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3.
  • Ai, Yue-Jie, 1982-, et al. (author)
  • Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase
  • 2011
  • In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 115:37, s. 10976-10982
  • Journal article (peer-reviewed)abstract
    • Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.
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4.
  • Abdel-Magied, Ahmed F., et al. (author)
  • Chemical and Photochemical Water Oxidation Mediated by an Efficient Single-Site Ruthenium Catalyst
  • 2016
  • In: ChemSusChem. - : Wiley. - 1864-5631 .- 1864-564X. ; 9:24, s. 3448-3456
  • Journal article (peer-reviewed)abstract
    • Water oxidation is a fundamental step in artificial photosynthesis for solar fuels production. In this study, we report a single-site Ru-based water oxidation catalyst, housing a dicarboxylate-benzimidazole ligand, that mediates both chemical and light-driven oxidation of water efficiently under neutral conditions. The importance of the incorporation of the negatively charged ligand framework is manifested in the low redox potentials of the developed complex, which allows water oxidation to be driven by the mild one-electron oxidant [Ru(bpy)(3)](3+) (bpy = 2,2'-bipyridine). Furthermore, combined experimental and DFT studies provide insight into the mechanistic details of the catalytic cycle.
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5.
  • Ai, Yue-Jie, et al. (author)
  • Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA
  • 2010
  • In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:44, s. 14096-14102
  • Journal article (peer-reviewed)abstract
    • The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.
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6.
  • Ai, Yue-Jie, et al. (author)
  • Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore
  • 2012
  • In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 14:38, s. 13409-13414
  • Journal article (peer-reviewed)abstract
    • We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.
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7.
  • Arafa, Wael A. A., et al. (author)
  • Dinuclear manganese complexes for water oxidation : evaluation of electronic effects and catalytic activity
  • 2014
  • In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 16:24, s. 11950-11964
  • Journal article (peer-reviewed)abstract
    • During recent years significant progress has been made towards the realization of a sustainable and carbon-neutral energy economy. One promising approach is photochemical splitting of H2O into O-2 and solar fuels, such as H-2. However, the bottleneck in such artificial photosynthetic schemes is the H2O oxidation half reaction where more efficient catalysts are required that lower the kinetic barrier for this process. In particular catalysts based on earth-abundant metals are highly attractive compared to catalysts comprised of noble metals. We have now synthesized a library of dinuclear Mn-2 (II,III) catalysts for H2O oxidation and studied how the incorporation of different substituents affected the electronics and catalytic efficiency. It was found that the incorporation of a distal carboxyl group into the ligand scaffold resulted in a catalyst with increased catalytic activity, most likely because of the fact that the distal group is able to promote proton-coupled electron transfer (PCET) from the high-valent Mn species, thus facilitating O-O bond formation.
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8.
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9.
  • Chen, Shi-Lu, et al. (author)
  • Phosphate Monoester Hydrolysis by Trinuclear Alkaline Phosphatase; DFT Study of Transition States and Reaction Mechanism
  • 2014
  • In: ChemPhysChem. - : Wiley. - 1439-4235 .- 1439-7641. ; 15:11, s. 2321-2330
  • Journal article (peer-reviewed)abstract
    • Alkaline phosphatase (AP) is a trinuclear metalloenzyme that catalyzes the hydrolysis of a broad range of phosphate monoesters to form inorganic phosphate and alcohol (or phenol). In this paper, by using density functional theory with a model based on a crystal structure, the AP-catalyzed hydrolysis of phosphate monoesters is investigated by calculating two substrates, that is, methyl and p-nitrophenyl phosphates, which represent alkyl and aryl phosphates, respectively. The calculations confirm that the AP reaction employs a ping-pong mechanism involving two chemical displacement steps, that is, the displacement of the substrate leaving group by a Ser102 alkoxide and the hydrolysis of the phosphoseryl intermediate by a Zn2-bound hydroxide. Both displacement steps proceed via a concerted associative pathway no matter which substrate is used. Other mechanistic aspects are also studied. Comparison of our calculations with linear free energy relationships experiments shows good agreement.
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11.
  • Das, Biswanath, et al. (author)
  • Water oxidation catalyzed by molecular di- and nonanuclear Fe complexes: importance of a proper ligand framework
  • 2016
  • In: Dalton Transactions. - : ROYAL SOC CHEMISTRY. - 1477-9226 .- 1477-9234. ; 45:34, s. 13289-13293
  • Journal article (peer-reviewed)abstract
    • The synthesis of two molecular iron complexes, a dinuclear iron(III,III) complex and a nonanuclear iron complex, based on the di-nucleating ligand 2,2-(2-hydroxy-5-methyl-1,3-phenylene)bis(1H-benzo[d]imidazole-4-carboxylic acid) is described. The two iron complexes were found to drive the oxidation of water by the one-electron oxidant [Ru(bpy)(3)](3+).
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12.
  • Hu, Maowei, et al. (author)
  • Efficient and Stable Dye-Sensitized Solar Cells Based on a Tetradentate Copper(II/I) Redox Mediator
  • 2018
  • In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 10:36, s. 30409-30416
  • Journal article (peer-reviewed)abstract
    • The identification of an efficient and stable redox mediator is of paramount importance for commercialization of dye-sensitized solar cells (DSCs). Herein, we report a new class of copper complexes containing diamine-dipyridine tetradentate ligands (L1 = N,N'-dibenzyl-N,N'-bis-(pyridin-2-ylmethyl)ethylenediamine; L2 = N,N'-dibenzyl-N,N'-bis (6-methyl-pyridin-2-ylmethyl)ethylenediamine) as redox mediators in DSCs. Devices constructed with [Cu(L2)](2+/+) redox couple afford an impressive power conversion efficiency (PCE) of 9.2% measured under simulated one sun irradiation (100 mW cm(-2), AM 1.5G), which is among the top efficiencies reported thus far for DSCs with copper complex-based redox mediators. Remarkably, the excellent air, photo, and electrochemical stability of the [Cu(L2)](2+/+) complexes renders an outstanding long-term stability of the whole DSC device, maintaining similar to 90% of the initial efficiency over 500 h under continuous full sun irradiation. This work unfolds a new platform for developing highly efficient and stable redox mediators for large-scale application of DSCs.
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13.
