101
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Tian B, Strid Å, Eriksson LA. Catalytic Roles of Active-Site Residues in 2-Methyl-3-hydroxypyridine-5-carboxylic Acid Oxygenase: An ONIOM/DFT Study. J Phys Chem B 2011; 115:1918-26. [DOI: 10.1021/jp111525p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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102
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Erdtman E, Bushnell EA, Gauld JW, Eriksson LA. Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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103
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Wu M, Eriksson LA. Absorption spectra of riboflavin--a difficult case for computational chemistry. J Phys Chem A 2011; 114:10234-42. [PMID: 20718485 DOI: 10.1021/jp104127r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computing accurate absorption spectra of riboflavin (RBF) has proven a difficult task for computational chemistry. Time-dependent density functional theory have herein been employed using a wide range of recent range-separated and hybrid meta functionals to investigate ultraviolet and visible spectra of RBF to determine if any progress has been made through recent developments. It is concluded that B3LYP and PBE0 perform the best throughout the entire test set. However, since all methods deviate from experimental results by at least 40 nm when computing the spectra in vacuum, two approaches to describe aqueous solution are implemented together with the MPWB1K, B3LYP, and PBE0 functionals: implicitly using integral equation formulation of the polarized continuum model (minor improvement) and explicitly through molecular dynamics (MD) simulations of the molecule embedded in a water cluster whereafter snapshots of RBF-water clusters are extracted and time-dependent density functional theory calculations performed. The resulting averaged spectra from the MD-simulated clusters show a constant blue-shift for all peaks by ∼20 nm compared to experimental data at the TD-B3LYP/6-31+G(d,p) level.
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104
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Eriksson ESE, Eriksson LA. The Influence of Cholesterol on the Properties and Permeability of Hypericin Derivatives in Lipid Membranes. J Chem Theory Comput 2011; 7:560-74. [DOI: 10.1021/ct100528u] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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105
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Eriksson ESE, Eriksson LA. Computational design of chlorin based photosensitizers with enhanced absorption properties. Phys Chem Chem Phys 2011; 13:11590-6. [DOI: 10.1039/c1cp20715f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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106
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dos Santos DJVA, Saenz-Méndez P, Eriksson LA, Guedes RC. Properties and behaviour of tetracyclic allopsoralen derivatives inside a DPPC lipid bilayer model. Phys Chem Chem Phys 2011; 13:10174-82. [DOI: 10.1039/c0cp02245d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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107
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Yang ZB, Zhang RB, Eriksson LA. A triplet mechanism for the formation of thymine–thymine (6-4) dimers in UV-irradiated DNA. Phys Chem Chem Phys 2011; 13:8961-6. [DOI: 10.1039/c0cp02830d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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108
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Eriksson ESE, Eriksson LA. Predictive power of long-range corrected functionals on the spectroscopic properties of tetrapyrrole derivatives for photodynamic therapy. Phys Chem Chem Phys 2011; 13:7207-17. [DOI: 10.1039/c0cp02792h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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109
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Gao L, Tu Y, Wegman P, Wingren S, Eriksson LA. Conformational Enantiomerization and Estrogen Receptor α Binding of Anti-Cancer Drug Tamoxifen and Its Derivatives. J Chem Inf Model 2010; 51:306-14. [DOI: 10.1021/ci100401t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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110
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Jarikote DV, Li W, Jiang T, Eriksson LA, Murphy PV. Towards echinomycin mimetics by grafting quinoxaline residues on glycophane scaffolds. Bioorg Med Chem 2010; 19:826-35. [PMID: 21195622 DOI: 10.1016/j.bmc.2010.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 11/23/2010] [Accepted: 12/03/2010] [Indexed: 11/25/2022]
Abstract
Echinomycin is a natural depsipeptide, which is a bisintercalator, inserting quinoxaline units preferentially adjacent to CG base pairs of DNA. Herein the design and synthesis of echinomycin mimetics based on grafting of two quinoxaline residues onto a macrocyclic scaffold (glycophane) is addressed. Binding of the compounds to calf-thymus DNA was studied using UV-vis and steady state fluorescence spectroscopy, as well as thermal denaturation. An interesting observation was enhancement of fluorescence emission for the peptidomimetics on binding to DNA, which contrasted with observations for echinomycin. Molecular dynamics simulations were exploited to explore in more detail if bis-intercalation to DNA was possible for one of the glycophanes. Bis-intercalating echinomycin complexes with DNA were found to be stable during 20ns simulations at 298K. However, the MD simulations of a glycophane complexed with a DNA octamer displayed very different behaviour to echinomycin and its quinoxaline units were found to rapidly migrate out from the intercalation site. Release of bis-intercalation strain occurred with only one of the quinoxaline chromophores remaining intercalated throughout the simulation. The distance between the quinoxaline residues in the glycophane at the end of the MD simulation was 7.3-7.5Å, whereas in echinomycin, the distance between the residues was ∼11Å, suggesting that longer glycophane scaffolds would be required to generate bis-intercalating echinomycin mimetics.
