1
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da Silva Oliveira DD, Paz F, Brito NPF, Krüger A, Martinho ACC, Lapierre TJWJD, de Oliveira Souza F, Maltarollo VG, Kronenberger T, Mendes MS, Nonato MC, Pilau EJ, Wrenger C, Wunderlich G, Rezende Júnior CDO. Synthesis, design, and optimization of a potent and selective series of pyridylpiperazines as promising antimalarial agents. Eur J Med Chem 2024; 275:116621. [PMID: 38944935 DOI: 10.1016/j.ejmech.2024.116621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 05/31/2024] [Accepted: 06/22/2024] [Indexed: 07/02/2024]
Abstract
An optimization of the pyridylpiperazine series against Plasmodium falciparum has been performed, exploring a structure-activity relationship carried out on the toluyl fragment of hit 1, a compound with low micromolar activity against Plasmodium falciparum discovered by high-throughput screening. After confirming the crucial role played by this aryl fragment in the antiplasmodial activity, the replacement of the ortho-methyl substituent of 1 by halogenated ones led to an improvement for four analogs, either in terms of potency, expected pharmacokinetics profile, or both. Further introduction of endocyclic nitrogens in this fragment identified two more optimized compounds, 20 and 23, which are expected to be much more metabolically stable than 1. Additional assessment of the cytotoxicity, Ligand Lipophilic Efficiency, potency against the chloroquine-resistant Dd2 strain and in silico ADMET predictions revealed a satisfactory profile for most compounds, ultimately identifying the four optimized compounds 7, 9, 20 and 23 as promising compounds for further lead optimization of this series against Plasmodium falciparum.
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Affiliation(s)
- Douglas Davison da Silva Oliveira
- Laboratório de Síntese de Candidatos a Fármacos, Institute of Chemistry, Federal University of Uberlândia (UFU), Uberlândia, MG, 38400-902, Brazil
| | - Franciarli Paz
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nícolas Peterson Ferreira Brito
- Laboratório de Síntese de Candidatos a Fármacos, Institute of Chemistry, Federal University of Uberlândia (UFU), Uberlândia, MG, 38400-902, Brazil
| | - Arne Krüger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Clara Cassiano Martinho
- Laboratório de Síntese de Candidatos a Fármacos, Institute of Chemistry, Federal University of Uberlândia (UFU), Uberlândia, MG, 38400-902, Brazil
| | | | - Felipe de Oliveira Souza
- Laboratório de Biomoléculas e Espectrometria de Massas (LaBioMass), State University of Maringá (UEM), Maringá, PR, 807020-900, Brazil
| | - Vinícius G Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Thales Kronenberger
- German Center for Infection Research (DZIF), Partner-site Tübingen, 72076, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Marina Sena Mendes
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil; Center for the Research and Advancement of Fragments and Molecular Targets, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil; Center for the Research and Advancement of Fragments and Molecular Targets, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-903, Brazil
| | - Eduardo Jorge Pilau
- Laboratório de Biomoléculas e Espectrometria de Massas (LaBioMass), State University of Maringá (UEM), Maringá, PR, 807020-900, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gerhard Wunderlich
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Celso de Oliveira Rezende Júnior
- Laboratório de Síntese de Candidatos a Fármacos, Institute of Chemistry, Federal University of Uberlândia (UFU), Uberlândia, MG, 38400-902, Brazil.
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2
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Gray M, Bowling PE, Herbert JM. Comment on "Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided". J Phys Chem A 2024. [PMID: 39190891 DOI: 10.1021/acs.jpca.4c00283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Affiliation(s)
- Montgomery Gray
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Paige E Bowling
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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3
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Mohan S, Rissanen K, Ward JS. Iodine(I) pnictogenate complexes as Iodination reagents. Commun Chem 2024; 7:159. [PMID: 39020074 PMCID: PMC11255316 DOI: 10.1038/s42004-024-01240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Halogen(I) complexes are widely used as halogenation reagents and traditionally feature homoleptic stabilising Lewis bases, though the recent revitalisation of iodine(I) carboxylate chemistry has provided isolable examples of heteroleptic iodine(I) complexes. This work reports iodine(I) pnictogenate complexes stabilised by a Lewis base (L), Ph2P(O)O─I─L, synthesised via cation exchange from the silver(I) precursor, (Ph2P(O)OAg)n. The complexes were characterised in both solution (1H, 1H-15N HMBC, 31P) and the solid state, and supplemented computationally by DFT studies. Interestingly, these iodine(I) pnictogenates demonstrate a range of stabilities, and have been found to excel as iodination reagents in comparison to carbonyl hypoiodites, with comparable reactivity to the eponymous Barluenga's reagent in the iodination of antipyrine.
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Affiliation(s)
- Sharath Mohan
- Department of Chemistry, University of Jyvaskyla, 40014, Jyväskylä, Finland
| | - Kari Rissanen
- Department of Chemistry, University of Jyvaskyla, 40014, Jyväskylä, Finland
| | - Jas S Ward
- Department of Chemistry, University of Jyvaskyla, 40014, Jyväskylä, Finland.
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4
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Namba N, Fujii S. Hydroboration of vinylsilanes providing diversity-oriented hydrophobic building blocks for biofunctional molecules. Org Biomol Chem 2024. [PMID: 38826124 DOI: 10.1039/d4ob00632a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Hydroboration of vinylsilanes with BH3 affords two silylethanol regioisomers. Herein, we investigated the regioisomeric ratio of hydroboration products from various vinylsilanes, focusing on the characteristic reaction profile. All investigated vinylsilanes afforded both regioisomers, and greater bulkiness increased the proportion of the Markovnikov products. The obtained silylethanols were used as hydrophobic building blocks for constructing nuclear progesterone receptor (PR) modulators. Notably, structural conversions from an α-isomer (silylethan-1-oxy derivative) to a β-isomer (2-silylethoxy derivative) caused complete activity-switching from a PR agonist to an antagonist. Our results indicate that silylethanols are useful for structural development, and vinylsilanes are a versatile source of hydrophobic building blocks for obtaining biofunctional molecules.
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Affiliation(s)
- Nao Namba
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
| | - Shinya Fujii
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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5
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Bowling PE, Dasgupta S, Herbert JM. Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. J Chem Inf Model 2024; 64:3912-3922. [PMID: 38648614 DOI: 10.1021/acs.jcim.4c00221] [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: 04/25/2024]
Abstract
In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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6
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Puttreddy R, Kumar P, Rissanen K. Pyridine Iodine(I) Cations: Kinetic Trapping as a Sulfonate Complexes. Chemistry 2024; 30:e202304178. [PMID: 38193788 DOI: 10.1002/chem.202304178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 01/10/2024]
Abstract
Seven pyridine iodine(I) sulfonate complexes were prepared and isolated at low temperatures and characterized by X-ray diffraction analysis. The inherently instable pyridine iodine(I) cations are stabilized by an oxygen of sulfonate anions via the I⋅⋅⋅O halogen bond. In these complexes, the iodine atom of the pyridine iodine(I) cation acts as an electron acceptor and the sulfonate oxygen as the electron donor. These complexes are stable enough in the crystalline state, yet decompose rapidly under ambient conditions, also being unstable in solution. The (pyridine)N-I bond lengths [2.140(3)-2.197(2) Å] and the I⋅⋅⋅O halogen bonds [2.345(6)-2.227(3) Å] are analogous to (imide)N-I⋅⋅⋅O-N-pyridine uncharged halogen-bonded complexes formed from N-haloimides and pyridine N-oxides, thus confirming the existence of elusive pyridine iodine(I) cation.
