1
|
Pascariu M, Bernasconi L, Krzystyniak M, Taylor J, Rudić S. Comprehensive Analysis of Methyl-β-D-ribofuranoside: A Multifaceted Spectroscopic and Theoretical Approach. J Phys Chem A 2024; 128:2111-2120. [PMID: 38469744 PMCID: PMC10961842 DOI: 10.1021/acs.jpca.4c00266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
This study presents a comprehensive analysis of the vibrational spectra of methyl-β-D-ribofuranoside. Employing a combination of inelastic neutron scattering, Raman, and infrared spectroscopy allows for the observation of all modes regardless of the selection rules. The experimental techniques were complemented by density functional theory computational methods using both gas-phase (Gaussian) and solid-state (CRYSTAL, CASTEP) approaches to provide an unambiguous assignment of the defining vibrational features. Two distinct structures of the molecule were identified in the unit cell, differentiated mainly by the orientation of the furanose ring O-H bonds. The low-energy region of the spectrum (<400 cm-1) is dominated by lattice vibrations and functional group rotation, while the midenergy region is dominated by out-of-plane bending motions of the furanose ring (400-900 cm-1) and by C-H bending in the methyl and methylene groups (1400-1600 cm-1). The high-energy region (>2800 cm-1) encompasses the C-H and O-H stretching modes and offers convincing evidence of at least one H-bonding interaction between the two structures of methyl-β-D-ribofuranoside.
Collapse
Affiliation(s)
- Matei Pascariu
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Leonardo Bernasconi
- Center
for Research Computing & Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Matthew Krzystyniak
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
| | - James Taylor
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
| | - Svemir Rudić
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, STFC, Harwell Campus, Chilton, Oxfordshire OX11 0QX, U.K.
| |
Collapse
|
2
|
Konieczna J, Wrońska K, Kalińska M, Liberek B, Nowacki A. Conformational preferences of guanine-containing threose nucleic acid building blocks in B3LYP studies. Carbohydr Res 2024; 537:109055. [PMID: 38373388 DOI: 10.1016/j.carres.2024.109055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/22/2024] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
In this paper, detailed and systematic gas-phase B3LYP conformational studies of four monomers of threose nucleic acid (TNA) with guanine attached at the C1' atom and bearing different substituents (OH, OP(=O)OH2 and OCH3) in the C2' and C3' positions of the α-l-threofuranose moiety are presented. All exocyclic single-bond (χ, ε and γ) rotations, as well as the ν0-ν4 endocyclic torsion angles, were taken into consideration. Three (threoguanosines TG1-TG3) or two (TG4) energy minima were found for the rotation about the χ torsion angle. The syn orientation (the A rotamer family) is strongly privileged in geometries TG1 and TG2, whereas the anti orientation (the C rotamer family) and the syn orientation are observed to be in equilibrium (with populations of 56% and 44%, respectively) for TG3. In the case of TG4, the high-anti orientation (the B rotamer family) turned out to be by far the most favourable, with the contribution exceeding 90% in equilibrium. Such a preference can be attributed to the inability of H-bonding between sugar and nucleobase and possibly because of the steric strains. The low-energy conformers of TG1-TG4 occupy the northeastern (P ∼ 40°) and/or southern (P ∼ 210°) parts of the pseudorotational wheel, which fits the A- and B-type DNA helices quite well. Additionally, in the case of TG4, some relatively stable geometries have the furanoid ring in conformation lying on the northwestern part of the pseudorotational wheel (P ∼ 288°).
Collapse
Affiliation(s)
- Justyna Konieczna
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland
| | - Karolina Wrońska
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland
| | - Marta Kalińska
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland
| | - Beata Liberek
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland
| | - Andrzej Nowacki
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308, Gdańsk, Poland.
