1
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Kumawat RL, Sherrill CD. High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs. J Chem Inf Model 2023; 63:3150-3157. [PMID: 37125692 DOI: 10.1021/acs.jcim.3c00428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
High-order quantum chemistry is applied to hydrogen-bonded natural DNA nucleobase pairs [adenine:thymine (A:T) and guanine:cytosine (G:C)] and non-natural Hachimoji nucleobase pairs [isoguanine:1-methylcytosine (B:S) and 2-aminoimidazo[1,2a][1,3,5]triazin-4(1H)-one:6-amino-5-nitropyridin-2-one (P:Z)] to see how the intermolecular interaction energies and their energetic components (electrostatics, exchange-repulsion, induction/polarization, and London dispersion interactions) vary among the base pairs. We examined the Hoogsteen (HG) geometries in addition to the traditional Watson-Crick (WC) geometries. Coupled-cluster theory through perturbative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit and high-order symmetry-adapted perturbation theory (SAPT) at the SAPT2+(3)(CCD)δMP2/aug-cc-pVTZ level are used to estimate highly accurate noncovalent interaction energies. Electrostatic interactions are the most attractive component of the interaction energies, but the sum of induction/polarization and London dispersion is nearly as large, for all base pairs and geometries considered. Interestingly, the non-natural Hachimoji base pairs interact more strongly than the corresponding natural base pairs, by -21.8 (B:S) and -0.3 (P:Z) kcal mol-1 in the WC geometries, according to CCSD(T)/CBS. This is consistent with the H-bond distances being generally shorter in the non-natural base pairs. The natural base pairs are energetically more stabilized in their Hoogsteen geometries than in their WC geometries. The Hoogsteen geometry makes the A:T base pair slightly more stable, by -0.8 kcal mol-1, and it greatly stabilizes the G:C+ base pair, by -15.3 kcal mol-1. The G:C+ stabilization is mainly due to the fact that C has typically added a proton when found in Hoogsteen geometries. By contrast, Hoogsteen geometries are substantially less favorable than WC geometries for non-natural Hachimoji base pairs, by 17.3 (B:S) and 13.8 (P:Z) kcal mol-1.
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Affiliation(s)
- Rameshwar L Kumawat
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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2
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Stone S, Ray D, Andricioaei I. Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA. J Chem Inf Model 2022; 62:6749-6761. [PMID: 36049242 PMCID: PMC9795553 DOI: 10.1021/acs.jcim.2c00519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Hoogsteen (HG) base pairing conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studies. However, the mechanism of the conformational transition is not well understood. A detailed understanding of the process of WC to HG base pair transition can provide a deeper understanding of DNA repair and recognition. In an earlier study, we explored the free energy landscape for this process using extensive computer simulation with the CHARMM36 force field. In this work, we study the impact of force field models in describing the WC to HG base pairing transition using meta-eABF enhanced sampling, quasi-harmonic entropy calculation, and nonbonded energy analysis. The secondary structures of both base pairing forms and the topology of the free energy landscapes were consistent over different force field models, although the relative free energy, entropy, and the interaction energies tend to vary. The relative stability of the WC and HG conformations is dictated by a delicate balance between the enthalpic stabilization and the reduced entropy of the structurally rigid HG structure. These findings highlight the impact that subtleties in force field models can have on accurately modeling DNA base pair dynamics and should stimulate further computational investigations into other dynamically important motions in DNA.
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Affiliation(s)
- Sharon
Emily Stone
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Dhiman Ray
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Ioan Andricioaei
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States,Department
of Physics and Astronomy, University of
California Irvine, Irvine, California 92697, United States,
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3
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Stasyuk OA, Solà M, Swart M, Fonseca Guerra C, Krygowski TM, Szatylowicz H. Effect of Alkali Metal Cations on Length and Strength of Hydrogen Bonds in DNA Base Pairs. Chemphyschem 2020; 21:2112-2126. [PMID: 32643813 DOI: 10.1002/cphc.202000434] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/01/2020] [Indexed: 01/25/2023]
Abstract
For many years, non-covalently bonded complexes of nucleobases have attracted considerable interest. However, there is a lack of information about the nature of hydrogen bonding between nucleobases when the bonding is affected by metal coordination to one of the nucleobases, and how the individual hydrogen bonds and aromaticity of nucleobases respond to the presence of the metal cation. Here we report a DFT computational study of nucleobase pairs interacting with alkali metal cations. The metal cations contribute to the stabilization of the base pairs to varying degrees depending on their position. The energy decomposition analysis revealed that the nature of bonding between nucleobases does not change much upon metal coordination. The effect of the cations on individual hydrogen bonds were described by changes in VDD charges on frontier atoms, H-bond length, bond energy from NBO analysis, and the delocalization index from QTAIM calculations. The aromaticity changes were determined by a HOMA index.
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Affiliation(s)
- Olga A Stasyuk
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Spain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Spain
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, C/ M. Aurèlia Capmany 69, 17003, Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Célia Fonseca Guerra
- Theoretical Chemistry, Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Leiden University, PO Box 9502, NL-2300 RA, Leiden, The Netherlands
| | | | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw, 00-664, Poland
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4
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Long MP, Alland S, Martin ME, Isborn CM. Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects. Phys Chem Chem Phys 2020; 22:5584-5596. [DOI: 10.1039/c9cp06844a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Classical molecular dynamics simulations reveal size-dependent trends of alkaline earth metal ions binding to DNA are due to ion size and hydration behavior.
