by beta-diketiminate and anilido-imine ligands have recently been reported (Aboelella et al., J Am Chem Soc 2004, 126, 16896; Reynolds et al., Inorg Chem 2005, 44, 6989) as potential biomimetic models for dopamine beta-monooxygenase (DbetaM) and peptidylglycine alpha-hydroxylating monooxygenase (PHM). However, in contrast to the enzymatic systems, these complexes fail to exhibit C--H hydroxylation activity (Reynolds et al., Chem Commun 2005, 2014). Quantum chemical characterization of the 1:1 Cu-O(2) model adducts and related species (Cu(III)-hydroperoxide, Cu(III)-oxo, and Cu(III)-hydroxide) indicates that the 1:1 Cu-O(2) adducts are unreactive toward substrates because of the weakness of the O--H bond that would be formed upon hydrogen-atom abstraction. This in turn is ascribed to the 1:1 adducts having both low reduction potentials and basicities. Cu(III)-oxo species on the other hand, determined to be intermediate between Cu(III)-oxo and Cu(II)-oxyl in character, are shown to be far more reactive toward substrates. Based on these results, design strategies for new DbetaM and PHM biomimetic ligands are proposed: new ligands should be made less electron rich so as to favor end-on dioxygen coordination in the 1:1 Cu-O(2) adducts. Comparison of the relative reactivities of the various copper-oxygen complexes as hydroxylating agents provides support for a Cu(II)-superoxide species as the intermediate responsible for substrate hydroxylation in DbetaM and PHM, and suggests that a Cu(III)-oxo intermediate would be competent in this process as well.
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Affiliation(s)
- Benjamin F Gherman
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, USA
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Schultz NE, Gherman BF, Cramer CJ, Truhlar DG. PdnCO (n = 1,2): Accurate Ab Initio Bond Energies, Geometries, and Dipole Moments and the Applicability of Density Functional Theory for Fuel Cell Modeling. J Phys Chem B 2006; 110:24030-46. [PMID: 17125374 DOI: 10.1021/jp064467t] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrode poisoning by CO is a major concern in fuel cells. As interest in applying computational methods to electrochemistry is increasing, it is important to understand the levels of theory required for reliable treatments of metal-CO interactions. In this paper we justify the use of relativistic effective core potentials for the treatment of PdCO and hence, by inference, for metal-CO interactions where the predominant bonding mechanism is charge transfer. We also sort out key issues involving basis sets and we recommend that bond energies of 17.2, 43.3, and 69.4 kcal/mol be used as the benchmark bond energy for dissociation of Pd2 into Pd atoms, PdCO into Pd and CO, and Pd2CO into Pd2 and CO, respectively. We calculated the dipole moments of PdCO and Pd2CO, and we recommend benchmark values of 2.49 and 2.81 D, respectively. Furthermore, we tested 27 density functionals for this system and found that only hybrid density functionals can qualitatively and quantitatively predict the nature of the sigma-donation/pi-back-donation mechanism that is associated with the Pd-CO and Pd2-CO bonds. The most accurate density functionals for the systems tested in this paper are O3LYP, OLYP, PW6B95, and PBEh.