| |
Collapse
|
3
|
Ishiwata A, Narita S, Kimura K, Tanaka K, Fujita K, Fushinobu S, Ito Y. Mechanism-based inhibition of GH127/146 cysteine glycosidases by stereospecifically functionalized l-arabinofuranosides. Bioorg Med Chem 2022; 75:117054. [PMID: 36334492 DOI: 10.1016/j.bmc.2022.117054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022]
Abstract
To understand the precise mechanism of the glycoside hydrolase (GH) family 127, a cysteine β-l-arabinofuranosidase (Arafase) - HypBA1 - has been isolated from Bifidobacterium longum in the human Gut microbiota, and the design and synthesis of the mechanism-based inhibitors such as l-Araf-haloacetamides have been carried out. The α-l-Araf-azide derivative was used as the monoglycosylamine equivalent to afford the l-Araf-chloroacetamides (α/β-1-Cl) as well as bromoacetamides (α/β-1-Br) in highly stereoselective manner through Staudinger reaction followed by amide formation with/without anomerization. Against HypBA1, the probes 1, especially in the case of α/β-1-Br inhibited the hydrolysis. Conformational implications of these observations are discussed in this manuscript. Additional examinations using l-Araf-azides (α/β-5) resulted in further mechanistic observations of the GH127/146 cysteine glycosidases, including the hydrolysis of β-5 as the substrate and oxidative inhibition by α-5 using the GH127 homologue.
Collapse
Affiliation(s)
- Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan.
| | - Satoru Narita
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Systems Engineering and Science, Shibaura Institute of Technology Saitama 337-8570, Japan
| | - Kenta Kimura
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Systems Engineering and Science, Shibaura Institute of Technology Saitama 337-8570, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Department of Chemical Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan.
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo 113-8647, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8647, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, Saitama 351-0198, Japan; Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
| |
Collapse
|
4
|
Nester K, Gaweda K, Plazinski W. A GROMOS Force Field for Furanose-Based Carbohydrates. J Chem Theory Comput 2019; 15:1168-1186. [DOI: 10.1021/acs.jctc.8b00838] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| |
Collapse
|
5
|
Stortz CA, Sarotti AM. Exhaustive exploration of the conformational landscape of mono- and disubstituted five-membered rings by DFT and MP2 calculations. RSC Adv 2019; 9:24134-24145. [PMID: 35527879 PMCID: PMC9069843 DOI: 10.1039/c9ra03524a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/18/2019] [Indexed: 11/21/2022] Open
Abstract
The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set. Our results showed that the conformational preference of these compounds was governed mainly by the specific characteristics of the substituents, with a minor influence of the level of theory employed. After a detailed analysis of the computational data, we found an interesting preference of the electronegative substituents to take pseudo-axial positions, whereas alkyl groups preferred adopting the pseudo-equatorial locations. Such preferences were pronounced with MP2 and M06-2X and underestimated by B3LYP. Despite each level of theory affording different landscapes in many cases, as a general trend, we noticed that M06-2X afforded much higher correlation with the MP2 results than B3LYP. The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set.![]()
Collapse
Affiliation(s)
- Carlos A. Stortz
- Universidad de Buenos Aires
- Facultad de Ciencias Exactas
- Departamento de Química Orgánica
- Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR)
- 1428 Buenos Aires
| | - Ariel M. Sarotti
- Instituto de Química Rosario (CONICET)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Rosario 2000
- Argentina
| |
Collapse
|
6
|
Shaaban IA. Conformational analysis, infrared/Raman spectral assignment, and electronic structural studies of 1,3-dimethyl-2-imidazolidinone using quantum chemical calculations. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
7
|
Bednarko J, Stachurski O, Wielińska J, Kozakiewicz K, Liberek B, Nowacki A. Threocytidines: Insight into the Conformational Preferences of Artificial Threose Nucleic Acid (TNA) Building Blocks in B3LYP Studies. J Mol Graph Model 2018; 80:157-172. [PMID: 29366882 DOI: 10.1016/j.jmgm.2018.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
Abstract
A systematic DFT conformational studies of four building blocks of TNA with cytosine attached to the C1' atom of the α-L-threofuranose moiety are presented. Structures bearing 2'-OR and 3'-OR substituents, where R represents H, CH3 and phosphate groups, were used in the studies using a B3LYP functional in the gas phase. The χ angle (C2-N1-C1'-O4'), the ν0-ν4 endocyclic torsion angles and the exocyclic torsion angles ε (X-O2'-C2'-C1') and γ (X-O3'-C3'-C2') geometry parameter variations were taken into consideration. Three energy minima, high-anti, anti and syn, were found for the rotation about the C1'-N1 bond. The high-anti orientation of the base with respect to the sugar moiety, turned out to be preferred, regardless of the substituents at the C2' and C3' positions. Other orientations are at least 1.65 kcal/mol higher in Gibbs free energy than the high-anti one. It has been shown that intramolecular H-bonds and the anomeric effect of phosphate groups strongly affect the conformational preferences of the studied compounds. Further, the structure of substituents attached to the sugar moiety influence the pucker of the furanoid ring. The furanoid ring in the global minima of the compound with two OH groups (TC1) in the 2' and 3' positions, and the compound having a 3'-phosphate group (TC2), adopt roughly the same conformation located at the southern range of the pseudorotation wheel, and thus are close to those found in the B type DNA helix. The low-energy high-anti rotamers of the geometry with the phosphate group attached to the sugar ring in the 2' position (TC3) and the geometry with two methoxyl groups (TC4) have their furanoid rings in conformations resembling those found in A DNA and RNA helices (the northern range of the pseudorotation wheel).