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111
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Erdtman E, Bushnell EAC, Gauld JW, Eriksson LA. Computational Insights into the Mechanism of Porphobilinogen Synthase. J Phys Chem B 2010; 114:16860-70. [DOI: 10.1021/jp103590d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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112
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Bushnell EAC, Erdtman E, Llano J, Eriksson LA, Gauld JW. The first branching point in porphyrin biosynthesis: A systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase. J Comput Chem 2010; 32:822-34. [DOI: 10.1002/jcc.21661] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 08/07/2010] [Indexed: 11/06/2022]
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113
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Wang R, Zhang RB, Eriksson LA. The Fate of H Atom Adducts to 3′-Uridine Monophosphate. J Phys Chem B 2010; 114:9617-21. [DOI: 10.1021/jp100116w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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114
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Tian B, Eriksson ESE, Eriksson LA. Can Range-Separated and Hybrid DFT Functionals Predict Low-Lying Excitations? A Tookad Case Study. J Chem Theory Comput 2010; 6:2086-94. [DOI: 10.1021/ct100148h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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115
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Tian B, Tu Y, Strid A, Eriksson LA. Hydroxylation and ring-opening mechanism of an unusual flavoprotein monooxygenase, 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase: a theoretical study. Chemistry 2010; 16:2557-66. [PMID: 20066695 DOI: 10.1002/chem.200902253] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hybrid meta-GGA density functional theory (the MPWB1K functional) was used to study the hydroxylation and ring-opening mechanism of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO). This enzyme catalyses the conversion of 2-methyl-3-hydroxypyridine-5-carboxylic acid (MHPC) to alpha-(N-acetylaminomethylene)succinic acid (AAMS), which is the essential ring-opening step in the bacterial degradation of vitamin B(6). MHPCO belongs to the flavin-containing aromatic hydroxylases family. However, MHPCO is capable of catalysing a subsequent aromatic ring-cleavage reaction to give acyclic products rather than hydroxylated aromatic ones. Our calculations show that the re-aromatisation of the hydroxylated intermediate occurs spontaneously in aqueous solution; this implies that the ring-opening process occurs inside the enzyme's active site, in which limited water is available. The instability of the hydroxylated intermediate of MHPCO is the main reason why acyclic products are formed. Previously proposed mechanisms for the ring-opening step were studied, and were shown to be less likely to occur (DeltaDeltaG(not equal298)>35 kcal mol(-1)). Two new pathways with reasonable barrier heights (DeltaDeltaG(not equal 298)<15 kcal mol(-1)) are reported herein, which are in accordance with all experimental information present to date.
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116
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Zhang RB, Eriksson LA. Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group. Phys Chem Chem Phys 2010; 12:3690-7. [PMID: 20358065 DOI: 10.1039/b921646d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2'OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3'-endo conformation of ribose.
