1
|
Astani EK, Iravani H, Sardari S. Theoretical investigation of the effects of diverse hydrogen-bonding characteristics on the 17O chemical shielding and electric field gradient tensors within the active sites of MraY AA bound to nucleoside antibiotics capuramycin, carbacaprazamycin, 3'-Hydroxymureidomycin A, and muraymycin D2. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 133:101960. [PMID: 39208660 DOI: 10.1016/j.ssnmr.2024.101960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/31/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
This study builds upon our prior researches and seeks to investigate and clarify the influences of various characteristics of hydrogen bonds (H-bonds) and charge transfer (CT) interactions, which were detected within the inhibitor binding pockets (labeled as the QM models I-IV) of MraYAA-capuramycin, MraYAA-carbacaprazamycin, MraYAA-3'-hydroxymureidomycin A, and MraYAA-muraymycin D2 complexes by QTAIM and NBO analyses from DFT QM/MM MD calculations, on the 17O chemical shielding (CS) and electric field gradient (EFG) tensors of carboxylate (Oδ), carbonyl (C═O), and hydroxyl (O-H) oxygens in these models. The 17O CS and EFG tensors of these three types of oxygens in QM models I-IV were calculated at the M06-2X/6-31G** level by including the solvent effects using the polarizable continuum model. From the computed 17O CS and EFG tensors in these models, it was found that the nuclear shielding, σiso, for carboxylate or carbonyl oxygen increases (shielding effect) as the H-bond length decreases and the percentage p-character of nOδ/nC═O lone pair partner in the CT interaction enhances. In contrast, the σiso (17O-H) decreases (deshielding effect) with a reduction in the H-bond length as well as with an enhancement in percentage s-character of the nOH lone pair/σ*O-H antibond. By reducing the H-bond length or by increasing p-character of the nOδ/nC═O lone pair, the 17Oδ/17O═C quadrupole coupling constant smoothly decreases, while the 17Oδ/17O═C asymmetry parameter smoothly increases. Moreover, these calculated parameters are in a good agreement with the experimental values. The information garnered here is valuable particularly for further understanding of empirical correlations between 17O NMR spectroscopic and H-bonding characteristics in the protein-ligand complexes.
Collapse
Affiliation(s)
- Elahe K Astani
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, 13169-43551, Iran; Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, 14115-175, Iran.
| | - Hossein Iravani
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, 14115-175, Iran
| | - Soroush Sardari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, 13169-43551, Iran
| |
Collapse
|
2
|
Wu G, Dai Y, Hung I, Gan Z, Terskikh V. 1H/ 17O Chemical Shift Waves in Carboxyl-Bridged Hydrogen Bond Networks in Organic Solids. J Phys Chem A 2024; 128:4288-4296. [PMID: 38748612 DOI: 10.1021/acs.jpca.4c01866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
We report solid-state 1H and 17O NMR results for four 17O-labeled organic compounds each containing an extensive carboxyl-bridged hydrogen bond (CBHB) network in the crystal lattice: tetrabutylammonium hydrogen di-[17O2]salicylate (1), [17O4]quinolinic acid (2), [17O4]dinicotinic acid (3), and [17O2]Gly/[17O2]Gly·HCl cocrystal (4). The 1H isotropic chemical shifts found for protons involved in different CBHB networks are between 8.2 and 20.5 ppm, which reflect very different hydrogen-bonding environments. Similarly, the 17O isotropic chemical shifts found for the carboxylate oxygen atoms in CBHB networks, spanning a large range between 166 and 341 ppm, are also remarkably sensitive to the hydrogen-bonding environments. We introduced a simple graphical representation in which 1H and 17O chemical shifts are displayed along the H and O atomic chains that form the CBHB network. In such a depiction, because wavy patterns are often observed, we refer to these wavy patterns as 1H/17O chemical shift waves. Typical patterns of 1H/17O chemical shift waves in CBHB networks are discussed. The reported 1H and 17O NMR parameters for the CBHB network models examined in this study can serve as benchmarks to aid in spectral interpretation for CBHB networks in proteins.
Collapse
Affiliation(s)
- Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston Ontario K7L 3N6, Canada
| | - Yizhe Dai
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston Ontario K7L 3N6, Canada
| | - Ivan Hung
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Zhehong Gan
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Victor Terskikh
- Metrology, National Research Council Canada, Ottawa K1A 0R6, Canada
| |
Collapse
|
3
|
Shen J, Terskikh V, Struppe J, Hassan A, Monette M, Hung I, Gan Z, Brinkmann A, Wu G. Solid-state 17O NMR study of α-d-glucose: exploring new frontiers in isotopic labeling, sensitivity enhancement, and NMR crystallography. Chem Sci 2022; 13:2591-2603. [PMID: 35340864 PMCID: PMC8890099 DOI: 10.1039/d1sc06060k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/31/2021] [Indexed: 01/03/2023] Open
Abstract
We report the first “total synthesis” of 17O-labeled d-glucose and its solid-state 17O NMR characterization with unprecedented sensitivity and resolution.
Collapse
Affiliation(s)
- Jiahui Shen
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Victor Terskikh
- Metrology, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - Alia Hassan
- Bruker Switzerland AG, Fällanden, Switzerland
| | - Martine Monette
- Bruker Biospin Ltd., 2800 High Point Drive, Suite 206, Milton, Ontario L9T 6P4, Canada
| | - Ivan Hung
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - Zhehong Gan
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - Andreas Brinkmann
- Metrology, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| |
Collapse
|
4
|
Hartman JD, Mathews A, Harper JK. Fast and Accurate Electric Field Gradient Calculations in Molecular Solids With Density Functional Theory. Front Chem 2021; 9:751711. [PMID: 34692646 PMCID: PMC8529703 DOI: 10.3389/fchem.2021.751711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/20/2021] [Indexed: 11/24/2022] Open
Abstract
Modern approaches for calculating electric field gradient (EFF) tensors in molecular solids rely upon plane-wave calculations employing periodic boundary conditions (PBC). In practice, models employing PBCs are limited to generalized gradient approximation (GGA) density functionals. Hybrid density functionals applied in the context of gauge-including atomic orbital (GIAO) calculations have been shown to substantially improve the accuracy of predicted NMR parameters. Here we propose an efficient method that effectively combines the benefits of both periodic calculations and single-molecule techniques for predicting electric field gradient tensors in molecular solids. Periodic calculations using plane-wave basis sets were used to model the crystalline environment. We then introduce a molecular correction to the periodic result obtained from a single-molecule calculation performed with a hybrid density functional. Single-molecule calculations performed using hybrid density functionals were found to significantly improve the agreement of predicted 17O quadrupolar coupling constants (C q ) with experiment. We demonstrate a 31% reduction in the RMS error for the predicted 17O C q values relative to standard plane-wave methods using a carefully constructed test set comprised of 22 oxygen-containing molecular crystals. We show comparable improvements in accuracy using five different hybrid density functionals and find predicted C q values to be relatively insensitive to the choice of basis set used in the single molecule calculation. Finally, the utility of high-accuracy 17O C q predictions is demonstrated by examining the disordered 4-Nitrobenzaldehyde crystal structure.