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Affiliation(s)
- Nathan E Schultz
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, USA
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Aboelella NW, Gherman BF, Hill LMR, York JT, Holm N, Young VG, Cramer CJ, Tolman WB. Effects of thioether substituents on the O2 reactivity of beta-diketiminate-Cu(I) complexes: probing the role of the methionine ligand in copper monooxygenases. J Am Chem Soc 2006; 128:3445-58. [PMID: 16522125 PMCID: PMC2593856 DOI: 10.1021/ja057745v] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The activation of dioxygen by dopamine beta-monooxygenase (DbetaM) and peptidylglycine alpha-hydroxylating monooxygenase (PHM) is postulated to occur at a copper site ligated by two histidine imidazoles and a methionine thioether, which is unusual because such thioether ligation is not present in other O2-activating copper proteins. To assess the possible role of the thioether ligand in O2 activation by DbetaM and PHM, two new ligands comprising beta-diketiminates with thioether substituents were synthesized and Cu(I) and Cu(II) complexes were isolated. The Cu(II) compounds are monomeric and exhibit intramolecular thioether coordination. While the Cu(I) complexes exhibit a multinuclear topology in the solid state, variable-temperature 1H NMR studies implicate equilibria in solution, possibly including monomers with intramolecular thioether coordination that are structurally defined by DFT calculations. Low-temperature oxygenation of solutions of the Cu(I) complexes generates stable 1:1 Cu/O2 adducts, which on the basis of combined experimental and theoretical studies adopt side-on "eta(2)" structures with negligible Cu-thioether bonding and significant peroxo-Cu(III) character. In contrast to previously reported findings with related ligands lacking the thioether group, however (cf., Aboelella; et al. J. Am. Chem. Soc. 2004, 126, 16896), purging the solutions of the thioether-containing adducts with argon results in conversion to bis(mu-oxo)dicopper(III) species. A role for the thioether in promoting loss of O2 from the 1:1 Cu/O2 adduct and facilitating trapping of the resulting Cu(I) complex to yield the bis(mu-oxo) species is proposed, and the possible relevance of this role to that of the methionine in the active sites of DbetaM and PHM is discussed.
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Affiliation(s)
- Nermeen W Aboelella
- Department of Chemistry, Center for Metals in Biocatalysis, and Minnesota Supercomputer Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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Heppner DE, Gherman BF, Tolman WB, Cramer CJ. Can an ancillary ligand lead to a thermodynamically stable end-on 1 : 1 Cu–O2adduct supported by a β-diketiminate ligand? Dalton Trans 2006:4773-82. [PMID: 17033702 DOI: 10.1039/b608980a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The finding that dioxygen binds end-on to the Cu(B) site in the crystal structure of a precatalytic complex of peptidylglycine alpha-hydroxylating monooxygenase has spurred the search for biomimetic model complexes exhibiting the same dioxygen coordination. Recent work has not only indicated that sterically hindered beta-diketiminate ligands (L(1)) could support side-on 1 : 1 Cu-O(2) adducts, but also that an end-on L(1)Cu(THF)O(2) structure occurs as an unstable intermediate in the oxygenation mechanism of the Cu(I) complex. In this work, density functional theory and multireference methods are used to determine the potential of ancillary ligands, X, other than THF to yield thermodynamically stable end-on L(1)CuXO(2) species. A diverse set of ligands X, comprising phosphines, thiophene, cyclic ethers, acetonitrile, para-substituted pyridines, N-heterocyclic carbenes, and ligands bearing hydrogen bond donors, has been considered in order to identify ligand characteristics which energetically favor end-on L(1)CuXO(2) over: a) reversion to the Cu(I) complex and dioxygen, b) isomerization to side-on L(1)CuXO(2), and c) decay to L(1)CuO(2) and X. Ancillary ligands with judiciously chosen degrees and orientation of steric bulk and which bear potential hydrogen bond donors to an end-on bound dioxygen moiety most favor oxygenation of L(1)CuX to yield end-on L(1)CuXO(2). Conversion to the side-on isomer can be deterred through the use of a sufficiently bulky ligand X, such as one that is at least the size of a 5-membered ring. Loss of X to give L(1)CuO(2) can be made prohibitively endergonic by employing ligands X which are highly electron donating and which backbond strongly with and sigma-donate significantly to copper.