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Affiliation(s)
| | - Serra Alland
- Department of Chemistry and Biochemistry
- University of Central Arkansas
- Arkansas 72035
- USA
| | - Madison E. Martin
- Department of Chemistry and Biochemistry
- University of Central Arkansas
- Arkansas 72035
- USA
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5
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Grauffel C, Dudev T, Lim C. Why Cellular Di/Triphosphates Preferably Bind Mg 2+ and Not Ca 2. J Chem Theory Comput 2019; 15:6992-7003. [PMID: 31714772 DOI: 10.1021/acs.jctc.9b00847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Di/triphosphates perform a multitude of essential tasks, being important components of many vital organic cofactors such as adenosine/guanosine di/triphosphate (ADP/GDP, ATP/GTP), flavin adenine dinucleotide, and nicotinamide adenine dinucleotide and its phosphate derivative. They are generally bound to cations inside cells, in particular Mg2+ in the case of ATP/GTP. Yet how their metal-binding modes depend on the number, charge, and solvent exposure of the polyphosphate group and how Mg2+and Ca2+ dications that coexist in cellular fluids compete for di/triphosphates in biological systems remain elusive. Using density functional theory calculations combined with a polarizable continuum model, we have determined the relative free energies and stabilities of the different binding modes of di- and triphosphate groups to Mg2+ and Ca2+. We show that the thermodynamic outcome of the competition between Mg2+ and Ca2+ for cellular di/triphosphates depends mainly on the oligomericity/charge and metal-binding mode of the phosphate ligand as well as the solvent exposure of the binding site. Increasing the charge and thus denticity of the phosphate ligand from bi- to tridentate in a buried binding pocket enhances the affinity of the host system for the stronger charge acceptor, Mg2+. The cellular di/triphosphates's intrinsic properties and the protein matrix allowing them to bind a dication bi/tridentately, along with the higher cytosolic concentration of Mg2+ compared to Ca2+, enables Mg2+ to outcompete Ca2+ in binding to these highly charged anions. This suggests an explanation for why nature has chosen Mg2+ but not Ca2+ to perform most of the essential tasks associated with biological triphosphates.
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Affiliation(s)
- Cédric Grauffel
- Institute of Biomedical Sciences , Academia Sinica , Taipei 11529 , Taiwan
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy , Sofia University , Sofia 1164 , Bulgaria
| | - Carmay Lim
- Institute of Biomedical Sciences , Academia Sinica , Taipei 11529 , Taiwan.,Department of Chemistry , National Tsing Hua University , Hsinchu 300 , Taiwan
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6
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Bhai S, Ganguly B. Role of backbones on the interaction of metal ions with deoxyribonucleic acid and peptide nucleic acid: A DFT study. J Mol Graph Model 2019; 93:107445. [PMID: 31494536 DOI: 10.1016/j.jmgm.2019.107445] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 11/30/2022]
Abstract
Metal ion interaction with deoxyribonucleic acid and peptide nucleic acid were studied using B3LYP-D3/6-311++g(d,p)//B3LYP/6-31 + G(d) level of theory in aqueous phase employing polarized continuum (PCM) model. This study reports the role of backbones on deoxyribonucleic acid and peptide nucleic acid for complexation with different metal ions. The systematic study performed with DFT calculations reveals that central binding (Type-4) shows the strongest binding compared to the other binding modes because of the involvement of the backbone as well as the nitrogenous bases. The charged backbone of DNA nucleotides contributes significantly towards binding with the metal ions. The deoxyguanosine monophosphate (dGMP) clearly indicates the strongest binding upon complexation with Mg2+ (-49.6 kcal/mol), Zn2+ (-45.3 kcal/mol) and Cu2+ (-148.4 kcal/mol), respectively. The neutral backbone of PNA also assists to complex the metal ions with PNA nucleotides. The Mg2+ and Cu2+ prefer to bind with the PNA-Cytosine (-32.9 kcal/mol & -132.9 kcal/mol) in central binding mode (type-4). PNA-Adenine-Zn2+ (-29.1 kcal/mol) is the preferred binding mode (type-4) compared to other modes of interaction for this metal ion with PNA-Adenine nucleotide. The Cu2+ ion showed the superior complexation ability with deoxyribonucleic acid and peptide nucleic acid compared to Mg2+ and Zn2+ ions. The cation-π complexation with the bases of nucleotides was also obtained with Cu2+ ion. The AIM (atoms in molecule) theory has been applied to examine the nature of the interaction of Mg2+, Zn2+, and Cu2+ ion to the deoxyribonucleic acid and peptide nucleic acid. The alkaline earth metal, Mg2+ ion shows electrostatic nature while interaction with deoxyribonucleic acid and peptide nucleic acid, however, the transition metal ions (Zn2+, Cu2+) showed partly covalent nature as well with deoxyribonucleic acid and peptide nucleic acid. The optical properties calculated for the binding of metal ions with deoxyribonucleic acid and peptide nucleic acid showed a diagnostic signature to ascertain the interaction of metal ions with such nucleotides. Cu2+ ion showed larger red shifts in the absorption spectrum values upon complexation with the DNAs and PNAs. The calculated results suggest that such metal ions would prefer to bind with the DNA compared to PNA in DNA-PNA duplexes. The preference for the binding of metal ions with DNA nucleotides is largely attributed to the contribution of charged backbones compared to the neutral PNA backbones.
