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Richer M, Heidar-Zadeh F, Ríos-Gutiérrez M, Yang XD, Ayers PW. Spin-Polarized Conceptual Density Functional Theory from the Convex Hull. J Chem Theory Comput 2024; 20:4616-4628. [PMID: 38819213 DOI: 10.1021/acs.jctc.4c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We present a new, nonarbitrary, internally consistent, and unambiguous framework for spin-polarized conceptual density-functional theory (SP-DFT). We explicitly characterize the convex hull of energy, as a function of the number of electrons and their spin, as the only accessible ground states in spin-polarized density functional theory. Then, we construct continuous linear and quadratic models for the energy. The nondifferentiable linear model exactly captures the simplicial geometry of the complex hull about the point of interest and gives exact representations for the conceptual DFT reactivity indicators. The continuous quadratic energy model is the paraboloid of maximum curvature, which most tightly encloses the point of interest and neighboring vertices. The quadratic model is invariant to the choice of coordinate system (i.e., {N, S} vs {Nα, Nβ}) and reduces to a sensible formulation of spin-free conceptual DFT in the appropriate limit. Using the quadratic model, we generalize the Parr functions {P+(r), P-(r)} (and their derivatives with respect to number of electrons) to this new spin-polarized framework, integrating the Parr function concept into the context of (spin-polarized) conceptual DFT, and extending it to include higher-order effects.
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Affiliation(s)
- Michelle Richer
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
| | - Farnaz Heidar-Zadeh
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Mar Ríos-Gutiérrez
- Department of Organic Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Xiaotian Derrick Yang
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul W Ayers
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. Selective enhancement of (6-4) photoproduct formation in dithymine dinucleotides driven by specific sugar puckering. Org Biomol Chem 2024; 22:3025-3034. [PMID: 38530278 DOI: 10.1039/d4ob00279b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Four dinucleotide analogs of thymidylyl(3'-5')thymidine (TpT) have been designed and synthesized with a view to increase the selectivity, with respect to CPD, of efficient UV-induced (6-4) photoproduct formation. The deoxyribose residues of these analogs have been modified to increase north and south conformer populations at 5'- and 3'-ends, respectively. Dinucleotides whose 5'-end north population exceeds ca. 60% and whose 3'-end population is almost completely south display a three-fold selective enhancement in (6-4) adduct production when exposed to UV radiation, compared to TpT. These experimental results undoubtedly provide robust foundations for studying the singular ground-state proreactive species involved in the (6-4) photoproduct formation mechanism.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Clément Denhez
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR des Sciences Exactes et Naturelles, Reims, France
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, CNRS UMR 7312, ICMR, URCATech, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, F-38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne-Ardenne, CNRS, ICMR, UFR de Pharmacie, Reims, France.
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Guégan F, Lamine W, Chermette H, Morell C. Comment on “Revisiting the definition of local hardness and hardness kernel” by C. A. Polanco-Ramirez, M. Franco-Pérez, J. Carmona-Espíndola, J. L. Gázquez and P. W. Ayers, Phys. Chem. Chem. Phys., 2017, 19, 12355. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp04100d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this comment we show that the derivation proposed Polanco-Ramirez et al. appears naturally in the Taylor expansion of the energy, showing that their whole construction is not artificially built.
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Affiliation(s)
- F. Guégan
- Université de Lyon
- Institut des Sciences Analytiques
- UMR 5280 CNRS
- Université Claude Bernard Lyon 1
- ENS de Lyon
| | - W. Lamine
- Université de Lyon
- Institut des Sciences Analytiques
- UMR 5280 CNRS
- Université Claude Bernard Lyon 1
- ENS de Lyon
| | - H. Chermette
- Université de Lyon
- Institut des Sciences Analytiques
- UMR 5280 CNRS
- Université Claude Bernard Lyon 1
- ENS de Lyon
| | - C. Morell
- Université de Lyon
- Institut des Sciences Analytiques
- UMR 5280 CNRS
- Université Claude Bernard Lyon 1
- ENS de Lyon
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Jawiczuk M. A theoretical study on the hydrogen bond and stability of cytosine and thymine dimers. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Moriou C, Denhez C, Plashkevych O, Coantic-Castex S, Chattopadhyaya J, Guillaume D, Clivio P. A minute amount of s-puckered sugars is sufficient for (6-4) photoproduct formation at the dinucleotide level. J Org Chem 2014; 80:615-9. [PMID: 25496131 DOI: 10.1021/jo502230n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The di-2'-α-fluoro analogue of thymidylyl(3',5')thymidine, synthesized to probe the effect of a minimum amount of S conformer on the photoreactivity of dinucleotides, is endowed with only 3% and 8% of S sugar conformation at its 5'- and 3'-end, respectively. This analogue gives rise to the (6-4) photoproduct as efficiently as the dithymine dinucleotide (74% and 66% at the 5'- and 3'-end, respectively) under 254 nm. Our results suggest that the 5'-N, 3'-S conformer gives rise to the (6-4) photoproduct.