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117
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MacIntyre MM, Martell JM, Eriksson LA. DFT study of five naphthalimide derivatives: Structures and redox properties. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.11.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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118
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Labet V, Morell C, Douki T, Cadet J, Eriksson LA, Grand A. Hydrolytic Deamination of 5,6-Dihydrocytosine in a Protic Medium: A Theoretical Study. J Phys Chem A 2010; 114:1826-34. [DOI: 10.1021/jp9049044] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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119
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Eriksson ESE, Santos DJVAD, Guedes RC, Eriksson LA. Properties and Permeability of Hypericin and Brominated Hypericin in Lipid Membranes. J Chem Theory Comput 2009; 5:3139-49. [DOI: 10.1021/ct9002702] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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120
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Saenz Méndez P, Eriksson LA, Ventura ON. Theoretical study of the structure of neutral, radical and anionic monoperoxo carbonic acid. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.07.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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121
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Matxain JM, Padro D, Ristilä M, Strid A, Eriksson LA. Evidence of high *OH radical quenching efficiency by vitamin B6. J Phys Chem B 2009; 113:9629-32. [PMID: 19558175 DOI: 10.1021/jp903023c] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of the utmost importance in the living cell. The antioxidative properties of pyridoxine (vitamin B6) have recently been discovered. Previous theoretical calculations have shown a high reactivity of pyridoxine toward hydroxyl radicals, where the latter preferably abstract H from either carbon of the two methanol substituents (C8 or C9). In this study, we have explored the reactivity of pyridoxine toward further hydroxyl radicals, considering as the first step the H abstraction from either C8 or C9, also including addition reactions and cyclization. Many of the reactions display similar DeltaG, and hence, the quenching of hydroxyl radicals by pyridoxine may undergo different pathways leading to a mix of products. In addition, we observe that pyridoxine, under high hydroxyl radical concentrations, may scavenge up to eight radicals, supporting its observed high antioxidant activity.
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122
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Musa KAK, Eriksson LA. Theoretical Assessment of Norfloxacin Redox and Photochemistry. J Phys Chem A 2009; 113:10803-10. [DOI: 10.1021/jp904671s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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123
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Karlsson BCG, O’Mahony J, Karlsson JG, Bengtsson H, Eriksson LA, Nicholls IA. Structure and Dynamics of Monomer−Template Complexation: An Explanation for Molecularly Imprinted Polymer Recognition Site Heterogeneity. J Am Chem Soc 2009; 131:13297-304. [DOI: 10.1021/ja902087t] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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124
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Musa KAK, Eriksson LA. Photodegradation Mechanism of Nonsteroidal Anti-Inflammatory Drugs Containing Thiophene Moieties: Suprofen and Tiaprofenic Acid. J Phys Chem B 2009; 113:11306-13. [DOI: 10.1021/jp904171p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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125
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Zhang RB, Eriksson LA. Distinct hydroxy-radical-induced damage of 3'-uridine monophosphate in RNA: a theoretical study. Chemistry 2009; 15:2394-402. [PMID: 19156657 DOI: 10.1002/chem.200801654] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
RNA strand scission and base release in 3'-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. The barriers of (C2'-)H2'(a) abstraction by the C6 radical site range from 11.2 to 20.0 kcal mol(-1) in the gas phase and 14.1 to 21.0 kcal mol(-1) in aqueous solution, indicating that the local surrounding governs the hydrogen-abstraction reaction in a stereoselective way. The calculated N1-C1' (N1-glycosidic bond) and beta-phosphate bond strengths show that homolytic and heterolytic bond-breaking processes are largely favored in each case, respectively. The barrier for beta-phosphate bond rupture is approximately 3.2-4.0 kcal mol(-1) and is preferred by 8-12 kcal mol(-1) over N1-glycosidic bond cleavage in both the gas phase and solution. The beta-phosphate bond-rupture reactions are exothermal in the gas phase and solution, whereas N1-C1' bond-rupture reactions require both solvation and thermal corrections at 298 K to be energetically favored. The presence of the ribose 2'-OH group and its formation of low-barrier hydrogen bonds with oxygen atoms of the 3'-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions.
