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Pereira RW, Ramabhadran RO. Accurate Computation of Aqueous p Kas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box p K-Yay Method. J Phys Chem A 2023; 127:9121-9138. [PMID: 37862610 DOI: 10.1021/acs.jpca.3c02977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The use of static electronic structure calculations to compute solution-phase pKas offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pKas of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pKas of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pKa units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pKas are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid-base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.
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Affiliation(s)
- Roshni W Pereira
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh 517507, India
- Centre for Atomic Molecular Optical Sciences and Technology (CAMOST), Tirupati, Andhra Pradesh 517507, India
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2
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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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3
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Sanz-Novo M, León I, Alonso ER, Alonso JL. Unleashing the shape of L-DOPA at last. Phys Chem Chem Phys 2021; 24:3546-3554. [PMID: 34908061 DOI: 10.1039/d1cp05066d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Herein, we report the first rotational study of neutral L-DOPA, an extensively used supramolecular synthon and an amino acid precursor of the neurotransmitters dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline) using broadband and narrowband Fourier transform microwave spectroscopies coupled with a laser ablation vaporization system. The spectroscopic parameters derived from the analysis of the rotational spectrum conclusively identify the existence of four distinct conformers of L-DOPA in the supersonic jet, further rejecting the previously reported catechol ring-induced conformational restriction. The analysis of the 14N nuclear quadrupole coupling hyperfine structure further revealed the orientation of the N-bearing functional group, proving the existence of stabilizing N-H⋯π interactions for the observed structures.
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Affiliation(s)
- Miguel Sanz-Novo
- Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopía y Bioespectroscopía Unidad Asociada CSIC, Parque Científico Uva Universidad de Valladolid, Paseo de Belén 5, Valladolid 47011, Spain.
| | - Iker León
- Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopía y Bioespectroscopía Unidad Asociada CSIC, Parque Científico Uva Universidad de Valladolid, Paseo de Belén 5, Valladolid 47011, Spain.
| | - Elena R Alonso
- Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopía y Bioespectroscopía Unidad Asociada CSIC, Parque Científico Uva Universidad de Valladolid, Paseo de Belén 5, Valladolid 47011, Spain.
| | - José L Alonso
- Espectroscopía Molecular (GEM), Edificio Quifima Laboratorios de Espectroscopía y Bioespectroscopía Unidad Asociada CSIC, Parque Científico Uva Universidad de Valladolid, Paseo de Belén 5, Valladolid 47011, Spain.
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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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5
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Studies on hydrogen bonding of adrenaline/acetone and adrenaline/methanol complexes: computational and experimental approach. Struct Chem 2021. [DOI: 10.1007/s11224-021-01773-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Theoretical investigation on hydrogen bond interaction between adrenaline and hydrogen sulfide. J Mol Model 2020; 26:354. [PMID: 33244644 DOI: 10.1007/s00894-020-04602-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/08/2020] [Indexed: 10/22/2022]
Abstract
In this study, we elucidated the formation of hydrogen bond between adrenaline (AD) and hydrogen sulfide utilizing computational studies. Six potential complexes were studied including geometrical parameters, energy, vibrational frequency, topological analysis, natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and NMR analysis. Moreover, these calculations were examined through DFT/ωB97XD/6-311G++(d,p) level. It was found that there are no indication on formation on hydrogen bonding between the two catecholic OHs where the one formed between the amino group and the hydroxyl oxygen atom of adrenaline monomer was broken in AS1 to form two new interactions namely SH...N and O1H1...S, while it retained in other complexes. Furthermore, the bond became stronger due to cooperativity in AS3 and AS6, for the presence of withdrawing effect of the phenyl ring, the H-bonds formed with the side chain oxygen atom. The adrenaline and H2S interaction was experimentally examined via FT-IR spectrometry and thin layer chromatography for confirmation of our theoretical study. Graphical abstract.
