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Chatziorfanou E, Romero AR, Chouchane L, Dömling A. Crystal Clear: Decoding Isocyanide Intermolecular Interactions through Crystallography. J Org Chem 2024; 89:957-974. [PMID: 38175810 PMCID: PMC10804414 DOI: 10.1021/acs.joc.3c02038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/13/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
The isocyanide group is the chameleon among the functional groups in organic chemistry. Unlike other multiatom functional groups, where the electrophilic and nucleophilic moieties are typically separated, isocyanides combine both functionalities in the terminal carbon. This unique feature can be rationalized using the frontier orbital concept and has significant implications for its intermolecular interactions and the reactivity of the functional group. In this study, we perform a Cambridge Crystallographic Database-supported analysis of isocyanide intramolecular interactions to investigate the intramolecular interactions of isocyanides in the solid state, excluding isocyanide-metal complexes. We discuss examples of different interaction classes, including the isocyanide as a hydrogen bond acceptor (RNC···HX), halogen bonding (RNC···X), and interactions involving the isocyanide and carbon atoms (RNC···C). The latter interaction serves as an intriguing illustration of a Bürgi-Dunitz trajectory and represents a crucial experimental detail in the well-known multicomponent reactions such as the Ugi- and Passerini-type mechanisms. Understanding the spectrum of intramolecular interactions that isocyanides can undergo holds significant implications in fields such as medicinal chemistry, materials science, and asymmetric catalysis.
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Affiliation(s)
- Eleftheria Chatziorfanou
- Innovative
Chemistry Group, Institute of Molecular and Translational Medicine,
Faculty of Medicine and Dentistry and Czech Advanced Technology and
Research Institute, Palacky University in
Olomouc, Olomouc 779 00, Czech Republic
| | - Atilio Reyes Romero
- Genetic
Intelligence Laboratory, Weill Cornell Medicine-Qatar, Qatar Foundation, P.O.
Box 24144, Doha, Qatar
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York 10021, United States
- Department
of Genetic Medicine, Weill Cornell Medicine, New York 10021, United States
| | - Lotfi Chouchane
- Genetic
Intelligence Laboratory, Weill Cornell Medicine-Qatar, Qatar Foundation, P.O.
Box 24144, Doha, Qatar
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York 10021, United States
- Department
of Genetic Medicine, Weill Cornell Medicine, New York 10021, United States
| | - Alexander Dömling
- Innovative
Chemistry Group, Institute of Molecular and Translational Medicine,
Faculty of Medicine and Dentistry and Czech Advanced Technology and
Research Institute, Palacky University in
Olomouc, Olomouc 779 00, Czech Republic
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Custer T, Szczepaniak U, Gronowski M, Piétri N, Couturier-Tamburelli I, Guillemin JC, Turowski M, Kołos R. Isomerization of cyanopropyne in solid argon. Phys Chem Chem Phys 2019; 21:13668-13678. [PMID: 31190036 DOI: 10.1039/c8cp06739b] [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
Cyanopropyne, CH3-C[triple bond, length as m-dash]C-CN, is a simple molecule whose photochemistry is still unexplored. Here we investigate the UV photolysis of this astrophysically significant nitrile trapped in solid argon. The FTIR study was assisted with 15N-isotopic substitution data and with DFT-level computations including the analyses of ground- and excited-state potential energy surfaces. Cyanopropyne was found to decay mainly via a two-step isomerization process. Infrared absorption spectra evolved to show signals from allenyl cyanide, CH2[double bond, length as m-dash]C[double bond, length as m-dash]CH-CN, which then further convert into propargyl cyanide, H-C[triple bond, length as m-dash]C-CH2-CN. Some evidence for the presence of allenyl isocyanide, propargyl isocyanide, 3-cyanocyclopropene, and 1,2,3-butatrien-1-imine under particular experimental conditions was also observed. Although cyano/isocyano interconversion has been observed during photolysis of other closely related species in solid argon matrices, including H-C[triple bond, length as m-dash]C-CN, no evidence could be found for production of 1-isocyano-1-propyne, CH3-C[triple bond, length as m-dash]C-NC for these experiments.
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Affiliation(s)
- Thomas Custer
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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3
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Custer T, Szczepaniak U, Gronowski M, Fabisiewicz E, Couturier-Tamburelli I, Kołos R. Density Functional Exploration of C4H3N Isomers. J Phys Chem A 2016; 120:5928-38. [PMID: 27341606 DOI: 10.1021/acs.jpca.6b03922] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecules having C4H3N stoichiometry are of astrophysical interest. Two of these, methylcyanoacetylene (CH3C3N) and its structural isomer allenyl cyanide (H2CCCHN), have been observed in interstellar space, while several more have been examined in laboratories. Here we describe, for a broad range of C4H3N isomers, density functional calculations (B3LYP/aug-cc-pVTZ) of molecular parameters including the energetics, geometries, rotational constants, electric dipole moments, polarizabilities, vibrational IR frequencies, IR absorption intensities, and Raman activities. Singlet-triplet splittings as well as singlet vertical electronic excitation energies are given for selected species. The identification of less stable C4H3N molecules, generated in ongoing spectroscopic experiments, relies heavily on these quantum chemical predictions.
