1
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Kabir M, Ghosh P, Gozem S. Electronic Structure Methods for Simulating Flavin's Spectroscopy and Photophysics: Comparison of Multi-reference, TD-DFT, and Single-Reference Wave Function Methods. J Phys Chem B 2024; 128:7545-7557. [PMID: 39074870 PMCID: PMC11317985 DOI: 10.1021/acs.jpcb.4c03748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 07/31/2024]
Abstract
The use of flavins and flavoproteins in photocatalytic, sensing, and biotechnological applications has led to a growing interest in computationally modeling the excited-state electronic structure and photophysics of flavin. However, there is limited consensus regarding which computational methods are appropriate for modeling flavin's photophysics. We compare the energies of low-lying excited states of flavin computed with time-dependent density functional theory (TD-DFT), equation-of-motion coupled cluster (EOM-EE-CCSD), scaled opposite-spin configuration interaction [SOS-CIS(D)], multiconfiguration pair-density functional theory (MC-PDFT), and several multireference perturbation theory (MR-PT2) methods. In the first part, we focus on excitation energies of the first singlet excited state (S1) of five different redox and protonation states of flavin, with the goal of finding a suitable active space for MR-PT2 calculations. In the second part, we construct two sets of one-dimensional potential energy surfaces connecting the S0 and S1 equilibrium geometries (S0-S1 path) and the S1 (π,π*) and S2 (n,π*) equilibrium geometries (S1-S2 path). The first path therefore follows a Franck-Condon active mode of flavin while the second path maps crossings points between low-lying singlet and triplet states in flavin. We discuss the similarities and differences in the TD-DFT, EOM-EE-CCSD, SOS-CIS(D), MC-PDFT and MR-PT2 energy profiles along these paths. We find that (TD-)DFT methods are suitable for applications such as simulating the spectra of flavins but are inconsistent with several other methods when used for some geometry optimizations and when describing the energetics of dark (n,π*) states. MR-PT2 methods show promise for the simulation of flavin's low-lying excited states, but the selection of orbitals for the active space and the number of roots used for state averaging must be done carefully to avoid artifacts. Some properties, such as the intersystem crossing geometry and energy between the S1 (π,π*) and T2 (n,π*) states, may require additional benchmarking before they can be determined quantitatively.
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Affiliation(s)
- Mohammad
Pabel Kabir
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Paulami Ghosh
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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2
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Monsia R, Bhattacharyya S. Virtual Screening of Molecules via Neural Fingerprint-based Deep Learning Technique. RESEARCH SQUARE 2024:rs.3.rs-4355625. [PMID: 38766198 PMCID: PMC11100899 DOI: 10.21203/rs.3.rs-4355625/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
A machine learning-based drug screening technique has been developed and optimized using convolutional neural network-derived fingerprints. The optimization of weights in the neural network-based fingerprinting technique was compared with fixed Morgan fingerprints in regard to binary classification on drug-target binding affinity. The assessment was carried out using six different target proteins using randomly chosen small molecules from the ZINC15 database for training. This new architecture proved to be more efficient in screening molecules that less favorably bind to specific targets and retaining molecules that favorably bind to it. Scientific contribution We have developed a new neural fingerprint-based screening model that has a significant ability to capture hits. Despite using a smaller dataset, this model is capable of mapping chemical space similar to other contemporary algorithms designed for molecular screening. The novelty of the present algorithm lies in the speed with which the models are trained and tuned before testing its predictive capabilities and hence is a significant step forward in the field of machine learning-embedded computational drug discovery.
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3
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Kılıç M, Ensing B. Redox Properties of Flavin in BLUF and LOV Photoreceptor Proteins from Hybrid QM/MM Molecular Dynamics Simulation. J Phys Chem B 2024; 128:3069-3080. [PMID: 38518376 DOI: 10.1021/acs.jpcb.3c06245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Flavins play an important role in many oxidation and reduction processes in biological systems. For example, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are common cofactors found in enzymatic proteins that use the special redox properties of these flavin molecules for their catalytic or photoactive functions. The redox potential of the flavin is strongly affected by its (protein) environment; however, the underlying molecular interactions of this effect are still unknown. Using hybrid quantum mechanics/molecular mechanics (QM/MM) simulation techniques, we have studied the redox properties of flavin in the gas phase, aqueous solution, and two different protein environments, in particular, a BLUF and a LOV photoreceptor domain. By mapping the changes in electrostatic potential and solvent structure, we gain insight into how specific polarization of the flavin by its environment tunes the reduction potential. We find also that accurate calculation of the reduction potentials of these systems by using the hybrid QM/MM approach is hampered by a too limited sampling of the counterion configurations and by artifacts at the QM/MM boundary. We make suggestions for how these issues can be overcome.
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Affiliation(s)
- Murat Kılıç
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Park 904, Amsterdam 1098 XH, The Netherlands
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Park 904, Amsterdam 1098 XH, The Netherlands
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4
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Silvestri G, Arrigoni F, Persico F, Bertini L, Zampella G, De Gioia L, Vertemara J. Assessing the Performance of Non-Equilibrium Thermodynamic Integration in Flavodoxin Redox Potential Estimation. Molecules 2023; 28:6016. [PMID: 37630271 PMCID: PMC10459689 DOI: 10.3390/molecules28166016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Flavodoxins are enzymes that contain the redox-active flavin mononucleotide (FMN) cofactor and play a crucial role in numerous biological processes, including energy conversion and electron transfer. Since the redox characteristics of flavodoxins are significantly impacted by the molecular environment of the FMN cofactor, the evaluation of the interplay between the redox properties of the flavin cofactor and its molecular surroundings in flavoproteins is a critical area of investigation for both fundamental research and technological advancements, as the electrochemical tuning of flavoproteins is necessary for optimal interaction with redox acceptor or donor molecules. In order to facilitate the rational design of biomolecular devices, it is imperative to have access to computational tools that can accurately predict the redox potential of both natural and artificial flavoproteins. In this study, we have investigated the feasibility of using non-equilibrium thermodynamic integration protocols to reliably predict the redox potential of flavodoxins. Using as a test set the wild-type flavodoxin from Clostridium Beijerinckii and eight experimentally characterized single-point mutants, we have computed their redox potential. Our results show that 75% (6 out of 8) of the calculated reaction free energies are within 1 kcal/mol of the experimental values, and none exceed an error of 2 kcal/mol, confirming that non-equilibrium thermodynamic integration is a trustworthy tool for the quantitative estimation of the redox potential of this biologically and technologically significant class of enzymes.