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Kooser K, Kivimäki A, Turunen P, Pärna R, Reisberg L, Kirm M, Valden M, Huttula M, Kukk E. Gas-phase endstation of electron, ion and coincidence spectroscopies for diluted samples at the FinEstBeAMS beamline of the MAX IV 1.5 GeV storage ring. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1080-1091. [PMID: 33566019 PMCID: PMC7336174 DOI: 10.1107/s1600577520007146] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 05/27/2020] [Indexed: 05/26/2023]
Abstract
Since spring 2019 an experimental setup consisting of an electron spectrometer and an ion time-of-flight mass spectrometer for diluted samples has been available for users at the FinEstBeAMS beamline of the MAX IV Laboratory in Lund, Sweden. The setup enables users to study the interaction of atoms, molecules, (molecular) microclusters and nanoparticles with short-wavelength (vacuum ultraviolet and X-ray) synchrotron radiation and to follow the electron and nuclear dynamics induced by this interaction. Test measurements of N2 and thiophene (C4H4S) molecules have demonstrated that the setup can be used for many-particle coincidence spectroscopy. The measurements of the Ar 3p photoelectron spectra by linear horizontal and vertical polarization show that angle-resolved experiments can also be performed. The possibility to compare the electron spectroscopic results of diluted samples with solid targets in the case of Co2O3 and Fe2O3 at the Co and Fe L2,3-absorption edges in the same experimental session is also demonstrated. Because the photon energy range of the FinEstBeAMS beamline extends from 4.4 eV up to 1000 eV, electron, ion and coincidence spectroscopy studies can be executed in a very broad photon energy range.
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Affiliation(s)
- Kuno Kooser
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
- Institute of Physics, University of Tartu, W. Ostwaldi 1, EE-50411 Tartu, Estonia
| | - Antti Kivimäki
- Nano and Molecular Systems Research Unit, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
- MAX IV Laboratory, Lund University, PO Box 118, SE-22100 Lund, Sweden
| | - Paavo Turunen
- Nano and Molecular Systems Research Unit, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Rainer Pärna
- Institute of Physics, University of Tartu, W. Ostwaldi 1, EE-50411 Tartu, Estonia
- MAX IV Laboratory, Lund University, PO Box 118, SE-22100 Lund, Sweden
| | - Liis Reisberg
- Institute of Physics, University of Tartu, W. Ostwaldi 1, EE-50411 Tartu, Estonia
- MAX IV Laboratory, Lund University, PO Box 118, SE-22100 Lund, Sweden
| | - Marco Kirm
- Institute of Physics, University of Tartu, W. Ostwaldi 1, EE-50411 Tartu, Estonia
| | - Mika Valden
- Surface Science Group, Laboratory of Photonics, Tampere University of Technology, FIN-33101, Tampere, Finland
| | - Marko Huttula
- Nano and Molecular Systems Research Unit, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Edwin Kukk
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
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Dezalay J, Broquier M, Soorkia S, Hirata K, Ishiuchi SI, Fujii M, Grégoire G. Excited-state proton transfer in protonated adrenaline revealed by cryogenic UV photodissociation spectroscopy. Phys Chem Chem Phys 2020; 22:11498-11507. [PMID: 32393956 DOI: 10.1039/d0cp01127d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report a comprehensive study of the structures and deactivation processes of protonated adrenaline through cryogenic UV photodissociation spectroscopy. Single UV and double-resonance UV-UV hole burning spectroscopies have been performed and compared to coupled-cluster SCS-CC2 calculations performed on the ground and first electronic states. Three conformers were assigned, two lowest energy gauche conformers along with a higher energy conformer with an extended structure which is indeed the global minimum in solution. This demonstrates the kinetic trapping of this high energy gas phase conformer during the electrospray process. At the band origin of all conformers, the main fragmentation channel is the Cα-Cβ bond cleavage, triggered by an excited state proton transfer to the catechol ring. Internal conversion leading to the water loss channel competes with the direct dissociation and tends to prevail with the increase of excess energy brought by the UV laser. Picosecond time-resolved pump-probe spectroscopy was performed to measure the excited state lifetimes of the three conformers of AdH+, which decay with the increase of excess energy in the ππ* state, from 2 ns at the band origin down to few hundreds of picoseconds 0.5 eV to the blue. Finally, about 0.8 eV above the band origin, the πσ* state is directly reached, leading to the opening of the H-loss channel.
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Affiliation(s)
- Jordan Dezalay
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, F-91405 Orsay, France.