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Affiliation(s)
- Thomas Custer
- Institute of Physical Chemistry, Polish Academy of Sciences , ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Urszula Szczepaniak
- Institute of Physical Chemistry, Polish Academy of Sciences , ul. Kasprzaka 44/52, 01-224 Warsaw, Poland.,Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Sud, Université Paris-Saclay , F-91405 Orsay, France
| | - Marcin Gronowski
- Institute of Physical Chemistry, Polish Academy of Sciences , ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Emilia Fabisiewicz
- Institute of Physical Chemistry, Polish Academy of Sciences , ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
| | | | - Robert Kołos
- Institute of Physical Chemistry, Polish Academy of Sciences , ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
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Benidar A, Bégué D, Richter F, Pouchan C, Lahcini M, Guillemin JC. Gas-Phase Infrared Spectra of Three Compounds of Astrochemical Interest: Vinyl, Allenyl, and Propargyl Isocyanides. Chemphyschem 2014; 16:848-54. [DOI: 10.1002/cphc.201402712] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/18/2014] [Indexed: 11/08/2022]
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Møllendal H, Samdal S, Guillemin JC. Microwave spectrum and intramolecular hydrogen bonding of 2-isocyanoethanol (HOCH(2)CH(2)N≡C). J Phys Chem A 2014; 118:3120-7. [PMID: 24694084 DOI: 10.1021/jp502212n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The microwave spectrum of 2-isocyanoethanol (HOCH2CH2NC) has been investigated in the 12-120 GHz spectral range. The assignment of this spectrum was severely complicated by the rapid transformation of 2-isocyanoethanol into its isomer 2-oxazoline, which has a rich and strong spectrum. This process appeared both in a gold-plated microwave cell and in a brass cell and is presumed to be catalyzed by metals or traces of base. The spectrum of one conformer was ultimately assigned. This form is stabilized by an intramolecular hydrogen bond between the hydroxyl group and the isocyano group and is the first gas-phase study ever of this kind of hydrogen bonding. The distance between the hydrogen atom of the hydroxyl group and the nitrogen and carbon atoms are as long as 256 and 298 pm, respectively, indicating that covalent contribution to the hydrogen bond is minimal. Electrostatic forces are much more important because the O-H and N≡C bonds are almost parallel and the corresponding bond moments are practically antiparallel. The microwave work has been augmented by quantum chemical calculations at the CCSD(T)/cc-pVTZ and MP2/cc-pVTZ levels of theory. Results of these calculations are generally in good agreement with experimental findings.
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Affiliation(s)
- Harald Møllendal
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo , Blindern, NO-0315 Oslo, Norway
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Samdal S, Grønås T, Møllendal H, Guillemin JC. Microwave Spectrum and Conformational Properties of 4-Isocyano-1-butene (H2C═CHCH2CH2N≡C). J Phys Chem A 2014; 118:1413-9. [DOI: 10.1021/jp4122134] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Svein Samdal
- Centre
for Theoretical and Computational Chemistry (CTCC), Department of
Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Terje Grønås
- Centre
for Theoretical and Computational Chemistry (CTCC), Department of
Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Harald Møllendal
- Centre
for Theoretical and Computational Chemistry (CTCC), Department of
Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Jean-Claude Guillemin
- Institut
des Sciences Chimiques de Rennes, École Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, 11 Allée de Beaulieu, CS 50837, 35708 Rennes Cedex
7, France
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Samdal S, Møllendal H, Guillemin JC. Microwave spectrum and conformational properties of 4-isocyano-1-butyne (HC≡CCH2CH2N≡C). J Phys Chem A 2013; 117:10304-10. [PMID: 24003874 DOI: 10.1021/jp407126x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microwave spectrum of 4-isocyano-1-butyne (HC≡CCH2CH2N≡C) has been investigated in the 12.4-77.6 GHz spectral region. The spectra of two rotamers denoted ap and sc were assigned. ap has an antiperiplanar arrangement for the C-C-C-N chain of atoms, whereas sc has synclinal conformation for this link. The ground state spectrum and three vibrationally excited state spectra of the lowest torsional vibration were assigned for ap, while the ground vibrational state spectrum was assigned for sc. The C-C-C-N dihedral angle was found to be 64.5(30)° in sc and exactly 180° in ap. ap was determined to be 2.9(6) kJ/mol lower in energy than sc from relative intensity measurements. The microwave study has been augmented with ab initio and DFT calculations employing the CCSD(T), MP2, and B3LYP methods with the cc-pVTZ basis set. A Natural Bond Order analysis has also been performed. Most, but not all, of the quantum chemical predictions agree satisfactorily with the experimental results.