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Affiliation(s)
- Surjit Bhai
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India.
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7
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Comprehensive understanding of multiple binding of D-penicillamine with Cu2+-hexa aqua complex: a DFT approach. Struct Chem 2019. [DOI: 10.1007/s11224-019-01365-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Dinuclear Metal-Mediated Guanine–Uracil Base Pairs: Theoretical Studies of GUM22+ (M = Cu, Ag, and Au) Ions. J CLUST SCI 2019. [DOI: 10.1007/s10876-019-01503-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Cao GJ. A dinuclear Cu(i)-mediated complex: Theoretical studies of the G 2Cu 2 4+ cluster ion. J Chem Phys 2018; 149:144308. [PMID: 30316268 DOI: 10.1063/1.5038366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recently, the T-Hg(ii)2-A base pair containing two equivalents of Hg(ii) has been prepared and characterized experimentally, which implies that there might exist considerable stable metal-mediated base pairs holding two neighbouring metal centers. Here we report a quantum chemical study on geometries, electronic structures, and bonding of various G2Cu2 4+ (G = guanine) isomers including one di-copper(i) unit. Different density functional methods [Becke 3-parameter-Lee-Yang-Parr, Perdew-Becke-Ernzerhof, Becke-Perdew, Density Functional Theory with Dispersion Corrections (DFT-D)] assign ambiguous relative energies to these isomers with the singlet and triplet states. High-level ab initio [domain-based local pair natural orbital (DLPNO) coupled-cluster with single and double excitations and DLPNO-coupled-cluster with single, double, and perturbative triple excitations] calculations confirm that the lowest-lying isomer of the G2Cu2 4+ ion has C 2h symmetry with the singlet state and is comparable to the singly and doubly charged homologues (G2Cu2 + and G2Cu2 2+). The extended transition state (ETS)-natural orbitals for the chemical valence (ETS-NOCV) calculations point out that it has larger instantaneous interaction energy and bond dissociation energy than the corresponding singly and doubly charged complexes due to its relatively stronger attractive energies and weaker Pauli repulsion. The orbital interactions in the quadruply charged cluster chiefly come from Cu2 4+ ← G⋯G π donations. The results may help the understanding of the bonding properties of other potential metal-base pair complexes with the electron transfer.
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Affiliation(s)
- Guo-Jin Cao
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
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10
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Li D, Han Y, Li H, Zhang P, Kang Q, Li Z, Shen D. The influence of isolated and penta-hydrated Zn 2+ on some of the intramolecular proton-transfer processes of thymine: a quantum chemical study. RSC Adv 2018; 8:11021-11026. [PMID: 35541537 PMCID: PMC9078977 DOI: 10.1039/c7ra13750h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/27/2018] [Indexed: 02/02/2023] Open
Abstract
Zinc cation (Zn2+) plays an important role in the chemistry of DNA base pairs. In this work, the influence of isolated and penta-hydrated Zn2+ on some of the intramolecular proton-transfer processes of thymine (T) is investigated by the density functional theory method. It is shown that the calculated binding energies between Zn2+ and T are exothermic in vacuum. Compared to T, Zn2+ increases the stability of tautomer T' by 28.7 kcal mol-1, promoting the intramolecular proton transfer of T. But in a micro-water environment, the attachment processes of Zn2+ to T hydrates, penta-hydrated Zn2+ to T, and penta-hydrated Zn2+ to T hydrates lead to the rearrangement of molecules and the redistribution of charges. The conventional T is still the most stable form and the influence of Zn2+ is much reduced and the proton transfer is thermodynamically unfavored. The detailed characterization is helpful to understand the genotoxicity of zinc ions.
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Affiliation(s)
- Dejie Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
| | - Ying Han
- National Engineering Research Center for Colloidal Materials, School of Chemistry and Chemical Engineering, Shandong University Jinan 250100 P. R. China
| | - Huijuan Li
- College of Chemical and Environmental Engineering, Shandong University of Science and Technology Qingdao 266590 P. R. China
| | - Ping Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
| | - Qi Kang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
| | - Zhihua Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
| | - Dazhong Shen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
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11
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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12
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Khalili B, Rimaz M. Interaction of l-proline with group IIB (Zn2+, Cd2+, Hg2+) metal cations in the gas and aqueous phases: a quantum computational study. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gas and aqueous phase complexation geometries, electronic interactions, and metal ion affinities of Zn2+, Cd2+, and Hg2+ metal cations with the two most stable conformations of l-proline complexes were studied. The complexes were optimized by density functional theory (B3LYP) using the 6-311++G(d,p) orbital basis set and relativistic pseudopotentials for the metal cations. The interactions of the metal cations at different nucleophilic sites of l-proline were considered as were three modes of interactions including salt bridged, charge solvated 1, and charge solvated 2, which are indicative of binding in a bidentate manner through the carboxylate group, carbonyl and hydroxyl oxygen, and carbonyl oxygen and the nitrogen atom of l-proline. All of the coordination patterns were characterized by both charge transfer and ionic interactions between l-proline and the metal cation. The metal ion affinity (MIA) and interaction energy were also computed for all of the complexes at both the gas and aqueous phases. Results showed that the order of MIA at the gas and aqueous phases are different. MIA order at the gas phase was in the order of Zn2+ > Hg2+ > Cd2+ whereas at the aqueous phase, the order of Zn2+ > Cd2+ > Hg2+ was obtained for MIA. The infrared stretching vibrational modes of the N–H and O–H groups of free l-proline were compared with l-proline–M2+ in both CS1 and CS2 coordination patterns at the gas phase and results showed a considerable shift to lower frequency during complexation process.