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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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Chojecki M, Rutkowska-Zbik D, Korona T. On the applicability of functional-group symmetry-adapted perturbation theory and other partitioning models for chiral recognition - the case of popular drug molecules interacting with chiral phases. Phys Chem Chem Phys 2019; 21:22491-22510. [PMID: 31588451 DOI: 10.1039/c9cp04056k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The applicability of symmetry-adapted perturbation theory (SAPT) and functional-group SAPT (F-SAPT) to study chiral recognition is investigated on an example of three popular chiral drug molecules: ibuprofen, norepinephrine, and baclofen, interacting with phenethylamine or proline - two molecules that are often used as chiral phases in chromatography. The comparison of the F-SAPT with the interacting quantum atoms (IQA) approach is also provided. Accurate estimation of energetic differences of the non-covalent intermolecular complexes composed of two chiral molecules is a necessary prerequisite for the possibility of a prediction of the chiral recognition. The SAPT method with interacting molecules described on the density functional theory level provides accurate total interaction energies, while the F-SAPT approach is the most useful in determining which functional groups are responsible for strengthening or weakening of the interaction between chiral molecules. The largest difference in the interaction energies has been calculated for the baclofen-phenethylamine and norepinephrine-phenethylamine pairs, while the smallest for the ibuprofen-proline and baclofen-proline ones. In most cases, the intermolecular interaction is found to be composed of a strong directional hydrogen bond, which was stabilized by two or more weaker non-covalent interactions between groups (in accordance with the phenomological three-point rule), but in several cases more subtle factors are responsible for larger stability of one diastereoisomer, like the stabilization of the conformation involving two noninteracting functional groups attached to a chiral atom through intramolecular attraction. Additionally, the simulated IR spectra were analyzed for all pairs of diastereoisomeric complexes and the red- and blue-shifts of characteristic bond vibrations were discussed in the context of inter-group interactions.
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Affiliation(s)
- Michał Chojecki
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland.
| | - Dorota Rutkowska-Zbik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland.
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Stable Parent Anions of Dopamine and Adrenaline: A New Form of Neurotransmitters. J Phys Chem B 2019; 123:7695-7699. [DOI: 10.1021/acs.jpcb.9b06223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Pei L, Li DZ, Zhang LJ. Theoretical insights into the hydrogen bonding interaction in the complexation of epinephrine with uracil. J Mol Model 2019; 25:252. [PMID: 31353431 DOI: 10.1007/s00894-019-4123-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/04/2019] [Indexed: 11/28/2022]
Abstract
The present study is aimed at probing the hydrogen bonding interaction between epinephrine and uracil by means of density functional theory calculations concerning their complexation's geometries, interaction energies, and vibrational frequencies. Geometry optimization was carried out giving 19 stable geometries of epinephrine-uracil complex with interaction energies in a range of - 21.51 to - 62.37 kJ mol-1 using the basis set superposition error (BSSE) correction. The analysis of structure and vibration shows that the hydrogen bonding elongates the length of corresponding bond O(N)-H and decreases the symmetric stretching vibrational frequency, which indicates red-shifted H-bonding interactions in all the geometries. Additionally, the analysis with theories of natural bond orbital (NBO), atoms in molecules (AIM), and the reduced density gradient (RDG) of hydrogen bonding properties and characteristics of the 19 geometries suggests that the hydrogen bonding in all the optimized structures of epinephrine-uracil complex is kind of a closed-shell interaction and mainly electrostatic dominant.
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Affiliation(s)
- Ling Pei
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou, 256603, Shandong, People's Republic of China.
| | - Da-Zhi Li
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou, 256603, Shandong, People's Republic of China
| | - Li-Juan Zhang
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou, 256603, Shandong, People's Republic of China
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Demianenko E, Rayevsky A, Soriano-Ursúa MA, Trujillo-Ferrara JG. Theoretical Coupling and Stability of Boronic Acid Adducts with Catecholamines. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180710101604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background:
Catecholamines combined with boric/boronic acids are attractive chemical
agents in drug design because some of their adducts have shown interesting biological activity.
Scant information exists about their stability.
Objective:
The aim of the present theoretical study was to explore the role of boron in molecules
that combine catecholamines and boric/boronic acids, with a particular interest in examining
stability.
Method:
The methodology was based on the US GAMESS program using DFT with the B3LYP
exchange-correlation functional and the 6-31G (d,p) split-valence basis set.