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Affiliation(s)
- David E Heppner
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, MN 55455, USA
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Hill LMR, Gherman BF, Aboelella NW, Cramer CJ, Tolman WB. Electronic tuning of β-diketiminate ligands with fluorinated substituents: effects on the O2-reactivity of mononuclear Cu(i) complexes. Dalton Trans 2006:4944-53. [PMID: 17047744 DOI: 10.1039/b609939d] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Copper(i) complexes with the beta-diketiminate ligands HC{C(R)N(Dipp)}{C(R')N(Dipp)}(-) (Dipp = C(6)H(3)(i)Pr(2-)2,6; L(1), R = CF(3), R' = CH(3); L(2), R = R' = CF(3)) have been isolated and fully characterized. On the basis of X-ray structural comparisons with the previously reported complex LCu(CH(3)CN) (L = HC{C(CH(3))N(Dipp)}(2)(-)), the ligand environments at the copper centers in the analogous nitrile adducts with L(1) and L(2) impose similar steric demands. L(1)Cu(CH(3)CN) reacts instantaneously at low temperature with O(2) to form a thermally-unstable intermediate with an isotope-sensitive vibration at 977 cm(-1) (928 cm(-1) with (18)O(2)), in accord with the peroxo O-O stretch associated with side-on coordination for LCu(O(2)). However, L(2)Cu(CH(3)CN) is unreactive toward O(2) even at room temperature. Evaluation of the redox potentials of the nitrile adducts and the CO stretching frequencies of the carbon monoxide adducts revealed an incremental adjustment of the electronic environment at the copper center that correlated with the extent of ligand fluorination. Furthermore, theoretical calculations (DFT, CASPT2) predicted that an increasing extent of Cu(ii)-superoxo character and end-on coordination of the O(2) moiety in the Cu/O(2) product (L(2) > L(1) > L) are accompanied by increases in the free energy for the oxygenation reaction, with L(2) unable to support a Cu/O(2) intermediate. Calculations also predict the 1 : 1 Cu/O(2) adducts to be unreactive with respect to hydrogen atom abstraction from hydrocarbon substrates on the basis of their stability towards both reduction and protonation.
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Affiliation(s)
- Lyndal M R Hill
- Department of Chemistry, Center for Metals in Biocatalysis, and Supercomputer Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, 55455-0431, USA
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Gherman BF, Heppner DE, Tolman WB, Cramer CJ. Models for dioxygen activation by the CuB site of dopamine β-monooxygenase and peptidylglycine α-hydroxylating monooxygenase. J Biol Inorg Chem 2005; 11:197-205. [PMID: 16344970 DOI: 10.1007/s00775-005-0066-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Accepted: 11/21/2005] [Indexed: 11/30/2022]
Abstract
On the basis of spectroscopic and crystallographic data for dopamine beta-monooxygenase and peptidylglycine alpha-hydroxylating monooxygenase (PHM), a variety of ligand sets have been used to model the oxygen-binding Cu site in these enzymes. Calculations which employed a combination of density functional and multireference second-order perturbation theory methods provided insights into the optimal ligand set for supporting eta (1) superoxo coordination as seen in a crystal structure of a precatalytic Cu/O(2) complex for PHM (Prigge et al. in Science 304:864-867, 2004). Anionic ligand sets stabilized eta (2) dioxygen coordination and were found to lead to more peroxo-like Cu-O(2) complexes with relatively exergonic binding free energies, suggesting that these adducts may be unreactive towards substrates. Neutral ligand sets (including a set of two imidazoles and a thioether), on the other hand, energetically favored eta (1) dioxygen coordination and exhibited limited dioxygen reduction. Binding free energies for the 1:1 adducts with Cu supported by the neutral ligand sets were also higher than with their anionic counterparts. Deviations between the geometry and energetics of the most analogous models and the PHM crystal structures suggest that the protein environment influences the coordination geometry at the Cu(B) site and increases the lability of water bound to the preoxygenated reduced form. Another implication is that a neutral ligand set will be critical in biomimetic models in order to stabilize eta (1) dioxygen coordination.
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Affiliation(s)
- Benjamin F Gherman
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA.
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Kinsinger CR, Gherman BF, Gagliardi L, Cramer CJ. How useful are vibrational frequencies of isotopomeric O2 fragments for assessing local symmetry? Some simple systems and the vexing case of a galactose oxidase model. J Biol Inorg Chem 2005; 10:778-89. [PMID: 16187071 DOI: 10.1007/s00775-005-0026-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 08/23/2005] [Indexed: 11/27/2022]
Abstract
The tendency for mixed-isotope O2 fragments to exhibit different stretching frequencies in asymmetric environments is examined with various levels of electronic structure theory for simple peroxides and peroxyl radicals, as well as for a variety of monocopper-O2 complexes. The study of the monocopper species is motivated by their relevance to the active site of galactose oxidase. Extensive theoretical work with an experimental model characterized by Jazdzewski et al. (J. Biol. Inorg. Chem. 8:381-393, 2003) suggests that the failure to observe a splitting between 16O18O and 18O16O isotopomers cannot be taken as evidence against end-on O2 coordination. Conformational analysis on an energetic basis, however, is complicated by biradical character inherent in all of the copper-O2 singlet structures.