Collapse
Affiliation(s)
- Joshua D. Hartman
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, United States
| | - Amanda Mathews
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, United States
| | - James K. Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, United States
| |
Collapse
|
5
|
Muniyappan S, Lin Y, Lee YH, Kim JH. 17O NMR Spectroscopy: A Novel Probe for Characterizing Protein Structure and Folding. BIOLOGY 2021; 10:biology10060453. [PMID: 34064021 PMCID: PMC8223985 DOI: 10.3390/biology10060453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022]
Abstract
Oxygen is a key atom that maintains biomolecular structures, regulates various physiological processes, and mediates various biomolecular interactions. Oxygen-17 (17O), therefore, has been proposed as a useful probe that can provide detailed information about various physicochemical features of proteins. This is attributed to the facts that (1) 17O is an active isotope for nuclear magnetic resonance (NMR) spectroscopic approaches; (2) NMR spectroscopy is one of the most suitable tools for characterizing the structural and dynamical features of biomolecules under native-like conditions; and (3) oxygen atoms are frequently involved in essential hydrogen bonds for the structural and functional integrity of proteins or related biomolecules. Although 17O NMR spectroscopic investigations of biomolecules have been considerably hampered due to low natural abundance and the quadruple characteristics of the 17O nucleus, recent theoretical and technical developments have revolutionized this methodology to be optimally poised as a unique and widely applicable tool for determining protein structure and dynamics. In this review, we recapitulate recent developments in 17O NMR spectroscopy to characterize protein structure and folding. In addition, we discuss the highly promising advantages of this methodology over other techniques and explain why further technical and experimental advancements are highly desired.
Collapse
Affiliation(s)
- Srinivasan Muniyappan
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea;
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea;
- Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
- Research Headquarters, Korea Brain Research Institute, Daegu 41068, Korea
- Correspondence: (Y.-H.L.); (J.H.K.)
| | - Jin Hae Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
- Correspondence: (Y.-H.L.); (J.H.K.)
| |
Collapse
|
6
|
Holmes ST, Vojvodin CS, Schurko RW. Dispersion-Corrected DFT Methods for Applications in Nuclear Magnetic Resonance Crystallography. J Phys Chem A 2020; 124:10312-10323. [DOI: 10.1021/acs.jpca.0c06372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Cameron S. Vojvodin
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Robert W. Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| |
Collapse
|
7
|
Chen D, Gao W, Jiang Q. Distinguishing the Structures of High-Pressure Hydrides with Nuclear Magnetic Resonance Spectroscopy. J Phys Chem Lett 2020; 11:9439-9445. [PMID: 33108187 DOI: 10.1021/acs.jpclett.0c02657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The structural characterization of high-pressure hydrides has encountered many difficulties mainly due to the weak X-ray scattering of hydrogen. Herein, we investigate the prospect of detecting the H3S and LaH10 structures with nuclear magnetic resonance (NMR) spectroscopy. Our calculations demonstrate that the different candidate structures of H3S (or LaH10) exhibit significant differences in the electric field gradient (EFG) tensor of the 33S (or 139La) sites, indicating that the NMR spectroscopy can well capture the structural differences, even the small changes in the atomic position, and hence can be used to effectively probe the structures and the phase transitions of H3S and LaH10. Our results clarify the relationship between the structures and the EFG tensor parameters and provide a potential means to detect the structures of high-pressure hydrides.
Collapse
Affiliation(s)
- Da Chen
- Key Laboratory of Automobile Materials, Ministry of Education, and School of Materials Science and Engineering, Jilin University, Changchun 130022, China
| | - Wang Gao
- Key Laboratory of Automobile Materials, Ministry of Education, and School of Materials Science and Engineering, Jilin University, Changchun 130022, China
| | - Qing Jiang
- Key Laboratory of Automobile Materials, Ministry of Education, and School of Materials Science and Engineering, Jilin University, Changchun 130022, China
| |
Collapse
|
8
|
Rinald A, Wu G. A Modified Townes-Dailey Model for Interpretation and Visualization of Nuclear Quadrupole Coupling Tensors in Molecules. J Phys Chem A 2020; 124:1176-1186. [PMID: 31968940 DOI: 10.1021/acs.jpca.0c00439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We propose a modified Townes-Dailey (TD) model to help interpret and visualize experimentally measurable nuclear quadrupole coupling tensors (thus the electric field gradient tensors) in molecules. We show that within the framework of the TD model each principal component of the nuclear quadrupole coupling tensor is directly related to a new quantity termed as the valence p-orbital population anisotropy (VPPA or ΔP) in the same direction. Although the proposed model is a simple reformulation of the original TD model thus does not introduce new physics, the concept of VPPA makes it possible to directly interpret as well as visualize in a much straightforward way the experimentally determined nuclear quadrupole coupling tensors in molecules. We illustrate the utilization of VPPA using nuclear quadrupole coupling tensors for 11B, 14N, 17O, 35Cl, 79Br, and 127I nuclei in a variety of molecules. We propose to use VPPA or ΔP ellipsoid representation as a means of visualizing/displaying nuclear quadrupole coupling tensors in the molecular frame. We show the usefulness of the VPPA concept in providing a unifying explanation for seemingly different types of molecular interactions such as hydrogen bonding, halogen bonding, and frustrated Lewis pairs. We further suggest that VPPA can be used as a universal measure of the ability of any element in the entire p-block of the periodic table (groups 13-16) to interact with nucleophiles (e.g., formation of chalcogen, pnictogen, tetrel, and triel bonds).