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Affiliation(s)
- Svein Samdal
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo , P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
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Samdal S, Møllendal H, Guillemin JC. Microwave Spectrum, Conformational Properties, and Dipole Moment of Cyclopropylmethyl Isocyanide (C3H5CH2NC). J Phys Chem A 2013; 117:5073-81. [DOI: 10.1021/jp403374k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Svein Samdal
- Centre for Theoretical and Computational
Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Harald Møllendal
- Centre for Theoretical and Computational
Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Jean-Claude Guillemin
- Institut des Sciences Chimiques
de Rennes, École Nationale Supérieure de Chimie de Rennes,
CNRS, UMR 6226, Avenue du Général
Leclerc, CS 50837, 35708 Rennes Cedex 7, France
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Samdal S, Møllendal H, Guillemin JC. Microwave spectra and barriers to internal rotation of Z- and E-1-propenyl isocyanide. J Phys Chem A 2012; 116:8833-9. [PMID: 22839412 DOI: 10.1021/jp304227u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A synthetic procedure yielding a mixture of Z- and E-1-propenyl isocyanide (CH(3)CH═CHNC) is described. The microwave spectrum of this mixture has been recorded in the 12-100 GHz spectral range, and the spectra of the Z and E isomers have been assigned for the first time. Most transitions of the Z form were split into two components of equal intensity due to tunneling of the methyl group, which allowed the barrier to internal rotation of this group to be determined as 4.0124(12) kJ/mol by fitting 568 transitions with a maximum value of J = 46 using the computer program Xiam. This fit had a root-mean-square deviation as large as 4.325. The same transitions were therefore fitted anew using the more sophisticated program Erham. This fit has a rms deviation marginally better (4.136) than the Xiam fit. No split MW lines were found for E-1-propenyl isocyanide. The absence of splittings is ascribed to a barrier to internal rotation of the methyl group that is significantly higher than the barrier of the Z isomer. It is concluded that the barrier must be larger than 6 kJ/mol for the E form. The experimental work was augmented by quantum chemical calculations at CCSD/cc-pVTZ, B3LYP/cc-pVTZ, and MP2/cc-pVTZ levels of theory. The CCSD method predicts rotational constants of the Z and E forms well. The B3LYP barriers to internal rotation of a series of substituted propenes were calculated and found to be in good agreement with experiments. Calculations of the quartic centrifugal distortion constants of the two 1-propenyl isocyanides by the B3LYP and MP2 methods were less successful.
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Affiliation(s)
- Svein Samdal
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
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Møllendal H, Samdal S, Guillemin JC. Microwave Spectrum and Conformational Composition of 2-Chloroethylisocyanide. J Phys Chem A 2011; 115:13474-81. [DOI: 10.1021/jp208580m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Harald Møllendal
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Svein Samdal
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Jean-Claude Guillemin
- Sciences Chimiques de Rennes, École Nationale Supérieure de Chimie de Rennes, CNRS UMR 6226, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
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Samdal S, Møllendal H, Guillemin JC. Microwave spectrum and conformational composition of 2-fluoroethylisocyanide. J Phys Chem A 2011; 115:9192-8. [PMID: 21718075 DOI: 10.1021/jp205024s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The microwave spectrum of 2-fluoroethylisocyanide, FCH(2)CH(2)N≡C, has been investigated in the whole 50-120 GHz spectral region. Selected portions of the spectrum in the range of 18-50 GHz have also been recorded. The microwave spectra of the ground state and vibrationally excited states of two conformers have been assigned. Accurate spectroscopic constants have been derived from a large number of microwave transitions. The F-C-C-N chain of atoms is antiperiplanar in one of these rotamers and synclinal in the second conformer. The energy difference between the two forms was obtained from relative intensity measurements. It was found that the synclinal conformer is favored over the antiperiplanar form by 0.7(5) kJ/mol. Quantum chemical calculations at the high CCSD/cc-pVTZ and B3LYP/cc-pVTZ levels of theory were performed. Most, but not all, of the spectroscopic constants predicted in these calculations are in good agreement with the experimental counterparts. The theoretical calculations correctly indicate that the F-C-C-N dihedral angle in the synclinal form is about 67° but underestimate the magnitude of the gauche effect and erroneously predict the antiperiplanar rotamer to be 1.3-1.6 kJ/mol more stable than the synclinal conformer.
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Affiliation(s)
- Svein Samdal
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway
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