scholarly journals Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

2019 ◽  
Vol 15 ◽  
pp. 145-159 ◽  
Author(s):  
Ferran Planas ◽  
Michael J McLeish ◽  
Fahmi Himo
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Thiamin Diphosphate ◽  
Diverse Range ◽  
Factors Affecting ◽  
Benzoylformate Decarboxylase ◽  
Carbon Carbon Bond ◽  
Activated State ◽  
Catalyzed Reactions ◽  
The Individual

Thiamin diphosphate (ThDP)-dependent enzymes constitute a large class of enzymes that catalyze a diverse range of reactions. Many are involved in stereospecific carbon–carbon bond formation and, consequently, have found increasing interest and utility as chiral catalysts in various biocatalytic applications. All ThDP-catalyzed reactions require the reaction of the ThDP ylide (the activated state of the cofactor) with the substrate. Given that the cofactor can adopt up to seven states on an enzyme, identifying the factors affecting the stability of the pre-reactant states is important for the overall understanding of the kinetics and mechanism of the individual reactions. In this paper we use density functional theory calculations to systematically study the different cofactor states in terms of energies and geometries. Benzoylformate decarboxylase (BFDC), which is a well characterized chiral catalyst, serves as the prototypical ThDP-dependent enzyme. A model of the active site was constructed on the basis of available crystal structures, and the cofactor states were characterized in the presence of three different ligands (crystallographic water, benzoylformate as substrate, and (R)-mandelate as inhibitor). Overall, the calculations reveal that the relative stabilities of the cofactor states are greatly affected by the presence and identity of the bound ligands. A surprising finding is that benzoylformate binding, while favoring ylide formation, provided even greater stabilization to a catalytically inactive tricyclic state. Conversely, the inhibitor binding greatly destabilized the ylide formation. Together, these observations have significant implications for the reaction kinetics of the ThDP-dependent enzymes, and, potentially, for the use of unnatural substrates in such reactions.

scholarly journals Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents

2020 ◽  
Author(s):  
Vivek Sundaram ◽  
Alexey V. Lyulin ◽  
Björn Baumeier
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Variable Number ◽  
Polymer Chains ◽  
Relaxation Processes ◽  
Polymer Backbone ◽  
Dynamics Simulations ◽  
The Individual

We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and variable number of pi-conjugated thiophene units in the backbone, used as donor material in organic photovoltaic devices. Available intra-fragment parameterizations of the individual fragment building blocks are combined with inter-fragment bonded and non-bonded parameters explicitly derived from density-functional theory calculations. To validate the force field we perform classical molecular dynamics simulations of single polymer chains with 1, 2, and 3 thiophenes in good and bad solvents, and of melts. We observe the expected dependence of the chain conformation on the solvent quality, with the chain collapsing in water, and swelling in chloroform. The glass transition temperature for the polymer melts is found to be in the range of 340K to 370K. Analysis of the mobility of the conjugated segments in the polymer backbone reveals two relaxation processes: a fast one with a characteristic time at room temperature on the order of 10ps associated with nearly harmonic vibrations and a slow one on the order of 100 associated with temperature activated cis-trans transitions.

Understanding the role of frustrated Lewis pairs as ligands in transition metal-catalyzed reactions

2020 ◽  
Vol 49 (10) ◽  
pp. 3129-3137 ◽  
Author(s):  
Jorge Juan Cabrera-Trujillo ◽  
Israel Fernández
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
State Of The Art ◽  
Density Functional Theory Calculations ◽  
Frustrated Lewis Pairs ◽  
Functional Theory ◽  
Catalyzed Reactions ◽  
Metal Catalyzed ◽  
Lewis Pairs

The role of frustrated Lewis pairs (FLPs) as ligands in gold(i) catalyzed-reactions has been computationally investigated by using state-of-the-art density functional theory calculations.

Understanding the Reaction Mechanism of Gold-Catalyzed Reactions of 2,1-Benzisoxazoles with Propiolates and Ynamides

2021 ◽  
Author(s):  
Zhaoyuan Yu ◽  
Shu-Juan Lin ◽  
Zhenyang Lin
Keyword(s):  
Density Functional Theory ◽  
Reaction Mechanism ◽  
Reaction Mechanisms ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Catalyzed Reactions

The detailed reaction mechanisms of gold-catalyzed reactions of 2,1-benzisoxazoles with propiolates and ynamides have been investigated with the aid of density functional theory calculations. Our investigation focused on the different...

scholarly journals Graphene Support Effects on Palladium Catalyzed Reactions

2019 ◽  
Vol 20 (2) ◽  
Author(s):  
Kathleen Dreyer
Keyword(s):  
Binding Energy ◽  
Palladium Catalysts ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Binding Energies ◽  
Catalytic Reactions ◽  
Graphene Interface ◽  
Palladium Catalyzed ◽  
Pd Clusters ◽  
Catalyzed Reactions

