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Faintich B, Parsons T, Balduf T, Caricato M. Theoretical Study of the Isotope Effect in Optical Rotation. J Phys Chem A 2024. [PMID: 39259613 DOI: 10.1021/acs.jpca.4c03728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
In this work, the isotope effect in optical rotation (OR) is examined by exploring structure-property relationships for H → D substitutions in chiral molecules. While electronic effects serve as the dominant source of optical activity, there is a non-negligible contribution from nuclear vibrations, which changes with isotopic substitution. We employ a test set of 50 small organic molecules: three-membered rings with varying heteroatoms (PCl, PH, S, NCl, NH, O, and NBr) and functional groups (Me, F), and simulations were run at the B3LYP/aug-cc-pVDZ level of theory. The objectives of this work are to determine locations of isotopic substitution that result in significant changes in the vibrational correction to the OR and to evaluate which vibrational modes and electronic response are the major contributors to the isotope effect. Molecules with more polarizable heteroatoms in the ring (e.g., S and P) have the largest change in the vibrational correction compared to the unsubstituted parent molecules. In many cases, isotopic substitution made to the hydrogens on the opposite side of the ring from the functional group provides the largest change in the OR. H/D wagging modes and C vibrations (for D-C centers) are the largest contributors to the isotope effect. This is explained with a molecular orbital decomposition analysis of the OR. The relevant vibrational modes affect the orbital transitions that are already significant at the equilibrium geometry. However, this effect is only large when polarizable heteroatoms are involved because the electron density surrounding them is diffuse enough to feel the subtle effect of change in mass due to isotopic substitution on the relevant vibrational modes.
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Affiliation(s)
- Brian Faintich
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Taylor Parsons
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Ty Balduf
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Marco Caricato
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
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2
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Forson E, Parsons T, Caricato M. First Principles Simulations of Optical Rotation of Chiral Molecular Crystals. Chirality 2024; 36:e23709. [PMID: 39101242 DOI: 10.1002/chir.23709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
In this work, we present simulations of the optical rotation (OR) for five molecular crystals at density functional theory level with periodic boundary conditions (DFT-PBC). Calculations are compared with experimental measurements and show semi-quantitative agreement with experimental data for three of the crystals: tartatic acid, benzil, and pentaerythritol. For the other two crystals, aspartic acid and glutamic acid, the calculated data are in qualitative agreement with, but two orders of magnitude smaller than, the experimental data. We provide some arguments that support the theoretical predictions and suggest that the experiments should be revisited. We also find that the position of H centers provided in experimental X-ray data is not sufficiently reliable for simulating OR, and better results are obtained when H atoms are allowed to relax while keeping heavier elements fixed at the experimental positions. Comparison with molecular cluster calculations with a better functional and a larger basis set indicate that the role of intermolecular interactions (reproduced with the PBC technique) is as or more important than the choice of model chemistry. Despite the current limitations in the level of theory that can be employed, these simulations provide a promising avenue to investigate the effect of intermolecular interactions on this sensitive electronic property of molecules and materials.
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Affiliation(s)
- Emmanuel Forson
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Taylor Parsons
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Marco Caricato
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
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3
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Feineis D, Bringmann G. Structural variety and pharmacological potential of naphthylisoquinoline alkaloids. THE ALKALOIDS. CHEMISTRY AND BIOLOGY 2024; 91:1-410. [PMID: 38811064 DOI: 10.1016/bs.alkal.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Naphthylisoquinoline alkaloids are a fascinating class of natural biaryl compounds. They show characteristic mono- and dimeric scaffolds, with chiral axes and stereogenic centers. Since the appearance of the last comprehensive overview on these secondary plant metabolites in this series in 1995, the number of discovered representatives has tremendously increased to more than 280 examples known today. Many novel-type compounds have meanwhile been discovered, among them naphthylisoquinoline-related follow-up products like e.g., the first seco-type (i.e., ring-opened) and ring-contracted analogues. As highlighted in this review, the knowledge on the broad structural chemodiversity of naphthylisoquinoline alkaloids has been decisively driven forward by extensive phytochemical studies on the metabolite pattern of Ancistrocladus abbreviatus from Coastal West Africa, which is a particularly "creative" plant. These investigations furnished a considerable number of more than 80-mostly new-natural products from this single species, with promising antiplasmodial activities and with pronounced cytotoxic effects against human leukemia, pancreatic, cervical, and breast cancer cells. Another unique feature of naphthylisoquinoline alkaloids is their unprecedented biosynthetic origin from polyketidic precursors and not, as usual for isoquinoline alkaloids, from aromatic amino acids-a striking example of biosynthetic convergence in nature. Furthermore, remarkable botanical results are presented on the natural producers of naphthylisoquinoline alkaloids, the paleotropical Dioncophyllaceae and Ancistrocladaceae lianas, including first investigations on the chemoecological role of these plant metabolites and their storage and accumulation in particular plant organs.