Results:
According to the current findings, the boron-containing compounds (BCCs) exhibit weaker
bonding to the hydroxyls on the ethylamine moiety than to those in the aromatic ring. The strongest
binding site of a hydroxyl group was often found to be in meta-position (relative to ethylamine
moiety) for boron-free compounds and in para-position for BCCs. Nonetheless, the methyl substituent
in the amino group was able to induce changes in this pattern. We analyzed feasible boronsubstituted
structures and assessed the relative strength of the respective C-B bonds, which allowed
for the identification of the favorable points for reaction and stability.
Conclusion:
It is feasible to form adducts by bonding on the amine and catechol sides of catecholamines.
The presence of boron stabilizes the adducts in para-position. Since some of these BCCs
are promising therapeutic agents, understanding the mechanisms of reaction is relevant for drug
design.
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Affiliation(s)
- Eugeniy Demianenko
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., Kyiv, 03164, Ukraine
| | - Alexey Rayevsky
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., Kyiv, 03164, Ukraine
| | - Marvin A. Soriano-Ursúa
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
| | - José G. Trujillo-Ferrara
- Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron s/n, Mexico City, 11340, Mexico
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Ganina TA, Chertkov VA. Dynamic Structure of Organic Compounds in Solution According to NMR Data and Quantum Chemical Calculations: III. Noradrenaline. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2019. [DOI: 10.1134/s107042801903014x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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El Guerdaoui A, Tijar R, Bourjila M, El Merbouh B, El Bouzaidi RD, El Gridani A. Conformational Space Analysis of Protected N-Formyl-L-Phenylalanine-N-Amide Amino Acid: Effects of the Intramolecular Basis Set Superposition Error. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Calabrese C, Maris A, Evangelisti L, Piras A, Parravicini V, Melandri S. Rotational Spectrum and Conformational Analysis of N-Methyl-2-Aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters. Front Chem 2018. [PMID: 29520356 PMCID: PMC5827360 DOI: 10.3389/fchem.2018.00025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe an experimental and quantum chemical study for the accurate determination of the conformational space of small molecular systems governed by intramolecular non-covalent interactions. The model systems investigated belong to the biological relevant aminoalcohol's family, and include 2-amino-1-phenylethanol, 2-methylamino-1-phenylethanol, noradrenaline, adrenaline 2-aminoethanol, and N-methyl-2-aminoethanol. For the latter molecule, the rotational spectrum in the 6–18 and 59.6–74.4 GHz ranges was recorded in the isolated conditions of a free jet expansion. Based on the analysis of the rotational spectra, two different conformational species and 11 isotopologues were observed and their spectroscopic constants, including 14N-nuclear hyperfine coupling constants and methyl internal rotation barriers, were determined. From the experimental data a structural determination was performed, which was also used to benchmark accurate quantum chemical calculations on the whole conformational space. Atom in molecules and non-covalent interactions theories allowed the characterization of the position of the intramolecular non-covalent interactions and the energies involved, highlighting the subtle balance responsible of the stabilization of all the molecular systems.
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Affiliation(s)
- Camilla Calabrese
- Dipartimento di Chimica "G. Ciamician" dell'Università, Bologna, Italy
| | - Assimo Maris
- Dipartimento di Chimica "G. Ciamician" dell'Università, Bologna, Italy
| | - Luca Evangelisti
- Dipartimento di Chimica "G. Ciamician" dell'Università, Bologna, Italy
| | - Anna Piras
- Dipartimento di Chimica "G. Ciamician" dell'Università, Bologna, Italy
| | | | - Sonia Melandri
- Dipartimento di Chimica "G. Ciamician" dell'Università, Bologna, Italy
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El Guerdaoui A, El Merbouh B, Tijar R, Bourjila M, El Bouzaidi RD, El Gridani A, El Mouhtadi M. An exhaustive conformational analysis of N -formyl- l -tyrosinamide using a genetic algorithm for multimodal search. CR CHIM 2017. [DOI: 10.1016/j.crci.2016.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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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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20
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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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21
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Ishiuchi SI, Yamada K, Oba H, Wako H, Fujii M. Gas phase ultraviolet and infrared spectroscopy on a partial peptide of β2-adrenoceptor SIVSF-NH2 by a laser desorption supersonic jet technique. Phys Chem Chem Phys 2016; 18:23277-84. [DOI: 10.1039/c6cp04196e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Laser desorption supersonic jet laser spectroscopy has been applied to a penta-peptide, Ser-Ile-Val-Ser-Phe-NH2 (SIVSF-NH2), which is a partial sequence of a binding site in a β2-adrenaline receptor protein.