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Affiliation(s)
- Rakesh Puttreddy
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, FI-40014, Jyväskylä, Finland
| | - Parveen Kumar
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, FI-40014, Jyväskylä, Finland
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, P.O. BOX 35, FI-40014, Jyväskylä, Finland
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7
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Shen Y, Zhang S, Su Y, Qu Z, Ren H. Controlling the repair mechanisms of oxetanes through functional group substitution. Phys Chem Chem Phys 2023; 25:14511-14519. [PMID: 37190991 DOI: 10.1039/d3cp01019h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Intersystem crossing (ISC) plays a key role in the photolysis processes of oxetanes formed by benzophenone (BP)-like and thymine structures. In this work, we systematically explored the photophysical processes of oxetanes and ring-splitting products and investigated the effect of substituents on the repair mechanisms of oxetanes. The regioselectivity of oxetanes (head-to-head, HH and head-to-tail, HT) and the electron-donating and electron-withdrawing substituents, including CH3, OCH3 and NO2, were considered. It was found that the substituents influence the ISC rates of these compounds more by changing their spin-orbit coupling (SOC) coefficients rather than energy gaps. The SOC coefficients of HH-oxetanes are more affected by these groups than HT-oxetanes and products, and they have greater ISC rates on the whole. Besides, the insertion of substituents can alter the radiative and nonradiative decay rates, thereby transforming the photoinduced cycloreversion mechanisms of oxetanes. The ring-splitting reactions of non-substituted oxetanes could occur via two pathways of singlet and triplet manifolds. Furthermore, oxetanes with NO2 at the X site have the largest ISC rates but hardly undergo repair processes, while the introduction of electron-donating substituents can effectively promote the repair of oxetanes. The singlet ring-splitting reactions of HH-oxetanes are more inclined to occur after introducing CH3 and OCH3 at two sites. However, HT-oxeatnes with CH3 are more likely to undergo triplet repair processes and OCH3-substituted structures tend to originate cycloreversion in the singlet manifolds. Moreover, the introduction of CH3 and OCH3 at the Y site rather than the X site can more significantly accelerate the repair processes of HH-oxetanes. Contrarily, HT-oxetanes with electron-donating groups at the X site exhibit faster repair rates than those at the Y site. We hope this work can provide valuable insights into BP-like drugs and photosensitive DNA repair.
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Affiliation(s)
- Yan Shen
- School of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
| | - Shaoqin Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Yingli Su
- School of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
| | - Zexing Qu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Haisheng Ren
- School of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
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8
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Bowling PE, Broderick DR, Herbert JM. Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions. J Phys Chem Lett 2023; 14:3826-3834. [PMID: 37061921 DOI: 10.1021/acs.jpclett.3c00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Electronic structure calculations on enzymes require hundreds of atoms to obtain converged results, but fragment-based approximations offer a cost-effective solution. We present calculations on enzyme models containing 500-600 atoms using the many-body expansion, comparing to benchmarks in which the entire enzyme-substrate complex is described at the same level of density functional theory. When the amino acid fragments contain ionic side chains, the many-body expansion oscillates under vacuum boundary conditions but rapid convergence is restored using low-dielectric boundary conditions. This implies that full-system calculations in the gas phase are inappropriate benchmarks for assessing errors in fragment-based approximations. A three-body protocol retains sub-kilocalorie per mole fidelity with respect to a supersystem calculation, as does a two-body calculation combined with a full-system correction at a low-cost level of theory. These protocols pave the way for application of high-level quantum chemistry to large systems via rigorous, ab initio treatment of many-body polarization.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dustin R Broderick
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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9
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Ward JS, Martõnova J, Wilson LME, Kramer E, Aav R, Rissanen K. Carbonyl hypoiodites from pivalic and trimesic acid and their silver(I) intermediates. Dalton Trans 2022; 51:14646-14653. [PMID: 36093683 DOI: 10.1039/d2dt01988d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first tris(O-I-N) carbonyl hypoiodites have been synthesised based on trimesic acid and pyridine or 4-methylpyridine, with their structures definitively confirmed by single crystal X-ray diffraction (SCXRD). The more soluble carbonyl hypoiodites based on pivalic acid have also been studied via NMR, SCXRD, and computational analyses, enabling the study of the direct silver(I) precursor and intermediates of the resulting carbonyl hypoiodites generated using a range of substituted pyridines.
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Affiliation(s)
- Jas S Ward
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
| | - Jevgenija Martõnova
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Laura M E Wilson
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
| | - Eric Kramer
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
| | - Riina Aav
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, Jyväskylä 40014, Finland.
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10
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Alam B, Jiang H, Zimmerman PM, Herbert JM. State-specific solvation for restricted active space spin-flip (RAS-SF) wave functions based on the polarizable continuum formalism. J Chem Phys 2022; 156:194110. [PMID: 35597663 DOI: 10.1063/5.0091636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The restricted active space spin-flip (RAS-SF) formalism is a particular form of single-reference configuration interaction that can describe some forms of strong correlation at a relatively low cost and which has recently been formulated for the description of charge-transfer excited states. Here, we introduce both equilibrium and nonequilibrium versions of a state-specific solvation correction for vertical transition energies computed using RAS-SF wave functions, based on the framework of a polarizable continuum model (PCM). Ground-state polarization is described using the solvent's static dielectric constant and in the nonequilibrium solvation approach that polarization is modified upon vertical excitation using the solvent's optical dielectric constant. Benchmark calculations are reported for well-studied models of photo-induced charge transfer, including naphthalene dimer, C2H4⋯C2F4, pentacene dimer, and perylene diimide (PDI) dimer, several of which are important in organic photovoltaic applications. For the PDI dimer, we demonstrate that the charge-transfer character of the excited states is enhanced in the presence of a low-dielectric medium (static dielectric constant ɛ0 = 3) as compared to a gas-phase calculation (ɛ0 = 1). This stabilizes mechanistic traps for singlet fission and helps to explain experimental singlet fission rates. We also examine the effects of nonequilibrium solvation on charge-separated states in an intramolecular singlet fission chromophore, where we demonstrate that the energetic ordering of the states changes as a function of solvent polarity. The RAS-SF + PCM methodology that is reported here provides a framework to study charge-separated states in solution and in photovoltaic materials.
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Affiliation(s)
- Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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11
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Friedl C, Fedorov DG, Renger T. Towards a quantitative description of excitonic couplings in photosynthetic pigment-protein complexes: quantum chemistry driven multiscale approaches. Phys Chem Chem Phys 2022; 24:5014-5038. [PMID: 35142765 PMCID: PMC8865841 DOI: 10.1039/d1cp03566e] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/31/2021] [Indexed: 01/18/2023]
Abstract
A structure-based quantitative calculation of excitonic couplings between photosynthetic pigments has to describe the dynamical polarization of the protein/solvent environment of the pigments, giving rise to reaction field and screening effects. Here, this challenging problem is approached by combining the fragment molecular orbital (FMO) method with the polarizable continuum model (PCM). The method is applied to compute excitonic couplings between chlorophyll a (Chl a) pigments of the water-soluble chlorophyll-binding protein (WSCP). By calibrating the vacuum dipole strength of the 0-0 transition of the Chl a chromophores according to experimental data, an excellent agreement between calculated and experimental linear absorption and circular dichroism spectra of WSCP is obtained. The effect of the mutual polarization of the pigment ground states is calculated to be very small. The simple Poisson-Transition-charge-from-Electrostatic-potential (Poisson-TrEsp) method is found to accurately describe the screening part of the excitonic coupling, obtained with FMO/PCM. Taking into account that the reaction field effects of the latter method can be described by a scalar constant leads to an improvement of Poisson-TrEsp that is expected to provide the basis for simple and realistic calculations of optical spectra and energy transfer in photosynthetic light-harvesting complexes. In addition, we present an expression for the estimation of Huang-Rhys factors of high-frequency pigment vibrations from experimental fluorescence line-narrowing spectra that takes into account the redistribution of oscillator strength by the interpigment excitonic coupling. Application to WSCP results in corrected Huang-Rhys factors that are less than one third of the original values obtained by the standard electronic two-state analysis that neglects the above redistribution. These factors are important for the estimation of the dipole strength of the 0-0 transition of the chromophores and for the development of calculation schemes for the spectral density of the exciton-vibrational coupling.
