1
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Hinz DJ, Zhang L, Lee JK. Mass spectrometry in organic and bio-organic catalysis: Using thermochemical properties to lend insight into mechanism. MASS SPECTROMETRY REVIEWS 2022. [PMID: 35899315 DOI: 10.1002/mas.21797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this review, we discuss gas phase experimentation centered on the measurement of acidity and proton affinity of substrates that are useful for understanding catalytic mechanisms. The review is divided into two parts. The first covers examples of organocatalysis, while the second focuses on biological catalysis. The utility of gas phase acidity and basicity values for lending insight into mechanisms of catalysis is highlighted.
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Affiliation(s)
- Damon J Hinz
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Lanxin Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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2
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Zhang L, Hinz DJ, Kiruba GSM, Ding X, Lee JK. Gas‐phase experimental and computational studies of human hypoxanthine‐guanine phosphoribosyltransferase substrates: Intrinsic properties and biological implications. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lanxin Zhang
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey New Brunswick NJ USA
| | - Damon J. Hinz
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey New Brunswick NJ USA
| | | | - Xiao Ding
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey New Brunswick NJ USA
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey New Brunswick NJ USA
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3
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Krajewski AE, Lee JK. Nucleophilicity and Electrophilicity in the Gas Phase: Silane Hydricity. J Org Chem 2022; 87:1840-1849. [PMID: 35044778 DOI: 10.1021/acs.joc.1c02763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydricity is of great import as hydride transfer reactions are prominent in many processes, including organic synthesis, photoelectrocatalysis, and hydrogen activation. Herein, the kinetic hydricity of a series of silanes is examined in the gas phase. Most of these reactions have not heretofore been studied in vacuo and provide valuable data that can be compared to condensed-phase hydricity, to reveal the effects of solvent. Both experiments and computations are used to gain insight into mechanism and reactivity. In a broader sense, these studies also represent a first step toward systematically understanding nucleophilicity and electrophilicity in the absence of a solvent.
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Affiliation(s)
- Allison E Krajewski
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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4
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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5
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Krajewski AE, Lee JK. Gas-Phase Experimental and Computational Studies of 5-Halouracils: Intrinsic Properties and Biological Implications. J Org Chem 2021; 86:6361-6370. [PMID: 33891415 DOI: 10.1021/acs.joc.1c00183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gas-phase acidity and proton affinity (PA) of 5-halouracils (5-fluorouracil, 5-chlorouracil, 5-bromouracil, and 5-iodouracil) have been examined using both theoretical and experimental methods. This work represents a comprehensive study of the thermochemical properties of these nucleobases. Other than 5-fluorouracil acidity, the intrinsic acidity and PA of these halouracils have not been heretofore measured; these new experimental data provide a benchmark for the computational values. Furthermore, we examine these 5-halouracils in the context of the enzyme thymine DNA glycosylase (TDG), which is an enzyme that protects the genome by cleaving these substrates from DNA. Our gas-phase results are compared and contrasted to TDG excision rates to afford insights into the TDG mechanism.
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Affiliation(s)
- Allison E Krajewski
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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6
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Halder A, Kumar S, Valsson O, Reddy G. Mg 2+ Sensing by an RNA Fragment: Role of Mg 2+-Coordinated Water Molecules. J Chem Theory Comput 2020; 16:6702-6715. [PMID: 32941038 DOI: 10.1021/acs.jctc.0c00589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules selectively bind to specific metal ions to populate their functional active states, making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations, making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg2+, Ca2+, and K+) in the folding of a small RNA hairpin motif (5'-ucCAAAga-3') using unbiased all-atom molecular dynamics simulations. The advantage of studying this system is that it requires specific binding of a single metal ion to fold to its native state. We find that even for this small RNA, the folding free energy surface (FES) is multidimensional as different metal ions present in the solution can simultaneously facilitate folding. The FES shows that specific binding of a metal ion is indispensable for its folding. We further show that in addition to the negatively charged phosphate groups, the spatial organization of electronegative nucleobase atoms drives the site-specific binding of the metal ions. Even though the binding site cannot discriminate between different metal ions, RNA folds efficiently only in a Mg2+ solution. We show that the rigid network of Mg2+-coordinated water molecules facilitates the formation of important interactions in the transition state. The other metal ions such as K+ and Ca2+ cannot facilitate the formation of such interactions. These results allow us to hypothesize possible metal-sensing mechanisms in large metalloriboswitches and also provide useful insights into the design of appropriate collective variables for studying large RNA molecules using enhanced sampling methods.
