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Jurku̅nas M, Talaikis M, Klimkevičius V, Pudžaitis V, Niaura G, Makuška R. Diblock Copolymers of Methacryloyloxyethyl Phosphorylcholine and Dopamine Methacrylamide: Synthesis and Real-Time Adsorption Dynamics by SEIRAS and RAIRS. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:5945-5958. [PMID: 38456424 PMCID: PMC10956495 DOI: 10.1021/acs.langmuir.3c03925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Amphiphilic diblock copolymers containing a block of 2-methacryloyloxyethyl phosphorylcholine (MPC) with unique properties to prevent nonspecific protein adsorption and enhance lubrication in aqueous media and a block of dopamine methacrylamide (DOPMA) distinguished by excellent adhesion performance were synthesized by reversible addition fragmentation chain transfer (RAFT) polymerization for the first time. The DOPMA monomer with an acetonide-protected catechol group (acetonide-protected dopamine methacrylamide (ADOPMA)) was used, allowing the prevention of undesirable side reactions during polymerization and oxidation during storage. The adsorption behavior of the diblock copolymers with protected and unprotected catechol groups on gold surfaces was probed using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy, surface-enhanced infrared absorption spectroscopy (SEIRAS), and reflection-absorption infrared spectroscopy (RAIRS). The copolymers pMPC-b-pADOPMA demonstrated physisorption with rapid adsorption and ultrasound-assisted desorption, while the copolymers pMPC-b-DOPMA exhibited chemical adsorption with slower dynamics but a stronger interaction with the gold surface. SEIRAS and RAIRS allowed proving the reorientation of the diblock copolymers during adsorption, demonstrating the exposure of the pMPC block toward the aqueous phase.
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Affiliation(s)
- Marijus Jurku̅nas
- Institute
of Chemistry, Vilnius University, Naugarduko Str. 24, 03225 Vilnius, Lithuania
| | - Martynas Talaikis
- Department
of Organic Chemistry, Center for Physical
Sciences and Technology (FTMC), Sauletekio Ave. 3, 10257 Vilnius, Lithuania
| | - Vaidas Klimkevičius
- Institute
of Chemistry, Vilnius University, Naugarduko Str. 24, 03225 Vilnius, Lithuania
| | - Vaidas Pudžaitis
- Department
of Organic Chemistry, Center for Physical
Sciences and Technology (FTMC), Sauletekio Ave. 3, 10257 Vilnius, Lithuania
| | - Gediminas Niaura
- Department
of Organic Chemistry, Center for Physical
Sciences and Technology (FTMC), Sauletekio Ave. 3, 10257 Vilnius, Lithuania
| | - Ričardas Makuška
- Institute
of Chemistry, Vilnius University, Naugarduko Str. 24, 03225 Vilnius, Lithuania
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Ben Faleh A, Warnke S, Van Wieringen T, Abikhodr AH, Rizzo TR. New Approach for the Identification of Isobaric and Isomeric Metabolites. Anal Chem 2023; 95:7118-7126. [PMID: 37119183 PMCID: PMC10173252 DOI: 10.1021/acs.analchem.2c04962] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The structural elucidation of metabolite molecules is important in many branches of the life sciences. However, the isomeric and isobaric complexity of metabolites makes their identification extremely challenging, and analytical standards are often required to confirm the presence of a particular compound in a sample. We present here an approach to overcome these challenges using high-resolution ion mobility spectrometry in combination with cryogenic vibrational spectroscopy for the rapid separation and identification of metabolite isomers and isobars. Ion mobility can separate isomeric metabolites in tens of milliseconds, and cryogenic IR spectroscopy provides highly structured IR fingerprints for unambiguous molecular identification. Moreover, our approach allows one to identify metabolite isomers automatically by comparing their IR fingerprints with those previously recorded in a database, obviating the need for a recurrent introduction of analytical standards. We demonstrate the principle of this approach by constructing a database composed of IR fingerprints of eight isomeric/isobaric metabolites and use it for the identification of these isomers present in mixtures. Moreover, we show how our fast IR fingerprinting technology allows to probe the IR fingerprints of molecules within just a few seconds as they elute from an LC column. This approach has the potential to greatly improve metabolomics workflows in terms of accuracy, speed, and cost.
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Affiliation(s)
- Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, CH-1025 Lausanne, Switzerland
| | - Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, CH-1025 Lausanne, Switzerland
| | - Teun Van Wieringen
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, CH-1025 Lausanne, Switzerland
| | - Ali H Abikhodr
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, CH-1025 Lausanne, Switzerland
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, CH-1025 Lausanne, Switzerland
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Intramolecular interactions (O-H∙∙∙O, C-H∙∙∙N, N-H∙∙∙π) in isomers of neutral, cation, and anion dopamine molecules: A DFT study on the influence of solvents (water and ethanol). J Mol Model 2023; 29:67. [PMID: 36773132 DOI: 10.1007/s00894-023-05466-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/01/2023] [Indexed: 02/12/2023]
Abstract
CONTEXT Dopamine (DA) is one of the most important neurotransmitters associated with numerous neural disorders. This investigation reports the intramolecular interactions present in the isomers of neutral (DA0), anionic (DA-), and cationic (DA+) dopamine isomers in gas, water, and ethanol mediums. Neutral and anion isomers have O-H∙∙∙O, C-H∙∙∙N intramolecular hydrogen bonds and N-H∙∙∙π interactions. All the interactions are electrostatic in nature. Isomers of cation dopamine show no intramolecular interactions in the solvent. Natural charges from natural bond orbital (NBO) analysis show that O-H∙∙∙O bonds and the N-H∙∙∙π interactions are the most and least polar, respectively. 1H NMR study reveals the inverse linear correlation between shielding constant and electron density in a solvent medium. HOMO-LUMO energy gap indicates higher stability for neutral and cationic forms of dopamine isomers in water and ethanol medium. METHODS We have optimized all the structural forms of dopamine molecule using the Becke three hybrid exchange and Lee-Yang-Parr correlation functional with Grimme's dispersion correction, B3LYP-D3(BJ), and aug-cc-pVTZ basis set using the Gaussian16 software. Vibrational frequency analysis with no imaginary frequencies confirms the nature of global minima. The solvent studies (water and ethanol) were carried out using the SCRF keyword and the polarisable continuum model (PCM) of Miertus and Tomasi. NBO analysis and NMR studies were also performed for all conformers. Topology analysis was explored using the software Multiwfn.
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Yamaguchi K, Hirata K, Ishiuchi SI, Fujii M. Ultraviolet and infrared spectra of mono-, di- and tri-hydrated clusters of protonated noradrenaline – Solvation and conformational variations. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Corinti D, Maccelli A, Chiavarino B, Schütz M, Bouchet A, Dopfer O, Crestoni ME, Fornarini S. Cation-π Interactions between a Noble Metal and a Polyfunctional Aromatic Ligand: Ag + (benzylamine). Chemistry 2022; 28:e202200300. [PMID: 35412692 PMCID: PMC9325466 DOI: 10.1002/chem.202200300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Indexed: 12/21/2022]
Abstract
The structure of an isolated Ag+ (benzylamine) complex is investigated by infrared multiple photon dissociation (IRMPD) spectroscopy complemented with quantum chemical calculations of candidate geometries and their vibrational spectra, aiming to ascertain the role of competing cation-N and cation-π interactions potentially offered by the polyfunctional ligand. The IRMPD spectrum has been recorded in the 800-1800 cm-1 fingerprint range using the IR free electron laser beamline coupled with an FT-ICR mass spectrometer at the Centre Laser Infrarouge d'Orsay (CLIO). The resulting IRMPD pattern points toward a chelate coordination (N-Ag+ -π) involving both the amino nitrogen atom and the aromatic π-system of the phenyl ring. The gas-phase reactivity of Ag+ (benzylamine) with a neutral molecular ligand (L) possessing either an amino/aza functionality or an aryl group confirms N- and π-binding affinity and suggests an augmented silver coordination in the product adduct ion Ag + ( benzylamine ) ( L ) .
