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Zhao H, Brånalt J, Perry M, Tyrchan C. The Role of Allylic Strain for Conformational Control in Medicinal Chemistry. J Med Chem 2023. [PMID: 37285219 DOI: 10.1021/acs.jmedchem.3c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
It is axiomatic in medicinal chemistry that optimization of the potency of a small molecule at a macromolecular target requires complementarity between the ligand and target. In order to minimize the conformational penalty on binding, both enthalpically and entropically, it is therefore preferred to have the ligand preorganized in the bound conformation. In this Perspective, we highlight the role of allylic strain in controlling conformational preferences. Allylic strain was originally described for carbon-based allylic systems, but the same principles apply to other types of structure with sp2 or pseudo-sp2 arrangements. These systems include benzylic (including heteroaryl methyl) positions, amides, N-aryl groups, aryl ethers, and nucleotides. We have derived torsion profiles from small molecule X-ray structures for these systems. Through multiple examples, we show how these effects have been applied in drug discovery and how they can be used prospectively to influence conformation in the design process.
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Affiliation(s)
- Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Jonas Brånalt
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Matthew Perry
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
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Onchoke KK, Chaudhry SN, Ojeda JJ. Vibrational and electronic spectra of 2-nitrobenzanthrone: An experimental and computational study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 153:402-414. [PMID: 26348130 DOI: 10.1016/j.saa.2015.08.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 08/18/2015] [Accepted: 08/30/2015] [Indexed: 06/05/2023]
Abstract
The environmental pollutant 2-nitrobenzanthrone (2-NBA) poses human health hazards, and is formed by atmospheric reactions of NOX gases with atmospheric particulates. Though its mutagenic effects have been studied in biological systems, its comprehensive spectroscopic experimental data are scarce. Thus, vibrational and optical spectroscopic analysis (UV-Vis, and fluorescence) of 2-NBA was studied using both experimental and density functional theory employing B3LYP method with 6-311+G(d,p) basis set. The scaled theoretical vibrational frequencies show good agreement to experiment to within ~5 cm(-1) and <20 cm(-1) for frequencies <1800 cm(-1) and 2700-3200 cm(-1), respectively. In addition, predictions of the DFT frequencies below 1800 cm(-1) yield an overall root mean square (RMS) of ±20.1 and ±20.6 cm(-1) for benzanthrone and 2-NBA, respectively. On the basis of normal coordinate analysis complete assignments of harmonic experimental infrared and Raman bands are made. The influence of the nitro group substitution upon the benzanthrone structure and symmetric CH vibrations, and electronic spectra is noted. This study is useful for the development of spectroscopy-mutagenicity relationships in nitrated polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Kefa K Onchoke
- Department of Chemistry & Biochemistry, Stephen F. Austin State University, Box 13006 - SFA Station, Nacogdoches, TX, 75962-3006, United States.
| | - Saad N Chaudhry
- Department of Chemistry & Biochemistry, Stephen F. Austin State University, Box 13006 - SFA Station, Nacogdoches, TX, 75962-3006, United States
| | - Jorge J Ojeda
- Department of Chemistry & Biochemistry, Stephen F. Austin State University, Box 13006 - SFA Station, Nacogdoches, TX, 75962-3006, United States
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Onchoke KK, Ojeda JJ. A DFT Study of Vibrational Spectra and Mutagenicity Predictions of Mononitrated Fluoranthenes. Polycycl Aromat Compd 2013. [DOI: 10.1080/10406638.2013.810654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Maekawa H, Ge NH. Picosecond Rotational Interconversion Adjacent to a C═O Bond Studied by Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2012; 116:11292-301. [DOI: 10.1021/jp306201t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025,
United States
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025,
United States
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Shen Q, Samdal S. The molecular structures and conformational compositions of 1,3 cyclohexanedione and 1,4 cyclohexanedione as determined by gas-phase electron diffraction and theoretical calculation. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.08.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Onchoke KK, Parks M. Experimental and theoretical study of vibrational spectra of 3-nitrofluoranthene. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.04.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Onchoke KK, Parks ME, Nolan AH. A DFT study of the vibrational spectra of 1-, and 2-nitrotriphenylene. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 74:579-587. [PMID: 19651536 DOI: 10.1016/j.saa.2009.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 07/04/2009] [Accepted: 07/07/2009] [Indexed: 05/28/2023]
Abstract
The infrared (IR) and Raman spectra, and intensities of triphenylene, 1-, and 2-nitrotriphenylene were investigated by the density functional theory (DFT, B3LYP method) with 6-311 +G** basis set. Normal mode assignments are proposed with particular emphasis on the nitro group vibrations. Compared to 2-nitrotriphenylene (2-NTRP) 1-nitrotriphenylene (1-NTRP) is predicted to show asymmetric nitro stretches at higher frequencies. Through the vibrational study, the structure-spectroscopic relationships of these nitro polycyclic aromatic hydrocarbons (nitro-PAHs) are made, and possible insights into their differential mutagenic potencies correlated. The geometrical distortions of the TRP structure upon nitro group substitution and correlations between structural parameters and vibrational data as well as structure-function relationships related to the mutagenicity of this important class of polycyclic aromatic hydrocarbons are discussed.
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Affiliation(s)
- Kefa K Onchoke
- Department of Chemistry, Stephen F. Austin State University, Nacogdoches, TX 75962-13006, USA.