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Affiliation(s)
- Céline Moriou
- †Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Clément Denhez
- ‡Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | | | - Stéphanie Coantic-Castex
- ‡Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | | | - Dominique Guillaume
- ‡Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | - Pascale Clivio
- ‡Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
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Douki T, Meador JA, Bérard I, Wack A. N4-methylation of cytosine drastically favors the formation of (6-4) photoproducts in a TCG context. Photochem Photobiol 2014; 91:102-8. [PMID: 25319211 DOI: 10.1111/php.12365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 10/13/2014] [Indexed: 11/27/2022]
Abstract
Methylation of cytosine is a common biological process both in prokaryotic and eukaryotic cells. In addition to 5-methylcytosine (5mC), some bacterial species contain in their genome N(4) -methylcytosine (N4mC). Methylation at C5 has been shown to enhance the formation of pyrimidine dimeric photoproducts but nothing is known of the effect of N4 methylation on UV-induced DNA damage. In the present work, we compared the yield and the nature of bipyrimidine photoproducts induced in a series of trinucleotides exhibiting a TXG sequence where X is either T, C, 5mC or N4mC. HPLC associated to tandem mass spectrometry was used to quantify cyclobutane pyrimidine dimers (CPD), (6-4) photoproducts (64PP) and their Dewar valence isomer. Methylation at position N4 was found to drastically increase the reactivity of C upon exposure to both UVC and UVB and to favor the formation of 64PP. In contrast methylation at C5 increased the yield of CPD at the expense of 64PP. In addition, enhancement of photoreactivity by C5 methylation was much higher in the UVB than in the UVC range. These results show the drastic effect of the methylation site on the photochemistry of cytosine.
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Affiliation(s)
- Thierry Douki
- University Grenoble Alpes, INAC-LCIB, LAN, Grenoble, France; CEA, INAC-SCIB, LAN, Grenoble, France
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Guégan F, Mignon P, Tognetti V, Joubert L, Morell C. Dual descriptor and molecular electrostatic potential: complementary tools for the study of the coordination chemistry of ambiphilic ligands. Phys Chem Chem Phys 2014; 16:15558-69. [DOI: 10.1039/c4cp01613k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The possibility to retrieve the coordinating properties of ligands by a combined dual descriptor and molecular electrostatic potential analysis is shown, yielding a potentially predictive tool of their ambiphilicity and selectivity.
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Affiliation(s)
- Frédéric Guégan
- Laboratoire des Sciences Analytiques
- UMR CNRS 5280
- Université Claude Bernard Lyon
- 1 69622 Villeurbanne Cedex, France
| | - Pierre Mignon
- Laboratoire des Sciences Analytiques
- UMR CNRS 5280
- Université Claude Bernard Lyon
- 1 69622 Villeurbanne Cedex, France
| | - Vincent Tognetti
- Normandy University
- COBRA UMR 6014 & FR 3038
- Université de Rouen
- INSA Rouen
- CNRS
| | - Laurent Joubert
- Normandy University
- COBRA UMR 6014 & FR 3038
- Université de Rouen
- INSA Rouen
- CNRS
| | - Christophe Morell
- Laboratoire des Sciences Analytiques
- UMR CNRS 5280
- Université Claude Bernard Lyon
- 1 69622 Villeurbanne Cedex, France
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Tognetti V, Morell C, Ayers PW, Joubert L, Chermette H. A proposal for an extended dual descriptor: a possible solution when Frontier Molecular Orbital Theory fails. Phys Chem Chem Phys 2013; 15:14465-75. [DOI: 10.1039/c3cp51169c] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Labet V, Jorge N, Morell C, Douki T, Grand A, Cadet J, Eriksson LA. UV-induced formation of the thymine–thymine pyrimidine (6-4) pyrimidone photoproduct – a DFT study of the oxetane intermediate ring opening. Photochem Photobiol Sci 2013; 12:1509-16. [DOI: 10.1039/c3pp50069a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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