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Affiliation(s)
- Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sunil Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Omar Valsson
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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7
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Chatterjee K, Dopfer O. Microhydration of protonated biomolecular building blocks: protonated pyrimidine. Phys Chem Chem Phys 2020; 22:13092-13107. [PMID: 32490447 DOI: 10.1039/d0cp02110e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protonation and hydration of biomolecules govern their structure, conformation, and function. Herein, we explore the microhydration structure in mass-selected protonated pyrimidine-water clusters (H+Pym-Wn, n = 1-4) by a combination of infrared photodissociation spectroscopy (IRPD) between 2450 and 3900 cm-1 and density functional theory (DFT) calculations at the dispersion-corrected B3LYP-D3/aug-cc-pVTZ level. We further present the IR spectrum of H+Pym-N2 to evaluate the effect of solvent polarity on the intrinsic molecular parameters of H+Pym. Our combined spectroscopic and computational approach unequivocally shows that protonation of Pym occurs at one of the two equivalent basic ring N atoms and that the ligands in H+Pym-L (L = N2 or W) preferentially form linear H-bonds to the resulting acidic NH group. Successive addition of water ligands results in the formation of a H-bonded solvent network which increasingly weakens the NH group. Despite substantial activation of the N-H bond upon microhydration, no intracluster proton transfer occurs up to n = 4 because of the balance of relative proton affinities of Pym and Wn and the involved solvation energies. Comparison to neutral Pym-Wn clusters reveals the drastic effects of protonation on microhydration with respect to both structure and interaction strength.
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Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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8
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Wang N, Lee JK. Gas-Phase and Ionic Liquid Experimental and Computational Studies of Imidazole Acidity and Carbon Dioxide Capture. J Org Chem 2019; 84:14593-14601. [PMID: 31647232 DOI: 10.1021/acs.joc.9b02193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The capture and storage of carbon dioxide are pressing environmental concerns. Nucleophilic capture by anions in ionic liquids, such as imidazolates, is a promising strategy. Herein, the gas-phase acidity of a series of imidazoles is examined both experimentally and computationally. The intrinsic acidity of these imidazoles has not heretofore been measured; these experimental data provide a benchmark for the computational values. The relationship between imidazole acidity and carbon dioxide capture is explored computationally, both in the gas phase and in ionic liquid. The improved understanding of imidazolate properties provided herein is important for the design and development of improved systems for carbon dioxide capture.
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Affiliation(s)
- Ning Wang
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08901 United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08901 United States
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9
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Xu J, Krajewski AE, Niu Y, Kiruba GSM, Lee JK. Kinetic hydricity of silane hydrides in the gas phase. Chem Sci 2019; 10:8002-8008. [PMID: 31853355 PMCID: PMC6837013 DOI: 10.1039/c9sc02118c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/09/2019] [Indexed: 12/01/2022] Open
Abstract
Gas-phase experimental and computational methods reveal unknown intrinsic hydricity/nucleophilicity and electrophilicity parameters.
Herein, gas phase studies of the kinetic hydricity of a series of silane hydrides are described. An understanding of hydricity is important as hydride reactions figure largely in many processes, including organic synthesis, photoelectrocatalysis, and hydrogen activation. We find that hydricity trends in the gas phase differ from those in solution, revealing the effect of solvent. Calculations and further experiments, including H/D studies, were used to delve into the reactivity and structure of the reactants. These studies also represent a first step toward systematically understanding nucleophilicity and electrophilicity in the absence of solvent.
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Affiliation(s)
- Jiahui Xu
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
| | - Allison E Krajewski
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
| | - Yijie Niu
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
| | - G S M Kiruba
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology , Rutgers The State University of New Jersey , New Brunswick , NJ 08901 , USA .
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10
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Fuchs E, Falschlunger C, Micura R, Breuker K. The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry. Nucleic Acids Res 2019; 47:7223-7234. [PMID: 31276590 PMCID: PMC6698743 DOI: 10.1093/nar/gkz574] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/15/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022] Open
Abstract
The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodiester backbone moiety on its 5'-side that facilitates preferential phosphodiester backbone bond cleavage upon vibrational excitation by low-energy collisionally activated dissociation. Removal of the basic N3 site by deaza-modification of adenine was found to abrogate preferential phosphodiester backbone bond cleavage. No such effects were observed for N1 or N7 of adenine. Importantly, we found that the pH of the solution used for generation of the multiply protonated, gaseous RNA ions by electrospray ionization affects phosphodiester backbone bond cleavage next to adenine, which implies that the protonation patterns in solution are at least in part preserved during and after transfer into the gas phase. Our study suggests that interactions between protonated adenine and phosphodiester moieties of RNA may play a more important mechanistic role in biological processes than considered until now.