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Affiliation(s)
- Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Kohei Yamada
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hikari Oba
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hiromichi Wako
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
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22
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YOOSEFIAN MEHDI, RAISSI HEIDAR, SOHEILI SAEEDEH. A comprehensive study of the structure, tautomeric properties, and conformational flexibility of 3-Hydroxy-propeneselenal. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0856-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Juárez-Jiménez J, Barril X, Orozco M, Pouplana R, Luque FJ. Assessing the suitability of the multilevel strategy for the conformational analysis of small ligands. J Phys Chem B 2014; 119:1164-72. [PMID: 25319869 DOI: 10.1021/jp506779y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Predicting the conformational preferences of flexible compounds is a challenging problem in drug design, where the recognition between ligand and receptor is affected by the ability of the interacting partners to adopt a favorable conformation for the binding. To explore the conformational space of flexible ligands and to obtain the relative free energy of the conformation wells, we have recently reported a multilevel computational strategy that relies on the predominant-state approximation-where the conformational space is partitioned into distinct conformational wells-and combines a low-level method for sampling the conformational minima and high-level ab initio calculations for estimating their relative stability. In this study, we assess the performance of the multilevel strategy for predicting the conformational preferences of a series of structurally related phenylethylamines and streptomycin in aqueous solution. The charged nature of these compounds and the chemical complexity of streptomycin make them a challenging test for the multilevel approach. Furthermore, we explore the suitability of using a molecular mechanics approach as a source of approximate ensembles in the first stage of the multilevel strategy. The results support the reliability of the multilevel approach for obtaining an accurate conformational ensemble of small (bio)organic molecules in aqueous solution.
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Affiliation(s)
- Jordi Juárez-Jiménez
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona , Avda. Prat de la Riba, 171, 08921 Santa Coloma de Gramenet, Spain
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24
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Nagy PI. Competing intramolecular vs. intermolecular hydrogen bonds in solution. Int J Mol Sci 2014; 15:19562-633. [PMID: 25353178 PMCID: PMC4264129 DOI: 10.3390/ijms151119562] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/17/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, the University of Toledo, Toledo, OH 43606-3390, USA.
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25
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Capello MC, Broquier M, Ishiuchi SI, Sohn WY, Fujii M, Dedonder-Lardeux C, Jouvet C, Pino GA. Fast Nonradiative Decay in o-Aminophenol. J Phys Chem A 2014; 118:2056-62. [DOI: 10.1021/jp411457v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcela C. Capello
- Instituto
de Investigaciones en Físico Química de Córdoba
(INFIQC) CONICET, UNC. Dpto. de Fisicoquímica, Facultad de
Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Michel Broquier
- Centre Laser de l’Université Paris Sud (CLUPS,
LUMAT FR 2764) Bât. 106, Univ
Paris-Sud 11, 91405 Orsay Cedex, France
- Institut des Sciences Moléculaires d’Orsay (ISMO,
UMR8624 CNRS) Bât. 210, Univ
Paris-Sud 11, 91405 Orsay Cedex, France
| | - Shun-Ichi Ishiuchi
- Chemical
Resources Laboratory and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku,Yokohama 226-8503, Japan
| | - Woon Y. Sohn
- Chemical
Resources Laboratory and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku,Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Chemical
Resources Laboratory and Integrated Research Institute, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku,Yokohama 226-8503, Japan
| | - Claude Dedonder-Lardeux
- Physique
des Interactions Ioniques et Moléculaires (PIIM), UMR-CNRS 7345 Aix-Marseille Université, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
| | - Christophe Jouvet
- Physique
des Interactions Ioniques et Moléculaires (PIIM), UMR-CNRS 7345 Aix-Marseille Université, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
| | - Gustavo A. Pino
- Instituto
de Investigaciones en Físico Química de Córdoba
(INFIQC) CONICET, UNC. Dpto. de Fisicoquímica, Facultad de
Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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26
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Ganesan A, Mohammadi N, Wang F. From building blocks of proteins to drugs: a quantum chemical study on structure–property relationships of phenylalanine, tyrosine and dopa. RSC Adv 2014. [DOI: 10.1039/c3ra47364c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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27
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Ishiuchi SI, Sone H, Fujii M. Laser Desorption Supersonic Jet Spectroscopy of Octopamine by Its Hydrochloride Salt. CHEM LETT 2013. [DOI: 10.1246/cl.130431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Hirokazu Sone
- Chemical Resources Laboratory, Tokyo Institute of Technology
| | - Masaaki Fujii
- Chemical Resources Laboratory, Tokyo Institute of Technology
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28
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Cabezas C, Peña I, López JC, Alonso JL. Seven Conformers of Neutral Dopamine Revealed in the Gas Phase. J Phys Chem Lett 2013; 4:486-490. [PMID: 26281745 DOI: 10.1021/jz302135h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The rotational spectrum of neutral dopamine has been investigated for the first time using a combination of Fourier transform microwave spectroscopy with laser ablation. The parameters extracted from the analysis of the spectrum unequivocally identify the existence of seven conformers of dopamine. (14)N nuclear quadrupole coupling interactions have been used to determine the orientation of the amino group probing the existence of stabilizing N-H···π interactions for all observed conformers.