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Affiliation(s)
- Doris Feineis
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany.
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4
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Mori T. Significance of Vibronic Coupling that Shapes Circularly Polarized Luminescence of Double Helicenes. Angew Chem Int Ed Engl 2024; 63:e202319702. [PMID: 38317539 DOI: 10.1002/anie.202319702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
The circularly polarized luminescence (CPL) spectra of S- and X-shaped double helicenes exhibit distinct vibrational structures and overall shape variations. In this study, we conducted an in-depth investigation into the vibronic effects influencing the CPL spectra of two double helicenes, namely DPC and DNH. Employing state-of-the-art computations utilizing the FC-HT1|VH model at the CAM-B3LYP/def2-TZVP level, we unveiled the paramount impact of Franck-Condon (FC), Herzberg-Teller (HT), and Duschinsky effects on their chiroptical responses. Our research underscores the pivotal role of structural deformations associated with the S1-to-S0 electronic transition in molding CPL spectra and wavelength-dependent dissymmetry (g) factor values, as well as the significance of HT effects in shaping and enhancing CPL responses. This extensive investigation not only advances our comprehension of the vibronic characteristics in configurationally distinct double helicenes but also offers valuable insights for the design of chiral molecules featuring controllable or finely-tunable CPL responses.
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Affiliation(s)
- Tadashi Mori
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka, 565-0871, Japan
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5
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Zhang N, Xu Y, Yue X, Xiong L, Li H, Chen L. Isolation, characterization and anti-inflammatory effect of alkaloids from the roots of Stemona tuberosa Lour. PHYTOCHEMISTRY 2024; 220:114013. [PMID: 38331134 DOI: 10.1016/j.phytochem.2024.114013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Six undescribed alkaloids, neotuberostemonol C (1), dehydrostenines C-D (2-3), tuberostemonines Q-R (10-11), and (6R,8R,8aR)-8-hydroxy-6-methyl-hexahydroindolizin-5-one (32), along with twenty-six known analogues were isolated from the dried roots of Stemona tuberosa Lour. The structures and absolute stereochemistry of these compounds were delineated by extensive spectroscopy (1D NMR, 2D NMR, HRESIMS), quantum chemical calculations of the electronic circular dichroism spectra, and pyridine-induced solvent shifts. Tuberostemonines Q-R (10-11) represent tuberostemonine skeleton alkaloids possessing an α-methyl-γ-butyrolactone moiety attached to C-3. In addition, all these isolated compounds were assayed for their inhibitory activity against LPS-induced NO production in RAW264.7 cells using Griess assay.
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Affiliation(s)
- Na Zhang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yang Xu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Xinyi Yue
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Liangliang Xiong
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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6
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Kumar A, Asthana A, Abraham V, Crawford TD, Mayhall NJ, Zhang Y, Cincio L, Tretiak S, Dub PA. Quantum Simulation of Molecular Response Properties in the NISQ Era. J Chem Theory Comput 2023; 19:9136-9150. [PMID: 38054645 DOI: 10.1021/acs.jctc.3c00731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Accurate modeling of the response of molecular systems to an external electromagnetic field is challenging on classical computers, especially in the regime of strong electronic correlation. In this article, we develop a quantum linear response (qLR) theory to calculate molecular response properties on near-term quantum computers. Inspired by the recently developed variants of the quantum counterpart of equation of motion (qEOM) theory, the qLR formalism employs "killer condition" satisfying excitation operator manifolds that offer a number of theoretical advantages along with reduced quantum resource requirements. We also used the qEOM framework in this work to calculate the state-specific response properties. Further, through noiseless quantum simulations, we show that response properties calculated using the qLR approach are more accurate than the ones obtained from the classical coupled-cluster-based linear response models due to the improved quality of the ground-state wave function obtained using the ADAPT-VQE algorithm.
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Affiliation(s)
- Ashutosh Kumar
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ayush Asthana
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Vibin Abraham
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - T Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Nicholas J Mayhall
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yu Zhang
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lukasz Cincio
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Pavel A Dub
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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7
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Peyton BG, Wang Z, Crawford TD. Reduced Scaling Real-Time Coupled Cluster Theory. J Phys Chem A 2023; 127:8486-8499. [PMID: 37782945 DOI: 10.1021/acs.jpca.3c05151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Real-time coupled cluster (CC) methods have several advantages over their frequency-domain counterparts, namely, response and equation of motion CC theories. Broadband spectra, strong fields, and pulse manipulation allow for the simulation of complex spectroscopies that are unreachable using frequency-domain approaches. Due to the high-order polynomial scaling, the required numerical time propagation of the CC residual expressions is a computationally demanding process. This scaling may be reduced by local correlation schemes, which aim to reduce the size of the (virtual) orbital space by truncation according to user-defined parameters. We present the first application of local correlation to real-time CC. As in previous studies of locally correlated frequency-domain CC, traditional local correlation schemes are of limited utility for field-dependent properties; however, a perturbation-aware scheme proves promising. A detailed analysis of the amplitude dynamics suggests that the main challenge is a strong time dependence of the wave function sparsity.