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126
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Schyman P, Eriksson LA, Laaksonen A. Hydrogen Abstraction from Deoxyribose by a Neighboring 3′-Uracil Peroxyl Radical. J Phys Chem B 2009; 113:6574-8. [DOI: 10.1021/jp9007569] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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127
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Erdtman E, dos Santos DJ, Löfgren L, Eriksson LA. Erratum to ‘Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer’ [Chem. Phys. Lett. 463 (2008) 178]. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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128
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Labet V, Morell C, Cadet J, Eriksson LA, Grand A. Hydrolytic Deamination of 5-Methylcytosine in Protic Medium—A Theoretical Study. J Phys Chem A 2009; 113:2524-33. [DOI: 10.1021/jp808902j] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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129
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Labet V, Grand A, Morell C, Cadet J, Eriksson LA. Mechanism of nitric oxide induced deamination of cytosine. Phys Chem Chem Phys 2009; 11:2379-86. [DOI: 10.1039/b818669c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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130
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Musa KAK, Eriksson LA. Photodegradation mechanism of the common non-steroid anti-inflammatory drug diclofenac and its carbazole photoproduct. Phys Chem Chem Phys 2009; 11:4601-10. [DOI: 10.1039/b900144a] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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131
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Omar S, Eriksson LA. Computational study of khellin excited states and photobinding to DNA. Photochem Photobiol Sci 2009; 8:1179-86. [DOI: 10.1039/b905147c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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132
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Musa KAK, Eriksson LA. Theoretical study of the phototoxicity of naproxen and the active form of nabumetone. J Phys Chem A 2008; 112:10921-30. [PMID: 18834087 DOI: 10.1021/jp805614y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory using the hybrid functional B3LYP has been employed in order to study the mechanisms of photoinduced decomposition of the closely related nonsteroidal anti-inflammatory drugs naproxen (NP) and 6-methoxy-2-naphthylacetic acid (MNAA; the active form of nabumetone). The photochemical properties and computed energies of various species obtained in this study show that both drugs dominate in their deprotonated forms at physiological pH. The deprotonated acids are unable to decarboxylate from their excited singlets; instead, they decarboxylate from their first excited triplet states with high efficiency, overcoming energy barriers less than 3 and 1 kcal/mol for MNAA and NP, respectively. The ultraviolet and visible spectra of the neutral, deprotonated, and decarboxylated moieties of MNAA and NP are more-or-less similar but with higher probabilites (oscillator strength) for the latter. This fact, as well as the higher reactivity of NP, is explained in terms of the electron-donating effect of the additional methyl group present in NP. Singlet oxygen, superoxide radical anion, and corresponding peroxyl radical species are expected to be formed in different steps throughout the proposed photodegradation pathways of both drugs, which give rise to their effects on biomolecules, for example, lipid peroxidation.
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133
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Labet V, Grand A, Cadet J, Eriksson LA. Deamination of the radical cation of the base moiety of 2'-deoxycytidine: a theoretical study. Chemphyschem 2008; 9:1195-203. [PMID: 18438773 DOI: 10.1002/cphc.200800154] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Five pathways leading to the deamination of cytosine (to uracil) after formation of its deprotonated radical cation are investigated in the gas phase, at the UB3LYP/6-311G(d,p) level of theory, and in bulk aqueous solvent. The most favorable pathway involves hydrogen-atom transfer from a water molecule to the N3 nitrogen of the deprotonated radical cation, followed by addition of the resulting hydroxyl radical to the C4 carbon of the cytosine derivative. Following protonation of the amino group (N4), the C4--N4 bond is broken with elimination of the NH3+(. ) and formation of a protonated uracil. The rate-determining step of this mechanism is hydrogen-atom transfer from a water molecule to the cytosine derivative. The associated free energy barrier is 70.2 kJ mol(-1).
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134
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Erdtman E, dos Santos DJ, Löfgren L, Eriksson LA. Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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135
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Zhang RB, Zhang K, Eriksson LA. Theoretical studies of damage to 3'-uridine monophosphate induced by electron attachment. Chemistry 2008; 14:2850-6. [PMID: 18213558 DOI: 10.1002/chem.200701324] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3'-O(P) bond ruptures of 3'-UMP (UMP=uridine monophosphate) and the protonated form 3'-UMPH with -1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3 LYP together with the 6-31+G(d,p) basis set. The glycosidic bond breakage reactions of the 3'UMP and 3'UMPH electron adducts are exothermic in both cases, with barrier heights of 19-20 kcal mol(-1) upon inclusion of bulk solvation. The effects of the charge state on the phosphate group are marginal, but the C2'-OH group destabilizes the transition structure of glycosidic bond rupture of 3'-UMPH in the gas phase by approximately 5.0 kcal mol(-1). This is in contrast with the C3'-O(P) bond ruptures induced by LEE in which the charge state on the phosphate influences the barrier heights and reaction energies considerably. The barrier towards C3'-O(P) bond dissociation in the 3'UMP electron adduct is higher in the gas phase than the one corresponding to glycosidic bond rupture and is dramatically influenced by the C2'-OH group and bulk salvation, which decreases the barrier to 14.7 kcal mol(-1). For the C3'-O(P) bond rupture of the 3'UMPH electron adduct, the reaction is exothermic and the barrier is even lower, 8.2 kcal mol(-1), which is in agreement with recent results for 3'-dTMPH and 5'-dTMPH (dTMPH=deoxythymidine monophosphate). Both the Mulliken atomic charges and unpaired-spin distribution play significant roles in the reactions.
