1
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Togo T, Tram L, Denton LG, ElHilali-Pollard X, Gu J, Jiang J, Liu C, Zhao Y, Zhao Y, Zheng Y, Zheng Y, Yang J, Fan P, Arkin MR, Härmä H, Sun D, Canan SS, Wheeler SE, Renslo AR. Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6. J Med Chem 2023; 66:9784-9796. [PMID: 37406165 PMCID: PMC10388292 DOI: 10.1021/acs.jmedchem.3c00590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Indexed: 07/07/2023]
Abstract
Heteroaromatic stacking interactions are important in drug binding, supramolecular chemistry, and materials science, making protein-ligand model systems of these interactions of considerable interest. Here we studied 30 congeneric ligands that each present a distinct heteroarene for stacking between tyrosine residues at the dimer interface of procaspase-6. Complex X-ray crystal structures of 10 analogs showed that stacking geometries were well conserved, while high-accuracy computations showed that heteroarene stacking energy was well correlated with predicted overall ligand binding energies. Empirically determined KD values in this system thus provide a useful measure of heteroarene stacking with tyrosine. Stacking energies are discussed in the context of torsional strain, the number and positioning of heteroatoms, tautomeric state, and coaxial orientation of heteroarene in the stack. Overall, this study provides an extensive data set of empirical and high-level computed binding energies in a versatile new protein-ligand system amenable to studies of other intermolecular interactions.
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Affiliation(s)
- Takaya Togo
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Linh Tram
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Laura G. Denton
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Xochina ElHilali-Pollard
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Jun Gu
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Jinglei Jiang
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Chenglei Liu
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yan Zhao
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yanlong Zhao
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yinzhe Zheng
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yunping Zheng
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Jingjing Yang
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Panpan Fan
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Harri Härmä
- Department
of Chemistry, University of Turku, 20500 Turku, Finland
| | - Deqian Sun
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Stacie S. Canan
- Departments of Chemistry
and Structural Biology, Elgia Therapeutics, La Jolla, California 92037, United States
| | - Steven E. Wheeler
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Adam R. Renslo
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
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2
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Pyo K, Matus MF, Hulkko E, Myllyperkiö P, Malola S, Kumpulainen T, Häkkinen H, Pettersson M. Atomistic View of the Energy Transfer in a Fluorophore-Functionalized Gold Nanocluster. J Am Chem Soc 2023. [PMID: 37377151 DOI: 10.1021/jacs.3c02292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Understanding the dynamics of Förster resonance energy transfer (FRET) in fluorophore-functionalized nanomaterials is critical for developing and utilizing such materials in biomedical imaging and optical sensing applications. However, structural dynamics of noncovalently bound systems have a significant effect on the FRET properties affecting their applications in solutions. Here, we study the dynamics of the FRET in atomistic detail by disclosing the structural dynamics of the noncovalently bound azadioxotriangulenium dye (KU) and atomically precise gold nanocluster (Au25(p-MBA)18, p-MBA = para-mercaptobenzoic acid) with a combination of experimental and computational methods. Two distinct subpopulations involved in the energy transfer process between the KU dye and the Au25(p-MBA)18 nanoclusters were resolved by time-resolved fluorescence experiments. Molecular dynamics simulations revealed that KU is bound to the surface of Au25(p-MBA)18 by interacting with the p-MBA ligands as a monomer and as a π-π stacked dimer where the center-to-center distance of the monomers to Au25(p-MBA)18 is separated by ∼0.2 nm, thus explaining the experimental observations. The ratio of the observed energy transfer rates was in reasonably good agreement with the well-known 1/R6 distance dependence for FRET. This work discloses the structural dynamics of the noncovalently bound nanocluster-based system in water solution, providing new insight into the dynamics and energy transfer mechanism of the fluorophore-functionalized gold nanocluster at an atomistic level.