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Affiliation(s)
- Christopher R Kinsinger
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA
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Abstract
Copper(I) complexes of sterically hindered anilido imine ligands o-C6H4{N(C6H3(i)Pr2)}{C(R)=NC6H3(i)Pr2}- (L(1), R = H; L(2), R = CH3) have been prepared and characterized by spectroscopic and X-ray crystallographic methods. These complexes are highly reactive with O2, and in the case of L2 the product of low-temperature oxygenation was fully characterized by spectroscopic, X-ray crystallographic, and computational methods. The resonance Raman spectrum features an isotope-sensitive vibration at 974 cm(-1) (Delta(18O) = 66 cm(-1)), consistent with assignment as an O-O stretch. Despite the asymmetric coordination environment provided by the supporting anilido imine ligand, the X-ray crystal structure confirms rather symmetric side-on binding of the O2 moiety to the copper center, and the O-O bond length of 1.392(2) Angstroms indicates that this intermediate has significant Cu(III)-peroxo character. Theoretical calculations support this interpretation and predict that while a fully optimized end-on singlet geometry can be obtained, it is higher in energy than the side-on isomer by 3.5 kcal mol(-1) at the CASPT2/TZP level.
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Affiliation(s)
- Anne M Reynolds
- Department of Chemistry, University of Minnesota, Minneapolis, 55455, USA
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Gherman BF, Lippard SJ, Friesner RA. Substrate hydroxylation in methane monooxygenase: quantitative modeling via mixed quantum mechanics/molecular mechanics techniques. J Am Chem Soc 2005; 127:1025-37. [PMID: 15656641 DOI: 10.1021/ja049847b] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using broken-symmetry unrestricted density functional theory quantum mechanical (QM) methods in concert with mixed quantum mechanics/molecular mechanics (QM/MM) methods, the hydroxylation of methane and substituted methanes by intermediate Q in methane monooxygenase hydroxylase (MMOH) has been quantitatively modeled. This protocol allows the protein environment to be included throughout the calculations and its effects (electrostatic, van der Waals, strain) upon the reaction to be accurately evaluated. With the current results, recent kinetic data for CH3X (X = H, CH3, OH, CN, NO2) substrate hydroxylation in MMOH (Ambundo, E. A.; Friesner, R. A.; Lippard, S. J. J. Am. Chem. Soc. 2002, 124, 8770-8771) can be rationalized. Results for methane, which provide a quantitative test of the protocol, including a substantial kinetic isotope effect (KIE), are in reasonable agreement with experiment. Specific features of the interaction of each of the substrates with MMO are illuminated by the QM/MM modeling, and the resulting effects upon substrate binding are quantitatively incorporated into the calculations. The results as a whole point to the success of the QM/MM methodology and enhance our understanding of MMOH catalytic chemistry. We also identify systematic errors in the evaluation of the free energy of binding of the Michaelis complexes of the substrates, which most likely arise from inadequate sampling and/or the use of harmonic approximations to evaluate the entropy of the complex. More sophisticated sampling methods will be required to achieve greater accuracy in this aspect of the calculation.