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Alessandro Maccelli
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Markus Schütz
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623, Berlin, Germany.,present address: Eagleyard Photonics GmbH, Rudower Chaussee 29, 12489, Berlin, Germany
| | - Aude Bouchet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623, Berlin, Germany.,present address: Université Lille LASIRE Lab Adv Spect Interact React & Environm Cite Sci, CNRS, UMR 8516, 59000, Lille, France
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623, Berlin, Germany
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, I-00185, Roma, Italy
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Hirata K, Kasai KI, Yoshizawa K, Grégoire G, Ishiuchi SI, Fujii M. Excited state dynamics of protonated dopamine: hydration and conformation effects. Phys Chem Chem Phys 2022; 24:10737-10744. [PMID: 35389419 DOI: 10.1039/d2cp00543c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic and vibrational spectroscopy in a cryogenic ion trap has been applied to protonated dopamine water clusters and assigned with the help of quantum chemistry calculations performed in the ground and electronic excited states. A dramatic hydration effect is observed when dopamine is solvated by three water molecules. The broad electronic spectra recorded for the bare and small water clusters containing protonated dopamine turn to sharp, well-resolved vibronic transitions in the 1-3 complex. This reflects the change induced by hydration in the photodynamics of protonated dopamine which is initially controlled by an excited state proton transfer (ESPT) reaction from the ammonium group toward the catechol ring. Interestingly, conformer selectivity is revealed in the 1-3 complex which shows two low lying energy conformers for which the ESPT reaction is prevented or not depending on the H-bond network formed between the dopamine and water molecules.
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Affiliation(s)
- Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Ken-Ichi Kasai
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Koki Yoshizawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Gilles Grégoire
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, F-91405 Orsay, France
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
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Chowdhury A, Singh PC. Role of the weak noncovalent interactions in the stability of the aggregated protonated dopamine in the aqueous solution: spectroscopic and quantum chemical calculation studies. J CHEM SCI 2022. [DOI: 10.1007/s12039-021-02014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Bio-Inspired Proanthocyanidins from Blueberries’ Surface Coating Prevents Red Blood Cell Agglutination on Urinary Silicon-Based Catheters. COATINGS 2022. [DOI: 10.3390/coatings12020172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Thrombosis can cause the occlusion of implantable medical devices, leading to the rejection of the device and subsequent mortality. Thrombosis is primarily induced by red blood aggregation and coagulation. The administration of anticoagulant drugs is generally used as a treatment to avoid these processes. Adverse effects such as bleeding in the event of an anticoagulant overdose, osteoporosis associated with prolonged use, hypersensitivity, and hives have been reported. New strategies such as biomolecule surface functionalization have recently been studied to overcome these problems. In this study, we report a novel coating composed of polydopamine (PDA) and proanthocyanidins (PACs) from blueberry extract to avoid red blood aggregation in short-term use medical devices such as silicone catheters. We showed that PDA formed stable films on silicone surfaces and PACs could be immobilized on PDA layers using laccase as a catalyst. The PDA–PACs films decreased surface hydrophilicity, increased surface roughness, and decreased plasma protein adsorption. The films were stable in phosphate buffer saline (PBS) and cell culture media. Furthermore, red blood cell adsorption and aggregation decreased. These effects are attributed to changes in the membrane fluidity that influences adhesion, the steric hindrance of the layers, and the low adsorption of plasma proteins on the PAC layer.
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Becher S, Berden G, Martens J, Oomens J, Heiles S. IRMPD Spectroscopy of [PC (4:0/4:0) + M] + (M = H, Na, K) and Corresponding CID Fragment Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2874-2884. [PMID: 34723538 DOI: 10.1021/jasms.1c00277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Glycerophospholipids (GPs) are highly abundant in eukaryotic cells and take part in numerous fundamental physiological processes such as molecular signaling. The GP composition of samples is often analyzed using mass spectrometry (MS), but identification of some structural features, for example, differentiation of stereospecific numbering (sn) isomers by well-established tandem MS (MS2) methods, is challenging. In particular, the formation of 1,3-dioxolane over 1,3-dioxane intermediates proposed to be responsible for the sn-selectivity of these tandem MS strategies has not been validated by spectroscopic methods. In this work, we present infrared multiple photon dissociation (IRMPD) spectra of phosphatidylcholine (PC) ions [PC 4:0/4:0 + H/Na/K]+ and [PC 4:0/4:0 + Na/K - 183]+ fragments generated by electrospray ionization (ESI)-MS and collision-induced dissociation (CID), respectively. IRMPD spectra of protonated, sodiated, and potassiated PC 4:0/4:0 differ in the phosphate- and ester-related bands, which are increasingly shifted to lower wavenumbers with higher adduct masses. Comparison of calculated and experimental IR spectra indicates the presence of multiple, two and one isomer(s) for [PC 4:0/4:0 + H]+, [PC 4:0/4:0 + Na]+, and [PC 4:0/4:0 + K]+, respectively. Isomers exhibiting pronounced sn-1 ester-ion interactions are computationally predicted to be energetically preferred for all species and are in line with experimental results. IRMPD spectra of [PC 4:0/4:0 + Na/K - 183]+ are presented and shed the first light on the fragment ion structures, rationalizing MS-based lipidomics strategies that aim to characterize the sn-isomerism of GPs.
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Affiliation(s)
- Simon Becher
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Giel Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Jonathan Martens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, 6525 ED Nijmegen, The Netherlands
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
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Chen Y, Li X, Zhan C, Lao Z, Li F, Dong X, Wei G. A Comprehensive Insight into the Mechanisms of Dopamine in Disrupting Aβ Protofibrils and Inhibiting Aβ Aggregation. ACS Chem Neurosci 2021; 12:4007-4019. [PMID: 34472835 DOI: 10.1021/acschemneuro.1c00306] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fibrillary aggregates of amyloid-β (Aβ) are the pathological hallmark of Alzheimer's disease (AD). Clearing Aβ deposition or inhibiting Aβ aggregation is a promising approach to treat AD. Experimental studies reported that dopamine (DA), an important neurotransmitter, can inhibit Aβ aggregation and disrupt Aβ fibrils in a dose-dependent manner. However, the underlying molecular mechanisms still remain mostly elusive. Herein, we investigated the effect of DA on Aβ42 protofibrils at three different DA-to-Aβ molar ratios (1:1, 2:1, and 10:1) using all-atom molecular dynamics simulations. Our simulations demonstrate that protonated DA at a DA-to-Aβ ratio of 2:1 exhibits stronger Aβ protofibril disruptive capacity than that at a molar-ratio of 1:1 by mostly disrupting the F4-L34-V36 hydrophobic core. When the ratio of DA-to-Aβ increases to 10:1, DA has a high probability to bind to the outer surface of protofibril and has negligible effect on the protofibril structure. Interestingly, at the same DA-to-Aβ ratio (10:1), a mixture of protonated (DA+) and deprotonated (DA0) DA molecules significantly disrupts Aβ protofibrils by the binding of DA0 to the F4-L34-V36 hydrophobic core. Replica-exchange molecular dynamics simulations of Aβ42 dimer show that DA+ inhibits the formation of β-sheets, K28-A42/K28-D23 salt-bridges, and interpeptide hydrophobic interactions and results in disordered coil-rich Aβ dimers, which would inhibit the subsequent fibrillization of Aβ. Further analyses reveal that DA disrupts Aβ protofibril and prevents Aβ dimerization mostly through π-π stacking interactions with residues F4, H6, and H13, hydrogen bonding interactions with negatively charged residues D7, E11, E22 and D23, and cation-π interactions with residues R5. This study provides a complete picture of the molecular mechanisms of DA in disrupting Aβ protofibril and inhibiting Aβ aggregation, which could be helpful for the design of potent drug candidates for the treatment/intervention of AD.