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Affiliation(s)
- Christian Friedl
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria.
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria.
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12
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Hermanns V, Scheurer M, Kersten NF, Abdellaoui C, Wachtveitl J, Dreuw A, Heckel A. Rethinking Uncaging: A New Antiaromatic Photocage Driven by a Gain of Resonance Energy. Chemistry 2021; 27:14121-14127. [PMID: 34363415 PMCID: PMC8519059 DOI: 10.1002/chem.202102351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 12/31/2022]
Abstract
Photoactivatable compounds for example photoswitches or photolabile protecting groups (PPGs, photocages) for spatiotemporal light control, play a crucial role in different areas of research. For each application, parameters such as the absorption spectrum, solubility in the respective media and/or photochemical quantum yields for several competing processes need to be optimized. The design of new photochemical tools therefore remains an important task. In this study, we exploited the concept of excited-state-aromaticity, first described by N. Colin Baird in 1971, to investigate a new class of photocages, based on cyclic, ground-state-antiaromatic systems. Several thio- and nitrogen-functionalized compounds were synthesized, photochemically characterized and further optimized, supported by quantum chemical calculations. After choosing the optimal scaffold, which shows an excellent uncaging quantum yield of 28 %, we achieved a bathochromic shift of over 100 nm, resulting in a robust, well accessible, visible light absorbing, compact new photocage with a clean photoreaction and a high quantum product (ϵ⋅Φ) of 893 M-1 cm-1 at 405 nm.
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Affiliation(s)
- Volker Hermanns
- Institute of Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Lau-Str. 760438FrankfurtGermany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityIm Neuenheimer Feld 20569120HeidelbergGermany
| | - Nils Frederik Kersten
- Institute of Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Lau-Str. 760438FrankfurtGermany
| | - Chahinez Abdellaoui
- Institute of Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityIm Neuenheimer Feld 20569120HeidelbergGermany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Lau-Str. 760438FrankfurtGermany
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13
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Milani G, Cavalluzzi MM, Altamura C, Santoro A, Perrone M, Muraglia M, Colabufo NA, Corbo F, Casalino E, Franchini C, Pisano I, Desaphy J, Carrieri A, Carocci A, Lentini G. Bioisosteric Modification of To042: Synthesis and Evaluation of Promising Use-Dependent Inhibitors of Voltage-Gated Sodium Channels. ChemMedChem 2021; 16:3588-3599. [PMID: 34519427 PMCID: PMC9293070 DOI: 10.1002/cmdc.202100496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/01/2021] [Indexed: 11/07/2022]
Abstract
Three analogues of To042, a tocainide-related lead compound recently reported for the treatment of myotonia, were synthesized and evaluated in vitro as skeletal muscle sodium channel blockers possibly endowed with enhanced use-dependent behavior. Patch-clamp experiments on hNav1.4 expressed in HEK293 cells showed that N-[(naphthalen-1-yl)methyl]-4-[(2,6-dimethyl)phenoxy]butan-2-amine, the aryloxyalkyl bioisostere of To042, exerted a higher use-dependent block than To042 thus being able to preferentially block the channels in over-excited membranes while preserving healthy tissue function. It also showed the lowest active transport across BBB according to the results of P-glycoprotein (P-gp) interacting activity evaluation and the highest cytoprotective effect on HeLa cells. Quantum mechanical calculations and dockings gave insights on the most probable conformation of the aryloxyalkyl bioisostere of To042 in solution and the target residues involved in the binding, respectively. Both approaches indicated the conformations that might be adopted in both the unbound and bound state of the ligand. Overall, N-[(naphthalen-1-yl)methyl]-4-[(2,6-dimethyl)phenoxy]butan-2-amine exhibits an interesting toxico-pharmacological profile and deserves further investigation.
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Affiliation(s)
- Gualtiero Milani
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Concetta Altamura
- Department of Biomedical Sciences and Human OncologySchool of MedicineUniversity of Bari Aldo Moro PoliclinicoPiazza Giulio Cesare70124BariItaly
| | - Antonella Santoro
- Department of Bioscience, Biotechnology and BiopharmaceuticsUniversity of Bari Aldo MoroVia Orabona 470125BariItaly
| | - Mariagrazia Perrone
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Marilena Muraglia
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Nicola Antonio Colabufo
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Filomena Corbo
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Elisabetta Casalino
- Department of Veterinary MedicineUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Carlo Franchini
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Isabella Pisano
- Department of Bioscience, Biotechnology and BiopharmaceuticsUniversity of Bari Aldo MoroVia Orabona 470125BariItaly
| | - Jean‐François Desaphy
- Department of Biomedical Sciences and Human OncologySchool of MedicineUniversity of Bari Aldo Moro PoliclinicoPiazza Giulio Cesare70124BariItaly
| | - Antonio Carrieri
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Alessia Carocci
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
| | - Giovanni Lentini
- Department of Pharmacy – Pharmaceutical SciencesUniversity of Bari Aldo MoroVia E. Orabona 470125BariItaly
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14
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Chakravarty C, Aksu H, Maiti B, Dunietz BD. Electronic Spectra of C 60 Films Using Screened Range Separated Hybrid Functionals. J Phys Chem A 2021; 125:7625-7632. [PMID: 34448570 DOI: 10.1021/acs.jpca.1c04908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We study computationally the electronic spectra of C60 thin films using the recently developed density functional theory (DFT) framework combining a screened range separated hybrid (SRSH) functional with a polarizable continuum model (PCM). The SRSH-PCM approach achieves excellent correspondence between the frontier orbital's energy levels and the ionization potential and electron affinity of the molecular system at the condensed phase and consequently leads to high quality electronic excitation energies when used in time-dependent DFT calculations. Our calculated excited states reproduce the experimentally main reported spectral peaks at the 3.6-4.6 eV energy range and when addressing excitonic effects also reproduce the red-shifted spectral feature. Notably, we analyze the low-lying peak at 2.7 eV and associate it to an excitonic state.