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Affiliation(s)
| | | | | | | | | | - Luca De Gioia
- Department of Biotechnology and Biosciences BtBs, University of Milano-Bicocca, Piazza dell’Ateneo Nuovo 1, 20126 Milan, Italy
| | - Jacopo Vertemara
- Department of Biotechnology and Biosciences BtBs, University of Milano-Bicocca, Piazza dell’Ateneo Nuovo 1, 20126 Milan, Italy
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5
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Laatsch BF, Brandt M, Finke B, Fossum CJ, Wackett MJ, Lowater HR, Narkiewicz-Jodko A, Le CN, Yang T, Glogowski EM, Bailey-Hartsel SC, Bhattacharyya S, Hati S. Polyethylene Glycol 20k. Does It Fluoresce? ACS OMEGA 2023; 8:14208-14218. [PMID: 37180871 PMCID: PMC10168656 DOI: 10.1021/acsomega.3c01124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 03/22/2023] [Indexed: 05/16/2023]
Abstract
Polyethylene glycol (PEG) is a polyether compound commonly used in biological research and medicine because it is biologically inert. This simple polymer exists in variable chain lengths (and molecular weights). As they are devoid of any contiguous π-system, PEGs are expected to lack fluorescence properties. However, recent studies suggested the occurrence of fluorescence properties in non-traditional fluorophores like PEGs. Herein, a thorough investigation has been conducted to explore if PEG 20k fluoresces. Results of this combined experimental and computational study suggested that although PEG 20k could exhibit "through-space" delocalization of lone pairs of electrons in aggregates/clusters, formed via intermolecular and intramolecular interactions, the actual contributor of fluorescence between 300 and 400 nm is the stabilizer molecule, i.e., 3-tert-butyl-4-hydroxyanisole present in the commercially available PEG 20k. Therefore, the reported fluorescence properties of PEG should be taken with a grain of salt, warranting further investigation.
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Affiliation(s)
- Bethany F. Laatsch
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Michael Brandt
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Brianna Finke
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Carl J. Fossum
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Miles J. Wackett
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Harrison R. Lowater
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Alex Narkiewicz-Jodko
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Christine N. Le
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Thao Yang
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Elizabeth M. Glogowski
- Department of Materials Science and Biomedical Engineering, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin, 54701, United States
| | - Scott C. Bailey-Hartsel
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54701, United States
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6
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Galuzzi B, Mirarchi A, Viganò EL, De Gioia L, Damiani C, Arrigoni F. Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. J Chem Inf Model 2022; 62:4748-4759. [PMID: 36126254 PMCID: PMC9554915 DOI: 10.1021/acs.jcim.2c00858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Indexed: 11/29/2022]
Abstract
Determining the redox potentials of protein cofactors and how they are influenced by their molecular neighborhoods is essential for basic research and many biotechnological applications, from biosensors and biocatalysis to bioremediation and bioelectronics. The laborious determination of redox potential with current experimental technologies pushes forward the need for computational approaches that can reliably predict it. Although current computational approaches based on quantum and molecular mechanics are accurate, their large computational costs hinder their usage. In this work, we explored the possibility of using more efficient QSPR models based on machine learning (ML) for the prediction of protein redox potential, as an alternative to classical approaches. As a proof of concept, we focused on flavoproteins, one of the most important families of enzymes directly involved in redox processes. To train and test different ML models, we retrieved a dataset of flavoproteins with a known midpoint redox potential (Em) and 3D structure. The features of interest, accounting for both short- and long-range effects of the protein matrix on the flavin cofactor, have been automatically extracted from each protein PDB file. Our best ML model (XGB) has a performance error below 1 kcal/mol (∼36 mV), comparing favorably to more sophisticated computational approaches. We also provided indications on the features that mostly affect the Em value, and when possible, we rationalized them on the basis of previous studies.