  • Huang, Genping, et al. (author)
  • Mechanism, reactivity, and selectivity of the iridium-catalyzed C(sp(3))-H borylation of chlorosilanes
  • 2015
  • In: Chemical Science. - : Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 6:3, s. 1735-1746
  • Journal article (peer-reviewed)abstract
    • The iridium-catalyzed C(sp(3))-H borylation of methylchlorosilanes is investigated by means of density functional theory, using the B3LYP and M06 functionals. The calculations establish that the resting state of the catalyst is a seven-coordinate Ir(V) species that has to be converted into an Ir(III)tris(boryl) complex in order to effect the oxidative addition of the C-H bond. This is then followed by a C-B reductive elimination to yield the borylated product, and the catalytic cycle is finally completed by the regeneration of the active catalyst over two facile steps. The two employed functionals give somewhat different conclusions concerning the nature of the rate-determining step, and whether reductive elimination occurs directly or after a prior isomerization of the Ir(V) hydride intermediate complex. The calculations reproduce quite well the experimentally-observed trends in the reactivities of substrates with different substituents. It is demonstrated that the reactivity can be correlated to the Ir-C bond dissociation energies of the corresponding Ir(V) hydride intermediates. The effect of the chlorosilyl group is identified to originate from the alpha-carbanion-stabilizing effect of the silicon, which is further reinforced by the presence of an electron-withdrawing chlorine substituent. Furthermore, the source of selectivity for the borylation of primary over secondary C(sp(3))-H can be explained on a steric basis, by repulsion between the alkyl group and the Ir/ligand moiety. Finally, the difference in the reactivity between C(sp(3))-H and C(sp(2))-H borylation is investigated and rationalized in terms of distortion/interaction analysis.
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14.
  • Jalilian, Ehsan, et al. (author)
  • Luminescence properties of monoclinic Cu4I4(Piperidine)4
  • 2011
  • In: Materials research bulletin. - : Elsevier Ltd.. - 0025-5408 .- 1873-4227. ; 46:8, s. 1192-1196
  • Journal article (peer-reviewed)abstract
    • A new modification of Cu4I4Pip4 has been synthesized under hydrothermal conditions. X-ray crystallography revealed that this compound crystallized in the monoclinic system and consists of a tetrahedral core with composition Cu4I4, in which each Cu atom is coordinated by a piperidine molecule via the N atom. In contrast to a previously reported modification of Cu4I4Pip4, the present modification shows luminescent properties when exposed to UV-light. In addition, we have used time-dependent density functional theory calculations to characterize both compounds in term of both absorption and emission.
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15.
  • Jalilian, Ehsan, et al. (author)
  • Luminescence properties of the Cu4I62- cluster
  • 2011
  • In: CrystEngComm. - : Royal Society of Chemistry (RSC). - 1466-8033. ; 13:14, s. 4729-4734
  • Journal article (peer-reviewed)abstract
    • Two new solvates were prepared in the system Cu(I) I using a solvolysis reaction. The structures for both of them were solved by X-ray crystallography, showing that they constitute two modifications of the same compound with the net formula [Cu4I6](P(C6H5)(4))(2)center dot 2OC(CH3)(2). Both types of crystals show vivid fluorescence when exposed to UV light. The formation of the first modification (I) seems to be preferred by kinetics and on ageing in the mother liquor it converts to modification (II). The Cu positions in (I) are disordered while those in (II) are fully ordered. The luminescent properties of both crystals were characterized using a confocal microscope and an excitation wavelength of 405 nm, resulting in fluorescence spectra with the intensities of 1.22 and 0.52 relative to the reference (fluorescein 10 mu M). Density functional theory calculations on the ordered Cu4I62- core of modification (II) show that the de-excitation from LUMO to HOMO is responsible for the luminescence. The calculated emission spectrum has a maximum at 531 nm in good agreement with the results from confocal microscopy.
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17.
  • Karlsson, Erik A., et al. (author)
  • Synthesis and Electron-Transfer Processes in a New Family of Ligands for Coupled Ru-Mn2 Complexes
  • 2014
  • In: ChemPlusChem. - : Wiley. - 2192-6506. ; 79:7, s. 936-950
  • Journal article (peer-reviewed)abstract
    • A series of [Ru(bpy)(3)](2+)-type (bpy= 2,2'-bipyridine) photosensitisers have been coupled to a ligand for Mn, which is expected to give a dinuclear complex that is active as a water oxidation catalyst. Unexpectedly, photophysical studies showed that the assemblies had very short lived excited states and that the decay patterns were complex and strongly dependent on pH. One dyad was prepared that was capable of catalysing chemical water oxidation by using [Ru(bpy)(3)](3+) as an oxidant. However, photochemical water oxidation in the presence of an external electron acceptor failed, presumably because the short excited-state lifetime precluded initial electron transfer to the added acceptor. The photophysical behaviour could be explained by the presence of an intricate excited-state manifold, as also suggested by time-dependent DFT calculations.
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18.
  • Kärkäs, Markus D., et al. (author)
  • Metal-Ligand Cooperation in Single-Site Ruthenium Water Oxidation Catalysts : A Combined Experimental and Quantum Chemical Approach
  • 2018
  • In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 57:17, s. 10881-10895
  • Journal article (peer-reviewed)abstract
    • Catalysts for oxidation of water to molecular oxygen are essential in solar-driven water splitting. In order to develop more efficient catalysts for this oxidatively demanding reaction, it is vital to have mechanistic insight in order to understand how the catalysts operate. Herein, we report the mechanistic details associated with the two Ru catalysts 1 and 2. Insight into the mechanistic landscape of water oxidation catalyzed by the two single-site Ru catalysts was revealed by the use of a combination of experimental techniques and quantum chemical calculations. On the basis of the obtained results, detailed mechanisms for oxidation of water by complexes 1 and 2 are proposed. Although the two complexes are structurally related, two deviating mechanistic scenarios are proposed with metal-ligand cooperation being an important feature in both processes. The proposed mechanistic platforms provide insight for the activation of water or related small molecules through nontraditional and previously unexplored routes.
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19.
  • Kärkäs, Markus D., et al. (author)
  • Molecular ruthenium water oxidation catalysts carrying non-innocent ligands : mechanistic insight through structure-activity relationships and quantum chemical calculations
  • 2016
  • In: Catalysis Science & Technology. - : Royal Society of Chemistry (RSC). - 2044-4753 .- 2044-4761. ; 6:5, s. 1306-1319
  • Journal article (peer-reviewed)abstract
    • Robust catalysts that mediate H2O oxidation are of fundamental importance for the development of novel carbon-neutral energy technologies. Herein we report the synthesis of a group of single-site Ru complexes. Structure-activity studies revealed that the individual steps in the oxidation of H2O depended differently on the electronic properties of the introduced ligand substituents. The mechanistic details associated with these complexes were investigated experimentally along with quantum chemical calculations. It was found that O-O bond formation for the developed Ru complexes proceeds via high-valent Ru-VI species, where the capability of accessing this species is derived from the non-innocent ligand architecture. This cooperative catalytic involvement and the ability of accessing Ru-VI are intriguing and distinguish these Ru catalysts from a majority of previously reported complexes, and might generate unexplored reaction pathways for activation of small molecules such as H2O.
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20.