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Affiliation(s)
- Benjamin F Gherman
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
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Aboelella NW, Kryatov SV, Gherman BF, Brennessel WW, Young VG, Sarangi R, Rybak-Akimova EV, Hodgson KO, Hedman B, Solomon EI, Cramer CJ, Tolman WB. Dioxygen Activation at a Single Copper Site: Structure, Bonding, and Mechanism of Formation of 1:1 Cu−O2 Adducts. J Am Chem Soc 2004; 126:16896-911. [PMID: 15612729 DOI: 10.1021/ja045678j] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To evaluate the fundamental process of O(2) activation at a single copper site that occurs in biological and catalytic systems, a detailed study of O(2) binding to Cu(I) complexes of beta-diketiminate ligands L (L(1) = backbone Me; L(2) = backbone tBu) by X-ray crystallography, X-ray absorption spectroscopy (XAS), cryogenic stopped-flow kinetics, and theoretical calculations was performed. Using synchrotron radiation, an X-ray diffraction data set for L(2)CuO(2) was acquired, which led to structural parameters in close agreement to theoretical predictions. Significant Cu(III)-peroxo character for the complex was corroborated by XAS. On the basis of stopped-flow kinetics data and theoretical calculations for the oxygenation of L(1)Cu(RCN) (R = alkyl, aryl) in THF and THF/RCN mixtures between 193 and 233 K, a dual pathway mechanism is proposed involving (a) rate-determining solvolysis of RCN by THF followed by rapid oxygenation of L(1)Cu(THF) and (b) direct, bimolecular oxygenation of L(1)Cu(RCN) via an associative process.
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Affiliation(s)
- Nermeen W Aboelella
- Department of Chemistry, Center for Metals in Biocatalysis, and Supercomputer Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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Abstract
The character of singlet (C(3)N(2)H(5))CuO(2) ranges smoothly between copper(III) peroxide and copper(II) superoxide with variation of the electronic character of the supporting beta-diketiminate ligand. Over the range of the variation, multireference second-order perturbation theory predicts the (1)A(1) singlet state always to be lower in energy than the lowest triplet state ((3)B(1)). The multideterminantal character of the biradical-like superoxide mesomer causes density functional theory sometimes to fail badly in predicting the relative energies of these same states, although its predictions of other properties, such as geometry, are of good quality.
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Affiliation(s)
- Benjamin F Gherman
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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Gherman BF, Goldberg SD, Cornish VW, Friesner RA. Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) Study of the Deacylation Reaction in a Penicillin Binding Protein (PBP) versus in a Class C β-Lactamase. J Am Chem Soc 2004; 126:7652-64. [PMID: 15198613 DOI: 10.1021/ja036879a] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The origin of the substantial difference in deacylation rates for acyl-enzyme intermediates in penicillin-binding proteins (PBPs) and beta-lactamases has remained an unsolved puzzle whose solution is of great importance to understanding bacterial antibiotic resistance. In this work, accurate, large-scale mixed ab initio quantum mechanical/molecular mechanical (QM/MM) calculations have been used to study the hydrolysis of acyl-enzyme intermediates formed between cephalothin and the dd-peptidase of Streptomyces sp. R61, a PBP, and the Enterobacter cloacae P99 cephalosporinase, a class C beta-lactamase. Qualitative and, in the case of P99, quantitative agreement was achieved with experimental kinetics. The faster rate of deacylation in the beta-lactamase is attributed to a more favorable electrostatic environment around Tyr150 in P99 (as compared to that for Tyr159 in R61) which facilitates this residue's function as the general base. This is found to be in large part accomplished by the ability of P99 to covalently bind the ligand without concurrent elimination of hydrogen bonds to Tyr150, which proves not to be the case with Tyr159 in R61. This work provides an essential foundation for further work in this area, such as selecting mutations capable of converting the PBP into a beta-lactamase.
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Affiliation(s)
- Benjamin F Gherman
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
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Abstract
Using broken-symmetry unrestricted Density Functional Theory, the mechanism of enzymatic dioxygen activation by the hydroxylase component of soluble methane monooxygenase (MMOH) is determined to atomic detail. After a thorough examination of mechanistic alternatives, an optimal pathway was identified. The diiron(II) state H(red) reacts with dioxygen to give a ferromagnetically coupled diiron(II,III) H(superoxo) structure, which undergoes intersystem crossing to the antiferromagnetic surface and affords H(peroxo), a symmetric diiron(III) unit with a nonplanar mu-eta(2):eta(2)-O(2)(2)(-) binding mode. Homolytic cleavage of the O-O bond yields the catalytically competent intermediate Q, which has a di (mu-oxo)diiron(IV) core. A carboxylate shift involving Glu243 is essential to the formation of the symmetric H(peroxo) and Q structures. Both thermodynamic and kinetic features agree well with experimental data, and computed spin-exchange coupling constants are in accord with spectroscopic values. Evidence is presented for pH-independent decay of H(red) and H(peroxo). Key electron-transfer steps that occur in the course of generating Q from H(red) are also detailed and interpreted. In contrast to prior theoretical studies, a requisite large model has been employed, electron spins and couplings have been treated in a quantitative manner, potential energy surfaces have been extensively explored, and quantitative total energies have been determined along the reaction pathway.