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Affiliation(s)
- Chandrima Chakravarty
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242-0001, United States
| | - Huseyin Aksu
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242-0001, United States
| | - Buddhadev Maiti
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242-0001, United States
| | - Barry D Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242-0001, United States
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15
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 476] [Impact Index Per Article: 158.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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16
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Carter-Fenk K, Mundy CJ, Herbert JM. Natural Charge-Transfer Analysis: Eliminating Spurious Charge-Transfer States in Time-Dependent Density Functional Theory via Diabatization, with Application to Projection-Based Embedding. J Chem Theory Comput 2021; 17:4195-4210. [PMID: 34189922 DOI: 10.1021/acs.jctc.1c00412] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
For many types of vertical excitation energies, linear-response time-dependent density functional theory (LR-TDDFT) offers a useful degree of accuracy combined with unrivaled computational efficiency, although charge-transfer excitation energies are often systematically and dramatically underestimated, especially for large systems and those that contain explicit solvent. As a result, low-energy electronic spectra of solution-phase chromophores often contain tens to hundreds of spurious charge-transfer states, making LR-TDDFT needlessly expensive in bulk solution. Intensity borrowing by these spurious states can affect intensities of the valence excitations, altering electronic bandshapes. At higher excitation energies, it is difficult to distinguish spurious charge-transfer states from genuine charge-transfer-to-solvent (CTTS) excitations. In this work, we introduce an automated diabatization that enables fast and effective screening of the CTTS acceptor space in bulk solution. Our procedure introduces "natural charge-transfer orbitals" that provide a means to isolate orbitals that are most likely to participate in a CTTS excitation. Projection of these orbitals onto solvent-centered virtual orbitals provides a criterion for defining the most important solvent molecules in a given excitation and be used as an automated subspace selection algorithm for projection-based embedding of a high-level description of the CTTS state in a lower-level description of its environment. We apply this method to an ab initio molecular dynamics trajectory of I-(aq) and report the lowest-energy CTTS band in the absorption spectrum. Our results are in excellent agreement with the experiment, and only one-third of the water molecules in the I-(H2O)96 simulation cell need to be described with LR-TDDFT to obtain excitation energies that are converged to <0.1 eV. The tools introduced herein will improve the accuracy, efficiency, and usability of LR-TDDFT in solution-phase environments.
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Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher J Mundy
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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17
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Petrillo G, Tavani C, Bianchi L, Benzi A, Cavalluzzi MM, Salvagno L, Quintieri L, De Palma A, Caputo L, Rosato A, Lentini G. Densely Functionalized 2-Methylideneazetidines: Evaluation as Antibacterials. Molecules 2021; 26:3891. [PMID: 34202191 PMCID: PMC8271477 DOI: 10.3390/molecules26133891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/27/2023] Open
Abstract
Twenty-two novel, variously substituted nitroazetidines were designed as both sulfonamide and urethane vinylogs possibly endowed with antimicrobial activity. The compounds under study were obtained following a general procedure recently developed, starting from 4-nitropentadienoates deriving from a common β-nitrothiophenic precursor. While being devoid of any activity against fungi and Gram-negative bacteria, most of the title compounds performed as potent antibacterial agents on Gram-positive bacteria (E. faecalis and three strains of S. aureus), with the most potent congener being the 1-(4-chlorobenzyl)-3-nitro-4-(p-tolyl)azetidine 22, which displayed potency close to that of norfloxacin, the reference antibiotic (minimum inhibitory concentration values 4 and 1-2 μg/mL, respectively). Since 22 combines a relatively efficient activity against Gram-positive bacteria and a cytotoxicity on eucharyotic cells only at 4-times higher concentrations (inhibiting concentration on 50% of the cultured eukaryotic cells: 36 ± 10 μM, MIC: 8.6 μM), it may be considered as a promising hit compound for the development of a new series of antibacterials selectively active on Gram-positive pathogens. The relatively concise synthetic route described herein, based on widely available starting materials, could feed further structure-activity relationship studies, thus allowing for the fine investigation and optimization of the toxico-pharmacological profile.
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Affiliation(s)
- Giovanni Petrillo
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, I-16146 Genoa, Italy; (C.T.); (L.B.); (A.B.)
| | - Cinzia Tavani
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, I-16146 Genoa, Italy; (C.T.); (L.B.); (A.B.)
| | - Lara Bianchi
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, I-16146 Genoa, Italy; (C.T.); (L.B.); (A.B.)
| | - Alice Benzi
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, I-16146 Genoa, Italy; (C.T.); (L.B.); (A.B.)
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona n. 4, 70126 Bari, Italy; (M.M.C.); (L.S.); (A.R.); (G.L.)
| | - Lara Salvagno
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona n. 4, 70126 Bari, Italy; (M.M.C.); (L.S.); (A.R.); (G.L.)
| | - Laura Quintieri
- Institute of Sciences of Food Production (CNR-ISPA) National Council of Research, Via G. Amendola, 122/O, 70126 Bari, Italy; (L.Q.); (L.C.)
| | - Annalisa De Palma
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona 4, 70126 Bari, Italy;
| | - Leonardo Caputo
- Institute of Sciences of Food Production (CNR-ISPA) National Council of Research, Via G. Amendola, 122/O, 70126 Bari, Italy; (L.Q.); (L.C.)
| | - Antonio Rosato
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona n. 4, 70126 Bari, Italy; (M.M.C.); (L.S.); (A.R.); (G.L.)
| | - Giovanni Lentini
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona n. 4, 70126 Bari, Italy; (M.M.C.); (L.S.); (A.R.); (G.L.)
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18
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Gnocchi D, Cavalluzzi MM, Mangiatordi GF, Rizzi R, Tortorella C, Spennacchio M, Lentini G, Altomare A, Sabbà C, Mazzocca A. Xanthenylacetic Acid Derivatives Effectively Target Lysophosphatidic Acid Receptor 6 to Inhibit Hepatocellular Carcinoma Cell Growth. ChemMedChem 2021; 16:2121-2129. [PMID: 33831272 DOI: 10.1002/cmdc.202100032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/02/2021] [Indexed: 12/22/2022]
Abstract
Despite the increasing incidence of hepatocellular carcinoma (HCC) worldwide, current pharmacological treatments are still unsatisfactory. We have previously shown that lysophosphatidic acid receptor 6 (LPAR6) supports HCC growth and that 9-xanthenylacetic acid (XAA) acts as an LPAR6 antagonist inhibiting HCC growth without toxicity. Here, we synthesized four novel XAA derivatives, (±)-2-(9H-xanthen-9-yl)propanoic acid (compound 4 - MC9), (±)-2-(9H-xanthen-9-yl)butanoic acid (compound 5 - MC6), (±)-2-(9H-xanthen-9-yl)hexanoic acid (compound 7 - MC11), and (±)-2-(9H-xanthen-9-yl)octanoic acid (compound 8 - MC12, sodium salt) by introducing alkyl groups of increasing length at the acetic α-carbon atom. Two of these compounds were characterized by X-ray powder diffraction and quantum mechanical calculations, while molecular docking simulations suggested their enantioselectivity for LPAR6. Biological data showed anti-HCC activity for all XAA derivatives, with the maximum effect observed for MC11. Our findings support the view that increasing the length of the alkyl group improves the inhibitory action of XAA and that enantioselectivity can be exploited for designing novel and more effective XAA-based LPAR6 antagonists.