Collapse
Affiliation(s)
- Andrew Rinald
- Department of Chemistry , Queen's University , 90 Bader Lane , Kingston , Ontario , Canada K7L 3N6
| | - Gang Wu
- Department of Chemistry , Queen's University , 90 Bader Lane , Kingston , Ontario , Canada K7L 3N6
| |
Collapse
|
9
|
Wu G. 17O NMR studies of organic and biological molecules in aqueous solution and in the solid state. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:135-191. [PMID: 31779879 DOI: 10.1016/j.pnmrs.2019.06.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 06/10/2023]
Abstract
This review describes the latest developments in the field of 17O NMR spectroscopy of organic and biological molecules both in aqueous solution and in the solid state. In the first part of the review, a general theoretical description of the nuclear quadrupole relaxation process in isotropic liquids is presented at a mathematical level suitable for non-specialists. In addition to the first-order quadrupole interaction, the theory also includes additional relaxation mechanisms such as the second-order quadrupole interaction and its cross correlation with shielding anisotropy. This complete theoretical treatment allows one to assess the transverse relaxation rate (thus the line width) of NMR signals from half-integer quadrupolar nuclei in solution over the entire range of motion. On the basis of this theoretical framework, we discuss general features of quadrupole-central-transition (QCT) NMR, which is a particularly powerful method of studying biomolecules in the slow motion regime. Then we review recent advances in 17O QCT NMR studies of biological macromolecules in aqueous solution. The second part of the review is concerned with solid-state 17O NMR studies of organic and biological molecules. As a sequel to the previous review on the same subject [G. Wu, Prog. Nucl. Magn. Reson. Spectrosc. 52 (2008) 118-169], the current review provides a complete coverage of the literature published since 2008 in this area.
Collapse
Affiliation(s)
- Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada.
| |
Collapse
|
10
|
Carnahan SL, Lampkin BJ, Naik P, Hanrahan MP, Slowing II, VanVeller B, Wu G, Rossini AJ. Probing O–H Bonding through Proton Detected 1H–17O Double Resonance Solid-State NMR Spectroscopy. J Am Chem Soc 2018; 141:441-450. [DOI: 10.1021/jacs.8b10878] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Scott L. Carnahan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| | - Bryan J. Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Pranjali Naik
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| | - Michael P. Hanrahan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| | - Igor I. Slowing
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Gang Wu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Aaron J. Rossini
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- U.S. DOE Ames Laboratory, Ames, Iowa 50011, United States
| |
Collapse
|
11
|
Shen J, Terskikh V, Wang X, Hung I, Gan Z, Wu G. A Quadrupole-Central-Transition 17O NMR Study of Nicotinamide: Experimental Evidence of Cross-Correlation between Second-Order Quadrupolar Interaction and Magnetic Shielding Anisotropy. J Phys Chem B 2018; 122:4813-4820. [PMID: 29683675 DOI: 10.1021/acs.jpcb.8b02417] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have examined the 17O quadrupole-central-transition (QCT) NMR signal from [17O]nicotinamide (vitamin B3) dissolved in glycerol. Measurements were performed at five magnetic fields ranging from 9.4 to 35.2 T between 243 and 363 K. We found that, in the ultraslow motion regime, cross-correlation between the second-order quadrupole interaction and magnetic shielding anisotropy is an important contributor to the transverse relaxation process for the 17O QCT signal of [17O]nicotinamide. While such a cross-correlation effect has generally been predicted by relaxation theory, we report here the first experimental evidence for this phenomenon in solution-state NMR for quadrupolar nuclei. We have discussed the various factors that determine the ultimate resolution limit in QCT NMR spectroscopy. The present study also highlights the advantages of performing QCT NMR experiments at very high magnetic fields (e.g., 35.2 T).
Collapse
Affiliation(s)
- Jiahui Shen
- Department of Chemistry , Queen's University , 90 Bader Lane , Kingston , Ontario , Canada K7L 3N6
| | - Victor Terskikh
- Department of Chemistry , Queen's University , 90 Bader Lane , Kingston , Ontario , Canada K7L 3N6.,Department of Chemistry , University of Ottawa , Ottawa , Ontario , Canada K1N 6N5
| | - Xiaoling Wang
- National High Magnetic Field Laboratory , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Ivan Hung
- National High Magnetic Field Laboratory , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Zhehong Gan
- National High Magnetic Field Laboratory , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310 , United States
| | - Gang Wu
- Department of Chemistry , Queen's University , 90 Bader Lane , Kingston , Ontario , Canada K7L 3N6
| |
Collapse
|
12
|
Keeler EG, Michaelis VK, Colvin MT, Hung I, Gor'kov PL, Cross TA, Gan Z, Griffin RG. 17O MAS NMR Correlation Spectroscopy at High Magnetic Fields. J Am Chem Soc 2017; 139:17953-17963. [PMID: 29111706 DOI: 10.1021/jacs.7b08989] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The structure of two protected amino acids, FMOC-l-leucine and FMOC-l-valine, and a dipeptide, N-acetyl-l-valyl-l-leucine (N-Ac-VL), were studied via one- and two-dimensional solid-state nuclear magnetic resonance (NMR) spectroscopy. Utilizing 17O magic-angle spinning (MAS) NMR at multiple magnetic fields (17.6-35.2 T/750-1500 MHz for 1H) the 17O quadrupolar and chemical shift parameters were determined for the two oxygen sites of each FMOC-protected amino acids and the three distinct oxygen environments of the dipeptide. The one- and two-dimensional, 17O, 15N-17O, 13C-17O, and 1H-17O double-resonance correlation experiments performed on the uniformly 13C,15N and 70% 17O-labeled dipeptide prove the attainability of 17O as a probe for structure studies of biological systems. 15N-17O and 13C-17O distances were measured via one-dimensional REAPDOR and ZF-TEDOR experimental buildup curves and determined to be within 15% of previously reported distances, thus demonstrating the use of 17O NMR to quantitate interatomic distances in a fully labeled dipeptide. Through-space hydrogen bonding of N-Ac-VL was investigated by a two-dimensional 1H-detected 17O R3-R-INEPT experiment, furthering the importance of 17O for studies of structure in biomolecular solids.