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Affiliation(s)
- Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, People’s Republic of China
| | - Chendi Zhan
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
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Hirata K, Kasai KI, Grégoire G, Ishiuchi SI, Fujii M. Hydration-controlled excited-state relaxation in protonated dopamine studied by cryogenic ion spectroscopy. J Chem Phys 2021; 155:151101. [PMID: 34686064 DOI: 10.1063/5.0066919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ultraviolet (UV) and infrared (IR) spectra of protonated dopamine (DAH+) and its hydrated clusters DAH+(H2O)1-3 are measured by cryogenic ion spectroscopy. DAH+ monomer and hydrated clusters with up to two water molecules show a broad UV spectrum, while it turns to a sharp, well-resolved one for DAH+-(H2O)3. Excited state calculations of DAH+(H2O)3 reproduce these spectral features. The conformer-selected IR spectrum of DAH+(H2O)3 is measured by IR dip spectroscopy, and its structure is assigned with the help of quantum chemical calculations. The excited state lifetime of DAH+ is much shorter than 20 ps, the cross correlation of the ps lasers, revealing a fast relaxation dynamics. The minimal energy path along the NH → π proton transfer coordinate exhibits a low energy barrier in the monomer, while this path is blocked by the high energy barrier in DAH+(H2O)3. It is concluded that the excited state proton transfer in DAH+ is inhibited by water-insertion.
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Affiliation(s)
- Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Ken-Ichi Kasai
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Gilles Grégoire
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama 226-8503, Japan
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Lončar A, Negrojević L, Dimitrić-Marković J, Dimić D. The reactivity of neurotransmitters and their metabolites towards various nitrogen-centered radicals: Experimental, theoretical, and biotoxicity evaluation. Comput Biol Chem 2021; 95:107573. [PMID: 34562727 DOI: 10.1016/j.compbiolchem.2021.107573] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/20/2021] [Accepted: 09/05/2021] [Indexed: 11/24/2022]
Abstract
In the past few years, there has been a certain interest in nitrogen-centered radicals, biologically important radicals that play a vital role in various processes and constitute many important biological molecules. In this paper, there was an attempt to bridge a gap in the literature that concerns the antiradical potency of monoamine neurotransmitters (dopamine, epinephrine, and norepinephrine) and their metabolites towards these radicals. The most probable radical quenching mechanism was determined for each radical out of three common mechanisms, namely Hydrogen Atom Transfer (HAT), Single Electron Transfer followed by the Proton Transfer (SET-PT), and Sequential Proton Loss Electron Transfer (SPLET). Marcus' theory was then used to determine the reaction rates for the electron transfer process. SPLET was the most probable mechanism for both reactions with the aminyl and hydrazyl radicals, while HAT and SPLET were plausible mechanisms for reactions with the imidazolyl radical. Special emphasis was put on the investigation of the substituent effect on the preferred mechanism. The necessity of both thermodynamic and kinetic parameters for the comparison of the antiradical potency of compounds was discussed. The same methodology was applied for the theoretical investigation of the reactivity towards DPPH⦁, a member of the hydrazyl radicals. An ecotoxicity analysis was performed to assess the impact the investigated radicals have on the ecosystem. Except for histidine, every other neutral form was either toxic or highly toxic to some of the analyzed marine organisms.
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Affiliation(s)
- Aleksandar Lončar
- Faculty of Physical Chemistry, University of Belgrade, Studentski Trg 12-16, 11000 Belgrade, Serbia
| | - Luka Negrojević
- Faculty of Physical Chemistry, University of Belgrade, Studentski Trg 12-16, 11000 Belgrade, Serbia
| | | | - Dušan Dimić
- Faculty of Physical Chemistry, University of Belgrade, Studentski Trg 12-16, 11000 Belgrade, Serbia.
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Yadav T, Brahmachari G, Karmakar I, Yadav P, Prasad A, Pathak A, Agarwal A, Kumar R, Mukherjee V, Pandey G, Bento R, Yadav N. Conformational and vibrational spectroscopic investigation of N-n‑butyl, S-2-nitro-1-(p-tolyl)ethyl dithiocarbamate – a bio-relevant sulfur molecule. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Zhu Z, Zhang J, Song Y, Chang C, Ren G, Shen J, Zhang Z, Ji T, Chen M, Zhao H. Broadband terahertz signatures and vibrations of dopamine. Analyst 2021; 145:6006-6013. [PMID: 32756617 DOI: 10.1039/d0an00771d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Dopamine (DA) is an essential neurotransmitter and hormone of the nervous system, its structural and conformational properties play critical roles in biological functions and signal transmission processes. Although this neuroactive molecule has been studied extensively, the low-frequency vibration features that are closely related to the conformation and molecular interactions in the terahertz (THz) band still remain unclear. In this study, a broadband THz time-domain spectroscopy (THz-TDS) system in the frequency band of 0.5-18 THz was used to characterize the unique THz fingerprint of DA. In addition, density functional theory (DFT) calculations were performed to analyze the vibrational properties of DA. The results suggest that each THz resonant absorption peak of DA corresponds to specific vibrational modes, and the collective vibration also exists in the broadband THz range. Moreover, the interactions between the DA ligand and the D2 and D3 receptors were investigated by docking, and the simulated THz spectra were obtained. The results indicate the dominant role of hydrogen bonding interactions and the specificity of molecular conformation. This work may help to understand the resonance coupling between THz electromagnetic waves and neurotransmitters.
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Affiliation(s)
- Zhongjie Zhu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
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15
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Beyond templating: Electronic structure impacts of aromatic cations in organic–inorganic antimony chlorides. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202000484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Singh VB. Spectroscopic Signatures and the Cation-π Interaction in Conformational Preferences of the Neurotransmitter Dopamine in Aqueous Solution. ACS Chem Neurosci 2021; 12:613-625. [PMID: 33523624 DOI: 10.1021/acschemneuro.0c00597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The precise determination of the neurotransmitter dopamine's conformational preferences in aqueous solution is crucial for understanding its neurobiological function. The first principle Møller-Plesset perturbation theory (MP2) and dispersion corrected density functional theory (DFT-D3) methods, employing the basis set aug-cc-pVDZ(/pVTZ), are used to reinvestigate the nine lowest-energy (isolated) structures of protonated dopamine (DAH+) in both gas and aqueous phases. DAH+ trans isomer t1 is found higher in energy than lowest-energy gauche isomer g+1 (g + 1) by 6.4 and 5.7 kJ mol-1, at the MP2 and B3LYP-D3 levels of theory, respectively, in the aqueous environment within the polarizable continuum model (PCM). We found that the solvated cation, NH3+, retains its attractive character, which supports the previous report that agonist DAH+ can be involved in cation (NH3+)-π interaction in the active states of the D2 dopamine receptor. The dispersion corrected DFT evaluation of anharmonicity allows us to confirm the most experimental frequencies and suggest some new interpretations. The IR and Raman spectra's influential band for both gauche and the trans conformers observed at 1287/1288 cm-1 were enhanced in aqueous solution. The experimental Raman spectrum for dopamine was compared with the conformer-specific computed Raman spectrum of protonated dopamine (DAH+). The intense Raman band at 1451 cm-1 indicates the necessity of DAH+ calculated values in interpreting the Raman spectra. The most intense Raman band at 750 cm-1 arises due to the trans DAH+, t1, revealed by MP2/aug-cc-pVDZ Raman spectra, indicating trans DAH+ dominance in the bulk DAH+ of extracellular fluid.