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Affiliation(s)
- Davide Gnocchi
- Interdisciplinary Department of Medicine, University of Bari, School of Medicine, Piazza G. Cesare, 11, 70124, Bari, Italy
| | - Maria M Cavalluzzi
- Department of Pharmacy - Drug Sciences, University of Bari Aldo Moro, via Orabona, 4, 70125, Bari, Italy
| | | | - Rosanna Rizzi
- Institute of Crystallography CNR, Via Amendola 122/o, 70126, Bari, Italy
| | - Cosimo Tortorella
- Interdisciplinary Department of Medicine, University of Bari, School of Medicine, Piazza G. Cesare, 11, 70124, Bari, Italy
| | - Mauro Spennacchio
- Department of Pharmacy - Drug Sciences, University of Bari Aldo Moro, via Orabona, 4, 70125, Bari, Italy.,Institute of Crystallography CNR, Via Amendola 122/o, 70126, Bari, Italy
| | - Giovanni Lentini
- Department of Pharmacy - Drug Sciences, University of Bari Aldo Moro, via Orabona, 4, 70125, Bari, Italy
| | - Angela Altomare
- Institute of Crystallography CNR, Via Amendola 122/o, 70126, Bari, Italy
| | - Carlo Sabbà
- Interdisciplinary Department of Medicine, University of Bari, School of Medicine, Piazza G. Cesare, 11, 70124, Bari, Italy
| | - Antonio Mazzocca
- Interdisciplinary Department of Medicine, University of Bari, School of Medicine, Piazza G. Cesare, 11, 70124, Bari, Italy
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19
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Aldaz CR, Wiley TE, Miller NA, Abeyrathna N, Liao Y, Zimmerman PM, Sension RJ. Experimental and Theoretical Characterization of Ultrafast Water-Soluble Photochromic Photoacids. J Phys Chem B 2021; 125:4120-4131. [PMID: 33872018 DOI: 10.1021/acs.jpcb.1c00644] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
UV-visible transient absorption spectroscopy and quantum mechanical simulations are combined to elucidate the photochemical mechanism of two metastable merocyanine/spiropyran photoacids, 2-[(E)-2-(2-hydroxyphenyl)ethenyl]-3,3-dimethyl-1-(3-sulfopropyl)-3H-indol-1-ium (phenylhydroxy-MCH) and 2-[(E)-2-(1H-indazol-7-yl)ethenyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium (indazole-MCH). Transient absorption spectra demonstrate that trans-acid isomerization to the cis form results in deprotonation on a picosecond time scale. Ring closure to form spiropyran follows promptly from the appropriate conformation or follows at longer time delays (≫3.5 ns) following a barrier crossing for single-bond isomerization to the appropriate conformation. Consistent with the results of Berton et al. [ Chem. Sci. 2020, 11, 8457-8468] , we find that cis-phenylhydroxy-MCH is a stronger acid than trans-phenylhydroxy-MCH. The decrease in pKa upon isomerization is further investigated to benchmark quantum chemical methods for their accuracy. Calculations were performed with nine levels of theory including continuum solvent models and explicit water. The calculations are not sufficient to describe the ΔpKa following isomerization of these photoacids, and more work is necessary to properly evaluate the physical basis for the acidity of the cis photoacids.
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Affiliation(s)
- Cody R Aldaz
- Department of Chemistry, University of Michigan, 930 North University Avenue Ann Arbor, Michigan 48109-1055, United States
| | - Theodore E Wiley
- Department of Chemistry, University of Michigan, 930 North University Avenue Ann Arbor, Michigan 48109-1055, United States
| | - Nicholas A Miller
- Department of Chemistry, University of Michigan, 930 North University Avenue Ann Arbor, Michigan 48109-1055, United States
| | - Nawodi Abeyrathna
- Department of Chemistry, Florida Institute of Technology Melbourne, Florida 32901-8636, United States
| | - Yi Liao
- Department of Chemistry, Florida Institute of Technology Melbourne, Florida 32901-8636, United States
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 North University Avenue Ann Arbor, Michigan 48109-1055, United States
| | - Roseanne J Sension
- Department of Chemistry, University of Michigan, 930 North University Avenue Ann Arbor, Michigan 48109-1055, United States
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20
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Herbert JM. Dielectric continuum methods for quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry The Ohio State University Columbus Ohio USA
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21
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Scott M, Rehn DR, Coriani S, Norman P, Dreuw A. Electronic circular dichroism spectra using the algebraic diagrammatic construction schemes of the polarization propagator up to third order. J Chem Phys 2021; 154:064107. [DOI: 10.1063/5.0038315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Mikael Scott
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kongens Lyngby, Denmark
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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22
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Nottoli M, Lipparini F. General formulation of polarizable embedding models and of their coupling. J Chem Phys 2020; 153:224108. [PMID: 33317291 DOI: 10.1063/5.0035165] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Univeristà di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Univeristà di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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23
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Aksu H, Paul SK, Herbert JM, Dunietz BD. How Well Does a Solvated Octa-acid Capsule Shield the Embedded Chromophore? A Computational Analysis Based on an Anisotropic Dielectric Continuum Model. J Phys Chem B 2020; 124:6998-7004. [PMID: 32787071 DOI: 10.1021/acs.jpcb.0c04032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The optical properties of chromophores embedded in a water-solvated dimer of octa-acid that forms a molecular-shaped capsule are investigated. In particular, we address the anisotropic dielectric environment that appears to blue-shift excitation energies compared to the free aqueous chromophores. Recently we reported that using an effective scalar dielectric constant ε ≈ 3 appears to reproduce the measured spectra of the embedded coumarins, suggesting that the capsule provides a significant, albeit not perfect, screening of the aqueous dielectric environment. Here, we report absorption energies using a theoretical treatment that includes continuum solvation affected by an anisotropic dielectric function reflecting the high-dielectric environment outside of the capsule and the low-dielectric region within. We report time-dependent density functional theory calculations using a range-separated functional with the Poisson boundary conditions that model the anisotropic dielectric environment. Our calculations find that the anisotropic environment due to the water-solvated hydrophobic capsule is equivalent to a homogeneous effective dielectric constant of ≈3. The calculated values also appear to reproduce measured absorption of the embedded coumarin, where we study the effect of the hydrophobic capsule on the excited state.
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Affiliation(s)
- Huseyin Aksu
- Department of Physics, Canakkale Onsekiz Mart University, 17100 Canakkale, Turkey.,Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Suranjan K Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Barry D Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
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24
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Chen W, Peng S, Zheng S. A theoretical study on electronic spectra of a novel series of metal substituted boron subphthalocyanine chloride. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:118018. [PMID: 31923793 DOI: 10.1016/j.saa.2019.118018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/16/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Boron subphthalocyanine chloride has been extensively studied by experimentalists and computational chemists due to its unique optical and electronic properties. It has been practical to modify the optical and physical properties of subphthalocyanine through axial, peripheral, and center substitutions or ring expansion. However, there have been few investigations on the substitution of central boron atom. In the present work, a new metal-substituted (center substitution of boron atom) series of boron subphthalocyanine chloride (metal = Fe, Co, Ni, Cu, and Zn) are theoretically designed utilizing modern density functional theory. The optimized results of this series in gas phase and with polarizable continuum model show that they may be chemically stable, and the predicted order of the stability of MSubPC is Fe>Cu>Ni>Co>Zn. Also, this new series of MSubPC molecules all becomes more non-planar and has much smaller dipole moments, which imply that they may be feasible for blend with organic acceptors. The HOMO-LUMO energy gaps of MSubPC (M=Co, Ni, Cu) are smaller than that of subPC. Furthermore, the wavelength of simulated absorption peaks of ZnSubPC and NiSubPC is red-shifted with respect to prototype subPC molecule in the visible region, and FeSubPC has noticeably stronger absorption strength than subPC because its excitation involves more orbital transitions and d electrons. The work here shows a new way to design photoelectric materials based on subphthalocyanine with center metal substitution.
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Affiliation(s)
- Wenlan Chen
- Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, School of Materials and Energy, Southwest University, Chongqing, China
| | - Suoping Peng
- Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, School of Materials and Energy, Southwest University, Chongqing, China
| | - Shaohui Zheng
- Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, School of Materials and Energy, Southwest University, Chongqing, China.