Collapse
Affiliation(s)
- Eric G Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Vladimir K Michaelis
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Michael T Colvin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Ivan Hung
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310, United States
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310, United States
| | - Timothy A Cross
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310, United States
| | - Zhehong Gan
- National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32310, United States
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| |
Collapse
|
13
|
|
14
|
Métro TX, Gervais C, Martinez A, Bonhomme C, Laurencin D. Unleashing the Potential of 17 O NMR Spectroscopy Using Mechanochemistry. Angew Chem Int Ed Engl 2017; 56:6803-6807. [PMID: 28455940 DOI: 10.1002/anie.201702251] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Indexed: 12/31/2022]
Abstract
17 O NMR spectroscopy has been the subject of vivid interest in recent years, because there is increasing evidence that it can provide unique insight into the structure and reactivity of many molecules and materials. However, due to the very poor natural abundance of oxygen-17, 17 O labeling is generally a prerequisite. This is a real obstacle for most research groups, because of the high costs and/or strong experimental constraints of the most frequently used 17 O-labeling schemes. Here, we show for the first time that mechanosynthesis offers unique opportunities for enriching in 17 O a variety of organic and inorganic precursors of synthetic interest. The protocols are fast, user-friendly, and low-cost, which makes them highly attractive for a broad research community, and their suitability for 17 O solid-state NMR applications is demonstrated.
Collapse
Affiliation(s)
- Thomas-Xavier Métro
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, Campus Triolet, Place E. Bataillon, CC 1703, 34095, Montpellier cedex 05, France
| | - Christel Gervais
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR 7574, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris, France
| | - Anthony Martinez
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253, CNRS, UM, ENSCM, Campus Triolet, Place E. Bataillon, CC1701, 34095, Montpellier cedex 05, France
| | - Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR 7574, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris, France
| | - Danielle Laurencin
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253, CNRS, UM, ENSCM, Campus Triolet, Place E. Bataillon, CC1701, 34095, Montpellier cedex 05, France
| |
Collapse
|
15
|
Métro TX, Gervais C, Martinez A, Bonhomme C, Laurencin D. Unleashing the Potential of17O NMR Spectroscopy Using Mechanochemistry. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas-Xavier Métro
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247, CNRS; Université de Montpellier, ENSCM, Campus Triolet; Place E. Bataillon, CC 1703 34095 Montpellier cedex 05 France
| | - Christel Gervais
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP); UMR 7574; Sorbonne Universités, UPMC Univ Paris 06; 4 Place Jussieu 75005 Paris France
| | - Anthony Martinez
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253, CNRS, UM, ENSCM; Campus Triolet; Place E. Bataillon, CC1701 34095 Montpellier cedex 05 France
| | - Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP); UMR 7574; Sorbonne Universités, UPMC Univ Paris 06; 4 Place Jussieu 75005 Paris France
| | - Danielle Laurencin
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253, CNRS, UM, ENSCM; Campus Triolet; Place E. Bataillon, CC1701 34095 Montpellier cedex 05 France
| |
Collapse
|
16
|
Holmes ST, Iuliucci RJ, Mueller KT, Dybowski C. Semi-empirical refinements of crystal structures using 17O quadrupolar-coupling tensors. J Chem Phys 2017; 146:064201. [DOI: 10.1063/1.4975170] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Robbie J. Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, USA
| | - Karl T. Mueller
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| |
Collapse
|
17
|
Tang AW, Kong X, Terskikh V, Wu G. Solid-State 17O NMR of Unstable Acyl-Enzyme Intermediates: A Direct Probe of Hydrogen Bonding Interactions in the Oxyanion Hole of Serine Proteases. J Phys Chem B 2016; 120:11142-11150. [PMID: 27731644 DOI: 10.1021/acs.jpcb.6b08798] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report preparation, trapping, and solid-state 17O NMR characterization of three unstable acyl-enzyme intermediates (≈ 26 kDa): p-N,N-dimethylamino-[17O]benzoyl-chymotrypsin, trans-o-methoxy-[17O]cinnamoyl-chymotrypsin, and trans-p-methoxy-[17O]cinnamoyl-chymotrypsin. We show that both the 17O chemical shifts and nuclear quadrupolar parameters obtained for these acyl-enzyme intermediates in the solid state are correlated with their deacylation rate constants measured in aqueous solution. With the aid of quantum mechanical calculations, the experimental 17O NMR parameters were interpreted as to reflect the hydrogen bonding interactions between the carbonyl (C═17O) functional group of the acyl moiety and the two NH groups from the protein backbone (Ser195 and Gly193) in the oxyanion hole, a general feature of all serine proteases. Our results further suggest that the 17O chemical shift and quadrupole coupling constant display distinctly different sensitivities toward different aspects of hydrogen bonding, such as hydrogen bond distance and direction. This work demonstrates the utility of 17O as a useful nuclear probe in NMR studies of enzymes.
Collapse
Affiliation(s)
- Aaron W Tang
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Xianqi Kong
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Victor Terskikh
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada.,Department of Chemistry, University of Ottawa , Ottawa, Ontario K1N 6N5, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University , 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| |
Collapse
|
18
|
Hartman JD, Kudla RA, Day GM, Mueller LJ, Beran GJO. Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals. Phys Chem Chem Phys 2016; 18:21686-709. [PMID: 27431490 DOI: 10.1039/c6cp01831a] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.
Collapse
Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, California 92521, USA.
| | | | | | | | | |
Collapse
|
19
|
Rorick A, Michael MA, Yang L, Zhang Y. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds. J Phys Chem B 2015; 119:11618-25. [PMID: 26274812 PMCID: PMC4583422 DOI: 10.1021/acs.jpcb.5b06536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.