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17
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Tang WK, Mu X, Li M, Martens J, Berden G, Oomens J, Chu IK, Siu CK. Formation of n → π + interaction facilitating dissociative electron transfer in isolated tyrosine-containing molecular peptide radical cations. Phys Chem Chem Phys 2021; 22:21393-21402. [PMID: 32940309 DOI: 10.1039/d0cp00533a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Long-range electron transfer in proteins can be rationalized as a sequential short-distance electron-hopping processes via amino acid residues having low ionization energy as relay stations. Tyrosine residues can serve as such redox-active intermediates through one-electron oxidation to form a π-radical cation at its phenol side chain. An electron transfer from a vicinal functional group to this π-electron hole completes an elementary step of charge migration. However, transient oxidized/reduced intermediates formed at those relay stations during electron transfer processes have not been observed. In this study, formation of analog reactive intermediates via electron donor-acceptor coupling is observed by using IRMPD action spectroscopy. An elementary charge migration at the molecular level in model tyrosine-containing peptide radical cations [M]˙+ in the gas phase is revealed with its unusual Cα-Cβ bond cleavage at the side chain of the N-terminal residue. This reaction is induced by the radical character of the N-terminal amino group (-NH2˙+) resulting from an n → π+ interaction between the nonbonding electron pair of NH2 (n) and the π-electron hole at the Tyr side chain (π+). The formation of -NH2˙+ is supported by the IRMPD spectrum showing a characteristic NH2 scissor vibration coupled with Tyr side-chain stretches at 1577 cm-1. This n → π+ interaction facilitates a dissociative electron transfer with NH2 as the relay station. The occurrence of this side-chain cleavage may be an indicator of the formation of reactive conformers featuring the n → π+ interaction.
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Affiliation(s)
- Wai Kit Tang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China.
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18
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Structural confirmation of biorelevant molecule N-iso-butyl, S-2-nitro-1-phenylethyl dithiocarbamate in gas phase and effect of fluorination. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Sarkar S, Chowdhury A, Singh PC. Multimodal Interactions of Dopamine Hydrochloride with the Groove Region of DNA: A Key Factor in the Enhanced Stability of DNA. J Phys Chem B 2019; 123:10700-10708. [DOI: 10.1021/acs.jpcb.9b09254] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Abhinanda Chowdhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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20
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Dimić D, Milanović Ž, Jovanović G, Sretenović D, Milenković D, Marković Z, Dimitrić Marković J. Comparative antiradical activity and molecular Docking/Dynamics analysis of octopamine and norepinephrine: the role of OH groups. Comput Biol Chem 2019; 84:107170. [PMID: 31810852 DOI: 10.1016/j.compbiolchem.2019.107170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022]
Abstract
Octopamine is a neurotransmitter in invertebrates and a phenol analog of norepinephrine. The crystallographic and spectral (UV-visUV, and NMR) characteristics of octopamine were investigated experimentally and theoretically by applying appropriate level of theory, B3LYP-D3BJ/6-311++G(d,p), which reproduced well the experimental bond lengths and angles. The intramolecular interactions governing the stability of conformers were described by NBO and QTAIM analyses. The antiradical potencies of octopamine and norepinephrine towards DPPH and ABTS+ were examined with special emphasis on the preferred mechanism and effect of catechol moiety. Several techniques were used to distinguish Hydrogen Atom Transfer (HAT) and Proton Coupled Electron Transfer (PCET) mechanisms for reaction with DPPH. The calculated rate constants of the reactions with both radicals showed that Sequential Proton Loss Electron Transfer (SPLET) mechanism was dominant both thermodynamically and kinetically, with values of thermodynamic functions and rate constants clearly proving the importance of the second hydroxyl group in structure. The Molecular Docking and afterward Molecular Dynamics calculations of formed complexes between octopamine/norepinephrine with β1- and β2- adrenergic receptors examined in details the interactions that lead to the formation of stable complexes. The number of strong interactions of amino acids with norepinephrine was higher, but the absence of hydroxyl group in octopamine did not lead to a significant change in the type of interactions and stability. The formed complexes showed higher flexibility of amino acids, similar compactness of structure as proteins and increased interatomic distances of the backbone when compared to pure proteins.
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Affiliation(s)
- Dušan Dimić
- Faculty of Physical Chemistry, University of Belgrade, 12-16 Studentski trg, 11000, Belgrade, Republic of Serbia
| | - Žiko Milanović
- Bioengineering Research and Development Center, Prvoslava Stojanovića 6, 34000, Kragujevac, Republic of Serbia
| | - Goran Jovanović
- Faculty of Physical Chemistry, University of Belgrade, 12-16 Studentski trg, 11000, Belgrade, Republic of Serbia
| | - Dragana Sretenović
- Faculty of Physical Chemistry, University of Belgrade, 12-16 Studentski trg, 11000, Belgrade, Republic of Serbia
| | - Dejan Milenković
- Bioengineering Research and Development Center, Prvoslava Stojanovića 6, 34000, Kragujevac, Republic of Serbia; Institute for Information Technologies, Department of Science, University of Kragujevac, Republic of Serbia
| | - Zoran Marković
- Institute for Information Technologies, Department of Science, University of Kragujevac, Republic of Serbia; Department of Chemical-Technological Sciences, State University of Novi Pazar, Vuka Karadžića bb, 36300, Novi Pazar, Republic of Serbia
| | - Jasmina Dimitrić Marković
- Faculty of Physical Chemistry, University of Belgrade, 12-16 Studentski trg, 11000, Belgrade, Republic of Serbia.
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21
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Gómez-Chavarín M, Prado-Prone G, Padilla P, Ramírez Santos J, Gutiérrez-Ospina G, García-Macedo JA. Dopamine Released from TiO 2 Semicrystalline Lattice Implants Attenuates Motor Symptoms in Rats Treated with 6-Hydroxydopamine. ACS OMEGA 2019; 4:7953-7962. [PMID: 31459884 PMCID: PMC6648478 DOI: 10.1021/acsomega.8b00626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 02/26/2019] [Indexed: 06/10/2023]
Abstract
The motor dysfunction featured by patients aggrieved by Parkinson's disease (PD) results from the reduction of dopamine (DA) availability in the caudate nucleus (CN). Restituting CN DA levels is therefore essential to ameliorate PD motor deficits. In this regard, nanotechnology may offer solutions to restore CN DA availability. DA, however, can be rapidly oxidized into toxic compounds if made available in situ, unprotected. Then, we tested whether a semicrystalline TiO2 lattice, implanted into the CN of 6-hydroxydopamine (6-OHDA)-lesioned, hemiparkinsonian rats, was able to release DA during a time window sufficient to attenuate motor symptoms while protecting it from the ongoing oxidation. Accordingly, implanted semicrystalline TiO2 lattices released incremental amounts of DA into the CN of lesioned rats. Motor symptoms were already attenuated by the 1st month and significantly reduced 2 months after implantation. These effects were specific since TiO2 lattices alone did not modify motor symptoms in lesioned rats. DA-unloaded or -loaded TiO2 lattices did not produce obvious symptoms of systemic or neurological toxicity nor significantly increased CN lipid peroxidation in implanted, lesioned rats at the time of sacrifice. Our results thus support that loaded TiO2 lattices are capable of releasing DA while protecting it from the ongoing oxidation when implanted into the brain. Their implantation does not cause noticeable systemic or local toxicity. On the contrary, they attenuated motor symptoms in hemiparkinsonian rats.