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Affiliation(s)
- Behzad Khalili
- Department of Chemistry, Faculty of Sciences, University of Guilan, P.O. Box 41335-1914 Rasht, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran
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13
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DFT investigation of the vibrational properties of GC Watson-Crick and Hoogsteen base pairs in the presence of Mg2+, Ca2+, and Cu2+ ions. J Mol Model 2014; 20:2220. [DOI: 10.1007/s00894-014-2220-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/23/2014] [Indexed: 11/26/2022]
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14
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Eizaguirre A, Mó O, Yáñez M, Salpin JY, Tortajada J. Modelling peptide-metal dication interactions: formamide-Ca2+ reactions in the gas phase. Org Biomol Chem 2013; 10:7552-61. [PMID: 22892540 DOI: 10.1039/c2ob26166a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The collision induced dissociation of formamide-Ca(2+) complexes produced in the gas phase through nanoelectrospray ionization yields as main products ions [CaOH](+), [HCNH](+), [Ca(NH(2))](+), HCO(+) and [Ca(NH(3))](2+) and possibly [Ca(H(2)O)](2+) and [C,O,Ca](2+), the latter being rather minor. The mechanisms behind these fragmentation processes have been established by analyzing the topology of the potential energy surface by means of B3LYP calculations carried out with a core-correlated cc-pWCVTZ basis set. The Ca(2+) complexes formed by formamide itself and formimidic acid play a fundamental role. The former undergoes a charge separation reaction yielding [Ca(NH(2))](+) + HCO(+), and the latter undergoes the most favorable Coulomb explosion yielding [Ca-OH](+) + [HCNH](+) and is the origin of a multistep mechanism which accounts for the observed loss of water and HCN. Conversely, the other isomer of formamide, amino(hydroxyl)carbene, does not play any significant role in the unimolecular reactivity of the doubly charged molecular cation.
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Affiliation(s)
- Ane Eizaguirre
- Departamento de Química, Módulo 13, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049, Madrid, Spain
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15
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Liang LJ, Huang CZ. Spectral study on the unique enhanced fluorescence of guanosine triphosphate by zinc ions. Talanta 2012; 104:198-203. [PMID: 23597910 DOI: 10.1016/j.talanta.2012.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 11/26/2022]
Abstract
Binding effect of guanosine triphosphate (GTP) with metal ions is involved in many biologically important processes, and so its investigation has been one interesting research focus for many chemical and biochemical research groups. In this contribution, we presented the unique fluorescence recovery and enhancement of GTP induced by Zn(II) based on the spectrofluorometric method. When excited at 280 nm, GTP is hardly fluorescent at the alkaline condition. However, the presence of Zn(II) caused an obvious fluorescence emission of GTP at 346 nm, and the binding molar ratio between GTP and Zn(II) had been proved to be 1. The investigations of binding property of various nucleotides with metal ions demonstrated that this fluorescence recovery and enhancement of GTP with Zn(II) was highly specific, which could successfully discriminate GTP from other structurally similar nucleotides including GDP and GMP. Furthermore, similar fluorescence response of the bacterial alarmone ppGpp to Zn(II) had also been identified.
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Affiliation(s)
- Li Jiao Liang
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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16
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Density functional theory study of interaction, bonding and affinity of group IIb transition metal cations with nucleic acid bases. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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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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18
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Romancová I, Chval Z, Předota M. Influence of the Environment on the Specificity of the Mg(II) Binding to Uracil. J Phys Chem A 2012; 116:1786-93. [DOI: 10.1021/jp208823f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ingrid Romancová
- Institute
of Physics
and Biophysics, Faculty of Science, University of South Bohemia, Branišovská 31, CZ-370
05 České Budějovice, Czech Republic
| | - Zdeněk Chval
- Department of Laboratory
Methods and Information Systems, Faculty of Health and
Social Studies, University of South Bohemia, J. Boreckého 27, CZ-370 11 České Budějovice,
Czech Republic
| | - Milan Předota
- Institute
of Physics
and Biophysics, Faculty of Science, University of South Bohemia, Branišovská 31, CZ-370
05 České Budějovice, Czech Republic
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19
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Marino T, Russo N, Toscano M, Pavelka M. Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations. Dalton Trans 2011; 41:1816-23. [PMID: 22159156 DOI: 10.1039/c1dt11028d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
B3LYP density functional based computations were performed in order to characterize the interactions present in some Cu(+), Ag(+), and Au(+) metal ion-mediated DNA and RNA base pairs from both structural and electronic points of view. Examined systems involve as ligands canonical Watson-Crick, Hoogsteen and Wobble base pairs. Two artificial Hoogsteen base pairs were also taken into account. Binding energy values indicate that complexes involving silver cations are less stable than those in which copper or gold are present, and propose a similar behaviour for these two latter ions. The nature of the bond linking metal ions and bases was described by the NBO analysis that suggests metal coordinative interactions to be covalent. An evaluation of the dispersion contributions for the investigated systems was performed with the B3LYP-D3 functional.