Collapse
Affiliation(s)
- Amber Rorick
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken NJ 07030, USA
| | - Matthew A. Michael
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken NJ 07030, USA
| | - Liu Yang
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken NJ 07030, USA
| | - Yong Zhang
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken NJ 07030, USA
| |
Collapse
|
20
|
Kong X, Terskikh V, Toubaei A, Wu G. A solid-state 17O NMR study of platinum-carboxylate complexes: carboplatin and oxaliplatin. CAN J CHEM 2015. [DOI: 10.1139/cjc-2015-0019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report synthesis and solid-state NMR characterization of two 17O-labeled platinum anticancer drugs: cis-diammine(1,1-cyclobutane-[17O4]dicarboxylato)platinum(II) (carboplatin) and ([17O4]oxalato)[(1R, 2R)-(−)-1,2-cyclohexanediamine)]platinum(II) (oxaliplatin). Both 17O chemical shift (CS) and quadrupolar coupling (QC) tensors were measured for the carboxylate groups in these two compounds. With the aid of plane wave DFT computations, the 17O CS and QC tensor orientations were determined in the molecular frame of reference. Significant changes in the 17O CS and QC tensors were observed for the carboxylate oxygen atom upon its coordination to Pt(II). In particular, the 17O isotropic chemical shifts for the oxygen atoms directly bonded to Pt(II) are found to be smaller (more shielded) by 200 ppm than those for the non-Pt-coordinated oxygen atoms within the same carboxylate group. Examination of the 17O CS tensor components reveals that such a large 17O coordination shift is primarily due to the shielding increase along the direction that is within the O=C–O–Pt plane and perpendicular to the O–Pt bond. This result is interpreted as due to the σ donation from the oxygen nonbonding orbital (electron lone pair) to the Pt(II) empty dyz orbital, which results in large energy gaps between σ(Pt–O) and unoccupied molecular orbitals, thus reducing the paramagnetic shielding contribution along the direction perpendicular to the O–Pt bond. We found that the 17O QC tensor of the carboxylate oxygen is also sensitive to Pt(II) coordination, and that 17O CS and QC tensors provide complementary information about the O–Pt bonding.
Collapse
Affiliation(s)
- Xianqi Kong
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| | - Victor Terskikh
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Abouzar Toubaei
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| |
Collapse
|
21
|
Perras FA, Kobayashi T, Pruski M. Natural Abundance (17)O DNP Two-Dimensional and Surface-Enhanced NMR Spectroscopy. J Am Chem Soc 2015; 137:8336-9. [PMID: 26098846 DOI: 10.1021/jacs.5b03905] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Due to its extremely low natural abundance and quadrupolar nature, the (17)O nuclide is very rarely used for spectroscopic investigation of solids by NMR without isotope enrichment. Additionally, the applicability of dynamic nuclear polarization (DNP), which leads to sensitivity enhancements of 2 orders of magnitude, to (17)O is wrought with challenges due to the lack of spin diffusion and low polarization transfer efficiency from (1)H. Here, we demonstrate new DNP-based measurements that extend (17)O solid-state NMR beyond its current capabilities. The use of the PRESTO technique instead of conventional (1)H-(17)O cross-polarization greatly improves the sensitivity and enables the facile measurement of undistorted line shapes and two-dimensional (1)H-(17)O HETCOR NMR spectra as well as accurate internuclear distance measurements at natural abundance. This was applied for distinguishing hydrogen-bonded and lone (17)O sites on the surface of silica gel; the one-dimensional spectrum of which could not be used to extract such detail. Lastly, this greatly enhanced sensitivity has enabled, for the first time, the detection of surface hydroxyl sites on mesoporous silica at natural abundance, thereby extending the concept of DNP surface-enhanced NMR spectroscopy to the (17)O nuclide.
Collapse
Affiliation(s)
| | | | - Marek Pruski
- †U.S. DOE Ames Laboratory, Ames, Iowa 50011-3020, United States.,‡Department of Chemistry, Iowa State University, Ames, Iowa 50011-3020, United States
| |
Collapse
|
22
|
Michaelis VK, Keeler EG, Ong TC, Craigen KN, Penzel S, Wren JEC, Kroeker S, Griffin RG. Structural Insights into Bound Water in Crystalline Amino Acids: Experimental and Theoretical (17)O NMR. J Phys Chem B 2015; 119:8024-36. [PMID: 25996165 PMCID: PMC4894719 DOI: 10.1021/acs.jpcb.5b04647] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate here that the (17)O NMR properties of bound water in a series of amino acids and dipeptides can be determined with a combination of nonspinning and magic-angle spinning experiments using a range of magnetic field strengths from 9.4 to 21.1 T. Furthermore, we propose a (17)O chemical shift fingerprint region for bound water molecules in biological solids that is well outside the previously determined ranges for carbonyl, carboxylic, and hydroxyl oxygens, thereby offering the ability to resolve multiple (17)O environments using rapid one-dimensional NMR techniques. Finally, we compare our experimental data against quantum chemical calculations using GIPAW and hybrid-DFT, finding intriguing discrepancies between the electric field gradients calculated from structures determined by X-ray and neutron diffraction.
Collapse
Affiliation(s)
- Vladimir K. Michaelis
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Eric G. Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Ta-Chung Ong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Kimberley N. Craigen
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Susanne Penzel
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - John E. C. Wren
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Scott Kroeker
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| |
Collapse
|
23
|
Kong X, Tang A, Wang R, Ye E, Terskikh V, Wu G. Are the amide bonds in N-acyl imidazoles twisted? A combined solid-state 17O NMR, crystallographic, and computational study. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0397] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report synthesis of 17O-labeling and solid-state 17O NMR measurements of three N-acyl imidazoles of the type R-C(17O)-Im: R = p-methoxycinnamoyl (MCA-Im), R = 4-(dimethylamino)benzoyl (DAB-Im), and R = 2,4,6-trimethylbenzoyl (TMB-Im). Solid-state 17O NMR experiments allowed us to determine for the first time the 17O quadrupole coupling and chemical shift tensors in this class of organic compounds. We also determined the crystal structures of these compounds using single-crystal X-ray diffraction. The crystal structures show that, while the C(O)–N amide bond in DAB-Im exhibits a small twist, those in MCA-Im and TMB-Im are essentially planar. We found that, in these N-acyl imidazoles, the 17O quadrupole coupling and chemical shift tensors depend critically on the torsion angle between the conjugated acyl group and the C(O)–N amide plane. The computational results from a plane-wave DFT approach, which takes into consideration the entire crystal lattice, are in excellent agreement with the experimental solid-state 17O NMR results. Quantum chemical computations also show that the dependence of 17O NMR parameters on the Ar–C(O) bond rotation is very similar to that previously observed for the C(O)–N bond rotation in twisted amides. We conclude that one should be cautious in linking the observed NMR chemical shifts only to the twist of the C(O)–N amide bond.