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136
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Schyman P, Eriksson LA, Zhang RB, Laaksonen A. Hydroxyl radical – Thymine adduct induced DNA damages. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.04.086] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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137
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Erdtman E, Eriksson LA. Theoretical Study of 5-Aminolevulinic Acid Tautomerization: A Novel Self-Catalyzed Mechanism. J Phys Chem A 2008; 112:4367-74. [DOI: 10.1021/jp7118197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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138
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Méndez PS, Guedes RC, dos Santos DJ, Eriksson LA. Theoretical prediction of binding modes and hot sequences for allopsoralen–DNA interaction. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.10.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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139
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140
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Grand A, Morell C, Labet V, Cadet J, Eriksson LA. *H atom and *OH radical reactions with 5-methylcytosine. J Phys Chem A 2007; 111:8968-72. [PMID: 17722896 DOI: 10.1021/jp0737799] [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: 11/29/2022]
Abstract
The reactions between either a hydrogen atom or a hydroxyl radical and 5-methylcytosine (5-MeCyt) are studied by using the hybrid kinetic energy meta-GGA functional MPW1B95. *H atom and *OH radical addition to positions C5 and C6 of 5-MeCyt, or *OH radical induced H-abstraction from the C5 methyl group, are explored. All systems are optimized in bulk solvent. The data presented show that the barriers to reaction are very low: ca. 7 kcal/mol for the *H atom additions and 1 kcal/mol for the reactions involving the *OH radical. Thermodynamically, the two C6 radical adducts and the *H-abstraction product are the most stable ones. The proton hyperfine coupling constants (HFCC), computed at the IEFPCM/MPW1B95/6-311++G(2d,2p) level, agree well with B3LYP results and available experimental and theoretical data on related thymine and cytosine radicals.
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141
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Zhang RB, Eriksson LA. A triplet mechanism for the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA. J Phys Chem B 2007; 110:7556-62. [PMID: 16599537 DOI: 10.1021/jp060196a] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction pathways for the photochemical formation of cyclobutane thymine dimers in DNA are explored using hybrid density functional theory techniques. It is concluded that the thymine-thymine [2 + 2] cycloaddition displays favorable energy barriers and reaction energies in both the triplet and the singlet excited states. The stepwise cycloaddition in the triplet excited state involves the initial formation of a diradical followed by ring closure via singlet-triplet interaction. The triplet mechanism is thus completely different from the concerted singlet state cycloaddition processes. The key geometric features and electron spin densities are also discussed. Bulk solvation has a major effect by reducing the barriers and increasing the diradical stabilities. The present results provide a rationale for the faster cycloreaction observed in the singlet excited states than in the triplet excited states.
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142
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Zhu C, Raber J, Eriksson LA. Hydrolysis process of the second generation platinum-based anticancer drug cis-amminedichlorocyclohexylamineplatinum(II). J Phys Chem B 2007; 109:12195-205. [PMID: 16852504 DOI: 10.1021/jp0518916] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrolysis process of the anticancer drug cis-amminedichlorocyclohexylamineplatinum(II) (JM118 or cis-[PtCl2(NH3)cyclohexylamine]) and the influence of solvent models therein have been studied using hybrid density functional theory (B3LYP). The aquation reactions leading to the activated drug forms a key step for the reaction with the target DNA. In this study, the stepwise hydrolysis, cis-[PtCl2(NH3)cyclohexylamine] + 2 H2O --> cis-[Pt(NH3)cyclohexylamine(OH2)2]2+ + 2 Cl- was explored, using three different models. Implicit solvent effects were incorporated through polarized continuum models. The stationary points on the potential energy surfaces for the first and second hydrolysis steps, proceeding via a general S(N)2 pathway, were fully optimized and characterized. It was found that the explicit solvent effects originating from the inclusion of extra water molecules into the system are significantly stronger than those arising from the bulk aqueous medium, especially for the second aquation step, emphasizing the use of appropriate models for these types of problems. In comparison with previous work on the parent compound cisplatin, a slower rate of hydrolysis is determined for the first (rate determining) reaction. The results furthermore imply that the doubly aquated form of JM118 will be the main DNA binding form of the drug. The results provide detailed energy profiles for the mechanism of hydrolysis of JM118, which may assist in understanding the reaction mechanism of the drug with the DNA target and in the design of novel Pt-containing anticancer drugs.