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Affiliation(s)
- Elisabeth Fuchs
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Falschlunger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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11
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Xu J, Mieres-Perez J, Sanchez-Garcia E, Lee JK. Gas-Phase Deprotonation of Benzhydryl Cations: Carbene Basicity, Multiplicity, and Rearrangements. J Org Chem 2019; 84:7685-7693. [PMID: 31008604 DOI: 10.1021/acs.joc.9b00496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many fundamental properties of carbenes, particularly basicity, remain poorly understood. Herein, an experimental and computational examination of the deprotonation of a series of benzhydryl cations has been undertaken. These studies represent the first attempt at providing experimental values for diarylcarbene basicities. Pathways to deprotonation, including whether the singlet or triplet carbene is formed, are probed. Because diarylcarbenes are expected to be among the strongest organic bases known, assessing the energetics of protonation of these species is of fundamental importance for a wide range of chemical processes.
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Affiliation(s)
- Jiahui Xu
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
| | - Joel Mieres-Perez
- Computational Biochemistry, Center of Medical Biotechnology , University of Duisburg-Essen , D-45141 Essen , Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology , University of Duisburg-Essen , D-45141 Essen , Germany
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
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12
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Halder A, Data D, Seelam PP, Bhattacharyya D, Mitra A. Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches. ACS OMEGA 2019; 4:7354-7368. [PMID: 31459834 PMCID: PMC6648064 DOI: 10.1021/acsomega.8b03689] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/12/2019] [Indexed: 06/10/2023]
Abstract
Noncoding RNA molecules are composed of a large variety of noncanonical base pairs that shape up their functionally competent folded structures. Each base pair is composed of at least two interbase hydrogen bonds (H-bonds). It is expected that the characteristic geometry and stability of different noncanonical base pairs are determined collectively by the properties of these interbase H-bonds. We have studied the ground-state electronic properties [using density functional theory (DFT) and DFT-D3-based methods] of all the 118 normal base pairs and 36 modified base pairs, belonging to 12 different geometric families (cis and trans of WW, WH, HH, WS, HS, and SS) that occur in a nonredundant set of high-resolution RNA crystal structures. Having addressed some of the limitations of the earlier approaches, we provide here a comprehensive compilation of the average energies of different types of interbase H-bonds (E HB). We have also characterized each interbase H-bond using 13 different parameters that describe its geometry, charge distribution at its bond critical point (BCP), and n → σ*-type charge transfer from filled π orbitals of the H-bond acceptor to the empty antibonding orbital of the H-bond donor. On the basis of the extent of their linear correlation with the H-bonding energy, we have shortlisted five parameters to model linear equations for predicting E HB values. They are (i) electron density at the BCP: ρ, (ii) its Laplacian: ∇2ρ, (iii) stabilization energy due to n → σ*-type charge transfer: E(2), (iv) donor-hydrogen distance, and (v) hydrogen-acceptor distance. We have performed single variable and multivariable linear regression analysis over the normal base pairs and have modeled sets of linear relationships between these five parameters and E HB. Performance testing of our model over the set of modified base pairs shows promising results, at least for the moderately strong H-bonds.
