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Makuvaza JT, Kokkin DL, Loman JL, Reid SA. C-H/π and C-H-O Interactions in Concert: A Study of the Anisole-Methane Complex using Resonant Ionization and Velocity Mapped Ion Imaging. J Phys Chem A 2019; 123:2874-2880. [PMID: 30860841 DOI: 10.1021/acs.jpca.9b01020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Noncovalent forces such as hydrogen bonding, halogen bonding, π-π stacking, and C-H/π and C-H/O interactions hold the key to such chemical processes as protein folding, molecular self-assembly, and drug-substrate interactions. Invaluable insight into the nature and strength of these forces continues to come from the study of isolated molecular clusters. In this work, we report on a study of the isolated anisole-methane complex, where both C-H/π and C-H/O interactions are possible, using a combination of theory and experiments that include mass-selected two-color resonant two-photon ionization spectroscopy, two-color appearance potential (2CAP) measurements, and velocity mapped ion imaging (VMI). Using 2CAP and VMI, we derive the binding energies of the complex in ground, excited, and cation radical states. The experimental values from the two methods are in excellent agreement, and they are compared with selected theoretical values calculated using density functional theory and ab initio methods. The optimized ground-state cluster geometry, which is consistent with the experimental observations, shows methane sitting above the ring, interacting with anisole via both C-H/π and C-H/O interactions, and this dual mode of interaction is reflected in a larger ground-state binding energy as compared with the prototypical benzene-methane system.
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Affiliation(s)
- James T Makuvaza
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Damian L Kokkin
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - John L Loman
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Scott A Reid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
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Tsuzuki S, Uchimaru T, Wakisaka A, Ono T. Magnitude and Directionality of Halogen Bond of Benzene with C6F5X, C6H5X, and CF3X (X = I, Br, Cl, and F). J Phys Chem A 2016; 120:7020-9. [PMID: 27525985 DOI: 10.1021/acs.jpca.6b06295] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Geometries of benzene complexes with C6F5X, C6H5X, and CF3X (X is I, Br, Cl, and F) were optimized, and their interaction energies were evaluated. The CCSD(T) interaction energies at the basis set limit (Eint) of C6F5X (X is I, Br, Cl, and F) with benzene were -3.24, -2.88, -2.31, and -0.92 kcal mol(-1). Eint of C6H5X (X is I, Br, and Cl) with benzene were -2.31, -1.97, and -1.48 kcal mol(-1). The fluorination of halobenzenes slightly enhances the attraction. Eint of CF3X (X is I, Br, Cl, and F) with benzene (-3.11, -2.74, -2.22, and -0.71 kcal mol(-1)) were very close to Eint of corresponding C6F5X with benzene. In contrast to the halogen bond of iodine and bromine with pyridine (n-type halogen bond acceptor) where the main cause of the attraction is the electrostatic interactions, that of halogen bond with benzene (p-type acceptor) is dispersion interaction. In the halogen bonds with p-type acceptors (halogen-π interactions), the electrostatic interactions and induction interactions are small. The overall orbital-orbital interactions are repulsive. The directionality of halogen bonds with p-type acceptors is very weak, owing to the weak electrostatic interactions, in contrast to the strong directionality of the halogen bonds with n-type acceptors and hydrogen bonds.
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Affiliation(s)
- Seiji Tsuzuki
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology , 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Tadafumi Uchimaru
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Akihiro Wakisaka
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology , 16-1 Onogawa, Tsukuba, 305-8569, Japan
| | - Taizo Ono
- Structural Materials Research Institute, National Institute of Advanced Industrial Science and Technology , 2266-98, Anagahora, Shimoshidami, Moriyama-ku, Nagoya, Aichi 463-8560 Japan
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Berg L, Mishra BK, Andersson CD, Ekström F, Linusson A. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes. Chemistry 2016; 22:2672-81. [DOI: 10.1002/chem.201503973] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Lotta Berg
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
| | | | | | - Fredrik Ekström
- CBRN Defense and Security; Swedish Defense Research Agency; 906 21 Umeå Sweden
| | - Anna Linusson
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
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Ishikawa T, Hayakawa D, Miyamoto H, Ozawa M, Ozawa T, Ueda K. Ab initio studies on the structure of and atomic interactions in cellulose IIII crystals. Carbohydr Res 2015; 417:72-7. [DOI: 10.1016/j.carres.2015.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 08/24/2015] [Accepted: 09/09/2015] [Indexed: 10/23/2022]
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Veljković DŽ, Medaković VB, Andrić JM, Zarić SD. C–H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study. CrystEngComm 2014. [DOI: 10.1039/c4ce00595c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of benzene and pyridine. These results can be very important for molecular recognition of DNA and RNA.
