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Rahimi R, Saban N, Bar I. Conformational Mapping, Interactions, and Fluorine Impact by Combined Spectroscopic Approaches and Quantum Chemical Calculations. J Phys Chem Lett 2024; 15:3658-3667. [PMID: 38534060 DOI: 10.1021/acs.jpclett.4c00301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Noncovalent interactions and their careful variation can be crucial in understanding molecular structures, conformational topographies, and properties. Here, we examine the fluorination impact on the structure and conformational behavior of 2-(2-fluorophenyl)ethyl alcohol (2-FPEAL) by monitoring the first individual ionization-loss-stimulated Raman spectra of the jet-cooled molecule. The comparison of two different broad-range spectra and predicted equivalents discloses two distinct structures. One possesses a folded side chain (gauche) and the other an extended chain (anti) with the terminal hydrogen atom pointing opposite or toward the fluorine side, indicating the improper previous tentative assignment of the latter. These conformers resemble and differ from the nonfluorinated analogue structures. Theoretical analyses reveal interconversion pathways of 2-FPEAL conformers during expansion and the delicate balance between attractive (C-H···F and O-H···π) and repulsive interactions. These findings show the achievements of our integrated approach, suggesting its potential for overcoming future structural challenges.
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Affiliation(s)
- Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Noga Saban
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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2
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Rahimi R, Saban N, Bar I. Synergistic Spectroscopic and Computational Characterization Evidencing the Preservation or Flipping of the Hydroxyl Group of 2-Phenylethyl Alcohol upon Single and Double Hydration. J Am Chem Soc 2023; 145:18455-18467. [PMID: 37561882 DOI: 10.1021/jacs.3c04762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Even apparently simple, obtaining and analyzing observations on molecules and clusters and unambiguously assigning their structures is challenging. We report here the first ionization-loss Raman spectra compared to quantum chemical predictions for establishing the structural preferences of hydrates of the neurotransmitters hydroxy analogue, 2-phenylethyl alcohol (PEAL). The spectra encode two monohydrates and two previously unnoticed dihydrates, consequences of water insertion and sidewise attachment to the O-H group of gauche PEALs, in PEAL-H2O and PEAL-(H2O)2, or the higher-energy gauche-trans PEAL in the latter. The electronic structures retain the stable PEAL or flip its O-H to convert the gauche-trans PEAL conformer to the global minimum-energy dihydrate. We disclose conventional and bifurcated hydrogen bonds and electron steric repulsions by noncovalent interaction analysis and correlations between the experimental O-H stretching vibrational frequencies and the O-H and H···X bond lengths and electron densities, pointing to implications on hydrate forms and our approach virtue.
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Affiliation(s)
- Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Noga Saban
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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Rahimi R, Shachar A, Bar I. Experimental/Computational Study on the Impact of Fluorine on the Structure and Noncovalent Interactions in the Monohydrated Cluster of ortho-Fluorinated 2-Phenylethylamine. J Am Chem Soc 2022; 144:8337-8346. [PMID: 35471862 DOI: 10.1021/jacs.2c02480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorine-containing medicinal compounds frequently allow modulation of physical-chemical properties. Here, we address the effect of fluorine, near the ethylamino side chain, on conformational flexibility and noncovalent interactions (NCIs) of the selected jet-cooled monohydrated cluster of 2-(2-fluoro-phenyl)-ethylamine (2-FPEA) by mass-selected resonance-enhanced two-photon ionization and ionization-loss stimulated Raman spectroscopies. Our results show that Raman spectral signatures of the 2-FPEA-H2O cluster match the scaled harmonic vibrational Raman frequencies, resulting from density functional theory calculations of the most stable 2-FPEA gauche conformer hydrogen-bonded (HB) to water, confirming the three-dimensional cluster structure. This predicted electronic structure, together with NCI analysis, allows visualization and assessment of the attractive and repulsive interactions. The comparison of the NCIs and revealed red (O-H and N-H stretches) and blue shifts (C-H stretches and CH2 out-of-plane bends) of the cluster to other class members confirm O-H···N, N-H···π, C-H···O, and C-H···F HB formation and their contribution to structure stabilization, uncovering the potential of the approach.