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Affiliation(s)
- Margarita Gómez-Chavarín
- Departamento
de Fisiología, Facultad de Medicina, Posgrado en Ciencia
e Ingeniería de Materiales, Departamento de Estado Sólido, Instituto
de Física, Unidad de Cromatografía, Instituto de Investigaciones Biomédicas, and Departamento
de Biología Celular y Fisiología, Instituto de Investigaciones
Biomédicas and Coordinación de Psicobiología
y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Gina Prado-Prone
- Departamento
de Fisiología, Facultad de Medicina, Posgrado en Ciencia
e Ingeniería de Materiales, Departamento de Estado Sólido, Instituto
de Física, Unidad de Cromatografía, Instituto de Investigaciones Biomédicas, and Departamento
de Biología Celular y Fisiología, Instituto de Investigaciones
Biomédicas and Coordinación de Psicobiología
y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Patricia Padilla
- Departamento
de Fisiología, Facultad de Medicina, Posgrado en Ciencia
e Ingeniería de Materiales, Departamento de Estado Sólido, Instituto
de Física, Unidad de Cromatografía, Instituto de Investigaciones Biomédicas, and Departamento
de Biología Celular y Fisiología, Instituto de Investigaciones
Biomédicas and Coordinación de Psicobiología
y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Jesús Ramírez Santos
- Departamento
de Fisiología, Facultad de Medicina, Posgrado en Ciencia
e Ingeniería de Materiales, Departamento de Estado Sólido, Instituto
de Física, Unidad de Cromatografía, Instituto de Investigaciones Biomédicas, and Departamento
de Biología Celular y Fisiología, Instituto de Investigaciones
Biomédicas and Coordinación de Psicobiología
y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Gabriel Gutiérrez-Ospina
- Departamento
de Fisiología, Facultad de Medicina, Posgrado en Ciencia
e Ingeniería de Materiales, Departamento de Estado Sólido, Instituto
de Física, Unidad de Cromatografía, Instituto de Investigaciones Biomédicas, and Departamento
de Biología Celular y Fisiología, Instituto de Investigaciones
Biomédicas and Coordinación de Psicobiología
y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Jorge A. García-Macedo
- Departamento
de Fisiología, Facultad de Medicina, Posgrado en Ciencia
e Ingeniería de Materiales, Departamento de Estado Sólido, Instituto
de Física, Unidad de Cromatografía, Instituto de Investigaciones Biomédicas, and Departamento
de Biología Celular y Fisiología, Instituto de Investigaciones
Biomédicas and Coordinación de Psicobiología
y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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22
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Simão A, Cabezas C, León I, Alonso ER, Mata S, Alonso JL. Elucidating the multiple structures of pipecolic acid by rotational spectroscopy. Phys Chem Chem Phys 2019; 21:4155-4161. [PMID: 30520481 PMCID: PMC6478119 DOI: 10.1039/c8cp06120c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complex conformational space of the non-proteinogenic cyclic amino acid pipecolic acid has been explored in the gas phase for the first time. Solid pipecolic acid samples were vaporized by laser ablation and expanded in a supersonic jet where the rotational spectral signatures owing to nine different conformers were observed by Fourier transform microwave spectroscopy. All species were identified by comparison of the experimental rotational and nuclear quadrupole coupling constants with those predicted theoretically. Observation of type-III conformers, leading to a difference when compared against the conformational behavior of the analog amino acid proline, has been interpreted by an increment in steric hindrance when increasing the number of carbons present in the ring.
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Affiliation(s)
- A Simão
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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23
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Yadav T, Mukherjee V. Conformational study of octopamine in gas phase and effect of hydrochloride. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 206:263-277. [PMID: 30121472 DOI: 10.1016/j.saa.2018.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/18/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
This work deals with the molecular modeling and vibrational spectra of all the twenty conformers of an important biomolecule octopamine which have been investigated using the DFT/B3LYP level of theory in combination with the 6-31++g(d,p) as a suitable basis set. The experimental FTIR and FTRaman spectra of octopamine neurotransmitter were recorded in the spectral region 400-4000 cm-1 and 50-4000 cm-1 respectively and correlated with the calculated spectra of the most stable conformer. The effect of hydrochloride on the important geometrical parameters of most stable conformer of octopamine was also studied. The normal coordinate analysis was performed to scale the theoretical frequencies and to calculate potential energy distributions for precise normal mode assignment. Most of the frequencies were in good agreement with experimental one. However, some have been modified. Natural bond orbital analysis was performed in order to confirm the stability of electronic structure of octopamine molecule. HOMO-LUMO analysis for all the twenty conformers was also performed to give the transition profile and to study the chemical reactivity of octopamine.
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Affiliation(s)
- T Yadav
- SUIIT, Sambalpur University, Odisha, India.
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24
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Badillo-Ramírez I, Landeros-Rivera B, de la O-Cuevas E, Vargas R, Garza J, Saniger JM. Interaction of 5-S-cysteinyl-dopamine with graphene oxide: an experimental and theoretical study for the detection of a Parkinson's disease biomarker. NEW J CHEM 2019. [DOI: 10.1039/c9nj03781k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spectroscopic and theoretical analysis in the adsorption of 5-S-Cys-DA over GO for the development of platform biosensors with Raman spectroscopy.
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Affiliation(s)
- Isidro Badillo-Ramírez
- Instituto de Ciencias Aplicadas y Tecnología
- Universidad Nacional Autónoma de México
- Circuito Exterior S/N
- Ciudad Universitaria
- Ciudad de México
| | - Bruno Landeros-Rivera
- División de Ciencias Básicas e Ingeniería
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México
- Mexico
| | | | - Rubicelia Vargas
- División de Ciencias Básicas e Ingeniería
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México
- Mexico
| | - Jorge Garza
- División de Ciencias Básicas e Ingeniería
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México
- Mexico
| | - José M. Saniger
- Instituto de Ciencias Aplicadas y Tecnología
- Universidad Nacional Autónoma de México
- Circuito Exterior S/N
- Ciudad Universitaria
- Ciudad de México
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25
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26
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Nandi R, Loitongbam L, De J, Jain V, Pal SK. Gold nanoparticle-mediated signal amplification of liquid crystal biosensors for dopamine. Analyst 2019; 144:1110-1114. [DOI: 10.1039/c8an02171f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new design was developed for detection of dopamine using a boronic acid based amphiphile at aqueous–liquid crystal interface. The detection was highly enhanced in presence of gold nanoparticles.
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Affiliation(s)
- Rajib Nandi
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Manauli-140306
- India
| | - Lisha Loitongbam
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Manauli-140306
- India
| | - Joydip De
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Manauli-140306
- India
| | - Varsha Jain
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Manauli-140306
- India
| | - Santanu Kumar Pal
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Manauli-140306
- India
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27
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Chumillas S, Palomäki T, Zhang M, Laurila T, Climent V, Feliu JM. Analysis of catechol, 4-methylcatechol and dopamine electrochemical reactions on different substrate materials and pH conditions. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.08.113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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28
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Yadav T, Mukherjee V. Structural confirmation and spectroscopic study of a biomolecule: Norepinephrine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 202:222-237. [PMID: 29793144 DOI: 10.1016/j.saa.2018.05.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/25/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
The present work deals with the conformational and vibrational spectroscopic study of an important bio-molecule named norepinephrine in gas phase. The FTIR and FTRaman spectrum of norepinephrine in amorphous form were recorded in wavenumber range 4000-400 cm-1 and 4000-50 cm-1 respectively. We have investigated twenty-seven stable conformational structures of norepinephrine molecule. All the calculations have been done using Density Functional Theory with exchange functional B3LYP incorporated with the 6-31++G(d, p) basis set. The effect of hydrochloride on different bond lengths, bond angles and dihedral angles in the most stable conformer has also been studied. The total potential energy distribution for both the most stable conformer and the most stable conformer in hydrochloride was performed with the help Normal coordinate analysis method. Most of the calculated vibrational frequencies are in good agreement with the experimental frequencies. The natural bond orbital analysis was also performed to ensure the stability of electronic structures of norepinephrine. To know chemical reactivity of norepinephrine molecule we have calculated the energy gap between HOMO and LUMO orbitals and it has found above 5 eV in all the conformers.