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Affiliation(s)
- Bruno
Giovanni Galuzzi
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
- SYSBIO
Centre of Systems Biology/ISBE.IT, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonio Mirarchi
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Edoardo Luca Viganò
- Istituto
di Ricerche Farmacologiche Mario Negri, Via Mario Negri 2, 20156 Milan, Italy
| | - Luca De Gioia
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Chiara Damiani
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
- SYSBIO
Centre of Systems Biology/ISBE.IT, Piazza della Scienza 2, 20126, Milan, Italy
| | - Federica Arrigoni
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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7
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Curtolo F, Arantes GM. Molecular properties and tautomeric equilibria of isolated flavins. J Comput Chem 2022; 43:1561-1572. [PMID: 35778728 DOI: 10.1002/jcc.26957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/09/2022] [Indexed: 11/05/2022]
Abstract
Flavins are employed as redox cofactors and chromophores in a plethora of flavoenzymes. Their versatility is an outcome of intrinsic molecular properties of the isoalloxazine ring modulated by the protein scaffold and surrounding solvent. Thus, an investigation of isolated flavins with high-level electronic-structure methods and with error assessment of the calculated properties will contribute to building better models of flavin reactivity. Here, we benchmarked ground-state properties such as electron affinity, gas-phase basicity, dipole moment, torsion energy, and tautomer stability for lumiflavins in all biologically relevant oxidation and charge states. Overall, multiconfigurational effects are small and chemical accuracy is achieved by coupled-cluster treatments of energetic properties. Augmented basis sets and extrapolations to the complete basis-set limit are necessary for consistent agreement with experimental energetics. Among DFT functionals tested, M06-2X shows the best performance for most properties, except gas-phase basicity, in which M06 and CAM-B3LYP perform better. Moreover, dipole moments of radical flavins show large deviations for all functionals studied. Tautomers with noncanonical protonation states are significantly populated at normal temperatures, adding to the complexity of modeling flavins. These results will guide future computational studies of flavoproteins and flavin chemistry by indicating the limitations of electronic-structure methodologies and the contributions of multiple tautomeric states.
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Affiliation(s)
- Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
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8
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Rhodes Z, Simoska O, Dantanarayana A, Stevenson KJ, Minteer SD. Using structure-function relationships to understand the mechanism of phenazine-mediated extracellular electron transfer in Escherichia coli. iScience 2021; 24:103033. [PMID: 34522869 PMCID: PMC8426270 DOI: 10.1016/j.isci.2021.103033] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/19/2021] [Accepted: 08/20/2021] [Indexed: 10/26/2022] Open
Abstract
Phenazines are redox-active nitrogen-containing heterocyclic compounds that can be produced by either bacteria or synthetic approaches. As an electron shuttles (mediators), phenazines are involved in several biological processes facilitating extracellular electron transfer (EET). Therefore, it is of great importance to understand the structural and electronic properties of phenazines that promote EET in microbial electrochemical systems. Our previous study experimentally investigated a phenazine-based library as an exogenous mediator system to facilitate EET in Escherichia coli. Herein, we combine our experimental data with density functional theory (DFT) calculations and multivariate linear regression modeling to understand the structure-function relationships in phenazine-based mediated EET. These calculations demonstrate that the computed redox properties of phenazines in lipophilic environments (e.g., cell membrane) correlate to experimental mediated current densities. Additional DFT-derived molecular properties were considered to develop a predictive model, which could be used in metabolic engineering approaches to introduce phenazines as endogenous mediators into bacteria.
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Affiliation(s)
- Zayn Rhodes
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Olja Simoska
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Keith J Stevenson
- Center for Energy Science and Technology, Skolkovo Institute of Science and Technology, Bolshoi Boulevard 30 Bld. 1, Moscow 121205, Russia
| | - Shelley D Minteer
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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9
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Wei Y, Zhou YM, Li YQ, Gao RY, Fu LM, Wang P, Zhang JP, Skibsted LH. Spatial effects of photosensitization on morphology of giant unilamellar vesicles. Biophys Chem 2021; 275:106624. [PMID: 34051444 DOI: 10.1016/j.bpc.2021.106624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/10/2021] [Accepted: 05/18/2021] [Indexed: 11/28/2022]
Abstract
Singlet oxygen (1O2) formed through photosensitization may initiate oxidative destruction of biomembranes, however, the influence from the spatial organization of photosensitizers (PS) relative to membranes remains unclear. To clarify this issue, we loaded riboflavin 5'-(dihydrogen phosphate) monosodium (FMN-Na) as a hydrophilic PS into the lumen of halloysite nanotubes (HNTs), and attached the nanoassemblies (FMN-Na@HNTs), via Pickering effects, to the outer surfaces of giant unilamellar vesicles (GUVs) of phospholipids. We also prepared GUVs dopped with lumiflavin (LF) as a lipophilic PS having a 1O2 quantum yield comparable to FMN-Na. FMN-Na capsulated in HNT was characterized by a longer triplet excited state lifetime (12.1 μs) compared to FMN-Na free in solution (7.5 μs), and FMN-Na in both forms efficiently generated 1O2 upon illumination. The spatio-effects of PS on the photosensitized morphological changes of membranes were studied using conventional optical microscopy by monitoring GUV morphological changes. Upon light exposure (400-440 nm), the GUVs attached with FMN-Na@HNT merely experienced membrane deformation starting from the original spherical shape, ascribed to Type II photosensitization with 1O2 as oxidant. In contrast, photooxidation of LF dopped GUVs mainly led to membrane coarsening and budding assigned to Type I photosensitization. The spatial effects of PS on photosensitized morphological changes were related to the different lipid oxidation products generated through Type I and Type II photosensitized lipid oxidation.
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Affiliation(s)
- Yuan Wei
- Department of Chemistry, Renmin University of China, No.59 Zhongguancun Street, 100872 Beijing, China.
| | - Yi-Ming Zhou
- Department of Chemistry, Renmin University of China, No.59 Zhongguancun Street, 100872 Beijing, China.
| | - Yu-Qian Li
- Department of Chemistry, Renmin University of China, No.59 Zhongguancun Street, 100872 Beijing, China.
| | - Rong-Yao Gao
- Department of Chemistry, Renmin University of China, No.59 Zhongguancun Street, 100872 Beijing, China.
| | - Li-Min Fu
- Department of Chemistry, Renmin University of China, No.59 Zhongguancun Street, 100872 Beijing, China.
| | - Peng Wang
- Department of Chemistry, Renmin University of China, No.59 Zhongguancun Street, 100872 Beijing, China.
| | - Jian-Ping Zhang
- Department of Chemistry, Renmin University of China, No.59 Zhongguancun Street, 100872 Beijing, China.
| | - Leif H Skibsted
- Department of Food Science, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark.