Collapse
Affiliation(s)
- Xianqi Kong
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| | - Aaron Tang
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| | - Ruiyao Wang
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| | - Eric Ye
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Victor Terskikh
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Gang Wu
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, ON K7L 3N6, Canada
| |
Collapse
|
24
|
Density functional theory (DFT) prediction of structural and spectroscopic parameters of cytosine using harmonic and anharmonic approximations. Struct Chem 2015. [DOI: 10.1007/s11224-015-0573-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
25
|
Abstract
Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.
Collapse
Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry
- Prague
- Czech Republic
| | | |
Collapse
|
26
|
Theodorou V, Skobridis K, Alivertis D, Gerothanassis IP. Synthetic methodologies in organic chemistry involving incorporation of [¹⁷O] and [¹⁸O] isotopes. J Labelled Comp Radiopharm 2014; 57:481-508. [PMID: 24996002 DOI: 10.1002/jlcr.3212] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/06/2014] [Accepted: 05/15/2014] [Indexed: 11/09/2022]
Abstract
This review is a critical survey of the literature that aims to highlight the most significant developments on synthetic strategies involving stable oxygen isotopes ([(17)O] and [(18)O]). The labeling methodologies are categorized in groups, according to the oxygen-containing functional group.
Collapse
Affiliation(s)
- Vassiliki Theodorou
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, GR-451 10, Greece
| | | | | | | |
Collapse
|
27
|
Petersen PAD, Silva AS, Gonçalves MB, Lapolli AL, Ferreira AMC, Carbonari AW, Petrilli HM. Cd hyperfine interactions in DNA bases and DNA of mouse strains infected with Trypanosoma cruzi investigated by perturbed angular correlation spectroscopy and ab initio calculations. Biochemistry 2014; 53:3446-56. [PMID: 24801145 DOI: 10.1021/bi401680h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work, perturbed angular correlation (PAC) spectroscopy is used to study differences in the nuclear quadrupole interactions of Cd probes in DNA molecules of mice infected with the Y-strain of Trypanosoma cruzi. The possibility of investigating the local genetic alterations in DNA, which occur along generations of mice infected with T. cruzi, using hyperfine interactions obtained from PAC measurements and density functional theory (DFT) calculations in DNA bases is discussed. A comparison of DFT calculations with PAC measurements could determine the type of Cd coordination in the studied molecules. To the best of our knowledge, this is the first attempt to use DFT calculations and PAC measurements to investigate the local environment of Cd ions bound to DNA bases in mice infected with Chagas disease. The obtained results also allowed the detection of local changes occurring in the DNA molecules of different generations of mice infected with T. cruzi, opening the possibility of using this technique as a complementary tool in the characterization of complicated biological systems.
Collapse
Affiliation(s)
- Philippe A D Petersen
- Departamento de Física de Materiais e Mecânica, Instituto de Física, Universidade de São Paulo , CEP 05508-090 São Paulo, SP, Brazil
| | | | | | | | | | | | | |
Collapse
|
28
|
Viger-Gravel J, Leclerc S, Korobkov I, Bryce DL. Direct Investigation of Halogen Bonds by Solid-State Multinuclear Magnetic Resonance Spectroscopy and Molecular Orbital Analysis. J Am Chem Soc 2014; 136:6929-42. [DOI: 10.1021/ja5013239] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jasmine Viger-Gravel
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Sophie Leclerc
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Ilia Korobkov
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - David L. Bryce
- Department
of Chemistry and Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada K1N 6N5
| |
Collapse
|
29
|
Exploring 11B and 15N NMR parameters of C70−2x (BN) x fullerenes (x = 3–25) in connection with local structures and curvature effects: a DFT study. MONATSHEFTE FUR CHEMIE 2014. [DOI: 10.1007/s00706-013-1103-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
30
|
Michaelis VK, Corzilius B, Smith AA, Griffin RG. Dynamic nuclear polarization of 17O: direct polarization. J Phys Chem B 2013; 117:14894-906. [PMID: 24195759 PMCID: PMC3922122 DOI: 10.1021/jp408440z] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dynamic nuclear polarization of (17)O was studied using four different polarizing agents: the biradical TOTAPOL and the monoradicals trityl and SA-BDPA, as well as a mixture of the latter two. Field profiles, DNP mechanisms, and enhancements were measured to better understand and optimize directly polarizing this low-gamma quadrupolar nucleus using both mono- and biradical polarizing agents. Enhancements were recorded at <88 K and were >100 using the trityl (OX063) radical and <10 with the other polarizing agents. The >10,000-fold savings in acquisition time enabled a series of biologically relevant small molecules to be studied with small sample sizes and the measurement of various quadrupolar parameters. The results are discussed with comparison to room temperature studies and GIPAW quantum chemical calculations. These experimental results illustrate the strength of high field DNP and the importance of radical selection for studying low-gamma nuclei.
