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Abstract
In this contribution, we provide a comprehensive overview of acyclic twisted amides, covering the literature since 1993 (the year of the first recognized report on acyclic twisted amides) through June 2020. The review focuses on classes of acyclic twisted amides and their key structural properties, such as amide bond twist and nitrogen pyramidalization, which are primarily responsible for disrupting nN to π*C═O conjugation. Through discussing acyclic twisted amides in comparison with the classic bridged lactams and conformationally restricted cyclic fused amides, the reader is provided with an overview of amidic distortion that results in novel conformational features of acyclic amides that can be exploited in various fields of chemistry ranging from organic synthesis and polymers to biochemistry and structural chemistry and the current position of acyclic twisted amides in modern chemistry.
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Affiliation(s)
- Guangrong Meng
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Jin Zhang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States.,College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Michal Szostak
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
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2
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Pace V, Holzer W, Meng G, Shi S, Lalancette R, Szostak R, Szostak M. Structures of Highly Twisted Amides Relevant to Amide N−C Cross-Coupling: Evidence for Ground-State Amide Destabilization. Chemistry 2016; 22:14494-8. [DOI: 10.1002/chem.201603543] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Vittorio Pace
- Department of Pharmaceutical Chemistry; Faculty of Life Sciences; University of Vienna; Althanstrasse 14 Vienna 1090 Austria
| | - Wolfgang Holzer
- Department of Pharmaceutical Chemistry; Faculty of Life Sciences; University of Vienna; Althanstrasse 14 Vienna 1090 Austria
| | - Guangrong Meng
- Department of Chemistry; Rutgers University; 73 Warren Street Newark NJ 07102 United States
| | - Shicheng Shi
- Department of Chemistry; Rutgers University; 73 Warren Street Newark NJ 07102 United States
| | - Roger Lalancette
- Department of Chemistry; Rutgers University; 73 Warren Street Newark NJ 07102 United States
| | - Roman Szostak
- Department of Chemistry; Wroclaw University; F. Joliot-Curie 14 Wroclaw 50-383 Poland
| | - Michal Szostak
- Department of Chemistry; Rutgers University; 73 Warren Street Newark NJ 07102 United States
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3
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Tukachev NV, Bataev VA, Abramenkov AV, Godunov IA. Structure and conformational dynamics of formamide molecule in the ground and lowest excited electronic states. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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4
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Szostak R, Aubé J, Szostak M. An efficient computational model to predict protonation at the amide nitrogen and reactivity along the C-N rotational pathway. Chem Commun (Camb) 2015; 51:6395-8. [PMID: 25766378 DOI: 10.1039/c5cc01034a] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Protonation of amides is critical in numerous biological processes, including amide bonds proteolysis and protein folding as well as in organic synthesis as a method to activate amide bonds towards unconventional reactivity. A computational model enabling prediction of protonation at the amide bond nitrogen atom along the C-N rotational pathway is reported. Notably, this study provides a blueprint for the rational design and application of amides with a controlled degree of rotation in synthetic chemistry and biology.