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25
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Crumbie RL, Chalmers G, Bhadbhade M, Griffith R. Exploration of the Differences between Amine and Thiolate Addition to Acetylenedicarboxylates. J Org Chem 2019; 84:14602-14610. [DOI: 10.1021/acs.joc.9b01392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robyn L. Crumbie
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, Sydney, NSW 2751, Australia
| | - Gareth Chalmers
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, Sydney, NSW 2751, Australia
| | - Mohan Bhadbhade
- School of Chemistry, UNSW Australia, Sydney, NSW 2052, Australia
| | - Renate Griffith
- School of Chemistry, UNSW Australia, Sydney, NSW 2052, Australia
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26
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Bhandari S, Dunietz BD. Quantitative Accuracy in Calculating Charge Transfer State Energies in Solvated Molecular Complexes Using a Screened Range Separated Hybrid Functional within a Polarized Continuum Model. J Chem Theory Comput 2019; 15:4305-4311. [DOI: 10.1021/acs.jctc.9b00480] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Srijana Bhandari
- Department of Chemistry & Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Barry D. Dunietz
- Department of Chemistry & Biochemistry, Kent State University, Kent, Ohio 44242, United States
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27
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Lange AW, Herbert JM, Albrecht BJ, You ZQ. Intrinsically smooth discretisation of Connolly's solvent-excluded molecular surface. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1644384] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Benjamin J. Albrecht
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Zhi-Qiang You
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
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28
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Matsumoto F, Sumino S, Iwai T, Ito T. Regioselectivity enhancement in synthesis of [70]fullerene derivatives by introduction of a branched structure. Org Biomol Chem 2019; 17:2629-2634. [PMID: 30768088 DOI: 10.1039/c8ob03144d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Regio-purity in [70]fullerene derivatives is of great importance to improve the power conversion efficiencies of organic photovoltaics. We found that the introduction of a branched structure to [70]PCBM enhanced the yield of α-isomers. The effect of the steric group in the reaction mechanism was theoretically investigated and a difference in the activation energies within specific pathways was revealed.
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Affiliation(s)
- Fukashi Matsumoto
- Research Division of Organic Materials, Osaka Research Institute of Industrial Science and Technology, 1-6-50, Morinomiya, Joto-ku, Osaka 536-8553, Japan.
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29
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Bhandari S, Cheung MS, Geva E, Kronik L, Dunietz BD. Fundamental Gaps of Condensed-Phase Organic Semiconductors from Single-Molecule Calculations using Polarization-Consistent Optimally Tuned Screened Range-Separated Hybrid Functionals. J Chem Theory Comput 2018; 14:6287-6294. [DOI: 10.1021/acs.jctc.8b00876] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Srijana Bhandari
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Margaret S. Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, United States
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
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30
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Fletcher K, Krämer M, Bunz UH, Dreuw A. The π-conjugation length determines the fluorescence quenching mechanism of aromatic aldehydes in water. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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Coons MP, Herbert JM. Quantum chemistry in arbitrary dielectric environments: Theory and implementation of nonequilibrium Poisson boundary conditions and application to compute vertical ionization energies at the air/water interface. J Chem Phys 2018; 148:222834. [DOI: 10.1063/1.5023916] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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32
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Pai SJ, Han SS. S E2 reaction in noncarbon system: Metal-halide catalysis for dehydrogenation of ammonia borane. Proc Natl Acad Sci U S A 2017; 114:13625-13630. [PMID: 29229814 PMCID: PMC5748185 DOI: 10.1073/pnas.1712137115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
An electrophilic substitution (SE) reaction of BN isosteres has been investigated for the dehydrogenation of ammonia borane (AB) by metal chlorides (MCl2) using various ab initio calculations. In contrast to the typical SE reaction occurring at the carbon atom, the nitrogen atom in AB serves as the reaction center for the SE reaction with the boron moiety as the leaving group when the MCl2 approaches the AB. The SE2 backside reaction is favored as a trigger step for the dehydrogenation of AB by the MCl2 The SE2 reaction is found for 3d-transition-metal chlorides (e.g., FeCl2, CoCl2, NiCl2, CuCl2, and ZnCl2), while PdCl2 leads to the dehydrogenation of AB by a direct B-H σ-bond activation, similar to most organometallic catalysts. Interestingly, the polymerization of AB promoted by MCl2 can be explained with the similar SE2 mechanism, and the dehydrogenation of the BN derivative 3-methyl-1,2-BN-cyclopentane (CBN) bearing a carbon backbone ring also follows the SE2 reaction. In particular, the experimental observation that the use of metal-chloride catalysis decreases the by-products obtained during the hydrogenation of AB can be explained by our mechanism involving the SE2 reaction. This work is helpful for the development of novel metal-halide catalysts for practical hydrogen storage materials, including the BN moiety.
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Affiliation(s)
- Sung Jin Pai
- Computational Science Research Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Sang Soo Han
- Computational Science Research Center, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Republic of Korea
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33
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You ZQ, Herbert JM. Reparameterization of an Accurate, Few-Parameter Implicit Solvation Model for Quantum Chemistry: Composite Method for Implicit Representation of Solvent, CMIRS v. 1.1. J Chem Theory Comput 2016; 12:4338-46. [DOI: 10.1021/acs.jctc.6b00644] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhi-Qiang You
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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34
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Lipparini F, Mennucci B. Perspective: Polarizable continuum models for quantum-mechanical descriptions. J Chem Phys 2016; 144:160901. [DOI: 10.1063/1.4947236] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Filippo Lipparini
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, D55128 Mainz, Germany
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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35
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Liu J, Herbert JM. Local Excitation Approximations to Time-Dependent Density Functional Theory for Excitation Energies in Solution. J Chem Theory Comput 2015; 12:157-66. [DOI: 10.1021/acs.jctc.5b00828] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jie Liu
- Department
of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department
of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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36
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Panetier JA, Letko CS, Tilley TD, Head-Gordon M. Computational Characterization of Redox Non-Innocence in Cobalt-Bis(Diaryldithiolene)-Catalyzed Proton Reduction. J Chem Theory Comput 2015; 12:223-30. [DOI: 10.1021/acs.jctc.5b00968] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Julien A. Panetier
- Joint
Center for Artificial Photosynthesis, Materials Sciences Division and ‡Chemical Sciences
Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
| | - Christopher S. Letko
- Joint
Center for Artificial Photosynthesis, Materials Sciences Division and ‡Chemical Sciences
Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
| | - T. Don Tilley
- Joint
Center for Artificial Photosynthesis, Materials Sciences Division and ‡Chemical Sciences
Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Joint
Center for Artificial Photosynthesis, Materials Sciences Division and ‡Chemical Sciences
Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
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37
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You ZQ, Mewes JM, Dreuw A, Herbert JM. Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models. J Chem Phys 2015; 143:204104. [DOI: 10.1063/1.4936357] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhi-Qiang You
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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38
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de Queiroz TB, Kümmel S. Tuned range separated hybrid functionals for solvated low bandgap oligomers. J Chem Phys 2015. [PMID: 26203008 DOI: 10.1063/1.4926468] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The description of charge transfer excitations has long been a challenge to time dependent density functional theory. The recently developed concept of "optimally tuned range separated hybrid (OT-RSH) functionals" has proven to describe charge transfer excitations accurately in many cases. However, describing solvated or embedded systems is yet a challenge. This challenge is not only computational but also conceptual, because the tuning requires identifying a specific orbital, typically the highest occupied one of the molecule under study. For solvated molecules, this orbital may be delocalized over the solvent. We here demonstrate that one way of overcoming this problem is to use a locally projected self-consistent field diagonalization on an absolutely localized molecular orbital expansion. We employ this approach to determine ionization energies and the optical gap of solvated oligothiophenes, i.e., paradigm low gap systems that are of relevance in organic electronics. Dioxane solvent molecules are explicitly represented in our calculations, and the ambiguities of straightforward parameter tuning in solution are elucidated. We show that a consistent estimate of the optimal range separated parameter (ω) at the limit of bulk solvation can be obtained by gradually extending the solvated system. In particular, ω is influenced by the solvent beyond the first coordination sphere. For determining ionization energies, a considerable number of solvent molecules on the first solvation shell must be taken into account. We demonstrate that accurately calculating optical gaps of solvated systems using OT-RSH can be done in three steps: (i) including the chemical environment when determining the range-separation parameter, (ii) taking into account the screening due to the solvent, and (iii) using realistic molecular geometries.