  • Laine, Tanja M., et al. (author)
  • A Dinuclear Ruthenium-Based Water Oxidation Catalyst : Use of Non-Innocent Ligand Frameworks for Promoting Multi-Electron Reactions
  • 2015
  • In: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 21:28, s. 10039-10048
  • Journal article (peer-reviewed)abstract
    • Insight into how H2O is oxidized to O-2 is envisioned to facilitate the rational design of artificial water oxidation catalysts, which is a vital component in solar-to-fuel conversion schemes. Herein, we report on the mechanistic features associated with a dinuclear Ru-based water oxidation catalyst. The catalytic action of the designed Ru complex was studied by the combined use of high-resolution mass spectrometry, electrochemistry, and quantum chemical calculations. Based on the obtained results, it is suggested that the designed ligand scaffold in Ru complex 1 has a non-innocent behavior, in which metal-ligand cooperation is an important part during the four-electron oxidation of H2O. This feature is vital for the observed catalytic efficiency and highlights that the preparation of catalysts housing non-innocent molecular frameworks could be a general strategy for accessing efficient catalysts for activation of H2O.
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21.
  • Laine, Tanja M., et al. (author)
  • Efficient photochemical water oxidation by a dinuclear molecular ruthenium complex
  • 2015
  • In: Chemical Communications. - : Royal Society of Chemistry. - 1359-7345 .- 1364-548X. ; 51:10, s. 1862-1865
  • Journal article (peer-reviewed)abstract
    • Herein is described the preparation of a dinuclear molecular Ru catalyst for H2O oxidation. The prepared catalyst mediates the photochemical oxidation of H2O with an efficiency comparable to state-of-the-art catalysts.
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22.
  • Li, Ying-Ying, et al. (author)
  • Mechanism of Water Oxidation Catalyzed by a Mononuclear Manganese Complex
  • 2017
  • In: ChemSusChem. - : Wiley. - 1864-5631 .- 1864-564X. ; 10:5, s. 903-911
  • Journal article (peer-reviewed)abstract
    • The design and synthesis of biomimetic Mn complexes to catalyze oxygen evolution is a very appealing goal because water oxidation in nature employs a Mn complex. Recently, the mononuclear Mn complex [LMnII(H2O)(2)](2+) [1, L=Py2N(tBu)(2), Py= pyridyl] was reported to catalyze water oxidation electro-chemically at an applied potential of 1.23 V at pH 12.2 in aqueous solution. Density functional calculations were performed to elucidate the mechanism of water oxidation promoted by this catalyst. The calculations showed that 1 can lose two protons and one electron readily to produce [LMnIII(OH)(2)](+) (2), which then undergoes two sequential proton-coupled electron-transfer processes to afford [(LMnOO)-O-V](+) (4). The O-O bond formation can occur through direct coupling of the two oxido ligands or through nucleophilic attack of water. These two mechanisms have similar barriers of approximately 17 kcal mol(-1). The further oxidation of 4 to generate [(LMnO)-O-VI-O](2+) (5), which enables O-O bond formation, has a much higher barrier. In addition, ligand degradation by C-H activation has a similar barrier to that for the O-O bond formation, and this explains the relatively low turnover number of this catalyst.
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23.
  • Li, Ying-Ying, et al. (author)
  • Quantum Chemical Study of the Mechanism of Water Oxidation Catalyzed by a Heterotrinuclear Ru2Mn Complex
  • 2019
  • In: ChemSusChem. - : Wiley. - 1864-5631 .- 1864-564X. ; 12:5, s. 1101-1110
  • Journal article (peer-reviewed)abstract
    • The heterotrinuclear complex A {[Ru-II(H2O)(tpy)](2)(mu-[Mn-II(H2O)(2)(bpp)(2)])}(4+) [tpy=2,2 ':6 ',2 ''-terpyridine, bpp=3,5-bis(2-pyridyl)pyrazolate] was found to catalyze water oxidation both electrochemically and photochemically with [Ru(bpy)(3)](3+) (bpy=2,2 '-bipyridine) as the photosensitizer and Na2S2O8 as the electron acceptor in neutral phosphate buffer. The mechanism of water oxidation catalyzed by this unprecedented trinuclear complex was studied by density functional calculations. The calculations showed that a series of oxidation and deprotonation events take place from A, leading to the formation of complex 1 (formal oxidation state of Ru1(IV)Mn(III)Ru2(III)), which is the starting species for the catalytic cycle. Three sequential oxidations of 1 result in the generation of the catalytically competing species 4 (formal oxidation state of Ru1(IV)Mn(V)Ru2(IV)), which triggers the O-O bond formation. The direct coupling of two adjacent oxo ligands bound to Ru and Mn leads to the production of a superoxide intermediate Int1. This step was calculated to have a barrier of 7.2 kcal mol(-1) at the B3LYP*-D3 level. Subsequent O-2 release from Int1 turns out to be quite facile. Other possible pathways were found to be much less favorable, including water nucleophilic attack, the coupling of an oxo and a hydroxide, and the direct coupling pathway at a lower oxidation state ((RuMnRuIV)-Mn-IV-Ru-IV).
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24.
  • Liao, Rong-Zhen, et al. (author)
  • Antiferromagnetically coupled [Fe8S9] cluster catalyzed acetylene reduction in a nitrogenase-like enzyme DCCPCh : Insights from QM/MM calculations
  • 2021
  • In: Journal of Catalysis. - : Elsevier BV. - 0021-9517 .- 1090-2694. ; 398, s. 67-75
  • Journal article (peer-reviewed)abstract
    • QM/MM calculations have been used to elucidate the reaction mechanism of the reduction of acetylene to ethylene catalyzed by a nitrogenase-like enzyme DCCPCh with an unusual [Fe8S9] double-cubane cluster. Various plausible reaction pathways, involving different oxidation states and protonation states of the iron-sulfur cluster, have been analyzed to find the most favorable one. The acetylene substrate bridges to the [Fe8S8] cluster via its triple bond in a μ-(bis-η2) coordination mode. After a proton-coupled electron transfer reduction of the reactant complex, the acetylene reduction may be described to proceed via a special “double-electron transfer induced proton transfer” mechanism, deduced from the principal interacting orbital analysis. The anti-ferromagnetically coupled [Fe8S8] cluster delivers a pair of α- and β-electrons to the substrate, concertedly but asynchronously with a proton transfer mediated by the second-shell Lys147 residue to one of the acetylene carbon atoms. Subsequently, the second proton-coupled electron transfer proceeds, followed by protonation of the substrate to afford the ethylene product. During the two-electron reaction, the oxidation states of the [Fe8S8] cluster cycle from [FeII6FeIII2], to [FeII7FeIII], to [FeII5FeIII3], and back to [FeII6FeIII2].
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25.