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Affiliation(s)
- T Yadav
- SUIIT, Sambalpur University, Odisha, India
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29
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Yadav T, Mukherjee V. Interpretation of IR and Raman spectra of dopamine neurotransmitter and effect of hydrogen bond in HCl. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.066] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Martens J, Berden G, Bentlage H, Coene KLM, Engelke UF, Wishart D, van Scherpenzeel M, Kluijtmans LAJ, Wevers RA, Oomens J. Unraveling the unknown areas of the human metabolome: the role of infrared ion spectroscopy. J Inherit Metab Dis 2018; 41:367-377. [PMID: 29556837 PMCID: PMC5959965 DOI: 10.1007/s10545-018-0161-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 11/30/2022]
Abstract
The identification of molecular biomarkers is critical for diagnosing and treating patients and for establishing a fundamental understanding of the pathophysiology and underlying biochemistry of inborn errors of metabolism. Currently, liquid chromatography/high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy are the principle methods used for biomarker research and for structural elucidation of small molecules in patient body fluids. While both are powerful techniques, several limitations exist that often make the identification of unknown compounds challenging. Here, we describe how infrared ion spectroscopy has the potential to be a valuable orthogonal technique that provides highly-specific molecular structure information while maintaining ultra-high sensitivity. Here, we characterize and distinguish two well-known biomarkers of inborn errors of metabolism, glutaric acid for glutaric aciduria and ethylmalonic acid for short-chain acyl-CoA dehydrogenase deficiency, using infrared ion spectroscopy. In contrast to tandem mass spectra, in which ion fragments can hardly be predicted, we show that the prediction of an IR spectrum allows reference-free identification in the case that standard compounds are either commercially or synthetically unavailable. Finally, we illustrate how functional group information can be obtained from an IR spectrum for an unknown and how this is valuable information to, for example, narrow down a list of candidate structures resulting from a database query. Early diagnosis in inborn errors of metabolism is crucial for enabling treatment and depends on the identification of biomarkers specific for the disorder. Infrared ion spectroscopy has the potential to play a pivotal role in the identification of challenging biomarkers.
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Affiliation(s)
- Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands.
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Herman Bentlage
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands
| | - Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Udo F Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - David Wishart
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Monique van Scherpenzeel
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands.
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED, Nijmegen, The Netherlands.
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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31
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Dimić D, Milenković D, Dimitrić Marković J, Marković Z. Antiradical activity of catecholamines and metabolites of dopamine: theoretical and experimental study. Phys Chem Chem Phys 2018; 19:12970-12980. [PMID: 28480927 DOI: 10.1039/c7cp01716b] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The importance of molecules with antiradical potency that are produced in the human body has significantly increased. Among others, neurotransmitters and their metabolites act as the first line of defense against oxidative stress in the peripheral endocrine and the central nervous systems. Dopamine (DO), epinephrine (EP), norepinephrine (NE), l-DOPA, catechol, and three metabolites of dopamine (3-methoxytyramine (3-MT), homovanillic acid (HO), and 3,4-dihydrophenylacetic acid (DOPAC)) were investigated for their antiradical potency via computational methods and DPPH assay. Density functional theory calculations were used to determine the most probable reaction mechanism based on the thermodynamic parameters. These results suggested that hydrogen atom transfer (HAT)/proton-coupled electron transfer (PCET) and sequential proton loss electron transfer (SPLET) mechanisms are preferable in polar solvents. Several techniques were employed to differentiate between HAT and PCET mechanisms via examination of the transition state structures. Kinetic studies of HAT/PCET and electron transfer (ET) reactions, the second step of SPLET, have proven that ET is much faster for an order of 105-106. Based on this, it was concluded that SPLET was the dominant mechanism for the antiradical activity towards DPPH radicals in polar solvents. The findings suggest that all the investigated molecules can be classified as excellent antiradical scavengers, except for 3-MT and homovanillic acid.
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Affiliation(s)
- D Dimić
- Faculty of Physical Chemistry, University of Belgrade, 12-16 Studentski trg, 11000 Belgrade, Republic of Serbia
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32
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Jašíková L, Roithová J. Infrared Multiphoton Dissociation Spectroscopy with Free-Electron Lasers: On the Road from Small Molecules to Biomolecules. Chemistry 2018; 24:3374-3390. [PMID: 29314303 DOI: 10.1002/chem.201705692] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 01/07/2023]
Abstract
Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the structure of isolated, mass-selected ions in the gas phase. This method has been widely used since it became available at free-electron laser (FEL) user facilities. Thus, in this Minireview, we examine the use of IRMPD/FEL spectroscopy for investigating ions derived from small molecules, metal complexes, organometallic compounds and biorelevant ions. Furthermore, we outline new applications of IRMPD spectroscopy to study biomolecules.
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Affiliation(s)
- Lucie Jašíková
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Jana Roithová
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 43, Czech Republic
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33
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Corinti D, Gregori B, Guidoni L, Scuderi D, McMahon TB, Chiavarino B, Fornarini S, Crestoni ME. Complexation of halide ions to tyrosine: role of non-covalent interactions evidenced by IRMPD spectroscopy. Phys Chem Chem Phys 2018; 20:4429-4441. [PMID: 29372198 DOI: 10.1039/c7cp06657k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The binding motifs in the halide adducts with tyrosine ([Tyr + X]-, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950-1950 and 2800-3700 cm-1. Extensive quantum chemical calculations at B3LYP, B3LYP-D3 and MP2 levels of theory have been performed using the 6-311++G(d,p) basis set to determine the geometry, relative energy and vibrational properties of likely isomers and interpret the measured spectra. A diagnostic carbonyl stretching band at ∼1720 cm-1 from the intact carboxylic group characterizes the IRMPD spectra of both [Tyr + X]- and [nitroTyr + X]-, revealing that the canonical isomers (maintaining intact amino and carboxylic functions) are the prevalent structures. The spectroscopic evidence reveals the presence of multiple non-covalent forms. The halide complexes of tyrosine conform to a mixture of plane and phenol isomers. The contribution of phenol-bound isomers is sensitive to anion size, increasing from chloride to iodide, consistent with the decreasing basicity of the halide, with relative amounts depending on the relative energies of the respective structures. The stability of the most favorable phenol isomer with respect to the reference plane geometry is in fact 1.3, -2.1, -6.8 kJ mol-1, for X = Cl, Br, I, respectively. The change in π-acidity by ring nitration also stabilizes anion-π interactions yielding ring isomers for [nitroTyr + X]-, where the anion is placed above the face of the aromatic ring.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", P.le A. Moro 5, I-00185 Roma, Italy.
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34
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Dimić DS, Milenković DA, Marković JMD, Marković ZS. Thermodynamic and kinetic analysis of the reaction between biological catecholamines and chlorinated methylperoxy radicals. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1414967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Dušan S. Dimić
- Faculty of Physical Chemistry, University of Belgrade, Belgrade, Republic of Serbia
| | - Dejan A. Milenković
- Bioengineering Research and Development Center, Kragujevac, Republic of Serbia
| | | | - Zoran S. Marković
- Department of Chemical-Technological Sciences, State University of Novi Pazar, Novi Pazar, Republic of Serbia
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Bernhard D, Holzer C, Dietrich F, Stamm A, Klopper W, Gerhards M. The Structure of Diphenyl Ether-Methanol in the Electronically Excited and Ionic Ground States: A Combined IR/UV Spectroscopic and Theoretical Study. Chemphyschem 2017; 18:3634-3641. [PMID: 29024275 DOI: 10.1002/cphc.201700722] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/24/2017] [Indexed: 11/06/2022]
Abstract
Diphenyl ether offers competing docking sites for methanol: the ether oxygen acts as a common hydrogen-bond acceptor and the π system of each phenyl ring allows for OH-π interactions driven by electrostatic, induction, and dispersion forces. Based on investigations in the electronic ground state (S0 ), we present a detailed study of the electronically excited state (S1 ) and the ionic ground state (D0 ), in which an impact on the structural preference is expected compared with the S0 state. Dispersion forces in the electronically excited state were analyzed by comparing the computed binding energies at the coupled-cluster-singles (CCS) and approximate coupled-cluster-singles-doubles levels of theory (CC2 approximation). By applying UV/IR/UV spectroscopy, we found a more strongly bound OH-π structure in the S1 state compared with the S0 state, in agreement with spin-component-scaled CC2 calculations. A structural rearrangement into a non-hydrogen-bonded structure takes places upon ionization in the D0 state, which was revealed by using IR photodissociation spectroscopy and confirmed by theory.