Collapse
Affiliation(s)
- Justyna Bednarko
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308 Gdańsk, Poland
| | - Oktawian Stachurski
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308 Gdańsk, Poland
| | - Justyna Wielińska
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308 Gdańsk, Poland
| | - Karol Kozakiewicz
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308 Gdańsk, Poland
| | - Beata Liberek
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308 Gdańsk, Poland
| | - Andrzej Nowacki
- Faculty of Chemistry, Department of Organic Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80-308 Gdańsk, Poland
| |
Collapse
|
8
|
Walczak D, Nowacki A, Trzybiński D, Samaszko-Fiertek J, Myszka H, Sikorski A, Liberek B. Conformational studies of N-(α-d-glucofuranurono-6,3-lactone)- and N-(methyl β-d-glucopyranuronate)-p-nitroanilines. Carbohydr Res 2017; 446-447:85-92. [PMID: 28554013 DOI: 10.1016/j.carres.2017.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/28/2017] [Accepted: 05/13/2017] [Indexed: 10/19/2022]
Abstract
N-(α-d-Glucofuranurono-6,3-lactone)-p-nitroaniline and N-(methyl β-d-glucopyranuronate)-p-nitroaniline were obtained as crystalline solids. The single-crystal X-ray diffraction, NMR data and DFT calculations for N-(α-d-glucofuranurono-6,3-lactone)-p-nitroaniline indicate that this N-furanoside adopts a 3T2/3E-like conformation in the crystal lattice, solution and gas phase. Thus, the structure of recorded for N-furanoside 1H NMR spectrum is indicative of the 3T2/3E region of the pseudorotational itinerary for furanose derivatives with α-d-gluco, β-L-ido and α-d-xylo configurations. Moreover, it is concluded that the 1T2/E2/3T2/3E region of the pseudorotational itinerary for furanose derivatives with d-gluco, L-ido and d-xylo configurations should be characterised by the lack of coupling between H2 and H3 protons, irrespective of the anomeric configuration. Such a lack of vicinal coupling is characteristic for some of the trans-oriented furanose ring protons. The single-crystal X-ray diffraction and NMR data for N-(methyl β-d-glucopyranuronate)-p-nitroaniline indicate that this N-glucuronide adopts the 4C1 conformation, both in the crystal lattice and solution. The occurrence of anomeric effects in the presented N-glycosides is discussed. The crystal structure analysis of both N-glycosides gives evidence that the amine group in p-nitroaniline is planar due to the nitrogen sp2 hybridisation.