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Affiliation(s)
| | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
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39
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Lee MH, Geva E, Dunietz BD. The Effect of Interfacial Geometry on Charge-Transfer States in the Phthalocyanine/Fullerene Organic Photovoltaic System. J Phys Chem A 2015; 120:2970-5. [DOI: 10.1021/acs.jpca.5b06196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Myeong H. Lee
- Department
of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, U.K
| | - Eitan Geva
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Barry D. Dunietz
- Department
of Chemistry, Kent State University, Kent, Ohio 44242, United States
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40
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Jurss JW, Khnayzer RS, Panetier JA, El Roz KA, Nichols EM, Head-Gordon M, Long JR, Castellano FN, Chang CJ. Bioinspired design of redox-active ligands for multielectron catalysis: effects of positioning pyrazine reservoirs on cobalt for electro- and photocatalytic generation of hydrogen from water. Chem Sci 2015; 6:4954-4972. [PMID: 29142725 PMCID: PMC5664355 DOI: 10.1039/c5sc01414j] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 06/09/2015] [Indexed: 01/18/2023] Open
Abstract
Mononuclear metalloenzymes in nature can function in cooperation with precisely positioned redox-active organic cofactors in order to carry out multielectron catalysis. Inspired by the finely tuned redox management of these bioinorganic systems, we present the design, synthesis, and experimental and theoretical characterization of a homologous series of cobalt complexes bearing redox-active pyrazines. These donor moieties are locked into key positions within a pentadentate ligand scaffold in order to evaluate the effects of positioning redox non-innocent ligands on hydrogen evolution catalysis. Both metal- and ligand-centered redox features are observed in organic as well as aqueous solutions over a range of pH values, and comparison with analogs bearing redox-inactive zinc(ii) allows for assignments of ligand-based redox events. Varying the geometric placement of redox non-innocent pyrazine donors on isostructural pentadentate ligand platforms results in marked effects on observed cobalt-catalyzed proton reduction activity. Electrocatalytic hydrogen evolution from weak acids in acetonitrile solution, under diffusion-limited conditions, reveals that the pyrazine donor of axial isomer 1-Co behaves as an unproductive electron sink, resulting in high overpotentials for proton reduction, whereas the equatorial pyrazine isomer complex 2-Co is significantly more active for hydrogen generation at lower voltages. Addition of a second equatorial pyrazine in complex 3-Co further minimizes overpotentials required for catalysis. The equatorial derivative 2-Co is also superior to its axial 1-Co congener for electrocatalytic and visible-light photocatalytic hydrogen generation in biologically relevant, neutral pH aqueous media. Density functional theory calculations (B3LYP-D2) indicate that the first reduction of catalyst isomers 1-Co, 2-Co, and 3-Co is largely metal-centered while the second reduction occurs at pyrazine. Taken together, the data establish that proper positioning of non-innocent pyrazine ligands on a single cobalt center is indeed critical for promoting efficient hydrogen catalysis in aqueous media, akin to optimally positioned redox-active cofactors in metalloenzymes. In a broader sense, these findings highlight the significance of electronic structure considerations in the design of effective electron-hole reservoirs for multielectron transformations.
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Affiliation(s)
- Jonah W Jurss
- Department of Chemistry , University of California , Berkeley , California 94720 , USA . ; ;
- Department of Chemistry and Biochemistry , University of Mississippi , University , MS 38677 , USA
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - Rony S Khnayzer
- Department of Chemistry , North Carolina State University , Raleigh , NC 27695-8204 , USA .
- Department of Natural Sciences , Lebanese American University , Beirut 1102-2801 , Chouran , Lebanon
| | - Julien A Panetier
- Department of Chemistry , University of California , Berkeley , California 94720 , USA . ; ;
- Materials Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - Karim A El Roz
- Department of Chemistry , North Carolina State University , Raleigh , NC 27695-8204 , USA .
| | - Eva M Nichols
- Department of Chemistry , University of California , Berkeley , California 94720 , USA . ; ;
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - Martin Head-Gordon
- Department of Chemistry , University of California , Berkeley , California 94720 , USA . ; ;
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - Jeffrey R Long
- Department of Chemistry , University of California , Berkeley , California 94720 , USA . ; ;
- Materials Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - Felix N Castellano
- Department of Chemistry , North Carolina State University , Raleigh , NC 27695-8204 , USA .
| | - Christopher J Chang
- Department of Chemistry , University of California , Berkeley , California 94720 , USA . ; ;
- Department of Molecular and Cell Biology , University of California , Berkeley , California 94720 , USA
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
- Howard Hughes Medical Institute , University of California , Berkeley , California 94720 , USA
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41
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Herbert JM. The Quantum Chemistry of Loosely-Bound Electrons. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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42
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Manna AK, Balamurugan D, Cheung MS, Dunietz BD. Unraveling the Mechanism of Photoinduced Charge Transfer in Carotenoid-Porphyrin-C60 Molecular Triad. J Phys Chem Lett 2015; 6:1231-1237. [PMID: 26262978 DOI: 10.1021/acs.jpclett.5b00074] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Photoinduced charge transfer (CT) plays a central role in biologically significant systems and in applications that harvest solar energy. We investigate the relationship of CT kinetics and conformation in a molecular triad. The triad, consisting of carotenoid, porphyrin, and fullerene is structurally flexible and able to acquire significantly varied conformations under ambient conditions. With an integrated approach of quantum calculations and molecular dynamics simulations, we compute the rate of CT at two distinctive conformations. The linearly extended conformation, in which the donor (carotenoid) and the acceptor (fullerene) are separated by nearly 50 Å, enables charge separation through a sequential CT process. A representative bent conformation that is entropically dominant, however, attenuates the CT, although the donor and the acceptor are spatially closer. Our computed rate of CT at the linear conformation is in good agreement with measured values. Our work provides unique fundamental understanding of the photoinduced CT process in the molecular triad.