Collapse
Affiliation(s)
- Vladimir K. Michaelis
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | | | | | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| |
Collapse
|
31
|
Theoretically describing the 17O magnetic shielding constant of biomolecular systems: uracil and 5-fluorouracil in water environment. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1424-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
32
|
Kong X, Shan M, Terskikh V, Hung I, Gan Z, Wu G. Solid-State 17O NMR of Pharmaceutical Compounds: Salicylic Acid and Aspirin. J Phys Chem B 2013; 117:9643-54. [DOI: 10.1021/jp405233f] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xianqi Kong
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, K7L 3N6, Canada
| | - Melissa Shan
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, K7L 3N6, Canada
| | - Victor Terskikh
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, K7L 3N6, Canada
- National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A
0R6, Canada
| | - Ivan Hung
- Center of Interdisciplinary
Magnetic
Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United
States
| | - Zhehong Gan
- Center of Interdisciplinary
Magnetic
Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United
States
| | - Gang Wu
- Department
of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario, K7L 3N6, Canada
| |
Collapse
|
33
|
ESRAFILI MEHDID, MOHAMMADIRAD NAFISEH. A DFT INVESTIGATION ON BASIS SET SIZE AND HYDROGEN-BONDING EFFECTS ON 17O AND 2H NQR PARAMETERS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A systematic theoretical study on various maleic acid (MA) clusters has been carried out employing density functional theory (DFT) methods. The performance of two different functionals namely B3LYP and M06 in the prediction of geometries, 17 O and 2 H nuclei quadrupole coupling constant (CQ) values of the MA clusters has been assessed comparing the results to those experimental data. For DFT calculations, several basis sets have been used, including the recently developed Jensen's polarization-consistent basis set families, pcJ-n and pcS-n (n = 0,1,2,3). Calculations at the basis set limit indicate that the value of CQ(2 H ) in monomer MA, changes by 0.01–0.04 kHz for each of the final two basis set increments, and seems reasonable to conclusion that the pcJ-3 result is within a few kHz of the basis set limit. Convergence with respect to basis set size was found to be very good, and the pcJ-1 and pcS-1 basis sets provided a good compromise between the basis set limit and computational expense. In most cases, the differences between B3LYP and M06 results for a given basis set are in a range of 1–2%. On the other hand, no systematic changes in the CQ(17 O ) or CQ(2 H ) were found for basis sets larger than double-ζ. Thus, the usual assumption that double-ζ basis set (pcJ-1 and pcS-1) results in the acceptable CQ values, seems to be valid in the case of 17 O and 2 H nuclei.
Collapse
Affiliation(s)
- MEHDI D. ESRAFILI
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - NAFISEH MOHAMMADIRAD
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| |
Collapse
|
34
|
Shaghaghi H, Ebrahimi HP, Bahrami Panah N, Tafazzoli M. Layer selection effect on solid state 13C and 15N chemical shifts calculation using ONIOM approach. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2013; 51-52:31-36. [PMID: 23414630 DOI: 10.1016/j.ssnmr.2013.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/15/2013] [Accepted: 01/21/2013] [Indexed: 06/01/2023]
Abstract
Solid state (13)C and (15)N chemical shifts of uracil and imidazole have been calculated using a 2-layer ONIOM approach at 32 levels of theory. The effect of electron correlation between two layers has been investigated by choosing two different kinds of layer selection. Factorial design has been applied as a multivariate technique to analyze the effect of wave function and layer selection on solid state (13)C and (15)N chemical shifts calculations. PBEPBE/6-311+G(d,p) was recommended as an optimally selected level of theory for high layer in both models. It is illustrated that considering the electron correlation of two layers of ONIOM models is important factor to calculate solid state (15)N chemical shifts. The agreement between the calculated and experimental values of solid state (13)C and (15)N chemical shifts using ONIOM (PBEPBE/6-311+G(d,p):AM1) for both uracil and imidazole confirmed the reliability of the selected wave functions and layer selection.
Collapse
Affiliation(s)
- Hoora Shaghaghi
- Department of Chemistry, Sharif University of Technology, Tehran, Iran
| | | | | | | |
Collapse
|
35
|
Baggioli A, Crescenzi O, Field MJ, Castiglione F, Raos G. Computational 17O-NMRspectroscopy of organic acids and peracids: comparison of solvation models. Phys Chem Chem Phys 2013; 15:1130-40. [DOI: 10.1039/c2cp43021e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
36
|
Dračínský M, Hodgkinson P. A molecular dynamics study of the effects of fast molecular motions on solid-state NMR parameters. CrystEngComm 2013. [DOI: 10.1039/c3ce40612a] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
37
|
Kong X, O’Dell LA, Terskikh V, Ye E, Wang R, Wu G. Variable-Temperature 17O NMR Studies Allow Quantitative Evaluation of Molecular Dynamics in Organic Solids. J Am Chem Soc 2012; 134:14609-17. [DOI: 10.1021/ja306227p] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xianqi Kong
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario K7L 3N6, Canada
| | - Luke A. O’Dell
- National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A
0R6, Canada
| | - Victor Terskikh
- National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A
0R6, Canada
| | - Eric Ye
- Department of
Chemistry, University of Ottawa, 10 Marie
Curie Private, Ottawa,
Ontario K1N 6N5, Canada
| | - Ruiyao Wang
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston,
Ontario K7L 3N6, Canada
| |
Collapse
|
38
|
Michaelis VK, Markhasin E, Daviso E, Herzfeld J, Griffin RG. Dynamic Nuclear Polarization of Oxygen-17. J Phys Chem Lett 2012; 3:2030-2034. [PMID: 23024834 PMCID: PMC3459188 DOI: 10.1021/jz300742w] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Oxygen-17 detected DNP NMR of a water/glycerol glass enabled an 80-fold enhancement of signal intensities at 82 K, using the biradical TOTAPOL. The >6,000-fold savings in acquisition time enables (17)O-(1)H distance measurements and heteronuclear correlation experiments. These experiments are the initial demonstration of the feasibility of DNP NMR on quadrupolar (17)O.
Collapse
Affiliation(s)
- Vladimir K Michaelis
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA, 02139
| | | | | | | | | |
Collapse
|
39
|
Goswami M, Madhu PK. Combining dipolar-quadrupolar correlation spectroscopy with isotropic shift resolution in magic-angle-spinning 17O NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 219:4-12. [PMID: 22595292 DOI: 10.1016/j.jmr.2012.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Revised: 03/05/2012] [Accepted: 03/17/2012] [Indexed: 05/31/2023]
Abstract
We explore the effect of heteronuclear dipolar recoupling on the satellite and multiple-quantum transitions of a half-integer-spin quadrupolar nucleus coupled to a single spin-12. A three-dimensional experiment is introduced that resolves different quadrupolar sites whilst allowing simultaneous extraction of the quadrupolar coupling constants, asymmetry parameters of the electric field gradient, and the isotropic shifts of the quadrupolar nucleus. The experiment also enables estimation of the heteronuclear dipolar coupling constant between the spin-1/2 and half-integer spin quadrupolar nucleus. The relative orientation of the dipolar tensor with respect to the quadrupolar tensor can be estimated by comparing experiments and simulations. Experimental results are shown on a sample of brucite, Mg((17)OH)(2), where the (1)H-(17)O bond distance is estimated.