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Affiliation(s)
- Antarip Halder
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology
(IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Dhruv Data
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology
(IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Preethi P. Seelam
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology
(IIIT-H), Gachibowli, Hyderabad 500032, India
| | - Dhananjay Bhattacharyya
- Computational
Science Division, Saha Institute of Nuclear
Physics(SINP), 1/AF,
Bidhannagar, Kolkata 700064, India
| | - Abhijit Mitra
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology
(IIIT-H), Gachibowli, Hyderabad 500032, India
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13
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Lu W, Liu J. Deprotonated guanine·cytosine and 9-methylguanine·cytosine base pairs and their "non-statistical" kinetics: a combined guided-ion beam and computational study. Phys Chem Chem Phys 2018; 18:32222-32237. [PMID: 27849082 DOI: 10.1039/c6cp06670d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a guided-ion beam mass spectrometric study on collision-induced dissociation (CID) of deprotonated guanine(G)·cytosine(C) base pairs and their 9-methylguanine (9MG) analogue with Xe, including measurements of product cross sections as a function of collision energy and determination of dissociation thresholds. DFT, RI-MP2 and DLPNO-CCSD(T) calculations and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling were performed to elucidate structures and kinetics. The experiment and theoretical study have provided considerable insight into tautomerization, intra-base-pair proton transfer and dissociation of deprotonated G·C and 9MG·C. In contrast to the previously reported lowest-energy deprotonated base pair structure G·[C-H1]- that consists of H-bonded neutral guanine and N1-deprotonated cytosine, we found that proton transfer from guanine N1 to cytosine N3 within G·[C-H1]- (or 9MG·[C-H1]-) leads to another slightly more stable conformer denoted as G·[C-H1]-_PT1 (or 9MG·[C-H1]-_PT1). The conventional (non-proton-transferred) and the proton-transferred conformers are close in energy and interconvert quickly, but they can be distinguished by dissociation products. The conventional structure dissociates into deprotonated cytosine and neutral guanine, while the other dissociates into deprotonated guanine and neutral cytosine. The two dissociation asymptotes have similar threshold energies, but surprisingly the CID product mass spectra of deprotonated G·C and 9MG·C are both overwhelmingly dominated by deprotonated G or 9MG, with their branching ratios greater than RRKM predictions by one to two orders of magnitude. The proton-transferred structures of deprotonated base pairs and the "unexpected" non-statistical kinetics provide new leads for understanding purine-pyrimidine interactions, forming rare nucleobase tautomers, and base pair opening.
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Affiliation(s)
- Wenchao Lu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. and Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. and Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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14
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Vušurović J, Schneeberger E, Breuker K. Interactions of Protonated Guanidine and Guanidine Derivatives with Multiply Deprotonated RNA Probed by Electrospray Ionization and Collisionally Activated Dissociation. ChemistryOpen 2017; 6:739-750. [PMID: 29226062 PMCID: PMC5715244 DOI: 10.1002/open.201700143] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/06/2017] [Indexed: 11/25/2022] Open
Abstract
Interactions of ribonucleic acid (RNA) with guanidine and guanidine derivatives are important features in RNA-protein and RNA-drug binding. Here we have investigated noncovalently bound complexes of an 8-nucleotide RNA and six different ligands, all of which have a guanidinium moiety, by using electrospray ionization (ESI) and collisionally activated dissociation (CAD) mass spectrometry (MS). The order of complex stability correlated almost linearly with the number of ligand atoms that can potentially be involved in hydrogen-bond or salt-bridge interactions with the RNA, but not with the proton affinity of the ligands. However, ligand dissociation of the complex ions in CAD was generally accompanied by proton transfer from ligand to RNA, which indicated conversion of salt-bridge into hydrogen-bond interactions. The relative stabilities and dissociation pathways of [RNA+m L-n H] n- complexes with different stoichiometries (m=1-5) and net charge (n= 2-5) revealed both specific and unspecific ligand binding to the RNA.
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Affiliation(s)
- Jovana Vušurović
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Eva‐Maria Schneeberger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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15
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16
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Zhu Y, Hamlow LA, He CC, Lee JK, Gao J, Berden G, Oomens J, Rodgers MT. Gas-Phase Conformations and N-Glycosidic Bond Stabilities of Sodium Cationized 2'-Deoxyguanosine and Guanosine: Sodium Cations Preferentially Bind to the Guanine Residue. J Phys Chem B 2017; 121:4048-4060. [PMID: 28355483 DOI: 10.1021/acs.jpcb.7b02906] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
2'-Deoxyguanosine (dGuo) and guanosine (Guo) are fundamental building blocks of DNA and RNA nucleic acids. In order to understand the effects of sodium cationization on the gas-phase conformations and stabilities of dGuo and Guo, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and complementary electronic structure calculations are performed. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ are compared to calculated IR spectra predicted for the stable low-energy structures computed for these species to determine the most favorable sodium cation binding sites, identify the structures populated in the experiments, and elucidate the influence of the 2'-hydroxyl substituent on the structures and IRMPD spectral features. These results are compared with those from a previous IRMPD study of the protonated guanine nucleosides to elucidate the differences between sodium cationization and protonation on structure. Energy-resolved collision-induced dissociation (ER-CID) experiments and survival yield analyses of protonated and sodium cationized dGuo and Guo are performed to compare the effects of these cations toward activating the N-glycosidic bonds of these nucleosides. For both [dGuo+Na]+ and [Guo+Na]+, the gas-phase structures populated in the experiments are found to involve bidentate binding of the sodium cation to the O6 and N7 atoms of guanine, forming a 5-membered chelation ring, with guanine found in both anti and syn orientations and C2'-endo (2T3 or 3T2) puckering of the sugar. The ER-CID results, IRMPD yields and the computed C1'-N9 bond lengths indicate that sodium cationization activates the N-glycosidic bond less effectively than protonation for both dGuo and Guo. The 2'-hydroxyl substituent of Guo is found to impact the preferred structures very little except that it enables a 2'OH···3'OH hydrogen bond to be formed, and stabilizes the N-glycosidic bond relative to that of dGuo in both the sodium cationized and protonated complexes.