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Affiliation(s)
- Arun K Manna
- †Department of Chemistry, Kent State University, 1787 Summit Street, Kent, Ohio 44242, United States
| | - D Balamurugan
- ∥Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Margaret S Cheung
- §Center for Theoretical Biological Physics, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Barry D Dunietz
- †Department of Chemistry, Kent State University, 1787 Summit Street, Kent, Ohio 44242, United States
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43
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Mewes JM, You ZQ, Wormit M, Kriesche T, Herbert JM, Dreuw A. Experimental Benchmark Data and Systematic Evaluation of Two a Posteriori, Polarizable-Continuum Corrections for Vertical Excitation Energies in Solution. J Phys Chem A 2015; 119:5446-64. [DOI: 10.1021/jp511163y] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jan-Michael Mewes
- Interdisciplinary
Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
| | - Zhi-Qiang You
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael Wormit
- Interdisciplinary
Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
| | - Thomas Kriesche
- Institute
for Physical Chemistry, Ruprechts-Karls University, 69120 Heidelberg, Germany
| | - John M. Herbert
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andreas Dreuw
- Interdisciplinary
Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
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44
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Zheng Z, Manna AK, Hendrickson HP, Hammer M, Song C, Geva E, Dunietz BD. Molecular structure, spectroscopy, and photoinduced kinetics in trinuclear cyanide bridged complex in solution: a first-principles perspective. J Am Chem Soc 2014; 136:16954-7. [PMID: 25424459 DOI: 10.1021/ja507131q] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the molecular structure of the solvated complex, [(NC)6Fe-Pt(NH3)4-Fe(CN)6](4-), and related dinuclear and mononuclear model complexes using first-principles calculations. Mixed nuclear complexes in both solution and crystal phases were widely studied as models for charge transfer (CT) reactions using advanced spectroscopical and electrochemical tools. In contrast to earlier interpretations, we find that the most stable gas phase and solvated geometries are substantially different from the crystal phase geometry, mainly due to variance in the underlying oxidation numbers of the metal centers. Specifically, in the crystal phase a Pt(IV) metal center resulting from Fe ← Pt backward electron transfers is stabilized by an octahedral ligand field, whereas in the solution phase a Pt(II) metal complex that prefers a square planar ligand field forms a CT salt by bridging to the iron complexes through long-range electrostatic interactions. The different geometry is shown to be consistent with spectroscopical data and measured CT rates of the solvated complex. Interestingly, we find that the experimentally indicated photoinduced process in the solvated complex is of backward CT (Fe ← Pt).
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Affiliation(s)
- Zilong Zheng
- Department of Chemistry, Kent State University , Kent, Ohio 44242, United States
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45
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Shao Y, Gan Z, Epifanovsky E, Gilbert AT, Wormit M, Kussmann J, Lange AW, Behn A, Deng J, Feng X, Ghosh D, Goldey M, Horn PR, Jacobson LD, Kaliman I, Khaliullin RZ, Kuś T, Landau A, Liu J, Proynov EI, Rhee YM, Richard RM, Rohrdanz MA, Steele RP, Sundstrom EJ, Woodcock HL, Zimmerman PM, Zuev D, Albrecht B, Alguire E, Austin B, Beran GJO, Bernard YA, Berquist E, Brandhorst K, Bravaya KB, Brown ST, Casanova D, Chang CM, Chen Y, Chien SH, Closser KD, Crittenden DL, Diedenhofen M, DiStasio RA, Do H, Dutoi AD, Edgar RG, Fatehi S, Fusti-Molnar L, Ghysels A, Golubeva-Zadorozhnaya A, Gomes J, Hanson-Heine MW, Harbach PH, Hauser AW, Hohenstein EG, Holden ZC, Jagau TC, Ji H, Kaduk B, Khistyaev K, Kim J, Kim J, King RA, Klunzinger P, Kosenkov D, Kowalczyk T, Krauter CM, Lao KU, Laurent AD, Lawler KV, Levchenko SV, Lin CY, Liu F, Livshits E, Lochan RC, Luenser A, Manohar P, Manzer SF, Mao SP, Mardirossian N, Marenich AV, Maurer SA, Mayhall NJ, Neuscamman E, Oana CM, Olivares-Amaya R, O’Neill DP, Parkhill JA, Perrine TM, Peverati R, Prociuk A, Rehn DR, Rosta E, Russ NJ, Sharada SM, Sharma S, Small DW, Sodt A, Stein T, Stück D, Su YC, Thom AJ, Tsuchimochi T, Vanovschi V, Vogt L, Vydrov O, Wang T, Watson MA, Wenzel J, White A, Williams CF, Yang J, Yeganeh S, Yost SR, You ZQ, Zhang IY, Zhang X, Zhao Y, Brooks BR, Chan GK, Chipman DM, Cramer CJ, Goddard WA, Gordon MS, Hehre WJ, Klamt A, Schaefer HF, Schmidt MW, Sherrill CD, Truhlar DG, Warshel A, Xu X, Aspuru-Guzik A, Baer R, Bell AT, Besley NA, Chai JD, Dreuw A, Dunietz BD, Furlani TR, Gwaltney SR, Hsu CP, Jung Y, Kong J, Lambrecht DS, Liang W, Ochsenfeld C, Rassolov VA, Slipchenko LV, Subotnik JE, Van Voorhis T, Herbert JM, Krylov AI, Gill PM, Head-Gordon M. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Mol Phys 2014. [DOI: 10.1080/00268976.2014.952696] [Citation(s) in RCA: 1769] [Impact Index Per Article: 176.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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46
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de Queiroz TB, Kümmel S. Charge-transfer excitations in low-gap systems under the influence of solvation and conformational disorder: Exploring range-separation tuning. J Chem Phys 2014; 141:084303. [DOI: 10.1063/1.4892937] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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Letko CS, Panetier JA, Head-Gordon M, Tilley TD. Mechanism of the Electrocatalytic Reduction of Protons with Diaryldithiolene Cobalt Complexes. J Am Chem Soc 2014; 136:9364-76. [DOI: 10.1021/ja5019755] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christopher S. Letko
- Joint Center
for Artificial Photosynthesis, †Materials Sciences Division and ‡Chemical Sciences
Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
| | - Julien A. Panetier
- Joint Center
for Artificial Photosynthesis, †Materials Sciences Division and ‡Chemical Sciences
Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Joint Center
for Artificial Photosynthesis, †Materials Sciences Division and ‡Chemical Sciences
Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
| | - T. Don Tilley
- Joint Center
for Artificial Photosynthesis, †Materials Sciences Division and ‡Chemical Sciences
Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
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48
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Faraji S, Wirz L, Dreuw A. Quantum chemical study of the enzymatic repair of T(6-4)C/C(6-4)T UV-photolesions by DNA photolyases. Chemphyschem 2013; 14:2817-24. [PMID: 23821498 DOI: 10.1002/cphc.201300223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Indexed: 11/10/2022]
Abstract
Several strategies have evolved to repair one of the abundant UV radiation-induced damages caused to DNA, namely the mutagenic pyrimidine (6-4) pyrimidone photolesions. DNA (6-4)-photolyases are enzymes repairing these lesions by a photoinitiated electron transfer. An important aspect of a possible repair mechanism is its generality and transferability to different (6-4) lesions. Therefore, previously suggested mechanisms for the repair of the T(6-4)T lesion are here transferred to the T(6-4)C and C(6-4)T lesions and investigated theoretically using quantum chemical methods. Despite the different functional groups of the pyrimidine bases involved, a general valid molecular mechanism was identified, in which the initial step is an electron transfer coupled to a proton transfer from the protonated HIS365 to the N3(') nitrogen of the 3(') pyrimidine, followed by an intramolecular OH/NH2 transfer in one concerted step, which does not require an oxetane/azetidine or isolated water/ammonia intermediate.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
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49
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Liu J, Liang W. Analytical second derivatives of excited-state energy within the time-dependent density functional theory coupled with a conductor-like polarizable continuum model. J Chem Phys 2013; 138:024101. [DOI: 10.1063/1.4773397] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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50
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Nippe M, Khnayzer RS, Panetier JA, Zee DZ, Olaiya BS, Head-Gordon M, Chang CJ, Castellano FN, Long JR. Catalytic proton reduction with transition metal complexes of the redox-active ligand bpy2PYMe. Chem Sci 2013. [DOI: 10.1039/c3sc51660a] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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