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Affiliation(s)
- Tiziana Marino
- Dipartimento di Chimica, Ponte P. Bucci Cubo 14C, Università degli Studi della Calabria, 87036 Arcavacata di Rende (CS), Italy.
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Liu W, Minier MA, Franz AH, Curtis M, Xue L. Synthesis of nucleobase-calix[4]arenes via click chemistry and evaluation of their complexation with alkali metal ions and molecular assembly. Supramol Chem 2011. [DOI: 10.1080/10610278.2011.632824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Wanbo Liu
- a Department of Chemistry , University of the Pacific , Stockton , CA , 95211 , USA
| | - Mikael A. Minier
- a Department of Chemistry , University of the Pacific , Stockton , CA , 95211 , USA
| | - Andreas H. Franz
- a Department of Chemistry , University of the Pacific , Stockton , CA , 95211 , USA
| | - Matthew Curtis
- a Department of Chemistry , University of the Pacific , Stockton , CA , 95211 , USA
| | - Liang Xue
- a Department of Chemistry , University of the Pacific , Stockton , CA , 95211 , USA
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21
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WANG NANA, LI PING, HU YI, BU YUXIANG, WANG WEIHUA, XIE XIAOYAN. ASSOCIATION OF URACIL WITH Zn2+ AND THE HYDRATED Zn2+: A DFT INVESTIGATION. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633607002927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The association behaviors between Uracil and Zn 2+ in vacuum and in the presence of extra water molecules have been investigated systematically using the density functional theory (DFT). In these systems, the interaction of Zn 2+ with the carbonyl oxygen O 4 is systematically favored relative to O 2. For Uracil- Zn 2+ complexes, the more stable coordination mode among the possible complexes corresponds to the bidentate one, where the monodentate coordination mode is about 37 kcal/mol higher in energy relative to the bidentate case. Correspondingly, the stabilities of these structures are enhanced due to the formations of the four-membered chelate ring in the bidentate coordination processes. In the monodentate coordination complexes, the hydration effects are larger than those in the bidentate coordination complexes. The most basic center in the Uracil remains the same regardless of whether introducing the water molecules to Zn 2+ or not. The calculated Zn 2+ bonding energies in Uracil- Zn 2+( H 2 O ) complexes are reduced in comparison to those of the unhydrated Uracil- Zn 2+ complexes. Moreover, investigations of stepwise hydration of Zn 2+ in the most stable Uracil- Zn 2+ complex suggest that the successive hydration effect on the Zn 2+ site can enhance the strength of C = O bond in the Uracil- Zn 2+ complexes and reduce the association interaction of Uracil with Zn 2+. Additionally, the most acidic site of Uracil has been changed from N 1- to N 3– H group before and after introducing the Zn 2+ and there is a significant increase in the overall acidity of the system.
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Affiliation(s)
- NANA WANG
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
| | - PING LI
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
| | - YI HU
- High-performance Computational Center, Shandong University, Jinan, 250100, P. R. China
| | - YUXIANG BU
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
- Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China
| | - WEIHUA WANG
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
| | - XIAOYAN XIE
- Department of Chemistry, Qufu Normal University, Qufu, 273165, P. R. China
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22
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Arshadi S, Bekhradnia A, Ebrahimnejad A. Feasibility study of hydrogen-bonded nucleic acid base pairs in gas and water phases — A theoretical study. CAN J CHEM 2011. [DOI: 10.1139/v11-124] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate the base pair binding probabilities for nucleic acid bases, numerous models were studied for contacts between adenine, thymine, guanine, cytosine, and uracil using density functional theory (DFT) in combination with the 6–311G* basis set. We obtained an assessment for the energy given by our calculations in gas and aqueous phases, which showed that it should be incorporated into hydrogen bonding and propeller rotational energies. The 42 complexes of base pairs (5 regular and 37 irregular base pairs) were proposed and their hydrogen-bonding (H-bonding) properties were verified. The hydrogen bonds in some irregular base pairs, including CC, UU, and TT (series 1), were stronger than in regular GC and AT base pairs. Also, the strength of the hydrogen bonds in the proposed base pairs, including CU, GG, GU, and TU (series 2), were similar to regular base pairs from an energetic point of view. The propeller rotations revealed a higher rotational barrier energy (6–7.5 kcal/mol; 1 cal = 4.184 J) for irregular base pairs (series 1 and 2) than regular GC and AT ones (1–3 kcal/mol). Nevertheless, the trend in these affinities of the complex contact probabilities and their biological properties were confirmed by our calculations.