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Affiliation(s)
- Y Zhu
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - C C He
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J K Lee
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - J Gao
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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17
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Raczyńska ED, Gal JF, Maria PC. Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase. Chem Rev 2016; 116:13454-13511. [PMID: 27739663 DOI: 10.1021/acs.chemrev.6b00224] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
| | - Jean-François Gal
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
| | - Pierre-Charles Maria
- Institut de Chimie de Nice (ICN) - UMR CNRS 7272, University Nice Sophia Antipolis , Parc Valrose, 06108 Nice Cedex 2, France
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18
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Wincel H. Microhydration of Deprotonated Nucleobases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1383-92. [PMID: 27178262 PMCID: PMC4942500 DOI: 10.1007/s13361-016-1411-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/17/2016] [Accepted: 04/19/2016] [Indexed: 06/05/2023]
Abstract
Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH (o) , ΔS (o) , and ΔG (o) , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data. Graphical Abstract ᅟ.
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Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland.
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19
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Kiruba GSM, Xu J, Zelikson V, Lee JK. Gas-Phase Studies of Formamidopyrimidine Glycosylase (Fpg) Substrates. Chemistry 2016; 22:3881-90. [DOI: 10.1002/chem.201505003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 11/08/2022]
Affiliation(s)
- G. S. M. Kiruba
- Department of Chemistry and Chemical Biology; Rutgers; The State University of New Jersey; New Brunswick NJ 08901 USA
| | - Jiahui Xu
- Department of Chemistry and Chemical Biology; Rutgers; The State University of New Jersey; New Brunswick NJ 08901 USA
| | - Victoria Zelikson
- Department of Chemistry and Chemical Biology; Rutgers; The State University of New Jersey; New Brunswick NJ 08901 USA
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology; Rutgers; The State University of New Jersey; New Brunswick NJ 08901 USA
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20
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Cho B, Wong MW. Unconventional Bifunctional Lewis-Brønsted Acid Activation Mode in Bicyclic Guanidine-Catalyzed Conjugate Addition Reactions. Molecules 2015; 20:15108-21. [PMID: 26295222 PMCID: PMC6331857 DOI: 10.3390/molecules200815108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 06/03/2015] [Accepted: 08/10/2015] [Indexed: 01/26/2023] Open
Abstract
DFT calculations have demonstrated that the unconventional bifunctional Brønsted-Lewis acid activation mode is generally applicable to a range of nucleophilic conjugate additions catalyzed by bicyclic guanidine catalysts. It competes readily with the conventional bifunctional Brønsted acid mode of activation. The optimal pro-nucleophiles for this unconventional bifunctional activation are acidic substrates with low pKa, while the best electrophiles are flexible 1,4-diamide and 1,4-diester conjugated systems.