  • Liao, Rong-Zhen, 1983-, et al. (author)
  • Dipeptide hydrolysis by the dinuclear zinc enzyme human renal dipeptidase: Mechanistic insights from DFT calculations
  • 2010
  • In: Journal of Inorganic Biochemistry. - : Elsevier BV. - 0162-0134 .- 1873-3344. ; 104:1, s. 37-46
  • Journal article (peer-reviewed)abstract
    • The reaction mechanism of the dinuclear zinc enzyme human renal dipeptidase is investigated using hybrid density functional theory. This enzyme catalyzes the hydrolysis of dipeptides and beta-lactam antibiotics. Two different protonation states in which the important active site residue Asp288 is either neutral or ionized were considered. In both cases, the bridging hydroxide is shown to be capable of performing the nucleophilic attack on the substrate carbonyl carbon from its bridging position, resulting in the formation of a tetrahedral intermediate. This step is followed by protonation of the dipeptide nitrogen, coupled with C-N bond cleavage. The calculations establish that both cases have quite feasible energy barriers. When the Asp288 is neutral, the hydrolytic reaction occurs with a large exothermicity. However, the reaction becomes very close to thermoneutral with an ionized Asp288. The two zinc ions are shown to play different roles in the reaction. Zn1 binds the amino group of the substrate, and Zn2 interacts with the carboxylate group of the substrate, helping in orienting it for the nucleophilic attack. In addition, Zn2 stabilizes the oxyanion of the tetrahedral intermediate, thereby facilitating the nucleophilic attack
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26.
  • Liao, Rong-Zhen, et al. (author)
  • Energetics for the Mechanism of Nickel-Containing Carbon Monoxide Dehydrogenase
  • 2019
  • In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 58:12, s. 7931-7938
  • Journal article (peer-reviewed)abstract
    • Nickel-containing carbon monoxide (CO) dehydrogenase is an enzyme that catalyzes the important reversible carbon dioxide reduction. Several high-resolution structures have been determined at various stages of the reduction, which can be used as good starting points for the present computational study. The cluster model is used in combination with a systematic application of the density functional theory as recently described. The results are in very good agreement with experimental evidence. There are a few important results. To explain why the X-ray structure for the reduced C-red1 state has an empty site on nickel, it is here suggested that the cluster has been over-reduced by X-rays and is therefore not the desired reduced state, which instead contains a bound CO on nickel. After an additional reduction, a hydride bound to nickel is suggested to play a role. In order to obtain energetics in agreement with experiments, it is concluded that one sulfide bridge in the Ni-Fe cluster should be protonated. The best test of the accuracy obtained is to compare the computed rate for reduction using -0.6 V with that for oxidation using -0.3 V, where good agreement was obtained. Obtaining a mechanism that is easily reversible is another demanding aspect of the modeling. Nickel oscillates between nickel(II) and nickel(I), while nickel(0) never comes in.
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27.
  • Liao, Rong-Zhen, et al. (author)
  • Mechanism and selectivity of the dinuclear iron benzoyl-coenzyme A epoxidase BoxB
  • 2015
  • In: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 6:5, s. 2754-2764
  • Journal article (peer-reviewed)abstract
    • Benzoyl-CoA epoxidase is a dinuclear iron enzyme that catalyzes the epoxidation reaction of the aromatic ring of benzoyl-CoA with chemo-, regio- and stereo-selectivity. It has been suggested that this enzyme may also catalyze the deoxygenation reaction of epoxide, suggesting a unique bifunctionality among the diiron enzymes. We report a density functional theory study of this enzyme aimed at elucidating its mechanism and the various selectivities. The epoxidation is suggested to start with the binding of the O-2 molecule to the diferrous center to generate a diferric peroxide complex, followed by concerted O-O bond cleavage and epoxide formation. Two different pathways have been located, leading to (2S,3R)-epoxy and (2R,3S)-epoxy products, with barriers of 17.6 and 20.4 kcal mol(-1), respectively. The barrier difference is 2.8 kcal mol(-1), corresponding to a diastereomeric excess of about 99 : 1. Further isomerization from epoxide to phenol is found to have quite a high barrier, which cannot compete with the product release step. After product release into solution, fast epoxide-oxepin isomerization and racemization can take place easily, leading to a racemic mixture of (2S,3R) and (2R,3S) products. The deoxygenation of epoxide to regenerate benzoyl-CoA by a diferrous form of the enzyme proceeds via a stepwise mechanism. The C2-O bond cleavage happens first, coupled with one electron transfer from one iron center to the substrate, to form a radical intermediate, which is followed by the second C3-O bond cleavage. The first step is rate-limiting with a barrier of only 10.8 kcal mol(-1). Further experimental studies are encouraged to verify our results.
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28.
  • Liao, Rong-Zhen, et al. (author)
  • Mechanism for O-O bond formation in a biomimetic tetranuclear manganese cluster - A density functional theory study
  • 2015
  • In: Journal of Photochemistry and Photobiology. B. - : Elsevier BV. - 1011-1344 .- 1873-2682. ; 152:Part A, s. 162-172
  • Journal article (peer-reviewed)abstract
    • Density functional theory calculations have been used to study the reaction mechanism of water oxidation catalyzed by a tetranuclear Mn-oxo cluster Mn4O4L6 (L = (C6H4)(2)PO4-). It is proposed that the O-O bond formation mechanism is different in the gas phase and in a water solution. In the gas phase, upon phosphate ligand dissociation triggered by light absorption, the O-O bond formation starting with both the Mn-4(III,III,IV,IV) and Mn-4(III,IV,IV,IV) oxidation states has to take place via direct coupling of two bridging oxo groups. The calculated barriers are 42.3 and 37.1 kcal/mol, respectively, and there is an endergonicity of more than 10 kcal/mol. Additional photons are needed to overcome these large barriers. In water solution, water binding to the two vacant sites of the Mn ions, again after phosphate dissociation triggered by light absorption, is thermodynamically and kinetically very favorable. The catalytic cycle is suggested to start from the Mn-4(III,III,III,IV) oxidation state. The removal of three electrons and three protons leads to the formation of a Mn-4(III,IV,IV,IV)-oxyl radical complex. The O-O bond formation then proceeds via a nucleophilic attack of water on the Mn-IV-oxyl radical assisted by a Mn-bound hydroxide that abstracts a proton during the attack. This step was calculated to be rate-limiting with a total barrier of 29.2 kcal/mol. This is followed by proton-coupled electron transfer, O-2 release, and water binding to start the next catalytic cycle.
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29.
  • Liao, Rong-Zhen, 1983-, et al. (author)
  • Mechanism of mycolic acid cyclopropane synthase : A theoretical study
  • 2011
  • In: Biochemistry. - : American Chemical Society. - 0006-2960 .- 1520-4995. ; 50:9, s. 1505-1513
  • Journal article (peer-reviewed)abstract
    • The reaction mechanism of mycolic acid cyclopropane synthase is investigated using hybrid density functional theory. The direct methylation mechanism is examined with a large model of the active site constructed on the basis of the crystal structure of the native enzyme. The important active site residue Glu140 is modeled in both ionized and neutral forms. We demonstrate that the reaction starts via the transfer of a methyl to the substrate double bond, followed by the transfer of a proton from the methyl cation to the bicarbonate present in the active site. The first step is calculated to be rate-limiting, in agreement with experimental kinetic results. The protonation state of Glu140 has a rather weak influence on the reaction energetics. In addition to the natural reaction, a possible side reaction, namely a carbocation rearrangement, is also considered and is shown to have a low barrier. Finally, the energetics for the sulfur ylide proposal, which has already been ruled out, is also estimated, showing a large energetic penalty for ylide formation.