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Affiliation(s)
- S. Arshadi
- Department of Chemistry, Payame Noor University, 1935-4697, I.R. of Iran
| | - A.R. Bekhradnia
- Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Mazandaran University of Medical Sciences, Sari, Iran
| | - A. Ebrahimnejad
- Department of Chemistry, Payame Noor University, 1935-4697, I.R. of Iran
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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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Otero-Navas I, Seminario JM. Molecular electrostatic potentials of DNA base-base pairing and mispairing. J Mol Model 2011; 18:91-101. [PMID: 21625905 DOI: 10.1007/s00894-011-1028-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 02/14/2011] [Indexed: 11/28/2022]
Abstract
An understanding of why adenine (A) pairs with thymine (T) and cytosine (C) with guanine (G) in DNA is very useful in the design of sensors and other related devices. We report the use of dissociation energies, geometries and molecular electrostatic potentials (MEPs) to justify the canonical (AT and CG) Watson-Crick pairs. We also analyze all mismatches in both configurations-cis and trans-with respect to their glycoside bonds. As expected, we found that the most stable pair configuration corresponds to CG, providing an energy criterion for that preferred configuration. The reason why A gets together with T is much more difficult to explain as the energy of this pair is smaller than the energy of some other mismatched pairs. We tested MEPs to see if they could shed light on this problem. Interestingly, MEPs yield a unique pattern (shape) for the two canonical cases but different shapes for the mismatches. A tunnel of positive potential surrounded by a negative one is found interconnecting the three H-bonds of CG and the two of AT. This MEP tunnel, assisted partially by energetics and geometrical criteria, unambiguously determine a distinctive feature of the affinity between A and T as well as that between G and C.
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Affiliation(s)
- Ivonne Otero-Navas
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
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25
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Sharma B, Rao JS, Sastry GN. Effect of Solvation on Ion Binding to Imidazole and Methylimidazole. J Phys Chem A 2011; 115:1971-84. [DOI: 10.1021/jp1120492] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Bhaskar Sharma
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, AP, India
| | - J. Srinivasa Rao
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, AP, India
| | - G. Narahari Sastry
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, AP, India
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26
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Cocinero EJ, Basterretxea FJ, Écija P, Lesarri A, Fernández JA, Castaño F. Conformational behaviour, hydrogen bond competition and intramolecular dynamics in vanillin derivatives: acetovanillone and 6-hydroxy-3-methoxyacetophenone. Phys Chem Chem Phys 2011; 13:13310-8. [DOI: 10.1039/c0cp02418j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Gloaguen E, de Courcy B, Piquemal JP, Pilmé J, Parisel O, Pollet R, Biswal HS, Piuzzi F, Tardivel B, Broquier M, Mons M. Gas-phase folding of a two-residue model peptide chain: on the importance of an interplay between experiment and theory. J Am Chem Soc 2010; 132:11860-3. [PMID: 20687601 DOI: 10.1021/ja103996q] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In order to assess the ability of theory to describe properly the dispersive interactions that are ubiquitous in peptide and protein systems, an isolated short peptide chain has been studied using both gas-phase laser spectroscopy and quantum chemistry. The experimentally observed coexistence of an extended form and a folded form in the supersonic expansion was found to result from comparable Gibbs free energies for the two species under the high-temperature conditions (< or = 320 K) resulting from the laser desorption technique used to vaporize the molecules. These data have been compared to results obtained using a series of quantum chemistry methods, including DFT, DFT-D, and post-Hartree-Fock methods, which give rise to a wide range of relative stabilities predicted for these two forms. The experimental observation was best reproduced by an empirically dispersion-corrected functional (B97-D) and a hybrid functional with a significant Hartree-Fock exchange term (M06-2X). In contrast, the popular post-Hartree-Fock method MP2, which is often used for benchmarking these systems, had to be discarded because of a very large basis-set superposition error. The applicability of the atomic counterpoise correction (ACP) is also discussed. This work also introduces the mandatory theoretical examination of experimental abundances. DeltaH(0 K) predictions are clearly not sufficient for discussion of folding, as the conformation inversion temperature is crucial to the conformation determination and requires taking into account thermodynamical corrections (DeltaG) in order to computationally isolate the most stable conformation.
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Affiliation(s)
- E Gloaguen
- CEA, IRAMIS, Service des Photons, Atomes et Molécules, and CNRS, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France
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28
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Eizaguirre A, Lamsabhi AM, Mó O, Yáñez M. Assisted intramolecular proton transfer in (uracil)2Ca2+ complexes. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0801-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Biswal HS, Shirhatti PR, Wategaonkar S. O−H···O versus O−H···S Hydrogen Bonding. 2. Alcohols and Thiols as Hydrogen Bond Acceptors. J Phys Chem A 2010; 114:6944-55. [DOI: 10.1021/jp102346n] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Himansu S. Biswal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
| | - Pranav R. Shirhatti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India 400 005
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Gresh N, Audiffren N, Piquemal JP, de Ruyck J, Ledecq M, Wouters J. Analysis of the Interactions Taking Place in the Recognition Site of a Bimetallic Mg(II)−Zn(II) Enzyme, Isopentenyl Diphosphate Isomerase. A Parallel Quantum-Chemical and Polarizable Molecular Mechanics Study. J Phys Chem B 2010; 114:4884-95. [DOI: 10.1021/jp907629k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Nicole Audiffren
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jean-Philip Piquemal
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jerome de Ruyck
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Marie Ledecq
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Johan Wouters
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
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31