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10
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Pakiari AH, Salarhaji M, Abdollahi T, Safapour M. The redox potential of flavin derivatives as a mediator in biosensors. J Mol Model 2021; 27:96. [PMID: 33641033 DOI: 10.1007/s00894-020-04650-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 12/16/2020] [Indexed: 11/28/2022]
Abstract
The two-electron reduction potential for a set of 393 flavin derivatives is presented in this article. These derivatives are substituted flavin on carbon 6, 7, 8, and 9 by coinage transition metals (Cu, Ag, and Au) and conjugated double bond hydrocarbons; and both groups are examined with and without functional groups such as OH, Cl, CH3, COOH, and NO2. In order to show the validity of the results, the reduction potential of human life molecules, which have experimental values, such as flavin adenine dinucleotide (FAD) and riboflavin (vitamin B2) is calculated. The experimental value for FAD is - 0.22 V, while the obtained theoretical value is - 0.21 V, and the corresponding values for riboflavin are - 0.18 and - 0.19 V, respectively. Theoretical calculations have been carried out by DFT procedure with a 6-31+G** basis set and BLYP xc-functional for coinage transition metals substitution, and MPW1PW9 xc-functionals for conjugated double bond hydrocarbon substitution. Both xc-functionals are chosen by the DFT calibration procedure.
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Affiliation(s)
- A H Pakiari
- Chemistry Department, College of Sciences, Shiraz University, Shiraz, 7194684795, Iran.
| | - M Salarhaji
- Chemistry Department, College of Sciences, Shiraz University, Shiraz, 7194684795, Iran
| | - T Abdollahi
- Young Researchers and Elite Club, Bushehr Branch, Islamic Azad University, Bushehr, 75149-44141, Iran
| | - M Safapour
- Chemistry Department, College of Sciences, Shiraz University, Shiraz, 7194684795, Iran
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11
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Etz BD, DuClos JM, Vyas S. Investigating the Photochemistry of C7 and C8 Functionalized N(5)-Ethyl-flavinium Cation: A Computational Study. J Phys Chem A 2020; 124:4193-4201. [PMID: 32337990 DOI: 10.1021/acs.jpca.0c01938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavins are a diverse set of compounds with a wide variety of biological and nonbiological applications. Applications of flavins receiving attention recently consist of electro- and photocatalytic oxidation of substrates for organic synthesis, bioengineered nanotechnology, and water splitting catalysts, among others. While there is vast knowledge regarding the structure-property relationships of flavins and their electrochemistry, there is much less work elucidating the structure property relationships as they pertain to flavinium photochemistry. Herein, we report the effect of molecular tailoring on the molecular properties of N(5)-ethyl-flavinium cation (Et-Fl+), a derivative of the biocatalytic coenzyme riboflavin, by incorporating electron withdrawing and donating groups at the C7 and C8 position of the isoalloxazine ring. The presence of electron withdrawing groups at the C8 position caused a red shift in the absorption spectrum, while the electron donating groups caused a blue shift. Functionalization at the C7 position had the opposite effect on the absorption spectrum. The effects of single substitution were relatively negated with simultaneous functionalization at both the C8 and C7 positions. Difference density plots indicate no change in the nature of the S1 excited state, which was confirmed by optimization of the excited state geometries. The results presented in this study indicate that functionalization of the isoalloxazine unit affects the photophysical properties of N(5)-ethyl-flavinium cations.
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Affiliation(s)
- Brian D Etz
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Julie M DuClos
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Shubham Vyas
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States
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12
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Letfus V, Jelić D, Bokulić A, Petrinić Grba A, Koštrun S. Rational design, synthesis and biological profiling of new KDM4C inhibitors. Bioorg Med Chem 2020; 28:115128. [DOI: 10.1016/j.bmc.2019.115128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022]
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13
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Kılıç M, Ensing B. Microscopic Picture of the Solvent Reorganization During Electron Transfer to Flavin in Water. J Phys Chem B 2019; 123:9751-9761. [PMID: 31647869 DOI: 10.1021/acs.jpcb.9b07250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The redox potential of molecular species is largely modulated by its molecular environment so that a change of the environment will lead to a different redox potential. However, a detailed molecular picture of reorganization of the environment upon reduction is still unclear. To unravel the details of the solvent reorganization during electron transfer, we have performed density functional theory-based molecular dynamics (DFT-MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations of the reduction of lumiflavin. Previously, we have calculated the reduction free energy curves of the redox half reactions of lumiflavin in water as a function of the instantaneous gap energy (ΔE) ( J. Chem. Theory Comput. 2013 , 9 , 3889 - 3899 ). In this work, we focus on finding the changes in the solvent environment that correlate with this ΔE reaction coordinate. Comparing the QM/MM simulations, in which the solvent is modeled with an empirical force field, with the (full) DFT-MD simulations, we find that the response through electronic polarization plays a significant role in the latter case. Also a small charge transfer between flavin and solvent is observed in the full DFT treatment. As a result, we find only in the case of the QM/MM model a strong correlation between ΔE and the (pairwise computed) electrostatic potential (ESP) at the flavin due to the solvent. By analyzing the contribution of the ESP at the flavin per solvent molecule, we cannot only distinguish between the different modes of hydration by solvent molecules that coordinate at the hydrophilic and hydrophobic sides of the flavin molecule but also quantify their contribution to the reorganization free energy by measuring the ESP fluctuations per solvent molecule.