Collapse
Affiliation(s)
- Dominik Walczak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Andrzej Nowacki
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Damian Trzybiński
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Henryk Myszka
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Artur Sikorski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Beata Liberek
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| |
Collapse
|
9
|
LeNouen D, Defoin A, Behr JB. Determination of the Relative Configuration and Conformational Analysis of Five-memberedN-Acyl-Iminosugars by Relevant3JCoupling Constants. ChemistrySelect 2016. [DOI: 10.1002/slct.201600287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Didier LeNouen
- Université de Haute-Alsace; Institut J. B. Donnet; 3 bis rue Alfred Werner F-68093 Mulhouse Cedex France
| | - Albert Defoin
- Université de Haute-Alsace; Institut J. B. Donnet; 3 bis rue Alfred Werner F-68093 Mulhouse Cedex France
| | - Jean-Bernard Behr
- Université de Reims-Champagne-Ardenne; ICMR-UMR 7312, BP 1039 F-51687 Reims Cedex 2 France
| |
Collapse
|
10
|
Wang X, Woods RJ. Insights into furanose solution conformations: beyond the two-state model. JOURNAL OF BIOMOLECULAR NMR 2016; 64:291-305. [PMID: 26968894 PMCID: PMC5115177 DOI: 10.1007/s10858-016-0028-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/08/2016] [Indexed: 05/15/2023]
Abstract
A two-state model is commonly used for interpreting ring conformations of furanoses based on NMR scalar (3) J-coupling constants, with the ring populating relatively narrow distributions in the North and the South of the pseudorotation itinerary. The validity of this simple approach has been questioned, and is examined here in detail employing molecular dynamics (MD) simulations with a new GLYCAM force field parameter set for furanoses. Theoretical (3) J-coupling constants derived from unrestrained MD simulations with the new furanose-specific parameters agreed with the experimental coupling constants to within 1 Hz on average. The results confirm that a two state model is a reasonable description for the ring conformation in the majority of methyl furanosides. However, in the case of methyl α-D-arabinofuranoside the ring populates a continuum of states from North to South via the eastern side of the pseudorotational itinerary. Two key properties are responsible for these differences. Firstly, East and West regions in β- and α-anomers, respectively, are destabilized by the absence of the anomeric effect. And, secondly, East or West conformations can be further destabilized by repulsive interactions among vicinal hydroxyl groups and ring oxygen atoms when the vicinal hydroxyl groups are in syn-configurations (such as in ribose and lyxose) more so than when in anti (arabinose, xylose).
Collapse
Affiliation(s)
- Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
11
|
Lavoie S, Ouellet M, Fleury PY, Gauthier C, Legault J, Pichette A. Complete (1)H and (13)C NMR assignments of a series of pergalloylated tannins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:168-174. [PMID: 26352595 DOI: 10.1002/mrc.4328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/31/2015] [Accepted: 08/03/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Serge Lavoie
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 boul. de l'Université, Chicoutimi, Québec, G7H 2B1, Canada
| | - Michael Ouellet
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 boul. de l'Université, Chicoutimi, Québec, G7H 2B1, Canada
| | - Pierre-Yves Fleury
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 boul. de l'Université, Chicoutimi, Québec, G7H 2B1, Canada
| | - Charles Gauthier
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 boul. de l'Université, Chicoutimi, Québec, G7H 2B1, Canada
- Institut de Chimie IC2MP, Université de Poitiers, CNRS-UMR 7285, Équipe Synthèse Organique, 4 rue Michel Brunet, 86073, Poitiers Cedex-9, France
| | - Jean Legault
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 boul. de l'Université, Chicoutimi, Québec, G7H 2B1, Canada
| | - André Pichette
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 boul. de l'Université, Chicoutimi, Québec, G7H 2B1, Canada
| |
Collapse
|
12
|
Écija P, Uriarte I, Spada L, Davis BG, Caminati W, Basterretxea FJ, Lesarri A, Cocinero EJ. Furanosic forms of sugars: conformational equilibrium of methyl β-d-ribofuranoside. Chem Commun (Camb) 2016; 52:6241-4. [DOI: 10.1039/c6cc01180b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The rotational spectrum of the isolated ribofuranoside unit, the biologically active sugar form, revealed two structures with a similar puckering to the RNA units in crystals.
Collapse
Affiliation(s)
- Patricia Écija
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Iciar Uriarte
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Lorenzo Spada
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | | | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 1-40126 Bologna
- Italy
| | - Francisco J. Basterretxea
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Emilio J. Cocinero
- Departamento de Química Física
- Facultad de Ciencia y Tecnología
- Universidad del País Vasco (UPV/EHU)
- 48080 Bilbao
- Spain
| |
Collapse
|
13
|
Taha HA, Castillo N, Roy PN, Lowary TL. Conformational Studies of Methyl β-d-Arabinofuranoside Using the AMBER/GLYCAM Approach. J Chem Theory Comput 2015; 5:430-8. [PMID: 26610115 DOI: 10.1021/ct800384h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Furanosides are important constituents of a number of glycoconjugates from many microorganisms. The highly flexible nature of these furanosyl moieties is believed to contribute significantly to their role in biological processes. Therefore, an understanding of the conformational preferences of these molecules is an important area of research. As part of a larger program involved in the conformational analysis of mycobacterial oligofuranosides, molecular dynamics simulations on methyl β-d-arabinofuranoside (3) have been carried out using the AMBER forcefield and the GLYCAM carbohydrate parameter set. This approach was used to predict the rotamer population distribution about the hydroxymethyl group (C4-C5 bond) as well as the ring puckering of this flexible ring system. Comparison of the conformer distributions obtained during the simulation of 3 using the TIP3P water model with those obtained by analysis of (1)H-(1)H coupling constant data indicated that this water model was insufficient to describe the solvation of this system. However, the use of the TIP4P and TIP5P models led to improved agreement with conformer populations obtained from NMR data.