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Krasnokutski SA, Lee JS, Yang DS. High-resolution electron spectroscopy and structures of lithium-nucleobase (adenine, uracil, and thymine) complexes. J Chem Phys 2010; 132:044304. [DOI: 10.1063/1.3299278] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Systematic theoretical investigations on the tautomers of thymine in gas phase and solution. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.09.047] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Cerón-Carrasco JP, Requena A, Michaux C, Perpète EA, Jacquemin D. Effects of Hydration on the Proton Transfer Mechanism in the Adenine−Thymine Base Pair. J Phys Chem A 2009; 113:7892-8. [DOI: 10.1021/jp900782h] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - C. Michaux
- Laboratorie de Chimie Biologique Structurale, Facultés Universitaires Notre-Dame de la Paix Rue de Bruxelles, 61. 5000 Namur, Belgium
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34
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Wu Y, Sa R, Li Q, Wei Y, Wu K. Theoretical studies on the bonding of Cd2+ to adenine and thymine: Tautomeric equilibrium and metalation in base pairing. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2008.11.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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35
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Brancolini G, Di Felice R. Electronic Properties of Metal-Modified DNA Base Pairs. J Phys Chem B 2008; 112:14281-90. [DOI: 10.1021/jp806419t] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Giorgia Brancolini
- National Research Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41100 Modena, Italy
| | - Rosa Di Felice
- National Research Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41100 Modena, Italy
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36
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Krasnokutski SA, Lei Y, Lee JS, Yang DS. Pulsed-field ionization photoelectron and IR-UV resonant photoionization spectroscopy of Al-thymine. J Chem Phys 2008; 129:124309. [DOI: 10.1063/1.2985858] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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38
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de Courcy B, Piquemal JP, Gresh N. Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization? J Chem Theory Comput 2008; 4:1659-68. [DOI: 10.1021/ct800200j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Benoit de Courcy
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris, France UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris, France UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris, France UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France, and CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
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39
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Zhang AG, Qin M, Zhou ZY, Jia ZK, Hou RY. A density functional theory study of interaction between formamide and guanine. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2008. [DOI: 10.1134/s0036024408070169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Li Y, Xia YL, Jiang Y, Yan XP. Extracting stoichiometry, thermodynamics, and kinetics for the interaction of DNA with cadmium ion by capillary electrophoresis on-line coupled with electrothermal atomic absorption spectrometry. Electrophoresis 2008; 29:1173-9. [PMID: 18232028 DOI: 10.1002/elps.200700674] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Understanding the binding of cadmium with DNA is of great importance for elucidating the mechanism of cadmium genotoxicity and carcinogenicity. In the present work, CE on-line coupled with electrothermal atomic absorption spectrometry was employed to study the binding electrophoretic behaviors, stoichiometry, thermodynamics, and kinetics for the interaction of cadmium cation (Cd(II)) with DNA. The stoichiometry (Cd(II) to DNA (as the concentration of base pairs)) for the interaction was determined to be 1:5. Two types of binding sites on DNA were observed with the binding constants of 10(6) and 10(5) L/mol, respectively, showing strong affinity of Cd(II) to DNA. The interaction of Cd(II) with both types of binding sites on DNA were driven by negative enthalpy change with a large positive entropy change. The binding of Cd(II) to DNA followed a first-order kinetics for Cd(II) with the apparent activation energy of 45.7 +/- 1.9 kJ/mol. The results obtained in present investigation would be helpful to understanding the genotoxicity and carcinogenicity of cadmium.
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Affiliation(s)
- Yan Li
- Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, People's Republic of China
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41
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Lamsabhi AM, Mó O, Yáñez M, Boyd RJ. Gas-Phase Interaction of Calcium (Ca2+) with Seleno Derivatives of Uracil. J Chem Theory Comput 2008; 4:1002-11. [DOI: 10.1021/ct800017j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Al Mokhtar Lamsabhi
- Departamento de Química C-9, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, and Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3 Canada
| | - Otilia Mó
- Departamento de Química C-9, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, and Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3 Canada
| | - Manuel Yáñez
- Departamento de Química C-9, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, and Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3 Canada
| | - Russell J. Boyd
- Departamento de Química C-9, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid, Spain, and Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4J3 Canada
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42
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Noguera M, Bertran J, Sodupe M. Cu2+/+ cation coordination to adenine--thymine base pair. Effects on intermolecular proton-transfer processes. J Phys Chem B 2008; 112:4817-25. [PMID: 18358032 DOI: 10.1021/jp711982g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Intermolecular proton-transfer processes in the Watson & Crick adenine-thymine Cu+ and Cu2+ cationized base pairs have been studied using the density functional theory (DFT) methods. Cationized systems subject to study are those resulting from cation coordination to the main basic sites of the base pair, N7 and N3 of adenine and O2 of thymine. For Cu+ coordinated to N7 or N3 of adenine, only the double proton-transferred product is found to be stable, similarly to the neutral system. However, when Cu+ interacts with thymine, through the O2 carbonyl atom, the single proton transfer from thymine to adenine becomes thermodynamically spontaneous, and thus rare forms of the DNA bases may spontaneously appear. For Cu2+ cation, important effects on proton-transfer processes appear due to oxidation of the base pair, which stabilizes the different single proton-transfer products. Results for hydrated systems show that the presence of the water molecules interacting with the metal cation (and their mode of coordination) can strongly influence the ability of Cu2+ to induce oxidation on the base pair.