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Hooshyar H, Rahemi H, Akhbari Shad MH, Khezri B. Density functional and Møller–Plesset studies of cyclobutanone⋯HF and ⋯HCl complexes. J Mol Model 2008; 15:525-36. [DOI: 10.1007/s00894-008-0364-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2007] [Accepted: 09/22/2008] [Indexed: 10/21/2022]
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Chen KH, Lii JH, Fan Y, Allinger NL. Molecular mechanics (MM4) study of amines. J Comput Chem 2007; 28:2391-412. [PMID: 17486561 DOI: 10.1002/jcc.20737] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The MM4 force field has been extended to include aliphatic amines. About 20 amines have been examined to obtain a set of useful molecular mechanics parameters for this class. The vibrational spectra of seven amines (172 frequencies) calculated by MM4 have an overall rms error of 27 cm(-1), compared with corresponding MM4 value of 24 cm(-1) for alkanes. The rms and signed average errors of the moments of inertia of nine simple amines compared with the experimental data were 0.18% and -0.004%, respectively. The heats of formation of 30 amines were also studied. The MM4 weighted standard deviation is 0.41 kcal/mol, compared with experiment. Electronegativity effects occur in the hydrocarbon portion of an amine from the nitrogen, and are accounted for by including electronegativity induced changes in bond lengths and angles, and induced dipole-dipole interactions in the molecule. Negative hyperconjugation results from the presence of the lone pair of electrons on nitrogen, and leads to the Bohlmann bands in the infrared, and also to strong and unusual geometric changes in the molecules (Bohlmann effect), all of which are fairly well accounted for. The conformational energies in amines appear to be less straightforward than those for most other classes of molecules, apparently because of the Bohlmann effect, and these are probably not yet completely understood. In general, the agreement between the MM4 calculated results and the available data is reasonably good.
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Affiliation(s)
- Kuo-Hsiang Chen
- Department of Chemistry, Center for Computational Chemistry, Chemistry Annex, University of Georgia, Athens, Georgia 30605-2526, USA
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Chen KH, Lii JH, Walker GA, Xie Y, Schaefer HF, Allinger NL. Molecular Mechanics (MM4) Study of Fluorinated Hydrocarbons. J Phys Chem A 2006; 110:7202-27. [PMID: 16737272 DOI: 10.1021/jp060430x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular mechanics study of small saturated hydrocarbons (up to C-6) substituted by up to six fluorines has been carried out with the MM4 force field. A parameter set has been developed for use in the calculation of bond lengths, bond angles, torsion angles, conformational energies, barriers to rotation, dipole moments, moments of inertia, and vibrational frequencies for these compounds. The results are mostly in fair to good agreement with experiment and ab initio calculations. The high electronegativity of fluorine leads to serious geometric consequences in these compounds, but these consequences can be dealt with adequately by suitable cross-terms in the force constant matrix, and by recognizing that some of the reference bond lengths and angles (l(0), theta(0)) and the corresponding stretching and bending constant parameters (k(s), k(theta)) that are usually thought of as constants must in fact be treated as functions of the electronegativity of the substituents. Additionally, the heavy mass of the fluorine (relative to the mass of hydrogen in alkanes) leads to large values for other cross-terms that were found to be unimportant in hydrocarbons. Conformational equilibria for polyfluorinated compounds are affected by the delta-two effect well-known in carbohydrates. A few larger fluorinated and polyfluorinated alkanes, including perfluoropropane, perfluorobutane, and Teflon, have also been studied.
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Affiliation(s)
- Kuo-Hsiang Chen
- Center for Computational Chemistry, Chemistry Annex, University of Georgia, Athens, 30602-2526, USA
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Onchoke KK, Hadad CM, Dutta PK. Structure and Vibrational Spectra of Mononitrated Benzo[a]pyrenes. J Phys Chem A 2005; 110:76-84. [PMID: 16392842 DOI: 10.1021/jp054881d] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecules benzo[a]pyrene (BaP) and 1-, 3-, and 6-nitrobenzo[a]pyrene (1-NBaP, 3-NBaP, 6-NBaP) are currently of significant interest due to their presence in respirable combustion exhaust particulates and their mutagenic and carcinogenic properties. Structure-function correlations as well as spectroscopic signatures for trace analysis are necessary for these benzo[a]pyrene derivatives. In this paper, detailed infrared and Raman spectroscopic data of BaP and its three mononitrated isomers are provided for the first time. By utilizing density functional theory (DFT, B3LYP method with 6-311+G basis set), the molecular geometries and the vibrational spectra are calculated. Good agreement is noted between the calculated and experimental geometry for BaP, and predictions of the vibrational data for all compounds are within approximately 5 cm-1 of the experimental data. Normal mode assignments are proposed with particular emphasis on the nitro group vibrations. The geometrical distortions of the BaP structure upon nitro group substitution and correlations between structural parameters and vibrational data as well as structure-function relationships related to the mutagenicity of this important class of polycyclic aromatic hydrocarbons are discussed.
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Affiliation(s)
- Kefa K Onchoke
- Department of Chemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, USA
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Langley CH, Lii JH, Allinger N. Molecular mechanics (MM4) calculations on carbonyl compounds. I-IV. J Comput Chem 2003. [DOI: 10.1002/jcc.1177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Affiliation(s)
- Charles H. Langley
- Computational Center for Molecular Structure and Design, Department of Chemistry, Chemistry Annex, The University of Georgia, Athens, Georgia 30602-2526
| | - Norman L. Allinger
- Computational Center for Molecular Structure and Design, Department of Chemistry, Chemistry Annex, The University of Georgia, Athens, Georgia 30602-2526
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Langley CH, Lii JH, Allinger NL. Molecular mechanics calculations on carbonyl compounds. III. Cycloketones. J Comput Chem 2001. [DOI: 10.1002/jcc.1100] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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