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Ludwig V, da Costa Ludwig ZM, Modesto MDA, Rocha AA. Binding energies and hydrogen bonds effects on DNA-cisplatin interactions: a DFT-xTB study. J Mol Model 2024; 30:187. [PMID: 38801468 DOI: 10.1007/s00894-024-05983-4] [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: 02/25/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024]
Abstract
CONTEXT A systematic study of hydrogen bonds in base pairs and the interaction of cisplatin with DNA fragments was carried out. Structure, binding energies, and electron density were analyzed. xTB has proven to be an accurate method for obtaining structures and binding energies in DNA structures. Our xTB values for DNA base binding energy were in the same order and in some cases better than CAM-B3LYP values compared to experimental values. Double-stranded DNA-cisplatin structures have been calculated and the hydrogen bonds of water molecules are a decisive factor contributing to the preference for the cisplatin-Guanine interaction. Higher values of the water hydrogen bonding energies were obtained in cisplatin-Guanine structures. Furthermore, the electrostatic potential was used to investigate and improve the analysis of DNA-cisplatin structures. METHODS We applied the xTB method and the CAM-B3LYP functional combined with def2-SVP basis set to perform and analyze of the bonding energies of the cisplatin interaction and the effects of the hydrogen bonds. Results were calculated employing the xTB and the ORCA software.
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Affiliation(s)
- Valdemir Ludwig
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, CP 36036-330, Minas Gerais, Brasil.
| | - Zélia Maria da Costa Ludwig
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, CP 36036-330, Minas Gerais, Brasil
| | - Marlon de Assis Modesto
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, CP 36036-330, Minas Gerais, Brasil
| | - Arthur Augusto Rocha
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, CP 36036-330, Minas Gerais, Brasil
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Xue Y, Sexton TM, Yang J, Tschumper GS. Systematic analysis of electronic barrier heights and widths for concerted proton transfer in cyclic hydrogen bonded clusters: (HF) n, (HCl) n and (H 2O) n where n = 3, 4, 5. Phys Chem Chem Phys 2024; 26:12483-12494. [PMID: 38619858 DOI: 10.1039/d4cp00422a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The MP2 and CCSD(T) methods are paired with correlation consistent basis sets as large as aug-cc-pVQZ to optimize the structures of the cyclic minima for (HF)n, (HCl)n and (H2O)n where n = 3-5, as well as the corresponding transition states (TSs) for concerted proton transfer (CPT). MP2 and CCSD(T) harmonic vibrational frequencies confirm the nature of each minimum and TS. Both conventional and explicitly correlated CCSD(T) computations are employed to assess the electronic dissociation energies and barrier heights for CPT near the complete basis (CBS) limit for all 9 clusters. Results for (HF)n are consistent with prior studies identifying Cnh and Dnh point group symmetry for the minima and TSs, respectively. Our computations also confirm that CPT proceeds through Cs TS structures for the C1 minima of (H2O)3 and (H2O)5, whereas the process goes through a TS with D2d symmetry for the S4 global minimum of (H2O)4. This work corroborates earlier findings that the minima for (HCl)3, (HCl)4 and (HCl)5 have C3h, S4 and C1 point group symmetry, respectively, and that the Cnh structures are not minima for n = 4 and 5. Moreover, our computations show the TSs for CPT in (HCl)3, (HCl)4 and (HCl)5 have D3h, D2d, and C2 point group symmetry, respectively. At the CCSD(T) CBS limit, (HF)4 and (HF)5 have the smallest electronic barrier heights for CPT (≈15 kcal mol-1 for both), followed by the HF trimer (≈21 kcal mol-1). The barriers are appreciably higher for the other clusters (around 27 kcal mol-1 for (H2O)4 and (HCl)3; roughly 30 kcal mol-1 for (H2O)3, (H2O)5 and (HCl)4; up to 38 kcal mol-1 for (HCl)5). At the CBS limit, MP2 significantly underestimates the CCSD(T) barrier heights (e.g., by ca. 2, 4 and 7 kcal mol-1 for the pentamers of HF, H2O and HCl, respectively), whereas CCSD overestimates these barriers by roughly the same magnitude. Scaling the barrier heights and dissociation energies by the number of fragments in the cluster reveals strong linear relationships between the two quantities and with the magnitudes of the imaginary vibrational frequency for the TSs.