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Affiliation(s)
- Roman Szostak
- Department of Chemistry, Wroclaw University, F. Joliot-Curie 14, Wroclaw 50-383, Poland
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Szostak R, Aubé J, Szostak M. Determination of Structures and Energetics of Small- and Medium-Sized One-Carbon-Bridged Twisted Amides using ab Initio Molecular Orbital Methods: Implications for Amidic Resonance along the C–N Rotational Pathway. J Org Chem 2015; 80:7905-27. [DOI: 10.1021/acs.joc.5b00881] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roman Szostak
- Department of Chemistry, Wroclaw University, F. Joliot-Curie 14, Wroclaw 50-383, Poland
| | - Jeffrey Aubé
- Division of Chemical
Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michal Szostak
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
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6
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Affiliation(s)
- Michal Szostak
- Department of Medicinal Chemistry, University of Kansas, Delbert M. Shankel Structural Biology Center, 2034 Becker Drive, Lawrence, Kansas 66047
| | - Jeffrey Aubé
- Department of Medicinal Chemistry, University of Kansas, Delbert M. Shankel Structural Biology Center, 2034 Becker Drive, Lawrence, Kansas 66047
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Pazderková M, Profant V, Hodačová J, Šebestík J, Pazderka T, Novotná P, Urbanová M, Šafařík M, Buděšínský M, Tichý M, Bednárová L, Baumruk V, Maloň P. Nonplanar Tertiary Amides in Rigid Chiral Tricyclic Dilactams. Peptide Group Distortions and Vibrational Optical Activity. J Phys Chem B 2013; 117:9626-42. [DOI: 10.1021/jp405226k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
- Charles University in Prague, 121 16 Prague 2, Czech Republic
| | - Václav Profant
- Charles University in Prague, 121 16 Prague 2, Czech Republic
| | - Jana Hodačová
- Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | - Tomáš Pazderka
- Charles University in Prague, 121 16 Prague 2, Czech Republic
| | - Pavlína Novotná
- Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - Marie Urbanová
- Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | - Miloš Tichý
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
| | | | - Petr Maloň
- Institute of Organic Chemistry and Biochemistry AS CR, 166 10 Prague 6, Czech
Republic
- Charles University in Prague, 121 16 Prague 2, Czech Republic
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8
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Inter- versus intra-molecular cyclization of tripeptides containing tetrahydrofuran amino acids: a density functional theory study on kinetic control. J Mol Model 2012; 18:3181-97. [DOI: 10.1007/s00894-011-1326-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
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Andrushchenko V, Matějka P, Anderson DT, Kaminský J, Horníček J, Paulson LO, Bouř P. Solvent Dependence of the N-Methylacetamide Structure and Force Field. J Phys Chem A 2009; 113:9727-36. [DOI: 10.1021/jp9045512] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Pavel Matějka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - David T. Anderson
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Jan Horníček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Leif O. Paulson
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
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Dracínský M, Kaminský J, Bour P. Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging. J Chem Phys 2009; 130:094106. [PMID: 19275395 DOI: 10.1063/1.3081317] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in future quantum chemistry packages is desirable.
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Affiliation(s)
- Martin Dracínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic.
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Zheng A, Liu SB, Deng F. 13C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models. J Comput Chem 2009; 30:222-35. [DOI: 10.1002/jcc.21118] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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Albrecht M, Rice CA, Suhm MA. Elementary Peptide Motifs in the Gas Phase: FTIR Aggregation Study of Formamide, Acetamide, N-Methylformamide, and N-Methylacetamide. J Phys Chem A 2008; 112:7530-42. [DOI: 10.1021/jp8039912] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Merwe Albrecht
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Corey A. Rice
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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Benda L, Prokop A, Blechta V, Schraml J, Špirko V. Probing the Flexibility of Internal Rotation in Silylated Phenols with the NMR Scalar Spin−Spin Coupling Constants. J Phys Chem A 2008; 112:5167-74. [DOI: 10.1021/jp711809e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ladislav Benda
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo sq. 2., 166 10 Prague 6, Czech Republic, and Institute of Chemical Process Fundamentals of the ASCR, v.v.i., Rozvojová 135, 165 02, Prague 6, Czech Republic
| | - Alexandr Prokop
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo sq. 2., 166 10 Prague 6, Czech Republic, and Institute of Chemical Process Fundamentals of the ASCR, v.v.i., Rozvojová 135, 165 02, Prague 6, Czech Republic
| | - Vratislav Blechta
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo sq. 2., 166 10 Prague 6, Czech Republic, and Institute of Chemical Process Fundamentals of the ASCR, v.v.i., Rozvojová 135, 165 02, Prague 6, Czech Republic
| | - Jan Schraml
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo sq. 2., 166 10 Prague 6, Czech Republic, and Institute of Chemical Process Fundamentals of the ASCR, v.v.i., Rozvojová 135, 165 02, Prague 6, Czech Republic
| | - Vladimír Špirko
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo sq. 2., 166 10 Prague 6, Czech Republic, and Institute of Chemical Process Fundamentals of the ASCR, v.v.i., Rozvojová 135, 165 02, Prague 6, Czech Republic
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