  •  
30.
  • Liao, Rong-Zhen, et al. (author)
  • Mechanism of tungsten-dependent acetylene hydratase from quantum chemical calculations
  • 2010
  • In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 107:52, s. 22523-22527
  • Journal article (peer-reviewed)abstract
    • Acetylene hydratase is a tungsten-dependent enzyme that catalyzes the nonredox hydration of acetylene to acetaldehyde. Density functional theory calculations are used to elucidate the reaction mechanism of this enzyme with a large model of the active site devised on the basis of the native X-ray crystal structure. Based on the calculations, we propose a new mechanism in which the acetylene substrate first displaces the W-coordinated water molecule, and then undergoes a nucleophilic attack by the water molecule assisted by an ionized Asp13 residue at the active site. This is followed by proton transfer from Asp13 to the newly formed vinyl anion intermediate. In the subsequent isomerization, Asp13 shuttles a proton from the hydroxyl group of the vinyl alcohol to the α-carbon. Asp13 is thus a key player in the mechanism, but also W is directly involved in the reaction by binding and activating acetylene and providing electrostatic stabilization to the transition states and intermediates. Several other mechanisms are also considered but the energetic barriers are found to be very high, ruling out these possibilities.
  •  
31.
  • Liao, Rong-Zhen (author)
  • Mechanistic insights into dinuclear zinc enzymes from density functional theory studies
  • 2009
  • Licentiate thesis (other academic/artistic)abstract
    • In this thesis, quantum chemical methods have been used to shed light on the reaction mechanisms of several dinuclear zinc enzymes. The enzymes studied are involved in the hydrolysis of phosphates, amides, and carboxylic esters, namely RNase Z, Dihydroorotase (DHO), and N-acyl homoserine lactone hydrolase (AHL lactonase). The density functional method B3LYP, together with quite large active site models, was used to investigate these enzymatic reactions. Several plausible proposed mechanisms, involving protonation states of important active site residues (DHO), substrate orientations (AHL lactonase), have been considered. The calculated energetics can be used to assess the feasibility of the suggested reaction mechanisms. Based on the calculations and also on other related dinuclear zinc enzymes studied previously, some general mechanistic features have been uncovered. For all three enzymes, the nucleophilicity of the bridging hydroxide is shown to be sufficient to perform the nucleophilic attack on the substrates. During the attack, the negative charge is transferred from the bridging hydroxide to the substrate oxygen (P=O or C=O). For phosphate hydrolysis, an in line attack have been suggested for RNase Z. In addition, the two zinc ions in RNase Z are directly involved in stabilizing the negative charge in the penta-coordinated transition states. For carbonyl substrates, only one zinc ion participates in the oxygen anion stabilization in the transition states and the tetrahedral intermediates. Furthermore, the enzymes always use the zinc ion with less negatively-charged ligands to play such role. All the substrates investigated have poor leaving groups. Therefore, either the zinc ions or some active site residues help the cleavage of the scissile bond. For RNase Z, a Glu-His diad was suggested to protonate the leaving group. For DHO, an Asp residue was shown to transfer a proton from the bridging hydroxide to the leaving group nitrogen. For AHL lactonase, a zinc ion was also observed to stabilize the leaving oxygen anion.
  •  
32.
  • Liao, Rong-Zhen, et al. (author)
  • Metal Oxidation States for the O-O Bond Formation in the Water Oxidation Catalyzed by a Pentanuclear Iron Complex
  • 2018
  • In: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 8:12, s. 11671-11678
  • Journal article (peer-reviewed)abstract
    • Understanding the water oxidation mechanism, especially how the O-O bond formation takes place, provides crucial implication for the design of more efficient molecular catalysts for water oxidation in artificial photosynthesis. Density functional calculations have here been used to revisit the mechanism of O-O bond formation catalyzed by a pentanuclear iron complex. By comparing energetics for O-O bond formation at different oxidation states, it is suggested that the formally Fe-5(III,III,III,IV,IV) state is the best candidate for the coupling of two oxo groups, with a barrier of 17.3 kcal/mol, rather than the previously suggested lower oxidation state of Fe-5(II,II,III,IV,IV). Importantly, the first water insertion into the Fe-5(III,III,III,III,III) complex is associated with a barrier of 18.8 kcal/mol. The calculated barrier is somewhat overestimated as discussed in the text. Other possible reaction pathways, including water attack at the Fe-5(III,III,III,IV,IV) state, coupling of oxo and hydroxide at the Fe-5(III,III,III,III,IV) state, and coupling of two oxo groups at the Fe-5(III,III,IV,IV,IV) state, were found to have much higher barriers.
  •  
33.
  • Liao, Rong-Zhen, et al. (author)
  • On the mechanism of water oxidation catalyzed by a dinuclear ruthenium complex : a quantum chemical study
  • 2016
  • In: Catalysis Science & Technology. - : Royal Society of Chemistry (RSC). - 2044-4753 .- 2044-4761. ; 6:13, s. 5031-5041
  • Journal article (peer-reviewed)abstract
    • The development of efficient and robust catalysts for H2O oxidation is an essential element in solar water splitting. The reaction mechanism for a previously reported dinuclear Ru water oxidation catalyst (1) has been investigated in detail through quantum chemical calculations. The predicted mechanism starts from a Ru-2(III,III) complex with two aqua ligands. After three sequential oxidations, O-O bond formation occurs at a formal Ru-2(IV,V) state via the direct coupling of two adjacent oxo moieties while the water nucleophilic attack mechanism was found to be associated with a higher energy barrier. Two H2O molecules are then inserted with subsequent release of O-2, which was found to be the rate-limiting step with a barrier of 22.7 kcal mol(-1). In a previous work, it was revealed that the ligand scaffold in the studied Ru complex has a non-innocent function. Here, we further highlight this behavior, where the ligand was shown to mediate proton transfer events and accept/donate electrons during the catalytic cycle, which can significantly decrease the redox potentials and facilitate the access to high-valent redox states. This study provides further insight into the H2O oxidation mechanism and principles for designing improved catalysts for activation of small molecules, such as H2O.
  •  
34.
  • Liao, Rong-Zhen, et al. (author)
  • Origins of Stereoselectivity in Peptide-Catalyzed Kinetic Resolution of Alcohols
  • 2016
  • In: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 6:2, s. 1165-1171
  • Journal article (peer-reviewed)abstract
    • The origin of the stereoselectivity of the tetrapeptide-catalyzed kinetic resolution of trans-2-N-acetamidocyclohexanol is investigated by means of density functional theory calculations. Transition states for the functionalization of both (R,R) and (S,S) substrates were optimized considering all possible conformers. Due to the flexibility of the peptidic catalyst, a large number of transition states had to be located, and analysis of the geometries and energies allowed for the identification of the main factors that control the stereo selectivity.