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Affiliation(s)
- Yuan Xue
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA.
| | - Thomas More Sexton
- School of Arts and Sciences, Chemistry University of Mary, Bismark, ND 58504, USA.
| | - Johnny Yang
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA.
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA.
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Alshammari N, Platts JA. Theoretical study of copper binding to GHK peptide. Comput Biol Chem 2020; 86:107265. [PMID: 32371360 DOI: 10.1016/j.compbiolchem.2020.107265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 11/20/2022]
Abstract
We report ligand field molecular mechanics, density functional theory and semi-empirical studies on the binding of Cu(II) to GlyHisLys (GHK) peptide. Following exhaustive conformational searching using molecular mechanics, we show that relative energy and geometry of conformations are in good agreement between GFN2-xTB semi-empirical and B3LYP-D DFT levels. Conventional molecular dynamics simulation of Cu-GHK shows the stability of the copper-peptide binding over 100 ps trajectory. Four equatorial bonds in 3N1O coordination remain stable throughout simulation, while a fifth in apical position from C-terminal carboxylate is more fluxional. We also show that the automated conformer and rotamer search algorithm CREST is able to correctly predict the metal binding position from a starting point consisting of separated peptide, copper and water.
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Affiliation(s)
- Nadiyah Alshammari
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - James A Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK.
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Matsui T, Yamamoto K, Fujita T, Morihashi K. Molecular Dynamics and Quantum Chemical Approach for the Estimation of an Intramolecular Hydrogen Bond Strength in Okadaic Acid. J Phys Chem B 2018; 122:7233-7242. [DOI: 10.1021/acs.jpcb.8b03272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 760] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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Applications of hydrophobins: current state and perspectives. Appl Microbiol Biotechnol 2015; 99:1587-97. [PMID: 25564034 DOI: 10.1007/s00253-014-6319-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 01/07/2023]
Abstract
Hydrophobins are proteins exclusively produced by filamentous fungi. They self-assemble at hydrophilic-hydrophobic interfaces into an amphipathic film. This protein film renders hydrophobic surfaces of gas bubbles, liquids, or solid materials wettable, while hydrophilic surfaces can be turned hydrophobic. These properties, among others, make hydrophobins of interest for medical and technical applications. For instance, hydrophobins can be used to disperse hydrophobic materials; to stabilize foam in food products; and to immobilize enzymes, peptides, antibodies, cells, and anorganic molecules on surfaces. At the same time, they may be used to prevent binding of molecules. Furthermore, hydrophobins have therapeutic value as immunomodulators and can been used to produce recombinant proteins.