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Affiliation(s)
- Murat Kılıç
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Park 904 , 1098 XH , Amsterdam , The Netherlands
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Park 904 , 1098 XH , Amsterdam , The Netherlands
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14
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Bracker M, Dinkelbach F, Weingart O, Kleinschmidt M. Impact of fluorination on the photophysics of the flavin chromophore: a quantum chemical perspective. Phys Chem Chem Phys 2019; 21:9912-9923. [DOI: 10.1039/c9cp00805e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
10-Methylisoalloxazine (MIA) and its fluorinated derivatives (6-9F-MIA) were investigated by means of quantum chemistry, looking into the influence of fluorination on fluorescence, absorption and inter-system crossing (ISC) in vacuum and in aqueous solution.
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Affiliation(s)
- Mario Bracker
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Fabian Dinkelbach
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Oliver Weingart
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Martin Kleinschmidt
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- 40225 Düsseldorf
- Germany
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15
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Reinhardt CR, Hu QH, Bresnahan CG, Hati S, Bhattacharyya S. Cyclic Changes in Active Site Polarization and Dynamics Drive the 'Ping-pong' Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations. ACS Catal 2018; 8:12015-12029. [PMID: 31583178 DOI: 10.1021/acscatal.8b04193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quinone reductases belong to the family of flavin-dependent oxidoreductases. With the redox active cofactor, flavin adenine dinucleotide, quinone reductases are known to utilize a 'ping-pong' kinetic mechanism during catalysis in which a hydride is bounced back and forth between flavin and its two substrates. However, the continuation of this catalytic cycle requires product displacement steps, where the product of one redox half-cycle is displaced by the substrate of the next half-cycle. Using improved hybrid quantum mechanical/molecular mechanical simulations, both the catalytic hydride transfer and the product displacement reactions were studied in NRH:quinone oxidoreductase 2. Initially, the self-consistent charge-density functional tight binding theory was used to describe flavin ring and the substrate atoms, while embedded in the molecular mechanically-treated solvated active site. Then, for each step of the catalytic cycle, a further improvement of energetics was made using density functional theory-based corrections. The present study showcases an integrated interplay of solvation, protonation, and protein matrix-induced polarization as the driving force behind the thermodynamic wheel of the 'ping-pong' kinetics. Reported here is the first-principles model of the 'ping-pong' kinetics that portrays how cyclic changes in the active site polarization and dynamics govern the oscillatory hydride transfer and product displacement in this enzyme.
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Affiliation(s)
- Clorice R. Reinhardt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Quin H. Hu
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Caitlin G. Bresnahan
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
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16
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Cao X, Heinz N, Zhang J, Dolg M. The first water coordination sphere of lanthanide(iii) motexafins (Ln-Motex2+, Ln = La, Gd, Lu) and its effects on structures, reduction potentials and UV-vis absorption spectra. Theoretical studies. Phys Chem Chem Phys 2017; 19:20160-20171. [DOI: 10.1039/c7cp02861j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An explicit treatment of strongly bound water molecules is mandatory to calculate correct UV-vis absorption spectra of lanthanide(iii) motexafins.
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Affiliation(s)
- Xiaoyan Cao
- Institute for Theoretical Chemistry, University of Cologne
- D-50939 Cologne
- Germany
| | - Norah Heinz
- Institute for Theoretical Chemistry, University of Cologne
- D-50939 Cologne
- Germany
| | - Jun Zhang
- Department of Chemistry
- University of Illinois at Urbana Champaign
- Urbana
- USA
| | - Michael Dolg
- Institute for Theoretical Chemistry, University of Cologne
- D-50939 Cologne
- Germany
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17
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Reinhardt CR, Jaglinski TC, Kastenschmidt AM, Song EH, Gross AK, Krause AJ, Gollmar JM, Meise KJ, Stenerson ZS, Weibel TJ, Dison A, Finnegan MR, Griesi DS, Heltne MD, Hughes TG, Hunt CD, Jansen KA, Xiong AH, Hati S, Bhattacharyya S. Insight into the kinetics and thermodynamics of the hydride transfer reactions between quinones and lumiflavin: a density functional theory study. J Mol Model 2016; 22:199. [PMID: 27491848 DOI: 10.1007/s00894-016-3074-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/17/2016] [Indexed: 12/14/2022]
Abstract
The kinetics and equilibrium of the hydride transfer reaction between lumiflavin and a number of substituted quinones was studied using density functional theory. The impact of electron withdrawing/donating substituents on the redox potentials of quinones was studied. In addition, the role of these substituents on the kinetics of the hydride transfer reaction with lumiflavin was investigated in detail under the transition state (TS) theory assumption. The hydride transfer reactions were found to be more favorable for an electron-withdrawing substituent. The activation barrier exhibited a quadratic relationship with the driving force of these reactions as derived under the formalism of modified Marcus theory. The present study found a significant extent of electron delocalization in the TS that is stabilized by enhanced electrostatic, polarization, and exchange interactions. Analysis of geometry, bond-orders, and energetics revealed a predominant parallel (Leffler-Hammond) effect on the TS. Closer scrutiny reveals that electron-withdrawing substituents, although located on the acceptor ring, reduce the N-H bond order of the donor fragment in the precursor complex. Carried out in the gas-phase, this is the first ever report of a theoretical study of flavin's hydride transfer reactions with quinones, providing an unfiltered view of the electronic effect on the nuclear reorganization of donor-acceptor complexes.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tanner C Jaglinski
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Ashly M Kastenschmidt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Eun H Song
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Adam K Gross
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Alyssa J Krause
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Jonathan M Gollmar
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Kristin J Meise
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Zachary S Stenerson
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tyler J Weibel
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Andrew Dison
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Mackenzie R Finnegan
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Daniel S Griesi
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Michael D Heltne
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tom G Hughes
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Connor D Hunt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Kayla A Jansen
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Adam H Xiong
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA.