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143
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Sebastian ES, Matxain JM, Eriksson LA, Stote RH, Dejaegere A, Cossio FP, Lopez X. Metal Ion Dependent Adhesion Sites in Integrins: A Combined DFT and QMC Study on Mn2+. J Phys Chem B 2007; 111:9099-103. [PMID: 17608410 DOI: 10.1021/jp071065s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The theoretical study of relative energies of different spin states of Mn2+ has been carried out for the isolated cation and for structures in which the cation is coordinated to ligands that represent the first coordination shell in a protein environment that contains a metal ion dependent adhesion site (MIDAS, found in the ligand binding domain of protein LFA-1). The calculations determine whether the ligand field generated by a prototype protein environment affects the relative energies between high, intermediate, and low spin states. Geometry optimizations and vibrational frequency calculations were carried out at the B3LYP/SKBJ+* level of theory. Single point calculations were performed at the B3LYP/6-311++G(2df,2p) and diffusion monte carlo (DMC) levels for the refinement of the electronic energies. These calculations reveal important differences in the relative energies between high/low spin complexes obtained by B3LYP and DMC and show that although both DFT and DMC show similar trends, a higher level method such as DMC is necessary for a quantitative description of the interactions between Mn2+ and its natural ligands. (G)s of acetate-type ligand binding reactions were calculated that show that the higher the spin of the manganese complex, the lower the affinity for the ligand.
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144
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Mujika JI, Matxain JM, Eriksson LA, Lopez X. Resonance structures of the amide bond: the advantages of planarity. Chemistry 2007; 12:7215-24. [PMID: 16807968 DOI: 10.1002/chem.200600052] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Delocalization indexes based on magnitudes derived from electron-pair densities are demonstrated to be useful indicators of electron resonance in amides. These indexes, based on the integration of the two-electron density matrix over the atomic basins defined through the zero-flux condition, have been calculated for a series of amides at the B3LYP/6-31+G* level of theory. These quantities, which can be viewed as a measure of the sharing of electrons between atoms, behave in concordance with the traditional resonance model, even though they are integrated in Bader atomic basins. Thus, the use of these quantities overcomes contradictory results from analyses of atomic charges, yet keeps the theoretical appeal of using nonarbitrary atomic partitions and unambiguously defined functions such as densities and pair densities. Moreover, for a large data set consisting of 24 amides plus their corresponding rotational transition states, a linear relation was found between the rotational barrier for the amide and the delocalization index between the nitrogen and oxygen atoms, indicating that this parameter can be used as an ideal physical-chemical indicator of the electron resonance in amides.
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145
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Matxain JM, Ristilä M, Strid A, Eriksson LA. Theoretical Study of the Reaction of Vitamin B6 with1O2. Chemistry 2007; 13:4636-42. [PMID: 17348056 DOI: 10.1002/chem.200700002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Singlet oxygen is known to cause oxidative stress in cells, leading to severe damage (e.g., lipid peroxidation, membrane degradation, mutagenic alterations to DNA, protein misfunctionality). Recently, pyridoxine has been discovered to be capable of quenching singlet oxygen, however, the mechanism of this reaction remains essentially unknown. In this work, we have investigated four sets of reactions: 1) 1,3-addition to a double bond connected to a hydrogen-carrying group, resulting in the formation of allylic hydroperoxides; 2) [pi2+pi2] 1,2-cycloaddition to an isolated double bond, resulting in the formation of 1,2-peroxides; 3) 1,4-cycloaddition to a system containing at least two conjugated double bonds, resulting in the formation of the so-called 1,4-peroxides; 4) 1,4-addition to phenols and naphthols with the formation of hydroperoxide ketones. Thermodynamically, reaction 4 and the 6(9), 3(8), and 5(8) cases of reaction 1 are the most exergonic ones, with energies ranging from -16 to -18 kcal mol(-1). Furthermore, reaction 4 shows the lowest barrier through the reaction path, and is predicted to be the preferred mechanism for the pyridoxine + singlet-oxygen reaction, which is in agreement with previous experimental results.