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Affiliation(s)
- Bokun Cho
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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21
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Halder A, Halder S, Bhattacharyya D, Mitra A. Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study. Phys Chem Chem Phys 2015; 16:18383-96. [PMID: 25070186 DOI: 10.1039/c4cp02541e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protonated nucleobases have significant roles in facilitating catalytic functions of RNA, and in stabilizing different structural motifs. Reported pKa values of nucleobase protonation suggest that the population of neutral nucleobases is 10(3)-10(4) times higher than that of protonated nucleobases under physiological conditions (pH ∼ 7.4). Therefore, a molecular level understanding of various putative roles of protonated nucleobases cannot be achieved without addressing the question of how their occurrence propensities and stabilities are related to the free energy costs associated with the process of protonation under physiological conditions. With water as the proton donor, we use advanced QM methods to evaluate the site specific protonation propensities of nucleobases in terms of their associated free energy changes (ΔGprot). Quantitative follow up on the energetics of base pair formation and database search for evaluating their occurrence frequencies, reveal a lack of correlation between base pair stability and occurrence propensities on the one hand, and ease of protonation on the other. For example, although N7 protonated adenine (ΔGprot = 40.0 kcal mol(-1)) is found to participate in stable base pairing, base pairs involving N7 protonated guanine (ΔGprot = 36.8 kcal mol(-1)), on geometry optimization, converge to a minima where guanine transfers its extra proton to its partner base. Such observations, along with examples of weak base pairs involving N3 protonation of cytosine (ΔGprot = 37.0 kcal mol(-1)) are rationalized by analysing the protonation induced charge redistributions which are found to significantly influence, both positively and negatively, the hydrogen bonding potentials of different functional sites of individual nucleobases. Protonation induced charge redistribution is also found to strongly influence (i) the aromatic character of the rings of the participating bases and (ii) hydrogen bonding potential of the free edges of the protonated base pair. Comprehensive analysis of a non-redundant RNA crystal structure dataset further reveals that, while availability of stabilization possibilities determine the feasibility of occurrence of protonated bases, their occurrence context and specific functional roles are important factors determining their occurrence propensities.
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Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India.
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22
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Riml C, Glasner H, Rodgers MT, Micura R, Breuker K. On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent. Nucleic Acids Res 2015; 43:5171-81. [PMID: 25904631 PMCID: PMC4446422 DOI: 10.1093/nar/gkv288] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/24/2015] [Indexed: 12/18/2022] Open
Abstract
Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in ‘top-down’ strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)n+ and (M−nH)n− ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into c and y ions from phosphodiester bond cleavage.
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Affiliation(s)
- Christian Riml
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Heidelinde Glasner
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - M T Rodgers
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202-3489, United States
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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23
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Cole CA, Wang ZC, Snow TP, Bierbaum VM. Deprotonated Purine Dissociation: Experiments, Computations, and Astrobiological Implications. J Phys Chem A 2015; 119:334-43. [DOI: 10.1021/jp509012s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Callie A. Cole
- Department
of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, United States
| | - Zhe-Chen Wang
- Department
of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, United States
| | - Theodore P. Snow
- Department
of Astrophysical and Planetary Sciences, University of Colorado, 391 UCB, Boulder, Colorado 80309, United States
- Center
for Astrophysics and Space Astronomy, University of Colorado, 389 UCB, Boulder, Colorado 80309, United States
| | - Veronica M. Bierbaum
- Department
of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, United States
- Center
for Astrophysics and Space Astronomy, University of Colorado, 389 UCB, Boulder, Colorado 80309, United States
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24
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Chen M, Lee JK. Computational Studies of the Gas-Phase Thermochemical Properties of Modified Nucleobases. J Org Chem 2014; 79:11295-300. [DOI: 10.1021/jo502058w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mu Chen
- Department of Chemistry and
Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Jeehiun K. Lee
- Department of Chemistry and
Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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25
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Wilson KA, Wetmore SD. Complex Conformational Heterogeneity of the Highly Flexible O6-Benzyl-guanine DNA Adduct. Chem Res Toxicol 2014; 27:1310-25. [PMID: 24941023 DOI: 10.1021/tx500178x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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26
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Wang K, Chen M, Wang Q, Shi X, Lee JK. 1,2,3-Triazoles: Gas Phase Properties. J Org Chem 2013; 78:7249-58. [PMID: 23805820 DOI: 10.1021/jo4012738] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kai Wang
- Department of Chemistry and
Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Mu Chen
- Department of Chemistry and
Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Qiaoyi Wang
- C. Eugene Bennett Department
of Chemistry, West Virginia University,
Morgantown, West Virginia 26506, United States
| | - Xiaodong Shi
- C. Eugene Bennett Department
of Chemistry, West Virginia University,
Morgantown, West Virginia 26506, United States
| | - Jeehiun K. Lee
- Department of Chemistry and
Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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27
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Jissy AK, Konar S, Datta A. Molecular Switching Behavior in Isosteric DNA Base Pairs. Chemphyschem 2013; 14:1219-26. [DOI: 10.1002/cphc.201201083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Indexed: 12/22/2022]
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28
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Lanucara F, Crestoni ME, Chiavarino B, Fornarini S, Hernandez O, Scuderi D, Maitre P. Infrared spectroscopy of nucleotides in the gas phase 2. The protonated cyclic 3′,5′-adenosine monophosphate. RSC Adv 2013. [DOI: 10.1039/c3ra41117f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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29
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Feketeová L, Khairallah GN, Chan B, Steinmetz V, Maître P, Radom L, O'Hair RAJ. Gas-phase infrared spectrum and acidity of the radical cation of 9-methylguanine. Chem Commun (Camb) 2013; 49:7343-5. [DOI: 10.1039/c3cc43244k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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30
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Michelson AZ, Rozenberg A, Tian Y, Sun X, Davis J, Francis AW, O'Shea VL, Halasyam M, Manlove AH, David SS, Lee JK. Gas-phase studies of substrates for the DNA mismatch repair enzyme MutY. J Am Chem Soc 2012; 134:19839-50. [PMID: 23106240 PMCID: PMC4204490 DOI: 10.1021/ja309082k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The gas-phase thermochemical properties (tautomeric energies, acidity, and proton affinity) have been measured and calculated for adenine and six adenine analogues that were designed to test features of the catalytic mechanism used by the adenine glycosylase MutY. The gas-phase intrinsic properties are correlated to possible excision mechanisms and MutY excision rates to gain insight into the MutY mechanism. The data support a mechanism involving protonation at N7 and hydrogen bonding to N3 of adenine. We also explored the acid-catalyzed (non-enzymatic) depurination of these substrates, which appears to follow a different mechanism than that employed by MutY, which we elucidate using calculations.