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Affiliation(s)
- Carlos Cabezas
- Grupo de Espectroscopı́a Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Cientı́fico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Isabel Peña
- Grupo de Espectroscopı́a Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Cientı́fico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Juan C López
- Grupo de Espectroscopı́a Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Cientı́fico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
| | - José L Alonso
- Grupo de Espectroscopı́a Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Parque Cientı́fico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
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29
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Hydrogen-bonding interactions in adrenaline–water complexes: DFT and QTAIM studies of structures, properties, and topologies. J Mol Model 2012; 18:3113-23. [DOI: 10.1007/s00894-011-1325-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
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30
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Ishiuchi SI, Asakawa T, Mitsuda H, Miyazaki M, Chakraborty S, Fujii M. Gas-phase spectroscopy of synephrine by laser desorption supersonic jet technique. J Phys Chem A 2011; 115:10363-9. [PMID: 21819118 DOI: 10.1021/jp205267c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In our previous work, we found that synephrine has six conformers in the gas phase, while adrenaline, which is a catecholamine and has the same side chain as synephrine, has been reported to have only two conformers. To determine the conformational geometries of synephrine, we measured resonance enhanced multiphoton ionization, ultraviolet-ultraviolet hole burning, and infrared dip spectra by utilizing the laser desorption supersonic jet technique. By comparing the observed infrared spectra with theoretical ones, we assigned geometries except for the orientations of the phenolic OH group. Comparison between the determined structures of synephrine and those of 2-methylaminno-1-phenylethanol, which has the same side chain as synephrine but no phenol OH group, leads to the conclusion that the phenolic OH group in synephrine does not affect the conformational flexibility of the side chain. In the case of adrenaline, which is expected to have 12 conformers if there are no interactions between the catecholic OH groups and the side chain, some interactions possibly exist between them because only two conformations are observed. By estimation of the dipole-dipole interaction energy between partial dipole moments of the catecholic OH groups and the side chain, it was concluded that the dipole-dipole interaction stabilizes specific conformers which are actually observed.
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Affiliation(s)
- Shun-ichi Ishiuchi
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259, Yokahama 226-8503, Japan
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31
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Structural characterization by infrared multiple photon dissociation spectroscopy of protonated gas-phase ions obtained by electrospray ionization of cysteine and dopamine. Anal Bioanal Chem 2011; 399:2463-73. [DOI: 10.1007/s00216-010-4582-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 12/03/2010] [Accepted: 12/06/2010] [Indexed: 01/23/2023]
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32
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Ishiuchi SI, Mitsuda H, Asakawa T, Miyazaki M, Fujii M. Conformational reduction of DOPA in the gas phase studied by laser desorption supersonic jet laser spectroscopy. Phys Chem Chem Phys 2011; 13:7812-20. [DOI: 10.1039/c0cp02695f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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33
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Huang Z, Dai Y, Yu L. Density functional theory and topological analysis on the hydrogen bonding interactions in N-protonated adrenaline–DMSO complexes. Struct Chem 2010. [DOI: 10.1007/s11224-010-9621-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Lee DR, Galant NJ, Wang H, Mucsi Z, Setiadi DH, Viskolcz B, Csizmadia IG. Thermodynamic functions of molecular conformations of (2-fluoro-2-phenyl-1-ethyl)ammonium ion and (2-hydroxy-2-phenyl-1-ethyl)ammonium ion as models for protonated noradrenaline and adrenaline: first-principles computational study of conformations and thermodynamic functions for the noradrenaline and adrenaline models. J Phys Chem A 2009; 113:2507-15. [PMID: 19239211 DOI: 10.1021/jp807353n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper reports the structural and thermodynamic consequences of substitution of the OH group by the isoelectronic F-atom in the case of the adrenaline family of molecules. The conformational landscapes were explored for the two enantiomeric forms of N-protonated-beta-fluoro-beta-phenyl-ethylamine, also called (2-fluoro-2-phenyl-1-ethyl)-ammonium ion (Model 1) and that of