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Affiliation(s)
- Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Afik Shachar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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Shachar A, Kallos I, de Vries MS, Bar I. Revealing the Structure and Noncovalent Interactions of Isolated Molecules by Laser-Desorption/Ionization-Loss Stimulated Raman Spectroscopy and Quantum Calculations. J Phys Chem Lett 2021; 12:11273-11279. [PMID: 34767362 DOI: 10.1021/acs.jpclett.1c03336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The structural and dynamical characteristics of isolated molecules are essential, yet obtaining this information is difficult. We demonstrate laser-desorption jet-cooling/ionization-loss stimulated Raman spectroscopy to obtain Raman spectral signatures of nonvolatile molecules in the gas phase. The vibrational features of a test substance, the most abundant conformer of tryptamine, are compared and found to match those resulting from the scaled harmonic Raman spectrum obtained by density functional theory calculations. The vibrational signatures serve to identify the most prominent gauche conformer and evaluate its predicted electronic structure. These findings, together with noncovalent interaction (NCI) analysis, provide new insights into electron densities and reduced density gradients, assessing the hydrogen bonds (N-H···π and C-H···H-C) and interplay between attractive and repulsive NCIs affecting the structure. This approach accesses vibrational signatures of isolated nonvolatile molecules by tabletop lasers at uniform resolution and in a broad frequency range, promising great benefit to future studies.
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Affiliation(s)
- Afik Shachar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Itai Kallos
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Mattanjah S de Vries
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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Alghamdi M, Zhang J, Kong W. Doping with multiple cations and failure of charge transfer in large ionized helium droplets. J Chem Phys 2019; 151:134307. [PMID: 31594345 DOI: 10.1063/1.5123735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report experimental observations of aniline (A) cations and He2 + when aniline is doped into ionized helium droplets. Large droplets containing 108 atoms are bombarded by energetic electrons, resulting in more than one positive charge in one droplet. When aniline encounters the charged droplets, some are ionized via charge transfer, while others can remain neutral in the presence of He2 + when the mass-to-charge ratio (m/z) of the droplet is sufficiently large. Upon resonant excitation of the dopant An or An + (n ≥ 1), He2 + can be ejected. The excitation spectrum of He2 + becomes a juxtaposition of the spectra of An and An +. Moreover, an anticorrelation between the yields of He2 + and A+ is observed with increasing energies of the ionizing electrons. We attribute this result to the combined effect of reduction in m/z of the droplets and the different locations of He2 + and neutral An. Limited by the penetration depths of the ionizing electrons and further assisted by the Coulomb repulsion of coexisting cations, He2 + is located within 20 nm of the surface, while neutral An has an average position inside a large droplet. Upon resonant excitation of the interior An, He2 + is preferentially ejected. With increasing energies of the colliding electrons, the m/z of the droplets are reduced, leading to less effective charge shielding and more effective charge transfer, until ultimately, all He2 + can be neutralized to form A+.
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Affiliation(s)
- Maha Alghamdi
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, USA
| | - Jie Zhang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, USA
| | - Wei Kong
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, USA
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Mayorkas N, Bernat A, Izbitski S, Bar I. Vibrational and vibronic spectra of tryptamine conformers. J Chem Phys 2013; 138:124312. [DOI: 10.1063/1.4798218] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Mayorkas N, Izbitski S, Bernat A, Bar I. Simultaneous Ionization-Detected Stimulated Raman and Visible-Visible-Ultraviolet Hole-Burning Spectra of Two Tryptamine Conformers. J Phys Chem Lett 2012; 3:603-607. [PMID: 26286155 DOI: 10.1021/jz300026a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A key first step toward probing structures and interactions of individual conformers of isolated flexible molecules is uncovering their characteristic spectral signatures. Here, conformation-specific ionization-detected stimulated Raman (IDSR) and visible-visible-ultraviolet hole-burning spectra were measured simultaneously to determine the unique signatures of the two most stable conformers of tryptamine in the gas phase. These signatures together with the comparison of the IDSR spectra to the computationally predicted Raman spectra assisted in their characterization and structural identification. This new approach offers high selectivity and is foreseen to be an improved diagnostic tool for dissection of conformers of flexible molecules.