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Affiliation(s)
- Anna Zhachkina Michelson
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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31
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Aliakbar Tehrani Z, Shakourian-Fard M, Fattahi A. Computational investigation of thermochemical properties of non-natural C-nucloebases: different hydrogen-bonding preferences for non-natural Watson–Crick base pairs. Struct Chem 2012. [DOI: 10.1007/s11224-012-0115-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Psciuk BT, Lord RL, Munk BH, Schlegel HB. Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases. J Chem Theory Comput 2012; 8:5107-23. [PMID: 26593200 DOI: 10.1021/ct300550x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The oxidation potentials for N-methyl substituted nucleic acid bases guanine, adenine, cytosine, thymine, uracil, xanthine, and 8-oxoguanine were computed using B3LYP and CBS-QB3 with the SMD solvation model. Acid-base and tautomeric equilibria present in aqueous solution were accounted for by combining standard redox potentials with calculated pKa and tautomerization energies to produce an ensemble averaged pH dependent potential. Gas phase free energies were computed using B3LYP/aug-cc-pVTZ//B3LYP/6-31+G(d,p) and CBS-QB3. Solvation free energies were computed at the SMD/B3LYP/6-31+G(d,p) level of theory. Compared to experimental results, calculations with the CBS-QB3 level of theory have a mean absolute error (MAE) of ca. 1 kcal/mol for the gas phase proton affinity/gas phase basicity and an MAE of ca. 0.04 eV for the adiabatic/vertical ionization potentials. The B3LYP calculations have a MAE of ∼2 kcal/mol for the proton affinity/gas phase basicity data but systematically underestimated ionization potentials by 0.14-0.21 eV. Solvent cavities for charged solute species were rescaled uniformly by fitting computed pKa data to experimentally measured pKa values. After solvent cavity scaling, the MAEs for computed pKa's compared to experimental results are 0.7 for B3LYP and 0.9 for CBS-QB3. In acetonitrile, the computed E°(XH(+•)/XH) redox potentials are systematically lower than experimentally measured potentials by 0.21 V for CBS-QB3 and 0.33 V for B3LYP. However, the redox potentials relative to adenine are in very good agreement with experimental results, with MAEs of 0.10 V for CBS-QB3 and 0.07 V for B3LYP. In aqueous solution, B3LYP and CBS-QB3 have MAEs of 0.21 and 0.19 V for E7(X(•),H(+)/XH). Replacing the methyl substituent with ribose changes the calculated E7 potentials by 0.1-0.2 V. The calculated difference between the guanine and adenine oxidation potentials is too large compared to experimental results, but the calculated difference between guanine and 8-oxoguanine is in good agreement with the measured values.