Collapse
Affiliation(s)
- M Goswami
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | | |
Collapse
|
40
|
|
41
|
Brzyska A, Woliński K, Jaszuński M. Theoretical studies of the dependence of nuclear quadrupole coupling constants on intermolecular forces. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
|
42
|
Castiglione F, Baggioli A, Citterio A, Mele A, Raos G. Organic Peracids: A Structural Puzzle for 17O NMR and Ab Initio Chemical Shift Calculations. J Phys Chem A 2012; 116:1814-9. [DOI: 10.1021/jp210679y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Franca Castiglione
- Dipartimento di Chimica, Materiali e Ingegneria Chimica
“G. Natta”, Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
| | - Alberto Baggioli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica
“G. Natta”, Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
| | - Attilio Citterio
- Dipartimento di Chimica, Materiali e Ingegneria Chimica
“G. Natta”, Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
| | - Andrea Mele
- Dipartimento di Chimica, Materiali e Ingegneria Chimica
“G. Natta”, Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
| | - Guido Raos
- Dipartimento di Chimica, Materiali e Ingegneria Chimica
“G. Natta”, Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy
| |
Collapse
|
43
|
Abstract
AbstractTo investigate the influence of C-doping on the electrostatic structure properties in the frame work of density functional theory (DFT), we considered beryllium monoxide nanotubes (BeONTs), consisting of 60 Be and 60 O atoms. Full geometry optimizations are performed for all structures, i.e., all atoms are allowed to relax. Afterwards, the chemical shielding (CS) tensors are calculated for Be-9, O-17 and C-13 nuclei in the C-doped forms and also pristine models of the (10, 0) zigzag and (5, 5) armchair BeONTs. Formation energies indicate that C-doping of Be atom (CBe form) could be more favorable than C-doping of O atom (CO form) in both zigzag and armchair BeONTs. Gap energies and dipole moments detected the effects of dopant in the (5, 5) armchair models; however, those parameters did not indicate any significant changes in the C-doped (10, 0) zigzag BeONT models. The results show that the CS values for the Be and O atoms-contributed to the Be-C bonds or those atoms close to the C-doped region-in the CO form of BeONTs (zigzag and armchair) are changed. The same values only for the O atoms-contributed to the O-C bonds- in the CBe form of BeONTs (zigzag and armchair) are changed.
Collapse
|
44
|
Esrafili MD, Alizadeh V. Characterization of O–H⋯O interactions in linear and cyclic clusters of boric acid: An ab initio, DFT, QTAIM and NBO study. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.07.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
45
|
Esrafili MD. Intra- and inter-molecular interactions in salicylic acid — Theoretical calculations of 17O and 1H chemical shielding tensors and QTAIM analysis. CAN J CHEM 2011. [DOI: 10.1139/v11-105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A density functional theory (DFT) study was performed to examine intra- and inter-molecular hydrogen bond (HB) properties in crystalline salicylic acid (SA). BLYP, B3LYP, and M06 functionals with 6–311++G** basis set were employed to calculate NMR chemical shielding isotropy (σiso) and anisotropy (Δσ) at the sites of the 17O and 1H nuclei of SA. From this study, it appears that the intra- and inter-molecular O–H···O as well as C–H···O HBs around the SA molecule in the crystal lattice have a major influence on the chemical shielding tensors and more specifically on the carbonyl 17O isotropy value. The quantum theory of atoms in molecules (QTAIM) analysis was also employed to elucidate the interaction characteristics in SA H-bonded network. Based on QTAIM results, a partial covalent character is attributed to the intra- and inter-molecular O–H···O HBs in SA.
Collapse
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| |
Collapse
|
46
|
Esrafili MD, Alizadeh V. A theoretical investigation of hydrogen bonding effects on oxygen and hydrogen chemical shielding tensors of aspirin. Struct Chem 2011. [DOI: 10.1007/s11224-011-9810-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
47
|
karami L, Behzadi H, Hadipour NL, Mousavi-khoshdel M. Study of CO⋯HN Hydrogen bond interactions in amyloid beta (Aβ): A DFT study of the electric field gradient and CS tensors and NBO analysis. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.01.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
48
|
Latosińska JN, Seliger J, Zagar V, Burchardt DV. A comparative study of the hydrogen-bonding patterns and prototropism in solid 2-thiocytosine (potential antileukemic agent) and cytosine, as studied by 1H-14N NQDR and QTAIM/ DFT. J Mol Model 2011; 18:11-26. [PMID: 21445709 PMCID: PMC3249547 DOI: 10.1007/s00894-011-1021-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 02/13/2011] [Indexed: 02/03/2023]
Abstract
A potential antileukemic and anticancer agent, 2-thiocytosine (2-TC), has been studied experimentally in the solid state by 1H-14N NMR-NQR double resonance (NQDR) and theoretically by the quantum theory of atoms in molecules (QTAIM)/density functional theory (DFT). Eighteen resonance frequencies on 14N were detected at 180 K and assigned to particular nitrogen sites (−NH2, –N=, and –NH–) in 2-thiocytosine. Factors such as the nonequivalence of molecules (connected to the duplication of sites) and possible prototropic tautomerism (capable of modifying the type of site due to proton transfer) were taken into account during frequency assignment. The result of replacing oxygen with sulfur, which leads to changes in the intermolecular interaction pattern and molecular aggregation, is discussed. This study demonstrates the advantages of combining NQDR and DFT to extract detailed information on the H-bonding properties of crystals with complex H-bonding networks. Solid-state properties were found to have a profound impact on the stabilities and reactivities of both compounds. The experimental 1H-14N NQDR spectrum of 2-thiocytosine obtained at T = 180 K by the solid effect technique (left) and 3d distribution of the electron density Laplacian calculated by DFT (right) ![]()
Collapse
|
49
|
Behzadi H, Olyai MRTB, van der Spoel D. Probing 13C chemical shielding tensors in cryptolepine and two bromo-substituted analogs for antiplasmodial activity. J Mol Model 2011; 17:3289-97. [DOI: 10.1007/s00894-011-1009-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 02/02/2011] [Indexed: 11/30/2022]
|
50
|
|