Collapse
Affiliation(s)
- Hashem A Taha
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Norberto Castillo
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Pierre-Nicholas Roy
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Todd L Lowary
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| |
Collapse
|
14
|
Jana M, MacKerell AD. CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides. J Phys Chem B 2015; 119:7846-59. [PMID: 26018564 DOI: 10.1021/acs.jpcb.5b01767] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An empirical all-atom CHARMM polarizable force filed for aldopentofuranoses and methyl-aldopentofuranosides based on the classical Drude oscillator is presented. A single electrostatic model is developed for eight different diastereoisomers of aldopentofuranoses by optimizing the existing electrostatic and bonded parameters as transferred from ethers, alcohols, and hexopyranoses to reproduce quantum mechanical (QM) dipole moments, furanose-water interaction energies and conformational energies. Optimization of selected electrostatic and dihedral parameters was performed to generate a model for methyl-aldopentofuranosides. Accuracy of the model was tested by reproducing experimental data for crystal intramolecular geometries and lattice unit cell parameters, aqueous phase densities, and ring pucker and exocyclic rotamer populations as obtained from NMR experiments. In most cases the model is found to reproduce both QM data and experimental observables in an excellent manner, whereas for the remainder the level of agreement is in the satisfactory regimen. In aqueous phase simulations the monosaccharides have significantly enhanced dipoles as compared to the gas phase. The final model from this study is transferrable for future studies on carbohydrates and can be used with the existing CHARMM Drude polarizable force field for biomolecules.
Collapse
Affiliation(s)
- Madhurima Jana
- †Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street HSF II, Baltimore, Maryland 21201, United States.,‡Department of Chemistry, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India
| | - Alexander D MacKerell
- †Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street HSF II, Baltimore, Maryland 21201, United States
| |
Collapse
|
15
|
Lak P, Makeneni S, Woods RJ, Lowary TL. Specificity of furanoside-protein recognition through antibody engineering and molecular modeling. Chemistry 2014; 21:1138-48. [PMID: 25413161 DOI: 10.1002/chem.201405259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Indexed: 01/06/2023]
Abstract
Recognition of furanosides (five-membered ring sugars) by proteins plays important roles in host-pathogen interactions. In comparison to their six-membered ring counterparts (pyranosides), detailed studies of the molecular motifs involved in the recognition of furanosides by proteins are scarce. Here the first in-depth molecular characterization of a furanoside-protein interaction system, between an antibody (CS-35) and cell wall polysaccharides of mycobacteria, including the organism responsible for tuberculosis is reported. The approach was centered on the generation of the single chain variable fragment of CS-35 and a rational library of its mutants. Investigating the interaction from various aspects revealed the structural motifs that govern the interaction, as well as the relative contribution of molecular forces involved in the recognition. The specificity of the recognition was shown to originate mainly from multiple CH-π interactions and, to a lesser degree, hydrogen bonds formed in critical distances and geometries.