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Affiliation(s)
- Dominic Bernhard
- Fachbereich Chemie and Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663, Kaiserslautern, Germany
| | - Christof Holzer
- Institut für Physikalische Chemie, Abteilung für Theoretische Chemie, Karlsruher Institut für Technologie, KIT, Fritz-Haber-Weg 2, D-76131, Karlsruhe, Germany
| | - Fabian Dietrich
- Fachbereich Chemie and Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663, Kaiserslautern, Germany
| | - Anke Stamm
- Fachbereich Chemie and Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663, Kaiserslautern, Germany
| | - Wim Klopper
- Institut für Physikalische Chemie, Abteilung für Theoretische Chemie, Karlsruher Institut für Technologie, KIT, Fritz-Haber-Weg 2, D-76131, Karlsruhe, Germany
| | - Markus Gerhards
- Fachbereich Chemie and Research Center OPTIMAS, TU Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663, Kaiserslautern, Germany
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36
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Nikolić D, Macias C, Lankin DC, van Breemen RB. Collision-induced dissociation of phenethylamides: role of ion-neutral complexes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1385-1395. [PMID: 28558170 PMCID: PMC5555735 DOI: 10.1002/rcm.7915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/21/2017] [Accepted: 05/25/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Phenethylamides are a large group of naturally occurring molecules found both in the plant and animal kingdoms. In addition, they are used as intermediates for the synthesis of pharmaceutically important dihydro- and tetrahydroisoquinolines. To enable efficient characterization of this class of molecules, a detailed mass spectrometric fragmentation study of a broad series of analogs was carried out. METHODS The test compounds were synthesized using standard methods for amide bond formation. Low-energy high-resolution tandem mass spectra were acquired on a hybrid quadrupole/time-of-flight mass spectrometer using positive ion electrospray ionization. RESULTS A total of 26 analogs were investigated in the study. Fragmentation of phenethylamides was found to proceed via intermediate ion-neutral complexes. The complexes can break down via multiple pathways including dissociation, proton transfer, Friedel-Crafts acylation, and single electron transfer. The relative contribution of each of these pathways strongly depends on the structure of the coupling amine and acid. CONCLUSIONS A general scheme for the fragmentation of phenethylamides was developed. This study further extends the knowledge base of the ion-neutral complex by discovering Friedel-Crafts acylation as a novel reaction. The strong influence of minor structural modifications on the fragmentation patterns highlights the importance of testing many analogs in order to fully predict a fragmentation pattern of a particular class of molecules.
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Affiliation(s)
- Dejan Nikolić
- Corresponding Author: Dejan Nikolić, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612-7231, Telephone (312) 413-5867, FAX (312) 996-7107,
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37
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Dimić D, Milenković D, Marković Z, Marković JD. Structural and spectral analysis of 3-metoxytyramine, an important metabolite of dopamine. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.082] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Gregori B, Guidoni L, Crestoni ME, de Oliveira P, Houée-Levin C, Scuderi D. One-Electron Oxidation of Methionine-Containing Dipeptides of Reverse Sequence: Sulfur versus Sulfoxide Characterized by IRMPD Spectroscopy and Static and Dynamics DFT Simulations. J Phys Chem B 2017; 121:2083-2094. [DOI: 10.1021/acs.jpcb.6b12638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Leonardo Guidoni
- Dipartimento
di Scienza Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio 2, Coppito, L’Aquila I-64100, Italy
| | | | - Pedro de Oliveira
- Laboratoire
de Chimie Physique, Université Paris Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, Orsay Cedex 91405, France
| | - Chantal Houée-Levin
- Laboratoire
de Chimie Physique, Université Paris Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, Orsay Cedex 91405, France
| | - Debora Scuderi
- Laboratoire
de Chimie Physique, Université Paris Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, Orsay Cedex 91405, France
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39
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Bouchet A, Klyne J, Ishiuchi SI, Fujii M, Dopfer O. Conformation of protonated glutamic acid at room and cryogenic temperatures. Phys Chem Chem Phys 2017; 19:10767-10776. [DOI: 10.1039/c6cp08553a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Linear infrared spectroscopy of protonated glutamic acid in a cryogenic ion trap allows for the clear-cut and quantitative identification of the two conformers of this fundamental biomolecule.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- Berlin
- Germany
- Laboratory for Chemistry and Life Science
| | - Johanna Klyne
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- Berlin
- Germany
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute of Innovation Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of Innovation Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- Berlin
- Germany
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40
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Wako H, Ishiuchi SI, Kato D, Féraud G, Dedonder-Lardeux C, Jouvet C, Fujii M. A conformational study of protonated noradrenaline by UV–UV and IR dip double resonance laser spectroscopy combined with an electrospray and a cold ion trap method. Phys Chem Chem Phys 2017; 19:10777-10785. [DOI: 10.1039/c6cp08426e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In protonated noradrenaline, 3 folded and 2 extended conformers were identified under the ultra-cold condition.
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Affiliation(s)
- Hiromichi Wako
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Daichi Kato
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Géraldine Féraud
- CNRS
- Aix-Marseille Université
- PIIM UMR 7365
- Avenue Escadrille Normandie-Niémen
- 13397 Marseille Cedex 20
| | - Claude Dedonder-Lardeux
- CNRS
- Aix-Marseille Université
- PIIM UMR 7365
- Avenue Escadrille Normandie-Niémen
- 13397 Marseille Cedex 20
| | - Christophe Jouvet
- CNRS
- Aix-Marseille Université
- PIIM UMR 7365
- Avenue Escadrille Normandie-Niémen
- 13397 Marseille Cedex 20
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
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41
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Lee J, Ko J, Ryu J, Shin J, Kim H, Sohn D. Catechol grafted silica particles for enhanced adhesion to metal by coordinate bond. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.09.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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42
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Nieto P, Günther A, Berden G, Oomens J, Dopfer O. IRMPD Spectroscopy of Metalated Flavins: Structure and Bonding of Lumiflavin Complexes with Alkali and Coinage Metal Ions. J Phys Chem A 2016; 120:8297-8308. [PMID: 27690438 DOI: 10.1021/acs.jpca.6b08281] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavins are a fundamental class of biomolecules, whose photochemical properties strongly depend on their environment and their redox and metalation state. Infrared multiphoton dissociation (IRMPD) spectra of mass-selected isolated metal-lumiflavin ionic complexes (M+LF) are analyzed in the fingerprint range (800-1830 cm-1) to determine the bonding of lumiflavin with alkali (M = Li, Na, K, Cs) and coinage (M = Cu, Ag) metal ions. The complexes are generated in an electrospray ionization source coupled to an ion cyclotron resonance mass spectrometer and the IR free electron laser FELIX. Vibrational and isomer assignments of the IRMPD spectra are accomplished by comparison to quantum chemical calculations at the B3LYP/cc-pVDZ level, yielding structure, binding energy, bonding mechanism, and spectral properties of the complexes. The most stable binding sites identified in the experiments involve metal bonding to the oxygen atoms of the two available CO groups of LF. Hence, CO stretching frequencies are a sensitive indicator of both the metal binding site and the metal bond strength. More than one isomer is observed for M = Li, Na, and K, and the preferred CO binding site changes with the size of the alkali ion. For Cs+LF, only one isomer is identified, although the energies of the two most stable structures differ by less than 7 kJ/mol. While the M+-LF bonds for alkali ions are mainly based on electrostatic forces, substantial covalent contributions lead to stronger bonds for the coinage metal ions. Comparison between lumiflavin and lumichrome reveals substantial differences in the metal binding motifs and interactions due to the different flavin structures.