  •  
35.
  • Liao, Rong-Zhen, et al. (author)
  • Phosphate Hydrolysis by the Fe-2-Ca-3-Dependent Alkaline Phosphatase PhoX : Mechanistic Insights from DFT calculations
  • 2015
  • In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 54:24, s. 11941-11947
  • Journal article (peer-reviewed)abstract
    • PhoX is a pentanudear metalloenzyme that employs two ferric ions and three calcium ions to catalyze the hydrolysis of phosphomonoesters. On the basis of the X-ray structure of PhoX (Science 2014, 34S, 1170-1173), a model of the active site is designed, and quantum chemical calculations are used to investigate the reaction mechanism of this enzyme. The calculations support the experimental suggestion, in which the two high spin ferric ions interact in an antiferromagnetic fashion. The two step mechanism proposed by experimentalists has been investigated. The nudeophilic attack of a trinudear bridging oxo group on the phosphorus center was calculated to be the first step, which is concomitant with the departure of the phenolate, which is stabilized by a calcium ion. The second step is a reverse attack by a water molecule activated by a calciumbound hydroxide, leading to the regeneration of the bridging oxo group. The second step was calculated to have a barrier of 27.6 kcal/mol. The high barrier suggests that the alternative mechanism involving phosphate release directly from the active site seems to be more likely. All five metal ions are involved in the catalysis by stabilizing the pentacoordinated trigonal bipyramidal transition states.
  •  
36.
  • Liao, Rong-Zhen, 1983-, et al. (author)
  • Phosphate Mono- and Diesterase Activities of the Trinuclear Zinc Enzyme Nuclease P1—Insights from Quantum Chemical Calculations
  • 2010
  • In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 49:15, s. 6883-6888
  • Journal article (peer-reviewed)abstract
    • Nuclease P1 is a trinuclear zinc enzyme that catalyzes the hydrolysis of single-stranded DNA and RNA. Density functional calculations are used to elucidate the reaction mechanism of this enzyme with a model of the active site designed on the basis of the X-ray crystal structure. 2-Tetrahydrofuranyl phosphate and methyl 2-tetrahydrofuranyl phosphate substrates are used to explore the phosphomonoesterase and phosphodiesterase activities of this enzyme, respectively. The calculations reveal that for both activities, a bridging hydroxide performs an in-line attack on the phosphorus center, resulting in inversion of the configuration. Simultaneously, the P−O bond is cleaved, and Zn2 stabilizes the negative charge of the leaving alkoxide anion and assists its departure. All three zinc ions, together with Arg48, provide electrostatic stabilization to the penta-coordinated transition state, thereby lowering the reaction barrier.
  •  
37.
  • Liao, Rong-Zhen, et al. (author)
  • Photosystem II Like Water Oxidation Mechanism in a Bioinspired Tetranuclear Manganese Complex
  • 2015
  • In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 54:1, s. 342-351
  • Journal article (peer-reviewed)abstract
    • The synthesis of Mn-based catalysts to mimic the structural and catalytic properties of the oxygen-evolving complex in photosystem II is a long-standing goal for researchers. An interesting result in this field came with the synthesis of a Mn complex that enables water oxidation driven by the mild single-electron oxidant [Ru(bpy)(3)](3+). On the basis of hybrid density functional calculations, we herein propose a water oxidation mechanism for this bioinspired Mn catalyst, where the crucial O-O bond formation proceeds from the formal Mn-4(IV,IV,IV,V) state by direct coupling of a Mn-IV-bound terminal oxyl radical and a di-Mn bridging oxo group, a mechanism quite similar to the presently leading suggestion for the natural system. Of importance here is that the designed ligand is shown to be redox-active and can therefore store redox equivalents during the catalytic transitions, thereby alleviating the redox processes at the Mn centers.
  •  
38.
  • Liao, Rong-Zhen, et al. (author)
  • Possible water association and oxidation mechanisms for a recently synthesized Mn4Ca-complex
  • 2017
  • In: Journal of Catalysis. - : Elsevier BV. - 0021-9517 .- 1090-2694. ; 354, s. 169-181
  • Journal article (peer-reviewed)abstract
    • The laboratory synthesis of complexes to mimic the structure of the Mn4Ca cluster in the oxygen evolving complex (OEC) of photosystem II is a very challenging task to accomplish. The most encouraging breakthrough in this field was recently achieved with the synthesis of a Mn4Ca complex (Zhang et al., 2015) that shows a very similar core structure to the OEC. On the basis of density functional calculations, the structure and the redox potentials of this Mn4Ca complex in acetonitrile are obtained with very good agreement to experiments. A possible mechanism for water oxidation is more problematic. If only the thermodynamics is considered and assuming a standard state of 1 mol/L, it turns out that up to five water molecules can be inserted into the complex with only a small cost. This leads to a barrier for O-O bond formation which is 22.8 kcal/mol with an applied potential of 1.3 V. However, a study of the kinetics for the insertion of the critical water bridge between Mn3 and Mn4 indicates that the barrier for that process is quite high with 24.6 kcal/mol. A model where this water is not inserted also led to a rather high barrier for O-O bond formation with 31.7 kcal/mol with an applied potential of 1.3 V. However, the barrier decreases significantly to only 13.4 kcal/mol with an applied potential of 1.7 V. The different barrier originates from the different energetic penalty for the formation of the catalytic competent S-4 state. A major experimental problem discussed below, is the instability of the complex, which does not allow a high water concentration. The best calculated overall mechanism obtained is essentially the same as the leading suggestion for the OEC, where the critical O-O bond formation takes place at the S-4 state (formally Mn-4(IV,IV,IV,IV)) via direct coupling of a Mn-IV-oxyl radical and a di-Mn bridging oxo group.
  •  
39.
  • Liao, Rong-Zhen, 1983-, et al. (author)
  • Quantum chemical modeling of enzymatic reactions : The case of decarboxylation
  • 2011
  • In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 07:05, s. 1494-1501
  • Journal article (peer-reviewed)abstract
    • We present a systematic study of the decarboxylation step of the enzyme aspartate decarboxylase with the purpose of assessing the quantum chemical cluster approach for modeling this important class of decarboxylase enzymes. Active site models ranging in size from 27 to 220 atoms are designed, and the barrier and reaction energy of this step are evaluated. To model the enzyme surrounding, homogeneous polarizable medium techniques are used with several dielectric constants. The main conclusion is that when the active site model reaches a certain size, the solvation effects from the surroundings saturate. Similar results have previously been obtained from systematic studies of other classes of enzymes, suggesting that they are of a quite general nature.
  •  
40.