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Affiliation(s)
- Kyunglim Pyo
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, Jyväskylä FI-40014, Finland
| | - María Francisca Matus
- Nanoscience Center, Department of Physics, P.O. Box 35, University of Jyväskylä, Jyväskylä FI-40014, Finland
| | - Eero Hulkko
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, Jyväskylä FI-40014, Finland
- Nanoscience Center, Department of Biological and Environmental Sciences, P.O. Box 35, FI-40014, University of Jyväskylä, Jyväskylä FI-40014, Finland
| | - Pasi Myllyperkiö
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, Jyväskylä FI-40014, Finland
| | - Sami Malola
- Nanoscience Center, Department of Physics, P.O. Box 35, University of Jyväskylä, Jyväskylä FI-40014, Finland
| | - Tatu Kumpulainen
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, Jyväskylä FI-40014, Finland
| | - Hannu Häkkinen
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, Jyväskylä FI-40014, Finland
- Nanoscience Center, Department of Physics, P.O. Box 35, University of Jyväskylä, Jyväskylä FI-40014, Finland
| | - Mika Pettersson
- Nanoscience Center, Department of Chemistry, P.O. Box 35, University of Jyväskylä, Jyväskylä FI-40014, Finland
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3
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Bootsma AN, Doney AC, Wheeler SE. Predicting the Strength of Stacking Interactions between Heterocycles and Aromatic Amino Acid Side Chains. J Am Chem Soc 2019; 141:11027-11035. [DOI: 10.1021/jacs.9b00936] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Andrea N. Bootsma
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Analise C. Doney
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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4
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An Y, Doney AC, Andrade RB, Wheeler SE. Stacking Interactions between 9-Methyladenine and Heterocycles Commonly Found in Pharmaceuticals. J Chem Inf Model 2016; 56:906-14. [DOI: 10.1021/acs.jcim.5b00651] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yi An
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Analise C. Doney
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Rodrigo B. Andrade
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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5
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Semenov VE, Krylova ES, Galyametdinova IV, Chernova AV, Kharlamov SV, Latypov SK, Reznik VS. Synthesis and reactivity of acyclic and macrocyclic uracils bridged with five-membered heterocycles. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.07.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Mishra BK, Arey JS, Sathyamurthy N. Stacking and Spreading Interaction in N-Heteroaromatic Systems. J Phys Chem A 2010; 114:9606-16. [DOI: 10.1021/jp908941u] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brijesh Kumar Mishra
- Environmental Chemistry Modeling Laboratory, EPFL, 1015 Lausanne, Switzerland, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India, and Indian Institute of Science Education and Research Mohali, MGSIPAP Complex, Sector 26 Chandigarh 160019, India
| | - J. Samuel Arey
- Environmental Chemistry Modeling Laboratory, EPFL, 1015 Lausanne, Switzerland, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India, and Indian Institute of Science Education and Research Mohali, MGSIPAP Complex, Sector 26 Chandigarh 160019, India
| | - N. Sathyamurthy
- Environmental Chemistry Modeling Laboratory, EPFL, 1015 Lausanne, Switzerland, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India, and Indian Institute of Science Education and Research Mohali, MGSIPAP Complex, Sector 26 Chandigarh 160019, India
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7
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Alfonso I, Bru M, Burguete MI, García-Verdugo E, Luis S. Structural Diversity in the Self-Assembly of Pseudopeptidic Macrocycles. Chemistry 2010; 16:1246-55. [DOI: 10.1002/chem.200902196] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Studies on arene interactions in flexible pyrazolo[3,4-d]pyrimidine core based symmetrical ‘propylene/Leonard linker’ models: X-ray crystallographic evidence for disappearance of intramolecular stacking due to presence of chloro- or cyano-groups in place of methylsulfanyl or alkoxy substituents. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2008.12.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Hohenstein EG, Sherrill CD. Effects of heteroatoms on aromatic pi-pi interactions: benzene-pyridine and pyridine dimer. J Phys Chem A 2009; 113:878-86. [PMID: 19132847 DOI: 10.1021/jp809062x] [Citation(s) in RCA: 250] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Heteroatoms are found in many noncovalent complexes which are of biological importance. The effect of heteroatoms on pi-pi interactions is assessed via highly accurate quantum chemical computations for the two simplest cases of interactions between aromatic molecules containing heteroatoms, namely, benzene-pyridine and pyridine dimer. Benchmark quality estimated coupled-cluster through perturbative triples [CCSD(T)] binding energies are computed near the complete basis set limit. Comparisons to the benzene dimer are made to determine the contributions from heteroatoms. The presence of a heteroatom reduces the spatial extent of the pi-electron cloud and polarizability of pyridine as compared to benzene. As a result, the magnitude of the dispersion, exchange, and induction interactions in benzene-pyridine and pyridine dimer is generally reduced as compared to those for the benzene dimer. Benzene-pyridine and pyridine dimer bind more strongly than the benzene dimer in several configurations, and in contrast to the benzene dimer, parallel-displaced configurations can be significantly preferred over T-shaped configurations. Hydrogens para to a heteroatom are more effective "pi-hydrogen bond" donors, but aromatic rings with heteroatoms are worse "pi-hydrogen bond" acceptors.