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Affiliation(s)
- Pablo Nieto
- Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstrasse 36, D-10623 Berlin, Germany
| | - Alan Günther
- Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstrasse 36, D-10623 Berlin, Germany
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory , Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin , Hardenbergstrasse 36, D-10623 Berlin, Germany
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43
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Bouchet A, Schütz M, Chiavarino B, Crestoni ME, Fornarini S, Dopfer O. IR spectrum of the protonated neurotransmitter 2-phenylethylamine: dispersion and anharmonicity of the NH3(+)-π interaction. Phys Chem Chem Phys 2016; 17:25742-54. [PMID: 25757357 DOI: 10.1039/c5cp00221d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The structure and dynamics of the highly flexible side chain of (protonated) phenylethylamino neurotransmitters are essential for their function. The geometric, vibrational, and energetic properties of the protonated neutrotransmitter 2-phenylethylamine (H(+)PEA) are characterized in the N-H stretch range by infrared photodissociation (IRPD) spectroscopy of cold ions using rare gas tagging (Rg = Ne and Ar) and anharmonic calculations at the B3LYP-D3/(aug-)cc-pVTZ level including dispersion corrections. A single folded gauche conformer (G) protonated at the basic amino group and stabilized by an intramolecular NH(+)-π interaction is observed. The dispersion-corrected density functional theory calculations reveal the important effects of dispersion on the cation-π interaction and the large vibrational anharmonicity of the NH3(+) group involved in the NH(+)-π hydrogen bond. They allow for assigning overtone and combination bands and explain anomalous intensities observed in previous IR multiple-photon dissociation spectra. Comparison with neutral PEA reveals the large effects of protonation on the geometric and electronic structure.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, D-10623 Berlin, Germany.
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44
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Schütz M, Bouchet A, Chiavarino B, Crestoni ME, Fornarini S, Dopfer O. Effects of Aromatic Fluorine Substitution on Protonated Neurotransmitters: The Case of 2-Phenylethylamine. Chemistry 2016; 22:8124-36. [DOI: 10.1002/chem.201600798] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Markus Schütz
- Institut für Optik und Atomare Physik; Technische Universität Berlin; Hardenbergstr. 36 10623 Berlin Germany
| | - Aude Bouchet
- Institut für Optik und Atomare Physik; Technische Universität Berlin; Hardenbergstr. 36 10623 Berlin Germany
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco; Sapienza Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco; Sapienza Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco; Sapienza Università di Roma “La Sapienza”; P. le A. Moro 5 00185 Roma Italy
| | - Otto Dopfer
- Institut für Optik und Atomare Physik; Technische Universität Berlin; Hardenbergstr. 36 10623 Berlin Germany
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45
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Goyal A, Singhal S. Robust and economic reduction protocol employing immensely stable and leach-proof magnetically separable nanocomposites. RSC Adv 2016. [DOI: 10.1039/c6ra17387j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metals stabilized over modified magnetic ferrite nanoparticles (M@Dop@CoFe2O4) have been established as very stable, magnetically recyclable and leach-proof competent catalysts for the reduction of nitroarenes.
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Affiliation(s)
- Ankita Goyal
- Department of Chemistry
- Panjab University
- Chandigarh
- India-160014
| | - Sonal Singhal
- Department of Chemistry
- Panjab University
- Chandigarh
- India-160014
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46
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Schütz M, Bouchet A, Dopfer O. Infrared spectrum of the cold ortho-fluorinated protonated neurotransmitter 2-phenylethylamine: competition between NH+⋯π and NH+⋯F interactions. Phys Chem Chem Phys 2016; 18:26980-26989. [DOI: 10.1039/c6cp05915e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IR spectra of cold rare-gas tagged ions reveal the switch of the preferred conformation of the highly flexible side chain of a prototypical protonated neurotransmitter induced by site-specific aromatic fluorination.
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Affiliation(s)
- Markus Schütz
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Aude Bouchet
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- D-10623 Berlin
- Germany
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47
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Mayorkas N, Sachs H, Schütz M, Ishiuchi SI, Fujii M, Dopfer O, Bar I. Structural motifs of 2-(2-fluoro-phenyl)-ethylamine conformers. Phys Chem Chem Phys 2016; 18:1191-201. [DOI: 10.1039/c5cp06131h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibronic and vibrational spectra of 2-(2-fluoro-phenyl)-ethylamine (2-FPEA) conformers were measured in a molecular beam by resonant two-photon ionization (R2PI), ultraviolet–ultraviolet hole burning (UV–UV HB) spectroscopy, and ionization-loss stimulated Raman spectroscopy (ILSRS).
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Affiliation(s)
- Nitzan Mayorkas
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
| | - Hanan Sachs
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
| | - Markus Schütz
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Shun-ichi Ishiuchi
- Chemical Resources Laboratory
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Masaaki Fujii
- Chemical Resources Laboratory
- Tokyo Institute of Technology
- Yokohama 226-8503
- Japan
| | - Otto Dopfer
- Institut für Optik und Atomare Physik
- Technische Universität Berlin
- 10623 Berlin
- Germany
| | - Ilana Bar
- Department of Physics
- Ben-Gurion University of the Negev
- Beer-Sheva 84105
- Israel
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48
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Measurement, Interpretation and Use of Free Ligand Solution Conformations in Drug Discovery. PROGRESS IN MEDICINAL CHEMISTRY 2016; 55:45-147. [DOI: 10.1016/bs.pmch.2015.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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49
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Bouchet A, Schütz M, Dopfer O. Competing Insertion and External Binding Motifs in Hydrated Neurotransmitters: Infrared Spectra of Protonated Phenylethylamine Monohydrate. Chemphyschem 2015; 17:232-43. [PMID: 26584245 DOI: 10.1002/cphc.201500939] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 01/29/2023]
Abstract
Hydration has a drastic impact on the structure and function of flexible biomolecules, such as aromatic ethylamino neurotransmitters. The structure of monohydrated protonated phenylethylamine (H(+) PEA-H2 O) is investigated by infrared photodissociation (IRPD) spectroscopy of cold cluster ions by using rare-gas (Rg=Ne and Ar) tagging and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. Monohydration of this prototypical neurotransmitter gives an insight into the first step of the formation of its solvation shell, especially regarding the competition between intra- and intermolecular interactions. The spectra of Rg-tagged H(+) PEA-H2 O reveal the presence of a stable insertion structure in which the water molecule is located between the positively charged ammonium group and the phenyl ring of H(+) PEA, acting both as a hydrogen bond acceptor (NH(+) ⋅⋅⋅O) and donor (OH⋅⋅⋅π). Two other nearly equivalent isomers, in which water is externally H bonded to one of the free NH groups, are also identified. The balance between insertion and external hydration strongly depends on temperature.
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Affiliation(s)
- Aude Bouchet
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Markus Schütz
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623, Berlin, Germany.
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Yang J, Yuan Y, Zhao H. Theoretical study of the interactions of a graphene-on-Ni(111) composite with dopamine. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1123314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Junwei Yang
- Department of Mathematics and Physics, Shanghai Dianji University, Shanghai, China
| | - Yanhong Yuan
- Department of Mathematics and Physics, Shanghai Dianji University, Shanghai, China
| | - Hua Zhao
- Department of Mathematics and Physics, Shanghai Dianji University, Shanghai, China
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