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Affiliation(s)
- Marc Noguera
- Departament de Química, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain
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43
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Vázquez MV, Martínez A. Theoretical Study of Cytosine−Al, Cytosine−Cu and Cytosine−Ag (Neutral, Anionic and Cationic). J Phys Chem A 2008; 112:1033-9. [DOI: 10.1021/jp709813f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco-Vinicio Vázquez
- Instituto de Investigaciones en Materiales. Universidad Nacional Autónoma de México, Circuito Exterior Sin Número, Ciudad Universitaria, Apdo. Postal 70-360, México D. F., 04510, México
| | - Ana Martínez
- Instituto de Investigaciones en Materiales. Universidad Nacional Autónoma de México, Circuito Exterior Sin Número, Ciudad Universitaria, Apdo. Postal 70-360, México D. F., 04510, México
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44
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Trujillo C, Lamsabhi AM, Mó O, Yáñez M. The importance of the oxidative character of doubly charged metal cations in binding neutral bases. [Urea-M]2+ and [thiourea-M]2+ (M = Mg, Ca, Cu) complexes. Phys Chem Chem Phys 2008; 10:3229-35. [DOI: 10.1039/b802907e] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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45
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Trujillo C, Lamsabhi AM, Mó O, Yáñez M, Salpin JY. Interaction of Ca2+ with uracil and its thio derivatives in the gas phase. Org Biomol Chem 2008; 6:3695-702. [DOI: 10.1039/b810418b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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46
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Zhang Y, Huang K. The influence of the hydrated metal cations binding to adenine-N7 or adenine-N3 on the hydrogen bonding in adenine–thymine base pair: A comparative study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.07.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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47
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Mazzuca D, Russo N, Toscano M, Grand A. On the interaction of bare and hydrated aluminum ion with nucleic acid bases (U, T, C, A, G) and monophosphate nucleotides (UMP, dTMP, dCMP, dAMP, dGMP). J Phys Chem B 2007; 110:8815-24. [PMID: 16640440 DOI: 10.1021/jp055223w] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The B3LYP/6-311+G(2df,2p) density functional approach was used to study the interaction that aluminum trication, in the bare and hydrated forms, establishes with the nucleic acid bases and the corresponding monophosphate nucleotides. In this investigation, we determine equilibrium geometry of all possible complexes resulting from the attachment of the ion on the different binding sites selected on each ligand. The relative energies of complexes and metal ion affinities are also given. The most meaningful aspect was found to lie in the energetics of this interaction that underlines a very high affinity of aluminum ion for the examined biological systems.
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Affiliation(s)
- Donatella Mazzuca
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy
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48
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Hu X, Li H, Zhang L, Han S. Tautomerism of Uracil and 5-Bromouracil in a Microcosmic Environment with Water and Metal Ions. What Roles Do Metal Ions Play? J Phys Chem B 2007; 111:9347-54. [PMID: 17625822 DOI: 10.1021/jp0709454] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The base tautomerization processes of uracil/5-bromouracil were investigated in a microcosmic environment with both H2O and Na+ (W-M environment). It was found that uracil was more stable in the W-M environment than in the microcosmic environment with only water, which suggested that the metal ions and water work cooperated to maintain the classical nucleic acid bases. However, 5-bromouracil, a chemical mutagen, was found to be less stable than uracil in the W-M environment. Why the 5-bromouracil is easier to tautomerize and therefore induce gene mutation was explained to some extent. Further research revealed that the water molecule would assist the tautomerization in the W-M environment. However, the metal ions in different regions play absolutely opposite roles: in one region, the metal ions can prevent the base from tautomerizing, whereas in another region, the metal ion can assist the tautomerization process. Furthermore, from the viewpoint of ionization of the base, it seems BrU has a stronger tendency to lose the proton at N3, which is an intrinsic consequence of the bromine atom and is not affected by the metal cation.
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Affiliation(s)
- Xingbang Hu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
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49
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On the interactions of hydrated metal cations (Mg2+, Mn2+, Ni2+, Zn2+) with guanine–cytosine Watson–Crick and guanine–guanine reverse-Hoogsteen DNA base pairs. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.02.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Zhang RB, Eriksson LA. Effects of OH Radical Addition on Proton Transfer in the Guanine−Cytosine Base Pair. J Phys Chem B 2007; 111:6571-6. [PMID: 17506547 DOI: 10.1021/jp071772l] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Double proton transfer (PT) reactions in guanine-cytosine OH radical adducts are studied by the hybrid density functional B3LYP approach. Concerted and stepwise proton-transfer processes are explored between N1(H) on guanine (G) and N3 on cytosine (C), and between N4(H) on C and O6 on G. All systems except GC6OH display a concerted mechanism. 8OHGC has the highest dissociation energy and is 1.2 kcal/mol more stable than the nonradical GC base pair. The origin of the interactions are investigated through the estimation of intrinsic acid-basic properties of the *OH-X monomer (X = G or C). Solvent effects play a significant role in reducing the dissociation energy. The reactions including *OH-C adducts have significantly lower PT barriers than both the nonradical GC pair and the *OH-G adducts. All reactions are endothermic, with the GC6OH --> GC6OHPT reaction has the lowest reaction energy (4.6 kcal/mol). In accordance with earlier results, the estimated NBO charges show that the G moiety carries a slight negative charge (and C a corresponding positive one) in each adduct. The formation of a partial ion pair may be a potential factor leading to the PT reactions being thermodynamically unfavored.
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Affiliation(s)
- Ru bo Zhang
- The Institute for Chemical Physics and School of Science, Beijing Institute of Technology, Beijing 100081, China
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