  • Liao, Rong-Zhen, et al. (author)
  • Quantum Chemical Modeling of Homogeneous Water Oxidation Catalysis
  • 2017
  • In: ChemSusChem. - : Wiley. - 1864-5631 .- 1864-564X. ; 10:22, s. 4236-4263
  • Research review (peer-reviewed)abstract
    • The design of efficient and robust water oxidation catalysts has proven challenging in the development of artificial photosynthetic systems for solar energy harnessing and storage. Tremendous progress has been made in the development of homogeneous transition-metal complexes capable of mediating water oxidation. To improve the efficiency of the catalyst and to design new catalysts, a detailed mechanistic understanding is necessary. Quantum chemical modeling calculations have been successfully used to complement the experimental techniques to suggest a catalytic mechanism and identify all stationary points, including transition states for both O-O bond formation and O-2 release. In this review, recent progress in the applications of quantum chemical methods for the modeling of homogeneous water oxidation catalysis, covering various transition metals, including manganese, iron, cobalt, nickel, copper, ruthenium, and iridium, is discussed.
  •  
41.
  • Liao, Rong-Zhen, et al. (author)
  • Reaction mechanism of the dinuclear zinc enzyme N-acyl-L-homoserine lactone hydrolase : a quantum chemical study
  • 2009
  • In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 48:4, s. 1442-1448
  • Journal article (peer-reviewed)abstract
    • N-acyl-L-homoserine lactone hydrolase (AHL lactonase) is a dinuclear zinc enzyme responsible for the hydrolytic ring opening of AHLs, disrupting quorum sensing in bacteria. The reaction mechanism is investigated using hybrid density functional theory. A model of the active site is designed on the basis of the X-ray crystal structure, and stationary points along the reaction pathway are optimized and analyzed. Two possible mechanisms based on two different substrate orientations are considered. The calculations give support to a reaction mechanism that involves two major chemical steps: nucleophilic attack on the substrate carbonyl carbon by the bridging hydroxide and ring opening by direct ester C - O bond cleavage. The roles of the two zinc ions are analyzed. Zn1 is demonstrated to stabilize the charge of the tetrahedral intermediate, thereby facilitating the nucleophilic attack, while Zn2 stabilizes the charge of the alkoxide resulting from the ring opening, thereby lowering the barrier for the C - O bond cleavage.
  •  
42.
  • Liao, Rong-Zhen, 1983-, et al. (author)
  • Reaction Mechanism of the Trinuclear Zinc Enzyme Phospholipase C : A Density Functional Theory Study
  • 2010
  • In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:7, s. 2533-2540
  • Journal article (peer-reviewed)abstract
    • Phosphatidylcholine-preferring phospholipase C is a trinuclear zinc-dependent phosphodiesterase, catalyzing the hydrolysis of choline phospholipids. In the present study, density functional theory is used to investigate the reaction mechanism of this enzyme. Two possible mechanistic scenarios were considered with a model of the active site designed on the basis of the high resolution X-ray crystal structure of the native enzyme. The calculations show that a Zn1 and Zn3 bridging hydroxide rather than a Zn1 coordinated water molecule performs the nucleophilic attack on the phosphorus center. Simultaneously, Zn2 activates a water molecule to protonate the leaving group. In the following step, the newly generated Zn2 bound hydroxide makes the reverse attack, resulting in the regeneration of the bridging hydroxide. The first step is calculated to be rate-limiting with a barrier of 17.3 kcal/mol, in good agreement with experimental kinetic studies. The zinc ions are suggested to orient the substrate for nucleophilic attack and provide electrostatic stabilization to the dianionic penta-coordinated trigonal bipyramidal transition states, thereby lowering the barrier.
  •  
43.
  • Liao, Rong-Zhen, et al. (author)
  • Reaction Mechanism of Water Oxidation Catalyzed by Iron Tetraamido Macrocyclic Ligand Complexes - A DFT Study
  • 2014
  • In: European Journal of Inorganic Chemistry. - : Wiley. - 1434-1948 .- 1099-1948 .- 1099-0682. ; :4, s. 728-741
  • Journal article (peer-reviewed)abstract
    • Density functional calculations are used to elucidate the reaction mechanism of water oxidation catalyzed by iron tetra-amido macrocyclic ligand (TAML) complexes. The oxidation of the starting TAML-Fe3+-OH2 complex by removing three electrons and two protons leads to the formation of a key intermediate, TAML-Fe5+=O, which can undergo nucleophilic attack by either a water molecule or a nitrate ion. Both pathways involve attack on the oxo group and lead to the production of O-2. The water attack is more favoured and has a total barrier of 15.4 kcal/mol. The alternative nitrate attack pathway has a barrier of 19.5 kcal/mol. Nitrate functions as a cocatalyst by first donating an oxygen atom to the oxo group to form O-2 and a nitrite ion, which can then be reoxidized to regenerate a nitrate ion. Three possible competing pathways result in ligand modification, namely, water and nitrate attack on the ligand, as well as ligand amide oxidation. The water attack on the ligand has a low barrier of only 10.9 kcal/mol and leads to the opening of the benzene ring, which explains the observation of fast catalyst degradation. The lack of activity or lower activity of other catalysts with different substituents is also rationalized.
  •  
44.
  • Liao, Rong-Zhen, et al. (author)
  • The mechanism of hydrogen evolution in Cu(bztpen)-catalysed water reduction : a DFT study
  • 2015
  • In: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 44:21, s. 9736-9739
  • Journal article (peer-reviewed)abstract
    • The mechanism of water reduction catalysed by a mononuclear copper complex Cu(bztpen) (bztpen = N-benzyl-N, N', N'-tris(pyridine-2-ylmethyl) ethylenediamine) has been elucidated by DFT calculations, revealing that hydrogen evolution proceeds via coupling of a Cu(II)-hydride and a pendant pyridinium, and providing important implications for the future design of new catalytic systems for water reduction.
  •  
45.
  • Liao, Rong-Zhen, et al. (author)
  • Theoretical investigation of the reaction mechanism of the dinuclear zinc enzyme dihydroorotase
  • 2008
  • In: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 14:14, s. 4287-4292
  • Journal article (peer-reviewed)abstract
    • The reaction mechanism of the dinuclear zinc enzyme dihydroorotase was investigated by using hybrid density functional theory. This enzyme catalyzes the reversible interconversion of dihydroorotate and carbamoyl aspartate. Two reaction mechanisms in which the important active site residue Asp250 was either protonated or unprotonated were considered. The calculations establish that Asp250 must be unprotonated for the reaction to take place. The bridging hydroxide is shown to be capable of performing nucleophilic attack on the substrate from its bridging position and the role of Znβ is argued to be the stabilization of the tetrahedral intermediate and the transition state leading to it, thereby lowering the barrier for the nucleophilic attack. It is furthermore concluded that the rate-limiting step is the protonation of the amide nitrogen by Asp250 coupled with C-N bond cleavage, which is consistent with previous experimental findings from isotope labeling studies.
  •  
46.