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146
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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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147
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Tejero I, Gonzalez-Lafont A, Lluch JM, Eriksson LA. Theoretical Modeling of Hydroxyl-Radical-Induced Lipid Peroxidation Reactions. J Phys Chem B 2007; 111:5684-93. [PMID: 17472362 DOI: 10.1021/jp0650782] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The OH-radical-induced mechanism of lipid peroxidation, involving hydrogen abstraction followed by O2 addition, is explored using the kinetically corrected hybrid density functional MPWB1K in conjunction with the MG3S basis set and a polarized continuum model to mimic the membrane interior. Using a small nonadiene model of linoleic acid, it is found that hydrogen abstraction preferentially occurs at the mono-allylic methylene groups at the ends of the conjugated segment rather than at the central bis-allylic carbon, in disagreement with experimental data. Using a full linoleic acid, however, abstraction is correctly predicted to occur at the central carbon, giving a pentadienyl radical. The Gibbs free energy for abstraction at the central C11 is approximately 8 kcal/mol, compared to 9 kcal/mol at the end points (giving an allyl radical). Subsequent oxygen addition will occur at one of the terminal atoms of the pentadienyl radical fragment, giving a localized peroxy radical and a conjugated butadiene fragment, but is associated with rather high free energy barriers and low exergonicity at the CPCM-MPWB1K/MG3S level. The ZPE-corrected potential energy surfaces obtained without solvent effects, on the other hand, display considerably lower barriers and more exergonic reactions.
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148
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Durbeej B, Eriksson LA. On the Formation of Cyclobutane Pyrimidine Dimers in UV-irradiated DNA: Why are Thymines More Reactive?¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0780159otfocp2.0.co2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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149
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Musa KAK, Eriksson LA. Theoretical Assessment of Naphazoline Redoxchemistry and Photochemistry. J Phys Chem B 2007; 111:3977-81. [PMID: 17388561 DOI: 10.1021/jp070207f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The imidazoline derivative naphazoline (2-(1-naphtylmethyl)-2-imidazoline) is an alpha2-adrenergic agonist used as non-prescription eye and nasal preparations. Besides its functionality in generating vascoconstriction and decongestion in the patient, the toxicity, ROS generating capability, and recently also possible antioxidant capacity of the compound have been reported in the literature. In the current work the structural and electronic features of the drug are explored, using computational chemical tools. Electron affinities, ionization potentials, and excitation energies are reported, as well as charge and spin distributions of various forms of the drug. The difference in photochemical behavior between the protonated and unprotonated (basic) species is explained by the molecular orbital distributions, allowing for efficient excitation quenching in the basic structure but clear naphthalene to imidazolene charge transfer upon HOMO--> LUMO excitation in the protonated form, enabling larger intersystem crossing capability to the imidazole localized excited triplet and a resulting higher singlet oxygen quantum yield.
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150
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Abstract
UV-induced decarboxylation of the NSAID ketoprofen, followed by activation of molecular oxygen or formation of a decarboxylated peroxide adduct, is explored using computational quantum chemistry. The excited energy surfaces reveal that the neutral species will not decarboxylate, whereas the deprotonated acid decarboxylates spontaneously in the triplet state, and with an associated 3-5 kcal/mol barrier from several low-lying excited singlet states. The observed long lifetimes of the decarboxylated anion is explained in terms of the high stability of the triplet benzoyl ethyl species with protonated carbonylic oxygen, from which there is no obvious decay channel. Mechanisms for the generation of singlet oxygen and superoxide are discussed in detail. Addition of molecular oxygen to give the corresponding peroxyl radical capable of initiating propagating lipid peroxidation reactions is also explored. The computed data explains all features of the observed experimental observations made to date on the photodegradation of ketoprofen.
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