Palladium catalysts are often anchored to a support, such as graphitic carbon, to increase their overall surface area and facilitate catalytic reactions. There is a potential for interaction between the support and the catalyst, which can affect such reactions. At a certain palladium size threshold, it is hypothesized that the effects of the support on reactions on Pd are negligible. To determine this threshold, the Pd catalyst size and shape were varied (size was varied in the number of layers and number of Pd atoms, while shape ranged from hemispherical to spherical). The Pd clusters ranged from 2-5 layers and 38-293 atoms. Also, the graphene support was functionalized to different extents to test its effect on catalytic reactions on Pd. Initially, adsorption reactions of H*, O*, C*, OH*, and CH* onto supported Pd were tested to determine the effects of catalyst shape and size on the binding energy of such adsorbates. Periodic density functional theory calculations were used to determine these binding energies on bare Pd, Pd on a pure graphene support, and Pd on graphene functionalized with oxygen and hydroxide. These tests revealed that smaller Pd particles (about 100 atoms or fewer) are influenced by the support, showing large shifts in adsorbate binding energy from the pure graphene to the functionalized graphene. This shift in binding energy indicates that there are major changes in the catalytic behavior of sites upon which the adsorption reaction was tested, meaning that sites near the Pd-graphene interface might be affected by the support.

1,4,5,8-Tetraazafulvalene – Darstellung schwefelhaltiger Derivate und Zuordnung des Chromophors / 1,4,5,8-Tetraazafulvalenes – Synthesis of Sulfur-Containing Derivatives and Classification of the Chromophor

2004 ◽  
Vol 59 (4) ◽  
pp. 406-413 ◽  
Author(s):  
Christiane Kühn ◽  
R. Beckert ◽  
U.-W. Grummt ◽  
C. Käpplinger ◽  
E. Birckner
Keyword(s):  
Lipoic Acid ◽  
Density Functional ◽  
Tautomeric Form ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Different Types ◽  
Palladium Catalyzed ◽  
Catalyzed Reactions ◽  
Sulfur Containing

Abstract In order to obtain sulfur-containing tetraazafulvalenes the derivatives 1 - 3 were cross-coupled with different types of acetylenes via palladium-catalyzed reactions. Starting from the tetrabromoaryl derivative 3a, four bromine atoms could be replaced by 2-ethynylthiophene. Under analogous conditions, the methylsulfanyl esters 7 -11 could be obtained by employing 4-ethynylbenzoic acid 4-(methylsulfanyl)butylester 6. Lipoic acid could be integrated into tetraazafulvalenes successfully in a two step reaction. First, the Sonogashira coupling method yielded the compound 12 possessing two (4-anilino)ethynyl residues which were then condensed with lipoic acid to give derivative 13. Whereas the NMR data suggest the predominance of prototropic form A, UV/vis spectra of the deeply colored tetraazafulvalenes are in favor with structure B rather than with structure A. DFT calculations at the B3LYP/6-31G(d) level showed that tautomeric form B is about 60 kJ/mol more stable than A. In addition, time-dependent density functional theory calculations support the substructure of two crossed diazaheptamethinemerocyanines.

scholarly journals Function-oriented design of robust metal cocatalyst for photocatalytic hydrogen evolution on metal/titania composites

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dong Wang ◽  
Xue-Qing Gong
Keyword(s):  
Electron Transfer ◽  
Hydrogen Evolution ◽  
Density Functional ◽  
Metal Layer ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Metal Type ◽  
Surface Catalysis ◽  
The Individual ◽  
The Right

AbstractWhile the precise design of catalysts is one of ultimate goals in catalysis, practical strategies often fall short, especially for complicated photocatalytic processes. Here, taking the hydrogen evolution reaction (HER) as an example, we introduce a theoretical approach for designing robust metal cocatalysts supported on TiO2 using density functional theory calculations adopting on-site Coulomb correction and/or hybrid functionals. The approach starts with clarifying the individual function of each metal layer of metal/TiO2 composites in photocatalytic HER, covering both the electron transfer and surface catalysis aspects, followed by conducting a function-oriented optimization via exploring competent candidates. With this approach, we successfully determine and verify bimetallic Pt/Rh/TiO2 and Pt/Cu/TiO2 catalysts to be robust substitutes for conventional Pt/TiO2. The right metal type as well as the proper stacking sequence are demonstrated to be key to boosting performance. Moreover, we tentatively identify the tunneling barrier height as an effective descriptor for the important electron transfer process in photocatalysis on metal/oxide catalysts. We believe that this study pushes forward the frontier of photocatalyst design towards higher water splitting efficiency.

scholarly journals Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents

2020 ◽  
Author(s):  
Vivek Sundaram ◽  
Alexey V. Lyulin ◽  
Björn Baumeier
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Variable Number ◽  
Polymer Chains ◽  
Relaxation Processes ◽  
Polymer Backbone ◽  
Dynamics Simulations ◽  
The Individual