Collapse
Affiliation(s)
- Parnian Lak
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada)
| | | | | | | |
Collapse
|
16
|
Chlubnová I, Králová B, Dvořáková H, Hošek P, Spiwok V, Filipp D, Nugier-Chauvin C, Daniellou R, Ferrières V. The versatile enzyme Araf51 allowed efficient synthesis of rare pathogen-related β-d-galactofuranosyl-pyranoside disaccharides. Org Biomol Chem 2014; 12:3080-9. [DOI: 10.1039/c3ob42519c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
17
|
Richards MR, Bai Y, Lowary TL. Comparison between DFT- and NMR-based conformational analysis of methyl galactofuranosides. Carbohydr Res 2013; 374:103-14. [PMID: 23660004 DOI: 10.1016/j.carres.2013.03.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 11/26/2022]
Abstract
Galactofuranose (Galf) residues are found in a number of microbial polysaccharides, and knowledge of their conformation is key for developing a molecular-level understanding of their biological roles. To this end, we studied 180 conformations of methyl α- and β-Galf in aqueous solution (COSMO solvation model) using density functional theory (DFT). We compare the calculated low energy conformations to those determined from the program PSEUROT using (1)H NMR data. The lowest energy ring conformation for methyl α-Galf is (2)E, and this conformer is also the major solution conformation obtained by NMR spectroscopy. For methyl β-Galf, (4)E is the lowest energy ring conformation; however, DFT results do not agree with the solution NMR spectroscopic results. Additionally, we developed Galf-specific Karplus-like equations from these conformations.
Collapse
Affiliation(s)
- Michele R Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada
| | | | | |
Collapse
|
18
|
Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| |
Collapse
|
19
|
Guyenne S, León EI, Martín A, Pérez-Martín I, Suárez E. Intramolecular 1,8-Hydrogen Atom Transfer Reactions in Disaccharide Systems Containing Furanose Units. J Org Chem 2012; 77:7371-91. [DOI: 10.1021/jo301153u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sabrina Guyenne
- Instituto de Productos Naturales y Agrobiología del CSIC, Carretera de La Esperanza 3, 38206 La Laguna,
Tenerife, Spain
| | - Elisa I. León
- Instituto de Productos Naturales y Agrobiología del CSIC, Carretera de La Esperanza 3, 38206 La Laguna,
Tenerife, Spain
| | - Angeles Martín
- Instituto de Productos Naturales y Agrobiología del CSIC, Carretera de La Esperanza 3, 38206 La Laguna,
Tenerife, Spain
| | - Inés Pérez-Martín
- Instituto de Productos Naturales y Agrobiología del CSIC, Carretera de La Esperanza 3, 38206 La Laguna,
Tenerife, Spain
| | - Ernesto Suárez
- Instituto de Productos Naturales y Agrobiología del CSIC, Carretera de La Esperanza 3, 38206 La Laguna,
Tenerife, Spain
| |
Collapse
|
20
|
Islam SM, Roy PN. Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment. J Chem Theory Comput 2012; 8:2412-23. [DOI: 10.1021/ct200789w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Shahidul M. Islam
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| |
Collapse
|
21
|
Islam SM, Richards MR, Taha HA, Byrns SC, Lowary TL, Roy PN. Conformational Analysis of Oligoarabinofuranosides: Overcoming Torsional Barriers with Umbrella Sampling. J Chem Theory Comput 2011; 7:2989-3000. [DOI: 10.1021/ct200333p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Shahidul M. Islam
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Michele R. Richards
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Hashem A. Taha
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Simon C. Byrns
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| |
Collapse
|
22
|
Napolitano JG, Gavín JA, García C, Norte M, Fernández JJ, Daranas AH. On the configuration of five-membered rings: a spin-spin coupling constant approach. Chemistry 2011; 17:6338-47. [PMID: 21547972 DOI: 10.1002/chem.201100412] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Indexed: 11/06/2022]
Abstract
Five-membered rings are clearly among the most common structural motifs found in chemistry and biology. Nevertheless, the configuration of conformationally mobile five-membered rings is often difficult to assign from nuclear magnetic resonance (NMR) data. A simple, reliable, and efficient approach for the stereochemical analysis of five-membered rings based on the measurement of NMR coupling constants is presented. Density functional theory calculations using representative conformations of the full conformational space available to rings with different substitution patterns were used to identify differences between the accessible coupling constant values for cis and trans relative orientations of the substituents. The calculations were assessed experimentally using NMR data obtained from a number of models. This approach can be easily used to analyze different five-membered rings, such as oxolanes, cyclopentanes, furanosides and pyrrolidines, and their relative configuration can be determined without the need for making further conformational considerations.