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Sarmah A, Roy RK. A density functional reactivity theory (DFRT) based approach to understand the interaction of cisplatin analogues with protecting agents. J Comput Aided Mol Des 2014; 28:1153-73. [DOI: 10.1007/s10822-014-9790-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 08/23/2014] [Indexed: 01/24/2023]
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Jacquemin D, Zúñiga J, Requena A, Céron-Carrasco JP. Assessing the importance of proton transfer reactions in DNA. Acc Chem Res 2014; 47:2467-74. [PMID: 24849375 DOI: 10.1021/ar500148c] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although engineered by millions of years of evolution, the cellular machinery is not flawless, and errors regularly appear during DNA replication. The subsequent alteration of the stored genetic message results in a mutation and might be the starting point of important health disorders. The question therefore is what causes DNA mutations? All living organisms are constantly exposed to a number of external agents such as free radicals and to radiation, which may lead to induced mutations. There are also mutations happening without invoking the action of any exogenous element, the so-called spontaneous mutations. The former can be partially controlled by avoiding exposure to high-risk environments, while the latter are more intriguing because their origin is unclear and difficult to determine. As noted by Watson and Crick when they first discovered the DNA structure, the correct replication of DNA rests on the assumption that the base pairs remain in their most stable, canonical form. However, protons along the interbase hydrogen-bond network are not static entities. They can in fact interchange their positions in DNA bases through proton transfer (PT) reactions before strands unwind, giving rise to noncanonical structures defined as rare tautomers. The importance of these rare tautomers was also cleverly anticipated by Watson and Crick and some years later claimed by Löwdin to be a source of spontaneous mutations. In Watson and Crick's words: "It would be of interest to know the precise difference in free energy between the various tautomeric forms under physiological conditions." Unfortunately, rare tautomeric forms are very difficult to detect, so no direct and accurate free energy measure has been discerned. In contrast, theoretical chemistry is making good progress toward the quantification of PT reactions in DNA and their biological consequences. This Account touches upon the theoretical studies devoted to appraising the importance of rare tautomers as promoters of spontaneous mutations. We focus in particular on the crucial role played by the biological environment on DNA stability. It has now been demonstrated that valuable macroscopic predictions require not only highly accurate theories but also refined chemical models. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations performed on short but complete DNA sequence fragments emerge in this context as the most adequate tools. In addition, these methods can be used to quantify the effect of different external agents on the PT tautomeric equilibria and, eventually, to conveniently handle them. This is the case for the possible alteration of the naturally observed mutation rate by exposure to intense electric fields. Theoretical predictions envision in this respect promising applications of ultrashort electric pulses in medicine to selectively modify the mutated/canonical ratio in DNA.
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Affiliation(s)
- Denis Jacquemin
- CEISAM, UMR CNRS 6230, Université de Nantes, 2, Rue de la Houssinière, Nantes 44322 Cedex 3, France
- Institut Universitaire de France, 103 bd St Michel, Paris 75005 Cedex 5, France
| | - José Zúñiga
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
| | - Alberto Requena
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
| | - José Pedro Céron-Carrasco
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
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Chen HY, Chen HF, Kao CL, Yang PY, Hsu SCN. Interaction of electrons with cisplatin and the subsequent effect on DNA damage: a density functional theory study. Phys Chem Chem Phys 2014; 16:19290-7. [DOI: 10.1039/c4cp02306d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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10
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Kratochvílová I, Golan M, Vala M, Špérová M, Weiter M, Páv O, Šebera J, Rosenberg I, Sychrovský V, Tanaka Y, Bickelhaupt FM. Theoretical and Experimental Study of Charge Transfer through DNA: Impact of Mercury Mediated T-Hg-T Base Pair. J Phys Chem B 2014; 118:5374-81. [DOI: 10.1021/jp501986a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Irena Kratochvílová
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Faculty of Nuclear Physics
and Physical Engineering, Czech Technical University in Prague, Zikova 1, 160 00 Prague 6, Czech Republic
| | - Martin Golan
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Institute of Physics,
Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Martin Vala
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Miroslava Špérová
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Martin Weiter
- Materials
Research Centre, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, CZ-612 00 Brno, Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Jakub Šebera
- Institute
of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance
2, CZ-182 21 Prague
8, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy
of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, CZ-16610 Prague 6, Czech Republic
| | - Yoshiyuki Tanaka
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale