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Affiliation(s)
- Brian T Psciuk
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Richard L Lord
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Barbara H Munk
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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33
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Michelson AZ, Chen M, Wang K, Lee JK. Gas-Phase Studies of Purine 3-Methyladenine DNA Glycosylase II (AlkA) Substrates. J Am Chem Soc 2012; 134:9622-33. [DOI: 10.1021/ja211960r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anna Zhachkina Michelson
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
| | - Mu Chen
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
| | - Kai Wang
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
| | - Jeehiun K. Lee
- Department
of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick,
New Jersey 08901, United States
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34
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Michelson AZ, Petronico A, Lee JK. 2-Pyridone and Derivatives: Gas-Phase Acidity, Proton Affinity, Tautomer Preference, and Leaving Group Ability. J Org Chem 2011; 77:1623-31. [DOI: 10.1021/jo201991y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Anna Zhachkina Michelson
- Department of Chemistry and Chemical
Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
08901, United States
| | - Aaron Petronico
- Department of Chemistry and Chemical
Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
08901, United States
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical
Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
08901, United States
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35
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Liu M, Tran NT, Franz AK, Lee JK. Gas-Phase Acidity Studies of Dual Hydrogen-Bonding Organic Silanols and Organocatalysts. J Org Chem 2011; 76:7186-94. [DOI: 10.1021/jo201214x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Min Liu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Ngon T. Tran
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Annaliese K. Franz
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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36
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Uddin KM, Almatarneh MH, Shaw DM, Poirier RA. Mechanistic Study of the Deamination Reaction of Guanine: A Computational Study. J Phys Chem A 2011; 115:2065-76. [DOI: 10.1021/jp1120806] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kabir M. Uddin
- Department of Chemistry and ‡The Atlantic Computational Excellence Network, Memorial University, St. John’s, Newfoundland, Canada A1B 3X7
| | - Mansour H. Almatarneh
- Department of Chemistry and ‡The Atlantic Computational Excellence Network, Memorial University, St. John’s, Newfoundland, Canada A1B 3X7
| | - Dawn M. Shaw
- Department of Chemistry and ‡The Atlantic Computational Excellence Network, Memorial University, St. John’s, Newfoundland, Canada A1B 3X7
| | - Raymond A. Poirier
- Department of Chemistry and ‡The Atlantic Computational Excellence Network, Memorial University, St. John’s, Newfoundland, Canada A1B 3X7
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Galindo-Murillo R, Hernandez-Lima J, González-Rendón M, Cortés-Guzmán F, Ruíz-Azuara L, Moreno-Esparza R. π-Stacking between Casiopeinas® and DNA bases. Phys Chem Chem Phys 2011; 13:14510-5. [DOI: 10.1039/c1cp20183b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Interplay of thermochemistry and Structural Chemistry, the journal (volume 20, 2009) and the discipline. Struct Chem 2010. [DOI: 10.1007/s11224-010-9656-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Gardner MW, Li N, Ellington AD, Brodbelt JS. Infrared multiphoton dissociation of small-interfering RNA anions and cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:580-91. [PMID: 20129797 PMCID: PMC2847665 DOI: 10.1016/j.jasms.2009.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Revised: 12/21/2009] [Accepted: 12/22/2009] [Indexed: 05/13/2023]
Abstract
Infrared multiphoton dissociation (IRMPD) on a linear ion trap mass spectrometer is applied for the sequencing of small interfering RNA (siRNA). Both single-strand siRNAs and duplex siRNA were characterized by IRMPD, and the results were compared with that obtained by traditional ion trap-based collision induced dissociation (CID). The single-strand siRNA anions were observed to dissociate via cleavage of the 5' P-O bonds yielding c- and y-type product ions as well as undergo neutral base loss. Full sequence coverage of the siRNA anions was obtained by both IRMPD and CID. While the CID mass spectra were dominated by base loss ions, accounting for approximately 25% to 40% of the product ion current, these ions were eliminated through secondary dissociation by increasing the irradiation time in the IRMPD mass spectra to produce higher abundances of informative sequence ions. With longer irradiation times, however, internal ions corresponding to cleavage of two 5' P-O bonds began to populate the product ion mass spectra as well as higher abundances of [a - Base] and w-type ions. IRMPD of siRNA cations predominantly produced c- and y-type ions with minimal contributions of [a - Base] and w-type ions to the product ion current; the presence of only two complementary series of product ions in the IRMPD mass spectra simplified spectral interpretation. In addition, IRMPD produced high abundances of protonated nucleobases, [G + H](+), [A + H](+), and [C + H](+), which were not detected in the CID mass spectra due to the low-mass cut-off associated with conventional CID in ion traps. CID and IRMPD using short irradiation times of duplex siRNA resulted in strand separation, similar to the dissociation trends observed for duplex DNA. With longer irradiation times, however, the individual single-strands underwent secondary dissociation to yield informative sequence ions not obtained by CID.
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Affiliation(s)
- Myles W Gardner
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712-0165, USA
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