Collapse
Affiliation(s)
- José G Napolitano
- Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain
| | | | | | | | | | | |
Collapse
|
23
|
Taha HA, Castillo N, Sears DN, Wasylishen RE, Lowary TL, Roy PN. Conformational Analysis of Arabinofuranosides: Prediction of 3JH,H Using MD Simulations with DFT-Derived Spin−Spin Coupling Profiles. J Chem Theory Comput 2009; 6:212-22. [DOI: 10.1021/ct900477x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Hashem A. Taha
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Norberto Castillo
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Devin N. Sears
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Roderick E. Wasylishen
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Todd L. Lowary
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Pierre-Nicholas Roy
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, Gunning-Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2, and Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| |
Collapse
|
24
|
Hatcher E, Guvench O, MacKerell AD. CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B 2009; 113:12466-76. [PMID: 19694450 PMCID: PMC2741538 DOI: 10.1021/jp905496e] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides), and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids, and/or lipids when combined with existing CHARMM biomolecular force fields.
Collapse
Affiliation(s)
- Elizabeth Hatcher
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, 20 Penn Street HSF II, University of Maryland, Baltimore, Maryland 21201
| |
Collapse
|
25
|
Coxon B. Developments in the Karplus equation as they relate to the NMR coupling constants of carbohydrates. Adv Carbohydr Chem Biochem 2009; 62:17-82. [PMID: 19501704 DOI: 10.1016/s0065-2318(09)00003-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Bruce Coxon
- National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
26
|
Touboul D, Bouchoux G, Zenobi R. Gas-Phase Protonation Thermochemistry of Adenosine. J Phys Chem B 2008; 112:11716-25. [DOI: 10.1021/jp804786e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David Touboul
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland, and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | - Guy Bouchoux
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland, and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland, and Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| |
Collapse
|
27
|
Elias B, Creely C, Doorley GW, Feeney MM, Moucheron C, Kirsch-DeMesmaeker A, Dyer J, Grills DC, George MW, Matousek P, Parker AW, Towrie M, Kelly JM. Photooxidation of guanine by a ruthenium dipyridophenazine complex intercalated in a double-stranded polynucleotide monitored directly by picosecond visible and infrared transient absorption spectroscopy. Chemistry 2008; 14:369-75. [PMID: 17886324 DOI: 10.1002/chem.200700564] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Transient species formed by photoexcitation (400 nm) of [Ru(dppz)(tap)2]2+ (1) (dppz = dipyrido[3,2-a:2',3'-c]phenazine; tap=1,4,5,8-tetraazaphenanthrene) in aqueous solution and when intercalated into a double-stranded synthetic polynucleotide, [poly(dG-dC)]2, have been observed on a picosecond timescale by both visible transient absorption (allowing monitoring of the metal complex intermediates) and transient infrared (IR) absorption spectroscopy (allowing direct study of the DNA nucleobases). By contrast with its behavior when free in aqueous solution, excitation of 1 when bound to [poly(dG-dC)]2 causes a strong increase in absorbance at 515 nm due to formation of the reduced complex [Ru(dppz)(tap)2]+ (rate constant=(2.0+/-0.2) x 10(9) s(-1)). The subsequent reformation of 1 proceeds with a rate constant of (1.1+/-0.2) x 10(8) s(-1). When the process is carried out in D2O, the rates of formation and removal of [Ru(dppz)(tap)2]+ are reduced (rate constants (1.5+/-0.3) x 10(9) and (0.7+/-0.2) x 10(8) s(-1) respectively) consistent with proton-coupled electron transfer processes. Picosecond transient IR measurements in the 1540-1720 cm(-1) region in D2O solution confirm that the reduction of 1 intercalated into [poly(dG-dC)]2 is accompanied by bleaching of IR ground-state bands of guanine (1690 cm(-1)) and cytosine (1656 cm(-1)), each with similar rate constants.
Collapse
Affiliation(s)
- Benjamin Elias
- Service de Chimie Organique et Photochimie, CP 160/08, Université Libre de Bruxelles, 50 Avenue F.D. Roosevelt, 1050 Bruxelles, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Houseknecht JB, Lowary TL, Hadad CM. Gas- and Solution-Phase Energetics of the Methyl α- and β-d-Aldopentofuranosides. J Phys Chem A 2003. [DOI: 10.1021/jp027716w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Todd L. Lowary
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | | |
Collapse
|