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Affiliation(s)
- Nitzan Mayorkas
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Shay Izbitski
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Amir Bernat
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Smolarek S, Rijs AM, Hannam JS, Leigh DA, Drabbels M, Buma WJ. Conformational Flexibility of a Rotaxane Thread Probed by Electronic Spectroscopy in Helium Nanodroplets. J Am Chem Soc 2009; 131:12902-3. [DOI: 10.1021/ja905973v] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Szymon Smolarek
- University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédéral de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Anouk M. Rijs
- University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédéral de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jeffrey S. Hannam
- University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédéral de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - David A. Leigh
- University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédéral de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Marcel Drabbels
- University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédéral de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Wybren J. Buma
- University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, FOM Institute for Plasma Physics “Rijnhuizen”, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom, and Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédéral de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Vu TBC, Kalkman I, Meerts WL, Brand C, Svartsov YN, Wiedemann S, Weinkauf R, Schmitt M. The conformational landscape of 5-methoxytryptamine studied by rotationally resolved fluorescence spectroscopy and resonant ionization spectroscopy. Phys Chem Chem Phys 2009; 11:2433-40. [DOI: 10.1039/b819469f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Kong W, Pei L, Zhang J. Linear dichroism spectroscopy of gas phase biological molecules embedded in superfluid helium droplets. INT REV PHYS CHEM 2009. [DOI: 10.1080/01442350802573678] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Böhm M, Brause R, Jacoby C, Schmitt M. Conformational Relaxation Paths in Tryptamine. J Phys Chem A 2008; 113:488-55. [DOI: 10.1021/jp8087989] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcel Böhm
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany
| | - Robert Brause
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany
| | - Christoph Jacoby
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany
| | - Michael Schmitt
- Heinrich-Heine-Universität, Institut für Physikalische Chemie I, D-40225 Düsseldorf, Germany
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12
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Polarization spectroscopy of aluminum phthalocyanine hydroxide embedded in superfluid helium droplets. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.07.109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pei L, Zhang J, Kong W. Electronic polarization spectroscopy of metal phthalocyanine chloride compounds in superfluid helium droplets. J Chem Phys 2008; 127:174308. [PMID: 17994819 DOI: 10.1063/1.2803186] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the electronic polarization spectroscopy of two metal phthalocyanine chloride compounds (MPcCl, M=Al,Ga) embedded in superfluid helium droplets and oriented in a dc electric field. For both compounds, the laser induced fluorescence spectra show preference for perpendicular excitation relative to the orientation field. This result indicates that the permanent dipoles of both compounds are predominantly perpendicular to the transition dipole. Since the permanent dipole derives from the metal chloride, while the transition dipole derives from the phthalocyanine chromophore, in the plane of phthalocyanine, this qualitative result is not surprising. However, quantitative modeling reveals that this intuitive model is inadequate and that the transition dipole might have tilted away from the molecular plane of phthalocyanine. The out of plane component of the transition dipole amounts to approximately 10% if the permanent dipole is assumed to be approximately 4 debye. The origin for this tilt is puzzling, and we tentatively attribute it to the transition of nonbonding orbitals, either from the chlorine atom or from the bridge nitrogen atom, to the pi* orbitals of the phthalocyanine chromophore. On the other hand, although unlikely, we cannot completely exclude the possibility that both our high level density functional theory calculation and ab initio results severely deviate from reality. The droplet matrix induces redshifts in the origin of the electronic transition and produces discrete phonon wings. Nevertheless, in dc electric fields, all phonon wings and the zero phonon line demonstrate the same dependence on the polarization direction of the excitation laser. Although electronic excitation does couple to the superfluid helium matrix and the resulting phonon wings add complications to the electronic spectrum, this coupling does not affect the direction of the electronic transition dipole. Electronic polarization spectroscopy in superfluid helium droplets is thus still informative in revealing the permanent dipole and its relation relative to the transition dipole.
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Affiliation(s)
- Linsen Pei
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, USA
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