Modeling (ACMM), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Institute for Molecules and
Materials (IMM), Radboud University Nijmegen, Comeniuslaan 4, 6525 HP Nijmegen, The Netherlands
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12
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Gkionis K, Mutter ST, Platts JA. QM/MM description of platinum–DNA interactions: comparison of binding and DNA distortion of five drugs. RSC Adv 2013. [DOI: 10.1039/c3ra23041d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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Sarmah A, Roy RK. Understanding the preferential binding interaction of aqua-cisplatins with nucleobase guanine over adenine: a density functional reactivity theory based approach. RSC Adv 2013. [DOI: 10.1039/c2ra23223e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Nguyen TH, Arnesano F, Scintilla S, Rossetti G, Ippoliti E, Carloni P, Natile G. Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach. J Chem Theory Comput 2012; 8:2912-20. [DOI: 10.1021/ct300167m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Trung Hai Nguyen
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Fabio Arnesano
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
| | - Simone Scintilla
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
| | - Giulia Rossetti
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Emiliano Ippoliti
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Statistical and Biological Physics Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265,
I-34136 Trieste, Italy
| | - Giovanni Natile
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
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Cerón-Carrasco JP, Requena A, Jacquemin D. Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1188-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Cerón-Carrasco JP, Jacquemin D, Cauët E. Cisplatin cytotoxicity: a theoretical study of induced mutations. Phys Chem Chem Phys 2012; 14:12457-64. [DOI: 10.1039/c2cp40515f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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Cerón-Carrasco JP, Jacquemin D. Influence of Mg2+ on the Guanine-Cytosine Tautomeric Equilibrium: Simulations of the Induced Intermolecular Proton Transfer. Chemphyschem 2011; 12:2615-23. [DOI: 10.1002/cphc.201100264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/28/2011] [Indexed: 01/01/2023]
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19
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Nakanishi Y, Matsui T, Kitagawa Y, Shigeta Y, Saito T, Kataoka Y, Kawakami T, Okumura M, Yamaguchi K. Electron Conductivity in Modified Models of Artificial Metal–DNA Using Green’s Function-Based Elastic Scattering Theory. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20100207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Truflandier LA, Sutter K, Autschbach J. Solvent Effects and Dynamic Averaging of 195Pt NMR Shielding in Cisplatin Derivatives. Inorg Chem 2011; 50:1723-32. [DOI: 10.1021/ic102174b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lionel A. Truflandier
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Kiplangat Sutter
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
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22
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Hydrolysis and binding mechanism of AMD473 (cis-[PtCl2(NH3)(2-picoline)]) with guanine: A quantum mechanical study. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.05.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Miyachi H, Matsui T, Shigeta Y, Yamashita K, Hirao K. Possibility of multi-conformational structure of mismatch DNA nucleobase in the presence of silver(I) ions. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.06.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Miyachi H, Matsui T, Shigeta Y, Hirao K. Effects of mercury(ii) on structural properties, electronic structure and UV absorption spectra of a duplex containing thymine–mercury(ii)–thymine nucleobase pairs. Phys Chem Chem Phys 2010; 12:909-17. [DOI: 10.1039/b912807g] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Matsui T, Miyachi H, Nakanishi Y, Shigeta Y, Sato T, Kitagawa Y, Okumura M, Hirao K. Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNA. J Phys Chem B 2009; 113:12790-5. [PMID: 19708672 DOI: 10.1021/jp9045319] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We evaluated the stability, UV-vis spectra, and possibility of stacking of [S-M(II)-S] (M=Ni, Pd, Pt, S: hydroxypyridinethione) using density functional theory (DFT). We calculated the formation energies of modified bases with possible combinations of chalcogen atoms and metal cations. The results confirmed that [H-Ni(II)-H] (H: hydroxypyridone), [H-Cu(II)-H], and [S-Cu(II)-S] would form stable metal-base pairing; on the other hand, [H-Zn(II)-H], [S-Zn(II)-S], and [H-Pt(II)-H] would not. We predicted UV-vis excitations at 400-410 nm, mainly dominated by a d-pi* transition accompanied by a pi-pi* transition in [S-M(II)-S], where a metal-to-ligand charge transfer shifts the peak of S (without metal cations) by performing time-dependent density functional theory (TDDFT) calculations. By adding the Andersson-Langreth-Lundqvist van der Waals correction to the hybrid DFT results, we estimated the interaction energy between base pairs of [S-M(II)-S]. According to the results, the interaction between [S-M(II)-S] monomers for all cases is attractive, so that the selectivity of formation of the metal-containing DNA is governed mainly by the formation of the base pair in the aqueous phase and only slightly by the pi-pi stacking interaction between the modified bases.
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Affiliation(s)
- Toru Matsui
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8656, Japan.