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18
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Wijaya IMM, Domratcheva T, Iwata T, Getzoff ED, Kandori H. Single Hydrogen Bond Donation from Flavin N5 to Proximal Asparagine Ensures FAD Reduction in DNA Photolyase. J Am Chem Soc 2016; 138:4368-76. [PMID: 27002596 DOI: 10.1021/jacs.5b10533] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The spread of the absorbance of the stable FADH(•) radical (300-700 nm) allows CPD photolyase to highly efficiently form FADH(-), making it functional for DNA repair. In this study, FTIR spectroscopy detected a strong hydrogen bond, from FAD N5-H to the carbonyl group of the Asn378 side chain, that is modulated by the redox state of FAD. The observed characteristic frequency shifts were reproduced in quantum-mechanical models of the flavin binding site, which were then employed to elucidate redox tuning governed by Asn378. We demonstrate that enhanced hydrogen bonding of the Asn378 side chain with the FADH(•) radical increases thermodynamic stabilization of the radical state, and further ensures kinetic stabilization and accumulation of the fully reduced FADH(-) state.
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Affiliation(s)
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research , Jahnstrasse 29, Heidelberg 69120, Germany
| | | | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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19
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Sikdar S, Ghosh M, De Raychaudhury M, Chakrabarti J. Quantum Chemical Studies on Stability and Chemical Activities in Calcium Ion Bound Calmodulin Loops. J Phys Chem B 2015; 119:14652-9. [PMID: 26515023 DOI: 10.1021/acs.jpcb.5b09713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum chemical (QC) calculations for macromolecules require truncation of the molecule, highlighting the portion of interest due to heavy computation cost. As a result, an estimation of the effects of truncation is important to interpret the energy spectrum of such calculations. We perform density functional theory based QC calculations on calcium ion bound EF-hand loops of Calmodulin isolated from the crystal structure in an implicit solvent. We find that the terminal contributions of neutral capping are negligible across the entire ground-state energy spectrum. The coordination energy range and the nature of hybridization of the coordination state molecular orbitals remain qualitatively similar across these loops. While the HOMO and LUMO of loops in the N-terminal domain are dominated by the acidic aspartates, and the polar/hydrophobic residues, respectively, these levels of the C-terminal domain loops show strong localized electron density on the phenyl rings of the tyrosines. The Fukui index calculation identifies the hydroxyl oxygen in the phenyl ring of Y99 as a potent nucleophile. Our analysis indicates a general way of interpreting the electronic energy spectra to understand stability and functions of large biomolecules where the truncation of the molecule and, hence, the terminal capping effects are inevitable.
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Affiliation(s)
| | | | - Molly De Raychaudhury
- Department of Physics, West Bengal State University , Barasat, Kolkata 700126, India
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20
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Bresnahan CG, Reinhardt CR, Bartholow TG, Rumpel JP, North M, Bhattacharyya S. Effect of stacking interactions on the thermodynamics and kinetics of lumiflavin: a study with improved density functionals and density functional tight-binding protocol. J Phys Chem A 2014; 119:172-82. [PMID: 25490119 DOI: 10.1021/jp510020v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The π-π stacking interaction between lumiflavin and a number of π-electron-rich molecules has been studied by density functional theory using several new-generation density functionals. Six known lumiflavin-aromatic adducts were used and the models were evaluated by comparing the geometry and energetics with experimental results. The study found that dispersion-corrected and hybrid functionals with larger (>50%) Hartree-Fock exchanges produced superior results in modeling thermodynamic characteristics of these complexes. The functional producing the best energetics for these model systems was used to study the stacking interactions of lumiflavin with biologically relevant aromatic groups. Additionally, the reduction of flavin-in the presence of both a hydride donor and a nondonor π-electronic system was also studied. Weak interactions were observed in the stacked lumiflavin complexes of benzene, phenol, and indole, mimicking phenyl alanine, tryptophan, and tyrosine side chains, respectively, of an enzyme. The stacked complex of naphthalene and flavin showed little change in flavin's redox potential indicating insignificant effect on the thermodynamics of the hydride transfer reaction. In contrast, the hydride transfer reaction with the hydride donor N-methyl nicotinamide tells a different story, as the transition state was found to be strongly impacted by the stacking interactions. A comparison of performance between the density functional theory (DFT) and the computationally less expensive dispersion-corrected self-consistent density functional tight-binding (SCC-DFTB-D) theory revealed that the latter produces consistent energetics for this hydride transfer reaction and additional DFT-computed perturbative corrections could significantly improve these results.
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Affiliation(s)
- Caitlin G Bresnahan
- Department of Chemistry, University of Wisconsin-Eau Claire , Eau Claire, Wisconsin 54702, United States
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21
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Babanova S, Matanovic I, Atanassov P. Quinone-Modified Surfaces for Enhanced Enzyme-Electrode Interactions in Pyrroloquinoline-Quinone-Dependent Glucose Dehydrogenase Anodes. ChemElectroChem 2014. [DOI: 10.1002/celc.201402104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Redox reaction characteristics of riboflavin: A fluorescence spectroelectrochemical analysis and density functional theory calculation. Bioelectrochemistry 2014; 98:103-8. [DOI: 10.1016/j.bioelechem.2014.03.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/13/2014] [Accepted: 03/21/2014] [Indexed: 11/23/2022]
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23
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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24
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Langer J, Günther A, Seidenbecher S, Berden G, Oomens J, Dopfer O. Probing protonation sites of isolated flavins using IR spectroscopy: from lumichrome to the cofactor flavin mononucleotide. Chemphyschem 2014; 15:2550-62. [PMID: 24895155 DOI: 10.1002/cphc.201402146] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Indexed: 11/06/2022]
Abstract
Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B2), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600-1850 cm(-1)) by means of IR multiple-photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low-energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1-protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2- and N1-protonated tautomers. The frequencies and relative intensities of the two C=O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.