N-protonated-beta-hydroxy-beta-phenyl-ethylamine, also referred to as (2-hydroxy-2-phenyl-1-ethyl)-ammonium (Model 2) models of noradrenaline and adrenaline molecules. These full conformational studies were carried out by first principles of quantum mechanical computations at the B3LYP/6-31G(d,p) and G3MP2B3 levels of theory, using the Gaussian03 program. Also, frequency calculations of the stable structures were performed at the B3LYP/6-31G(d,p), and G3MP2B3 levels of theory. The thermodynamic functions (U, H, S, and G) of the various stable conformations of the title compounds were calculated at these levels of theory for the R and S stereoisomers. Relative values of the thermodynamic functions have been calculated with respect of the chosen reference conformers in which all relevant dihedral angles assumed anti orientation for the Model 1 and Model 2. Through the combination of both point and axis chirality, the enantiomeric and diastereomeric relationships of the six structures for each molecule investigated were established. Intramolecular hydrogen bonding interactions have been studied by the atoms in molecules (AIM) analysis of the electron density. The aromaticity of phenyl group has been determined by a selective hydrogenation protocol. The pattern of the extent of aromacity, due intramolecular interactions, varies very little between the two models studied.
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Affiliation(s)
- DongJin R Lee
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
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35
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Shields AE, van Mourik T. Comparison of ab Initio and DFT Electronic Structure Methods for Peptides Containing an Aromatic Ring: Effect of Dispersion and BSSE. J Phys Chem A 2007; 111:13272-7. [DOI: 10.1021/jp076496p] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ashley E. Shields
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
| | - Tanja van Mourik
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
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36
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Baker CM, Grant GH. The effect of solvation on biomolecular conformation: 2-amino-1-phenylethanol. J Phys Chem B 2007; 111:9940-54. [PMID: 17672488 DOI: 10.1021/jp071059w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecule neurotransmitters form one the most important classes of pharmaceutical molecules. While the behavior of these molecules in their neutral forms in the gas phase is well understood, their behavior in more biologically relevant scenarios (protonated and in aqueous solution) has received comparatively little attention. Here we address this problem by using molecular mechanics simulations to build up a detailed picture of the conformational behavior of 2-amino-1-phenylethanol, a noradrenaline analogue, in aqueous solution in both its neutral and protonated forms. For the sake of comparison, equivalent simulations are also performed on the gas-phase molecules and gas-phase hydrated clusters. These calculations reveal the important role that water has to play in determining the conformational preferences and dynamic behavior of the molecules. Water molecules are found to bridge between the various functional groups within the molecule, significantly affecting their relative stabilities in comparison to the gas-phase values. The reorganization of these solvation structures also provides a mechanism for conformational interconversion. The role of the solvent in mediating interactions between the various functional groups within the molecule suggests that in noradrenaline the catechol groups will be able to interact, albeit indirectly, with the other functional groups, thereby influencing the behavior of the molecule.
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Affiliation(s)
- Christopher M Baker
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, The University of Oxford, South Parks Road, Oxford, United Kingdom OX1 3QZ
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37
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Alagona G, Ghio C. Competitive H-bonds in vacuo and in aqueous solution for N-protonated adrenaline and its monohydrated complexes. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.02.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Macleod NA, Simons JP. Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase. Mol Phys 2007. [DOI: 10.1080/00268970701194285] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Macleod‡ NA, Simons JP. Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase – ARTICLE WITHDRAWN. Mol Phys 2006. [DOI: 10.1080/00268970601110340] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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41
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Miller III * TF, Clary DC. Torsional anharmonicity in the conformational thermodynamics of flexible molecules. Mol Phys 2005. [DOI: 10.1080/00268970500096145] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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