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Affiliation(s)
- Benjamin F Gherman
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
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Baik MH, Gherman BF, Friesner RA, Lippard SJ. Hydroxylation of methane by non-heme diiron enzymes: molecular orbital analysis of C-H bond activation by reactive intermediate Q. J Am Chem Soc 2002; 124:14608-15. [PMID: 12465971 DOI: 10.1021/ja026794u] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The electronic structures of key species involved in methane hydroxylation performed by the hydroxylase component of soluble methane monooxygenase (sMMO), as proposed previously on the basis of high-level density functional theory, were investigated. The reaction starts with initial approach of methane at one of the bridging oxo atoms in intermediate Q, a di(mu-oxo)diiron(IV) unit. This step is accompanied by a proton-coupled outer-sphere transfer of the first electron from a C-H sigma-bond in methane to one of the metal centers. The second electron transfer, also an outer-sphere electron transfer process, occurs along a two-component reaction pathway. Both redox reactions are strongly coupled to structural distortions of the diiron core. The electronic consequence and driving force of these distortions are intuitively explained by using the computed Kohn-Sham orbitals in the broken-symmetry framework to incorporate the experimentally observed antiferromagnetic coupling of the unpaired electrons at the metal centers. The broken-symmetry orbital scheme is essential for describing the C-H bond activation process in a consistent and complete manner, enabling derivation of both an intuitive and quantitative understanding of the most salient electronic features that govern the details of the hydroxylation.
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Affiliation(s)
- Mu-Hyun Baik
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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Guallar V, Gherman BF, Miller WH, Lippard SJ, Friesner RA. Dynamics of alkane hydroxylation at the non-heme diiron center in methane monooxygenase. J Am Chem Soc 2002; 124:3377-84. [PMID: 11916423 DOI: 10.1021/ja0167248] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Semiclassical molecular dynamics simulations have been combined with quantum chemistry calculations to provide detailed modeling of the methane and ethane hydroxylation reactions catalyzed by the hydroxylase enzymes of the soluble methane monooxygenase system. The experimental distribution of enantiomeric alcohols in the reaction of ethanes made chiral by the use of hydrogen isotopes is quantitatively reproduced and explained. The reaction dynamics involve a mixture of concerted and bound radical trajectories, and we characterize each of these reactive channels in detail. Diffusion of the bound radical intermediate at the active site core determines the global rate constant. The results also provide a qualitative rationale for the lack of ring-opened products derived from certain radical clock substrate probes and for the relative rate constants and kinetic isotope effects exhibited by a variety of substrates.
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Affiliation(s)
- Victor Guallar
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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Abstract
The catalytic pathways of soluble methane monooxygenase (sMMO) and cytochrome P450CAM, iron-containing enzymes, are described and compared. Recent extensive density functional ab initio electronic structure calculations have revealed many similarities in a number of the key catalytic steps, as well as some important differences. A particularly interesting and significant contrast is the role played by the protein in each system. For sMMO, the protein stabilizes various species in the catalytic cycle through a series of carboxylate shifts. This process is adequately described by a relatively compact model of the active site ( approximately 100 atoms), providing a reasonable description of the energetics of hydrogen atom abstraction. For P450CAM, in contrast, the inclusion of the full protein is necessary for an accurate description of the hydrogen atom abstraction.
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Affiliation(s)
- Victor Guallar
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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Gherman BF, Dunietz BD, Whittington DA, Lippard SJ, Friesner RA. Activation of the C-H bond of methane by intermediate Q of methane monooxygenase: a theoretical study. J Am Chem Soc 2001; 123:3836-7. [PMID: 11457123 DOI: 10.1021/ja0055108] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- B F Gherman
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, New York 10027, USA
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