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Affiliation(s)
- Judith Langer
- Technische Universität Berlin, Institut für Optik und Atomare Physik, Hardenbergstraße 36, D-10623 Berlin (Germany); Current address: Parque Tecnologico de San Sebastian, Paseo Miramon 182, Edif C, 20009 San Sebastian (Spain)
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25
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Computational Redox Potential Predictions: Applications to Inorganic and Organic Aqueous Complexes, and Complexes Adsorbed to Mineral Surfaces. MINERALS 2014. [DOI: 10.3390/min4020345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Kılıç M, Ensing B. Acidity constants of lumiflavin from first principles molecular dynamics simulations. Phys Chem Chem Phys 2014; 16:18993-9000. [DOI: 10.1039/c4cp01450b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DFT-based molecular dynamics simulations predict the acidity of lumiflavin in different redox states.
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Affiliation(s)
- Murat Kılıç
- Van't Hoff Institute for Molecular Science
- University of Amsterdam
- Amsterdam, The Netherlands
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Science
- University of Amsterdam
- Amsterdam, The Netherlands
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27
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Zhang T, Papson K, Ochran R, Ridge DP. Stability of Flavin Semiquinones in the Gas Phase: The Electron Affinity, Proton Affinity, and Hydrogen Atom Affinity of Lumiflavin. J Phys Chem A 2013; 117:11136-41. [DOI: 10.1021/jp406786a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Tianlan Zhang
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Kaitlin Papson
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Richard Ochran
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Douglas P. Ridge
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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28
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Kılıç M, Ensing B. First and Second One-Electron Reduction of Lumiflavin in Water—A First Principles Molecular Dynamics Study. J Chem Theory Comput 2013; 9:3889-99. [DOI: 10.1021/ct400088g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Murat Kılıç
- Van’t Hoff
Institute for Molecular Sciences,
University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The
Netherlands
| | - Bernd Ensing
- Van’t Hoff
Institute for Molecular Sciences,
University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The
Netherlands
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29
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Steele HM, Guillaumont D, Moisy P. Density functional theory calculations of the redox potentials of actinide(VI)/actinide(V) couple in water. J Phys Chem A 2013; 117:4500-5. [PMID: 23600693 DOI: 10.1021/jp401875f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The measured redox potential of an actinide at an electrode surface involves the transfer of a single electron from the electrode surface on to the actinide center. Before electron transfer takes place, the complexing ligands and molecules of solvation need to become structurally arranged such that the electron transfer is at its most favorable. Following the electron transfer, there is further rearrangement to obtain the minimum energy structure for the reduced state. As such, there are three parts to the total energy cycle required to take the complex from its ground state oxidized form to its ground state reduced form. The first part of the energy comes from the structural rearrangement and solvation energies of the actinide species before the electron transfer or charge transfer process; the second part, the energy of the electron transfer; the third part, the energy required to reorganize the ligands and molecules of solvation around the reduced species. The time resolution of electrochemical techniques such as cyclic voltammetry is inadequate to determine to what extent bond and solvation rearrangement occurs before or after electron transfer; only for a couple to be classed as reversible is it fast in terms of the experimental time. Consequently, the partitioning of the energy theoretically is of importance to obtain good experimental agreement. Here we investigate the magnitude of the instantaneous charge transfer through calculating the fast one electron reduction energies of AnO2(H2O)n(2+), where An = U, Np, and Pu, for n = 4-6, in solution without inclusion of the structural optimization energy of the reduced form. These calculations have been performed using a number of DFT functionals, including the recently developed functionals of Zhao and Truhlar. The results obtained for calculated electron affinities in the aqueous phase for the AnO2(H2O)5(2+/+) couples are within 0.04 V of accepted experimental redox potentials, nearly an order of magnitude improvement on previous calculated standard potentials E(0) values, obtained using both DFT and high level multireference approaches.
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Affiliation(s)
- Helen M Steele
- CEA, Nuclear Energy Division, RadioChemistry & Processes Department, F-30207 Bagnols sur Cèze, France.
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30
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Chen JJ, Chen W, He H, Li DB, Li WW, Xiong L, Yu HQ. Manipulation of microbial extracellular electron transfer by changing molecular structure of phenazine-type redox mediators. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:1033-1039. [PMID: 23244024 DOI: 10.1021/es304189t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Phenazines, as a type of electron shuttle, are involved in various biological processes to facilitate microbial energy metabolism and electron transfer. They constitute a large group of nitrogen-containing heterocyclic compounds, which can be produced by a diverse range of bacteria or by artificial synthesis. They vary significantly in their properties, depending mainly on the nature and position of substitutent group. Thus, it is of great interest to find out the most favorable substituent type and molecular structure of phenazines for electron transfer routes. Here, the impacts of the substituent group on the reduction potentials of phenazine-type redox mediators in aqueous solution were investigated by quantum chemical calculations, and the calculation results were further validated with experimental data. The results show that the reaction free energy was substantially affected by the location of substituent groups on the phenazine molecule and the protonated water clusters. For the main proton addition process, the phenazines substituted with electron-donating groups and those with electron-withdrawing groups interacted with different protonated water clusters, attributed to the proximity effect of water molecules on proton transfer. Thus, high energy conversion efficiency could be achieved by controlling electron flow route with appropriate substituted phenazines to reduce the biological energy acquisition. This study provides useful information for designing efficient redox mediators to promote electron transfer between microbes and terminal acceptors, which are essential to bioenergy recovery from wastes and environmental bioremediation.