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Cramer CJ, Truhlar DG. Density functional theory for transition metals and transition metal chemistry. Phys Chem Chem Phys 2009; 11:10757-816. [PMID: 19924312 DOI: 10.1039/b907148b] [Citation(s) in RCA: 1079] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.
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Affiliation(s)
- Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA.
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Matsui T, Sato T, Shigeta Y, Hirao K. Sequence-dependent proton-transfer reaction in stacked GC pair II: The origin of stabilities of proton-transfer products. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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QM/MM investigation into binding of square-planar platinum complexes to DNA fragments. J Biol Inorg Chem 2009; 14:1165-74. [DOI: 10.1007/s00775-009-0560-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 06/10/2009] [Indexed: 12/31/2022]
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Dans PD, Coitiño EL. Density Functional Theory Characterization and Descriptive Analysis of Cisplatin and Related Compounds. J Chem Inf Model 2009; 49:1407-19. [DOI: 10.1021/ci800421w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Pablo D. Dans
- Laboratorio de Química Teórica y Computacional (LQTC), Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República (UdelaR), Iguá 4225, 11400 Montevideo, Uruguay
| | - E. Laura Coitiño
- Laboratorio de Química Teórica y Computacional (LQTC), Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República (UdelaR), Iguá 4225, 11400 Montevideo, Uruguay
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Matsui T, Miyachi H, Sato T, Shigeta Y, Hirao K. Structural Origin of Copper Ion Containing Artificial DNA: A Density Functional Study. J Phys Chem B 2008; 112:16960-5. [DOI: 10.1021/jp8080707] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Toru Matsui
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hideaki Miyachi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Takeshi Sato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yasuteru Shigeta
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Kimihiko Hirao
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigouri-cho, Ako-gun, Hyogo 678-1297, Japan
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Shigeta Y, Miyachi H, Matsui T, Hirao K. Dynamic Quantum Isotope Effects on Multiple Proton-Transfer Reactions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.1230] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Munk BH, Burrows CJ, Schlegel HB. An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroiminodihydantoin by density functional theory. J Am Chem Soc 2008; 130:5245-56. [PMID: 18355018 DOI: 10.1021/ja7104448] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The potential energy surface for formation of 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-OG), guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) from 8-oxoguanine (8-oxoG) has been mapped out using B3LYP density functional theory, the aug-cc-pVTZ and 6-31+G(d,p) basis sets and the IEF-polarizable continuum model (PCM) solvation model. Three pathways for formation of 5-OH-OG from 8-oxoG were evaluated: (A) stepwise loss of two electrons and two protons to form the quinonoid intermediate 2-amino-7,9-dihydro-purine-6,8-dione (8-oxoG(ox)) followed by hydration; (B) stepwise loss of two electrons and one proton and net addition of hydroxide, in which the key step is nucleophilic addition to the 8-oxoG radical cation; and (C) stepwise loss of one electron and one proton and addition of hydroxyl radical to the 8-oxoG radical cation. The data suggest that all three pathways are energetically feasible mechanisms for the formation of 5-OH-OG, however, Pathway A may be kinetically favored over Pathway B. Although lower in energy, Pathway C may be of limited biological significance since it depends on the local concentration of hydroxyl radical. Pathways for hydrolysis and decarboxylation of 5-OH-OG to form Gh via either a carboxylic acid or substituted carbamic acid intermediate have been evaluated with the result that cleavage of the N1-C6 bond is clearly favored over that of the C5-C6 bond. Formation of Sp from 5-OH-OG via stepwise proton transfer and acyl migration or ring opening followed by proton transfer and ring closure have also been explored and suggest that deprotonation of the hydroxyl group facilitates a 1,2 acyl shift. Results of the calculations are consistent with experimental studies showing dependence of the Gh/Sp product ratio on pH. Under neutral and basic conditions, the data predict that formation of Sp is kinetically favored over the pathways for formation of Gh. Under acidic conditions, Gh is predicted to be the kinetically favored product.
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Affiliation(s)
- Barbara H Munk
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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