  • Liao, Rong-Zhen, 1983-, et al. (author)
  • Theoretical study of the chemoselectivity of tungsten-dependent acetylene hydratase
  • 2011
  • In: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 1:8, s. 937-944
  • Journal article (peer-reviewed)abstract
    • The tungsten-dependent enzyme acetylene hydratase catalyzes the hydration of acetylene to acetaldehyde. Very recently, we proposed a reaction mechanism for this enzyme based on density functional calculations (Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 22523). The mechanism involves direct coordination of the substrate to the tungsten ion, followed by a nucleophilic attack by a water molecule concerted with a proton transfer to a second-shell aspartate, which then reprotonates the substrate. Here, we use the same methodology to investigate the factors involved in the control of the chemoselectivity of this enzyme. The hydration reactions of three representative compounds (propyne, ethylene, and acetonitrile) are investigated using a large model of the active site. The energy of substrate binding to the metal ion and the barrier for the following nucleophilic attack are used to rationalize the experimental observations. It is shown that all three compounds have higher barriers for hydration compared with acetylene. In addition, propyne is shown to have a larger binding energy, explaining its behavior as a competitive inhibitor. Taken together, the results provide further corroboration of our suggested mechanism for acetylene hydratase
  •  
47.
  • Liao, Rong-Zhen, et al. (author)
  • Theoretical study of the RNA hydrolysis mechanism of the dinuclear zinc enzyme RNase Z
  • 2009
  • In: European Journal of Inorganic Chemistry. - Weinheim : Wiley. - 1434-1948 .- 1099-1948 .- 1099-0682. ; :20, s. 2967-2972
  • Journal article (peer-reviewed)abstract
    •  RNase Z is a dinuclear zinc enzyme that catalyzes the removal of the tRNA 3'-end trailer. Density functional theory is used to investigate the phosphodiester hydrolysis mechanism of this enzyme with a model of the active site constructed on the basis of the crystal structure. The calculations imply that the reaction proceeds through two steps. The first step is a nucleophihc attack by a bridging hydroxide coupled with protonation of the leaving group by a Glu-His diad. Subsequently, a water molecule activated by the same Glu-His diad makes a reverse attack, regenerating the bridging hydroxide. The second step is calculated to be the rate-limiting step with a barrier of 18 kcal/mol, in good agreement with experimental kinetic studies. Both zinc ions participate in substrate binding and orientation, facilitating nucleophilic attack. In addition, they act as electrophilic catalysts to stabilize the pentacoordinate trigonal-bipyramidal transition states.
  •  
48.
  • Liao, Rong-Zhen, 1983-, et al. (author)
  • Tungsten-dependent formaldehyde ferredoxin oxidoreductase : Reaction mechanism from quantum chemical calculations
  • 2011
  • In: Journal of Inorganic Biochemistry. - : Elsevier BV. - 0162-0134 .- 1873-3344. ; 105:7, s. 927-936
  • Journal article (peer-reviewed)abstract
    • Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus is a tungsten-dependent enzyme thatcatalyzes the oxidation of formaldehyde to formic acid. In the present study, quantum chemical calculationsare used to elucidate the reaction mechanism of this enzyme. Several possible mechanistic scenarios areinvestigated with a large model of the active site designed on the basis of the X-ray crystal structure of thenative enzyme. Based on the calculations, we propose a new mechanism in which the formaldehyde substratebinds directly to the tungsten ion.WVI=O then performs a nucleophilic attack on the formaldehyde carbon toform a tetrahedral intermediate. In the second step, which is calculated to be rate limiting, a proton istransferred to the second-shell Glu308 residue, coupled with a two-electron reduction of the tungsten ion.The calculated barriers for the mechanism are energetically very feasible and in relatively good agreementwith experimental rate constants. Three other second-shell mechanisms, including one previously proposedbased on experimental findings, are considered but ruled out because of their high barriers.
  •  
49.
  • Liao, Rong-Zhen, et al. (author)
  • Unraveling the Mechanism and Regioselectivity of the B12-Dependent Reductive Dehalogenase PceA
  • 2016
  • In: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 22:35, s. 12391-12399
  • Journal article (peer-reviewed)abstract
    • PceA is a cobalamin-dependent reductive dehalogenase that catalyzes the dechlorination of perchloroethylene to trichloroethylene and then to cis-dichloroethylene as the sole final product. The reaction mechanism and the regioselectivity of this enzyme are investigated by using density functional calculations. Four different substrates, namely, perchloroethylene, trichloroethylene, cis-dichloroethylene, and chlorotheylene, have been considered and were found to follow the same reaction mechanism pattern. The reaction starts with the reduction of Co-II to Co-I through a proton-coupled electron transfer process, with the proton delivered to a Tyr246 anion. This is followed by concerted C-Cl bond heterolytic cleavage and proton transfer from Tyr246 to the substrate carbon atom, generating a Co-III-Cl intermediate. Subsequently, a one-electron transfer leads to the formation of the Co-II-Cl product, from which the chloride and the dehalogenated product can be released from the active site. The substrate reactivity follows the trend perchloroethylene>trichloroethylene >> cis-dichloroethylene >> chlorotheylene. The barriers for the latter two substrates are significantly higher compared with those for perchloroethylene and trichloroethylene, implying that PceA does not catalyze their degradation. In addition, the formation of cis-dichloroethylene has a lower barrier by 3.8kcalmol(-1) than the formation of trans-dichloroethylene and 1,1-dichloroethylene, reproducing the regioselectivity. These results agree quite well with the experimental findings, which show cis-dichloroethylene as the sole product in the PceA-catalyzed dechlorination of perchloethylene and trichloroethylene.
  •  
50.
  • Liao, Rong-Zhen, et al. (author)
  • Which Oxidation State Initiates Dehalogenation in the B12-Dependent Enzyme NpRdhA : Co-II, COI or Co-0?
  • 2015
  • In: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 5:12, s. 7350-7358
  • Journal article (peer-reviewed)abstract
    • The quantum chemical cluster approach was used to elucidate the reaction mechanism of debromination catalyzed by the B12-dependent reductive dehalogenase NpRdliA. Various pathways, involving different oxidation states of the cobalt ion and different protonation states of the model, have been analyzed in order to find the most favorable one. We find that the reductive C Br cleavage takes place exclusively at the Co' state via a heterolytic pathway in the singlet state. Importantly, the C-H bond formation and the C Br bond cleavage proceeds via a concerted transition state, as opposed to the stepwise pathway suggested before. C Br cleavage at the Coll state has a very high barrier, and the reduction of Co' to Co is associated with a very negative potential; thus, reductive dehalogenation at Coll and Co can be safely ruled out. Examination of substrate with different halogen substitutions (F, Cl, Br, I) shows that the dehalogenation reactivity follows the order C I > C Br > C-C1 > C-F, and the barrier for defluorination is so high that NpRdhA cannot catalyze that reaction.
  •  
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