We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and variable number of pi-conjugated thiophene units in the backbone, used as donor material in organic photovoltaic devices. Available intra-fragment parameterizations of the individual fragment building blocks are combined with inter-fragment bonded and non-bonded parameters explicitly derived from density-functional theory calculations. To validate the force field we perform classical molecular dynamics simulations of single polymer chains with 1, 2, and 3 thiophenes in good and bad solvents, and of melts. We observe the expected dependence of the chain conformation on the solvent quality, with the chain collapsing in water, and swelling in chloroform. The glass transition temperature for the polymer melts is found to be in the range of 340K to 370K. Analysis of the mobility of the conjugated segments in the polymer backbone reveals two relaxation processes: a fast one with a characteristic time at room temperature on the order of 10ps associated with nearly harmonic vibrations and a slow one on the order of 100 associated with temperature activated cis-trans transitions.

scholarly journals Development and Testing of an All-Atom Force Field for Diketopyrrolopyrrole Polymers with Conjugated Substituents

2020 ◽  
Author(s):  
Vivek Sundaram ◽  
Alexey V. Lyulin ◽  
Björn Baumeier
Keyword(s):  
Force Field ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Variable Number ◽  
Polymer Chains ◽  
Relaxation Processes ◽  
Polymer Backbone ◽  
Dynamics Simulations ◽  
The Individual

We develop an all-atom force field for a series of diketopyrrolopyrrole polymers with two aromatic pyridine substituents and variable number of pi-conjugated thiophene units in the backbone, used as donor material in organic photovoltaic devices. Available intra-fragment parameterizations of the individual fragment building blocks are combined with inter-fragment bonded and non-bonded parameters explicitly derived from density-functional theory calculations. To validate the force field we perform classical molecular dynamics simulations of single polymer chains with 1, 2, and 3 thiophenes in good and bad solvents, and of melts. We observe the expected dependence of the chain conformation on the solvent quality, with the chain collapsing in water, and swelling in chloroform. The glass transition temperature for the polymer melts is found to be in the range of 340K to 370K. Analysis of the mobility of the conjugated segments in the polymer backbone reveals two relaxation processes: a fast one with a characteristic time at room temperature on the order of 10ps associated with nearly harmonic vibrations and a slow one on the order of 100 associated with temperature activated cis-trans transitions.

scholarly journals High-Resolution Spectroscopy of Bonding in a Novel BeP2N4Compound

2014 ◽  
Vol 20 (3) ◽  
pp. 664-670 ◽  
Author(s):  
Teresa Dennenwaldt ◽  
Jim Ciston ◽  
Ulrich Dahmen ◽  
Wai-Yim Ching ◽  
Florian J. Pucher ◽  
...  
Keyword(s):  
Energy Loss ◽  
Electron Energy ◽  
Density Functional ◽  
High Strength ◽  
Density Functional Theory Calculations ◽  
High Resolution Spectroscopy ◽  
Functional Theory ◽  
The Individual ◽  
Electron Energy Loss ◽  
Good Agreement

AbstractThe recently discovered compound BeP2N4that crystallizes in the phenakite-type structure has potential application as a high strength optoelectronic material. Therefore, it is important to analyze experimentally the electronic structure, which was done in the present work by monochromated electron energy-loss spectroscopy. The detection of Be is challenging due to its low atomic number and easy removal under electron bombardment. We were able to determine the bonding behavior and coordination of the individual atomic species including Be. This is evident from a good agreement between experimental electron energy-loss near-edge structures of the Be-K-, P-L2,3-, and N-K-edges and density functional theory calculations.

scholarly journals Visible Light-Induced Sulphide Anion-Catalysed Decarboxylative Alkylations in Batch and Continuous Flow

2021 ◽  
Author(s):  
Guangzu Wang ◽  
Mengting Liu ◽  
Deguang Liu ◽  
Zhiwei Qin
Keyword(s):  
Visible Light ◽  
Continuous Flow ◽  
Density Functional ◽  
High Efficiency ◽  
Density Functional Theory Calculations ◽  
Flow Process ◽  
One Pot ◽  
Diverse Range ◽  
High Yields ◽  
A Charge

We demonstrated herein a versatile protocol for visible-light-induced sulphide anion-catalysed decarboxylative cross-couplings. An array of primary, secondary, tertiary and amino acid-derived redox-active esters (RAEs) were all amenable substrates to undergo radical decarboxylation to be coupled with a diverse range of nucleophiles, creating challenging C(sp3)-C(sp3) and C(sp3)-C(sp2) bonds with high efficiency. We note that Katritzky’s salt and Togni’s reagent were also suitable substrates, affording deaminative alkylation and trifluoromethylation products in high yields. Density functional theory calculations and mechanism experiments indicate that a charge-transfer complex was formed between sulphide anions and RAEs in the amide solvent. Additionally, a one-pot two-step telescoped procedure and continuous-flow process further increase the synthetic utility of this catalytic system.

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