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Affiliation(s)
- Edward G Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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10
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Hayashi N, Higuchi H, Ninomiya K. X/π Interactions in Aromatic Heterocycles: Basic Principles and Recent Advances. TOPICS IN HETEROCYCLIC CHEMISTRY 2009. [DOI: 10.1007/7081_2008_15] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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11
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García B, Ibeas S, Ruiz R, Leal JM, Biver T, Boggioni A, Secco F, Venturini M. Solvent Effects on the Thermodynamics and Kinetics of Coralyne Self-Aggregation. J Phys Chem B 2008; 113:188-96. [DOI: 10.1021/jp807894a] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Begoña García
- Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Saturnino Ibeas
- Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Rebeca Ruiz
- Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - José M. Leal
- Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Tarita Biver
- Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Alessia Boggioni
- Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Fernando Secco
- Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Marcella Venturini
- Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain, and Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
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12
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Poudel PP, Chen J, Cammers A. Intramolecular π-Stacking in Isostructural Conformational Probes Depends Strongly on Charge Separation, a Proton NMR Study. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800663] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Healion DM, Schweigert IV, Mukamel S. Probing Multiple Core−Hole Interactions in the Nitrogen K-Edge of DNA Base Pairs by Multidimensional Attosecond X-ray Spectroscopy. A Simulation Study. J Phys Chem A 2008; 112:11449-61. [DOI: 10.1021/jp803824a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Daniel M. Healion
- Department of Chemistry, University of California Irvine, 456 Rowland Hall, Irvine, California 92697, and Department of Chemistry, University of California Irvine, 1102 Natural Sciences II, Irvine, California 92697,
| | - Igor V. Schweigert
- Department of Chemistry, University of California Irvine, 456 Rowland Hall, Irvine, California 92697, and Department of Chemistry, University of California Irvine, 1102 Natural Sciences II, Irvine, California 92697,
| | - Shaul Mukamel
- Department of Chemistry, University of California Irvine, 456 Rowland Hall, Irvine, California 92697, and Department of Chemistry, University of California Irvine, 1102 Natural Sciences II, Irvine, California 92697,
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14
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Copeland KL, Anderson JA, Farley AR, Cox JR, Tschumper GS. Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations. J Phys Chem B 2008; 112:14291-5. [PMID: 18922031 DOI: 10.1021/jp805528v] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.
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Affiliation(s)
- Kari L Copeland
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, USA
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15
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Adhikary A, Kumar A, Khanduri D, Sevilla MD. Effect of base stacking on the acid-base properties of the adenine cation radical [A*+] in solution: ESR and DFT studies. J Am Chem Soc 2008; 130:10282-92. [PMID: 18611019 PMCID: PMC4590776 DOI: 10.1021/ja802122s] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this study, the acid-base properties of the adenine cation radical are investigated by means of experiment and theory. Adenine cation radical (A*(+)) is produced by one-electron oxidation of dAdo and of the stacked DNA-oligomer (dA)6 by Cl2*(-) in aqueous glass (7.5 M LiCl in H2O and in D2O) and investigated by ESR spectroscopy. Theoretical calculations and deuterium substitution at C8-H and N6-H in dAdo aid in our assignments of structure. We find the pKa value of A*(+) in this system to be ca. 8 at 150 K in seeming contradiction to the accepted value of < or = 1 at ambient temperature. However, upon thermal annealing to > or = 160 K, complete deprotonation of A*(+) occurs in dAdo in these glassy systems even at pH ca. 3. A*(+) found in (dA)6 at 150 K also deprotonates on thermal annealing. The stability of A*(+) at 150 K in these systems is attributed to charge delocalization between stacked bases. Theoretical calculations at various levels (DFT B3LYP/6-31G*, MPWB95, and HF-MP2) predict binding energies for the adenine stacked dimer cation radical of 12 to 16 kcal/mol. Further DFT B3LYP/6-31G* calculations predict that, in aqueous solution, monomeric A*(+) should deprotonate spontaneously (a predicted pKa of ca. -0.3 for A*(+)). However, the charge resonance stabilized dimer AA*(+) is predicted to result in a significant barrier to deprotonation and a calculated pKa of ca. 7 for the AA*(+) dimer which is 7 pH units higher than the monomer. These theoretical and experimental results suggest that A*(+) isolated in solution and A*(+) in adenine stacks have highly differing acid-base properties resulting from the stabilization induced by hole delocalization within adenine stacks.
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Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
| | - Deepti Khanduri
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
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16
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Langner KM, Sokalski WA, Leszczynski J. Intriguing relations of interaction energy components in stacked nucleic acids. J Chem Phys 2007; 127:111102. [PMID: 17887817 DOI: 10.1063/1.2786983] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Major components of the interaction energy that define several approximate levels starting from second order Möller-Plesset theory were studied for 58 stacked nucleic acid dimers. They included typical B-DNA and A-DNA structures, and selected published geometries. A survey of the various terms yields an unexpected correlation between the Pauli exchange and dispersion or correlation terms, which holds for each class of similar planar geometries and for various basis sets. The geometries that exhibit these correlations span a specific range of molecular overlaps when compared to a model benzene-pyridine stacked dimer. Also, the relationship between electrostatic interactions and MP2 stabilization energies reported earlier is confirmed and a prediction interval of practical relevance is estimated.
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Affiliation(s)
- Karol M Langner
- Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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