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de Albuquerque Barros G, Henrique Morgon N. Finding reliable methodology for optical rotation and correct predictions of (s)-methyloxirane and (1R,5R)-β-pinene. Chirality 2022; 34:1197-1208. [PMID: 35670135 DOI: 10.1002/chir.23479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 12/25/2022]
Abstract
Theoretical calculations of optical rotation (OR), although important to predict absolute configurations (ACs) and corroborate experiments, require efficient methodology able to reproduce enantiomer specificity and real OR values. Also, troublesome molecules are recurring in the literature, such as (S)-methyloxirane and (1R,5R)-β-pinene. This study evaluates DFT functionals B3LYP, CAM-B3LYP, ωB97X-D, M06-2X, and PBE0 considering basis sets aug-cc-pVDZ, aug-cc-pVTZ, 6-311++G(2d,p), and 6-311++G(3df,2p) in OR prediction of 42 rigid organic molecules assessing cases with wrong enantiomeric determination comparing to available experimental data at wavelengths 355, 589, and 633 nm. Functionals CAM-B3LYP and ωB97X-D with aug-cc-pVTZ are indicated here to reproduce experimental values more accurately considering fewer number of wrong AC predictions, normalized RMSD values below 0.70, and a good approximation to experimental values in hierarchical cluster analysis. Methyloxirane AC was reproduced in CAM-B3LYP and PBE0, with [ α ] 355 = 6 . 94 $$ {\left[\alpha \right]}_{355}=6.94 $$ for CAM-B3LYP/aug-cc-pVTZ close to experimental value [ α ] 355 = 7 . 49 ± 0 . 30 $$ {\left[\alpha \right]}_{355}=7.49\pm 0.30 $$ . Good results were found for AC of β-pinene in M06-2X, CAM-B3LYP, and ωB97X-D while the latter in 6-311++G(3df,2p) obtained OR values of [ α ] 589 = 3 . 44 $$ {\left[\alpha \right]}_{589}=3.44 $$ and [ α ] 689 = 4 . 20 $$ {\left[\alpha \right]}_{689}=4.20 $$ close to experimental values [ α ] 589 = 2 . 8 $$ {\left[\alpha \right]}_{589}=2.8 $$ and [ α ] 689 = 4 . 66 ± 0 . 60 $$ {\left[\alpha \right]}_{689}=4.66\pm 0.60 $$ . The two molecules aforementioned are, for the first time, reported to give valid theoretical OR values in such simple methodologies. OR calculations were all performed after geometry optimization at the same level of theory, and analysis of different functional combinations for each step in β-pinene showed it can interfere with AC prediction even in rigid molecules.
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Affiliation(s)
| | - Nelson Henrique Morgon
- Department of Physical Chemistry, Institute of Chemistry, Campinas State University, Campinas, Brazil
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França BA, da Silva CO. Specific rotation of monosaccharides: a global property bringing local information. Phys Chem Chem Phys 2015; 16:13096-102. [PMID: 24853044 DOI: 10.1039/c4cp01316f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Carbohydrates generally occur in several conformations that may differ among themselves by energy values that are smaller than the accuracy of the most sophisticated theoretical methods used to determine them. In addition, the preferential orientations of the hydroxyl groups of these molecules cannot be identified by any experimental technique. Therefore, a method that is able to validate the absolute conformations (i.e., consisting of the orientations of the hydroxyl groups) of carbohydrates would be helpful to improve our knowledge about monosaccharides. SR has been used for this purpose, and here, we present a test to measure the specific rotation (SR) ability of a molecule that possesses not only many conformations, but also four adjacent chiral centers. The results show that the final SR value is a weighted average of a global property (obtained for each conformation), and the latter by its turn is influenced by each chiral center in a multi chiral system. By comparing the SR values calculated for the most abundant anomers of xylopyranose with those of the corresponding monochiral analogs obtained by saturation of three different chiral centers each time, the influence of each center on the global property is confirmed.
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Affiliation(s)
- Bruno A França
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, km 47, Seropédica, RJ 23897-000, Brazil.
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 743] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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Bauerfeldt GF, Cardozo TM, Pereira MS, da Silva CO. The anomeric effect: the dominance of exchange effects in closed-shell systems. Org Biomol Chem 2013; 11:299-308. [DOI: 10.1039/c2ob26818c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Andrade RR, da Silva CO. Specific rotation as a property to validate monosaccharide conformations. Carbohydr Res 2012; 350:62-7. [PMID: 22281178 DOI: 10.1016/j.carres.2011.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 11/28/2011] [Accepted: 12/13/2011] [Indexed: 11/15/2022]
Abstract
Specific rotation ([α](D)) values were calculated for the 15 conformations of xylopyranose that are the most stable in the gas phase and in aqueous solution. The effects of different theoretical descriptions and the medium on the geometry of the conformers and the [α](D) values are evaluated. Differences in [α](D) values found for the same conformer in all descriptions used were smaller than those found between any two different conformers in the same description. The difference between [α](D) values is prominent, even for two conformations that are distinguished from each other only by the orientation of one secondary hydroxyl group. This finding suggests that [α](D) values may potentially be used in the validation of monosaccharide conformations that are theoretically sampled.
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Affiliation(s)
- Renato R Andrade
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, km 47-Seropédica, Rio de Janeiro, Brazil
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Mazzeo G, Giorgio E, Rosini C, Fabris F, Fregonese E, Toniolo U, De Lucchi O. Synthesis, chiroptical properties, and their theoretical simulation of some highly rotating benzotricamphor derivatives. Chirality 2009; 21 Suppl 1:E86-97. [DOI: 10.1002/chir.20780] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Tartaglia S, Padula D, Scafato P, Chiummiento L, Rosini C. A Chemical/Computational Approach to the Determination of Absolute Configuration of Flexible and Transparent Molecules: Aliphatic Diols As a Case Study. J Org Chem 2008; 73:4865-73. [DOI: 10.1021/jo800516f] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sabina Tartaglia
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Daniele Padula
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Patrizia Scafato
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Lucia Chiummiento
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Carlo Rosini
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
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