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Affiliation(s)
- D. Ž. Veljković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - V. B. Medaković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - J. M. Andrić
- Innovation Center
- Department of Chemistry
- 11000 Belgrade, Serbia
| | - S. D. Zarić
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Department of Chemistry
- Texas A&M University at Qatar
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Witts RN, Hopson EC, Koballa DE, Van Boening TA, Hopkins NH, Patterson EV, Nagan MC. Backbone-base interactions critical to quantum stabilization of transfer RNA anticodon structure. J Phys Chem B 2013; 117:7489-97. [PMID: 23742318 DOI: 10.1021/jp400084p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transfer RNA (tRNA) anticodons adopt a highly ordered 3'-stack without significant base overlap. Density functional theory at the M06-2X/6-31+G(d,p) level in combination with natural bond orbital analysis was utilized to calculate the intramolecular interactions within the tRNA anticodon that are responsible for stabilizing the stair-stepped conformation. Ten tRNA X-ray crystal structures were obtained from the PDB databank and were trimmed to include only the anticodon bases. Hydrogenic positions were added and optimized for the structures in the stair-stepped conformation. The sugar-phosphate backbone has been retained for these calculations, revealing the role it plays in RNA structural stability. It was found that electrostatic interactions between the sugar-phosphate backbone and the base provide the most stability, rather than the traditionally studied interbase stacking. Base-stacking interactions, though present, were weak and inconsistent. Aqueous solvation was found to have little effect on the intramolecular interactions.
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Affiliation(s)
- Rachel N Witts
- Department of Chemistry, Truman State University, 100 East Normal, Kirksville, Missouri 63501, USA
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Dragelj JL, Janjić GV, Veljković DŽ, Zarić SD. Crystallographic and ab initio study of pyridine CH–O interactions: linearity of the interactions and influence of pyridine classical hydrogen bonds. CrystEngComm 2013. [DOI: 10.1039/c3ce40759d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tavagnacco L, Engström O, Schnupf U, Saboungi ML, Himmel M, Widmalm G, Cesàro A, Brady JW. Caffeine and sugars interact in aqueous solutions: a simulation and NMR study. J Phys Chem B 2012; 116:11701-11. [PMID: 22897449 PMCID: PMC3477616 DOI: 10.1021/jp303910u] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 m solution of α-D-glucopyranose, at a caffeine concentration of 0.083 m, a single caffeine in a 3 m solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 m solution of sucrose (table sugar). Parallel nuclear magnetic resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol.
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Affiliation(s)
| | - Olof Engström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, SWEDEN
| | - Udo Schnupf
- Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Marie-Louise Saboungi
- Centre de Recherche sur la Matière Divisée, 1 bis rue de la Férollerie, 45071 Orléans, FRANCE
| | - Michael Himmel
- National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401-3393
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, SWEDEN
| | - Attilio Cesàro
- Department of Life Sciences, University of Trieste, Trieste, ITALY
| | - John W. Brady
- Department of Food Science, Cornell University, Ithaca, NY 14853
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Galland N, Kone S, Le Questel JY. Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry. J Comput Aided Mol Des 2012; 26:1111-26. [PMID: 22972560 DOI: 10.1007/s10822-012-9602-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/05/2012] [Indexed: 11/29/2022]
Abstract
A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.
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Affiliation(s)
- Nicolas Galland
- UMR CNRS 6230, Chimie Et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UFR Sciences & Techniques, Université de Nantes, NANTES Cedex, France
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Kumbhar NM, Kumbhar BV, Sonawane KD. Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNA(Phe). J Mol Graph Model 2012; 38:174-85. [PMID: 23073221 DOI: 10.1016/j.jmgm.2012.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 07/18/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
Abstract
Conformational preferences of hypermodified nucleic acid base hydroxywybutine (OHyW) have been studied using quantum chemical single point semi-empirical PM3 method. Automated geometry optimization using semi-empirical RM1, molecular mechanics force field (MMFF) along with ab-initio HF-SCF (6-31G** basis set) and DFT (B3LYP/6-31G** basis set) calculations have also been made to compare the salient features. Molecular electrostatic potentials (MEPs) depict the polarities of hydroxywybutine (OHyW) side chain. Another conformational study showed that hydroxywybutosine side chain interacts with adjacent bases within the anticodon loop of tRNA(Phe). The solvent accessible surface area (SASA) calculations revealed the structural role of hydroxywybutine in anticodon loop. Explicit molecular dynamics (MD) simulation has been done over the PM3 most stable structure of OHyW. The hydroxywybutine side chain prefers 'distal' conformation i.e. spreads away from the cyclic five membered imidazole moiety of modified tricyclic guanine base. The predicted preferred conformation of hydroxywybutine may prevent extended Watson-Crick base pairing during protein biosynthesis process. This conformation of OHyW stabilized by intramolecular interactions between O(6)⋯HO(16), O(6)⋯HC(15) and O(20)⋯HC(17). Further stabilization is also expected from interactions between O(22)⋯HC(16) and O(23)⋯HC(15). Explicit molecular dynamics (MD) simulation over the PM3 most stable structure of OHyW support the preferred geometry by preserving the 'distal' orientation of hydroxywybutine side chain and intramolecular hydrogen bonding interactions. MD simulation study revealed the role of hydroxyl group of OHyW to avoid fluctuations and prevent multiple iso-energetic conformations of hydroxywybutine side chain as compared to wybutine (yW).
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Affiliation(s)
- Navanath M Kumbhar
- Department of Biotechnology, Shivaji University, Kolhapur 416004, Maharashtra-MS, India
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