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Affiliation(s)
- Jie-Jie Chen
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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31
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Brdarić TP, Marković ZS, Milenković D, Dimitrić Marković JM. A joint application of vibrational spectroscopic and quantum mechanical methods in quantitative analysis of baicalein structure. MONATSHEFTE FUR CHEMIE 2012. [DOI: 10.1007/s00706-012-0805-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Chen S, Hossain MS, Foss FW. Organocatalytic Dakin Oxidation by Nucleophilic Flavin Catalysts. Org Lett 2012; 14:2806-9. [DOI: 10.1021/ol3010326] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuai Chen
- The University of Texas at Arlington, Department of Chemistry and Biochemistry, Arlington, Texas 76019-0065, United States
| | - Mohammad S. Hossain
- The University of Texas at Arlington, Department of Chemistry and Biochemistry, Arlington, Texas 76019-0065, United States
| | - Frank W. Foss
- The University of Texas at Arlington, Department of Chemistry and Biochemistry, Arlington, Texas 76019-0065, United States
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33
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Borštnar R, Repič M, Kamerlin SCL, Vianello R, Mavri J. Computational Study of the pKa Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B. J Chem Theory Comput 2012; 8:3864-70. [PMID: 26593027 DOI: 10.1021/ct300119u] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Monoamine oxidase (MAO), which exists in two isozymic forms, MAO A and MAO B, is an important flavoenzyme responsible for the metabolism of amine neurotransmitters such as dopamine, serotonin, and norepinephrine. Despite extensive research effort, neither the catalytic nor the inhibition mechanisms of MAO have been completely understood. There has also been dispute with regard to the protonation state of the substrate upon entering the active site, as well as the identity of residues that are important for the initial deprotonation of irreversible acetylenic inhibitors, in accordance with the recently proposed mechanism. Therefore, in order to investigate features essential for the modes of action of MAO, we have calculated pKa values of three relevant tyrosine residues in the MAO B active site, with and without dopamine bound as the substrate (as well as the pKa of the dopamine itself in the active site). The calculated pKa values for Tyr188, Tyr398, and Tyr435 in the complex are found to be shifted upward to 13.0, 13.7, and 14.7, respectively, relative to 10.1 in aqueous solution, ruling out the likelihood that they are viable proton acceptors. The altered tyrosine pKa values could be rationalized as an interplay of two opposing effects: insertion of positively charged bulky dopamine that lowers tyrosine pKa values, and subsequent removal of water molecules from the active site that elevates tyrosine pKa values, in which the latter prevails. Additionally, the pKa value of the bound dopamine (8.8) is practically unchanged compared to the corresponding value in aqueous solution (8.9), as would be expected from a charged amine placed in a hydrophobic active site consisting of aromatic moieties. We also observed potentially favorable cation-π interactions between the -NH3(+) group on dopamine and aromatic moieties, which provide a stabilizing effect to the charged fragment. Thus, we offer here theoretical evidence that the amine is most likely to be present in the active site in its protonated form, which is similar to the conclusion from experimental studies of MAO A (Jones et al. J. Neural Trans.2007, 114, 707-712). However, the free energy cost of transferring the proton from the substrate to the bulk solvent is only 1.9 kcal mol(-1), leaving open the possibility that the amine enters the chemical step in its neutral form. In conjunction with additional experimental and computational work, the data presented here should lead toward a deeper understanding of mechanisms of the catalytic activity and irreversible inhibition of MAO B, which can allow for the design of novel and improved MAO B inhibitors.
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Affiliation(s)
- Rok Borštnar
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Matej Repič
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Shina Caroline Lynn Kamerlin
- Department of Cell and Molecular Biology, Uppsala University , Uppsala Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Robert Vianello
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Quantum Organic Chemistry Group, Ruđer Bošković Institute , Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Janez Mavri
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence , Dunajska 156, SI-1000 Ljubljana, Slovenia
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Lande ADL, Babcock NS, Řezáč J, Lévy B, Sanders BC, Salahub DR. Quantum effects in biological electron transfer. Phys Chem Chem Phys 2012; 14:5902-18. [DOI: 10.1039/c2cp21823b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mueller RM, North MA, Yang C, Hati S, Bhattacharyya S. Interplay of flavin's redox states and protein dynamics: an insight from QM/MM simulations of dihydronicotinamide riboside quinone oxidoreductase 2. J Phys Chem B 2011; 115:3632-41. [PMID: 21410212 PMCID: PMC3070059 DOI: 10.1021/jp1107922] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Dihydronicotinamide riboside quinone oxidoreductase 2 is known to catalyze a two-electron reduction of quinone to hydroquinone using its cofactor, flavin adenine dinucleotide. Using quantum mechanical/molecular mechanical simulations, we have computed the reorganization free energies of the electron and proton transfer processes of flavin in the free state as well as when it is bound in the active site of the enzyme. The calculated energetics for electron transfer processes demonstrate that the enzyme active site lowers the reorganization energy for the redox process as compared to the enzyme-free aqueous state. This is most apparent in the two electron reduction step, which eliminates the possibility of flavosemiquinone generation. In addition, essential dynamics study of the simulated motions revealed spectacular changes in the principal components of atomic fluctuations upon reduction of flavin. This alteration of active site dynamics provides an insight into the "ping-pong" kinetics exhibited by the enzyme upon a change in the redox state of the enzyme-bound flavin. A charge perturbation analysis provides further support that the observed change in dynamics is correlated with the change in energetics due to the altered electrostatic interactions between the flavin ring and the active site residues. This study shows that the effect of electrostatic preorganization goes beyond the chemical catalysis as it strongly impacts the postcatalytic intrinsic protein dynamics.
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Affiliation(s)
- Robyn M Mueller
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, USA
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