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Affiliation(s)
- Benjamin G Peyton
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Zhe Wang
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - T Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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8
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Parsons T, Balduf T, Caricato M. On the choice of coordinate origin in length gauge optical rotation calculations. Chirality 2023; 35:708-717. [PMID: 37137811 DOI: 10.1002/chir.23575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023]
Abstract
In this work, we explore the issue of origin dependence in optical rotation (OR) calculations in the length dipole gauge (LG) using standard approximate methods belonging to density functional theory (DFT) and coupled cluster (CC) theory. We use the origin-invariant LG approach, LG(OI), that we recently proposed as reference for the calculations, and we study whether a proper choice of coordinate origin and molecular orientation can be made such that diagonal elements of the LG-OR tensor match those of the LG(OI) tensor. Using a numerical search algorithm, we show that multiple spatial orientations can be found where the LG and LG(OI) results match. However, a simple analytical procedure provides a spatial orientation where the origin of the coordinate system is close to the center of mass of the molecule. At the same time, we also show that putting the origin at the center of mass is not an ideal choice for every molecule (relative errors in the OR up to 70% can be obtained in out test set). Finally, we show that the choice of coordinate origin based on the analytical procedure is transferable across different methods and it is superior to putting the origin in the center of mass or center of nuclear charge. This is important because the LG(OI) approach is trivial to implement for DFT, but not necessarily for nonvariational methods in the CC family. Therefore, one can determine an optimal coordinate origin at DFT level and use it for standard LG-CC response calculations.
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Affiliation(s)
- Taylor Parsons
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Ty Balduf
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Marco Caricato
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
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9
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Monti M, Stener M, Coccia E. Electronic circular dichroism from real-time propagation in state space. J Chem Phys 2023; 158:084102. [PMID: 36859092 DOI: 10.1063/5.0136392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In this paper, we propose to compute the electronic circular dichroism (ECD) spectra of chiral molecules using a real-time propagation of the time-dependent Schrödinger equation (TDSE) in the space of electronic field-free eigenstates, by coupling TDSE with a given treatment of the electronic structure of the target. The time-dependent induced magnetic moment is used to compute the ECD spectrum from an explicit electric perturbation. The full matrix representing the transition magnetic moment in the space of electronic states is generated from that among pairs of molecular orbitals. In the present work, we show the ECD spectra of methyloxirane, of several conformers of L-alanine, and of the Λ-Co(acac)3 complex, computed from a singly excited ansatz of time-dependent density functional theory eigenstates. The time-domain ECD spectra properly reproduce the frequency-domain ones obtained in the linear-response regime and quantitatively agree with the available experimental data. Moreover, the time-domain approach to ECD allows us to naturally go beyond the ground-state rotationally averaged ECD spectrum, which is the standard outcome of the linear-response theory, e.g., by computing the ECD spectra from electronic excited states.
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Affiliation(s)
- M Monti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - M Stener
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - E Coccia
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
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10
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Kowalski K. Sub-system self-consistency in coupled cluster theory. J Chem Phys 2023; 158:054101. [PMID: 36754799 DOI: 10.1063/5.0125696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In this article, we provide numerical evidence indicating that the single-reference coupled-cluster (CC) energies can be calculated alternatively to their copybook definition. We demonstrate that the CC energy can be reconstructed by diagonalizing the effective Hamiltonians describing correlated sub-systems of the many-body system. In the extreme case, we provide numerical evidence that the CC energy can be reproduced through the diagonalization of the effective Hamiltonian describing sub-system composed of a single electron. These properties of the CC formalism can be exploited to design protocols to define effective interactions in sub-systems used as probes to calculate the energy of the entire system and introduce a new type of self-consistency for approximate CC approaches.
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Affiliation(s)
- Karol Kowalski
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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11
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Ji HF. A general method to predict optical rotations of chiral molecules from their structures. RSC Adv 2023; 13:4775-4780. [PMID: 36760291 PMCID: PMC9900718 DOI: 10.1039/d2ra08290j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
The relationship of the chiroptical response of a molecule to its absolution configuration does not exist now. In this letter, I intend to report a general rule with exceptions to predict the sign of optical rotation of chiral molecules with a RCHXY structure from their absolute configurations using the Hammett constant, σ p, which is based on the electron withdrawing/donating power of functional groups. In this rule, a priority list of functional groups based on the electron withdrawing powers of the groups are used. When the lowest priority group is in the back of the molecule, a clockwise arrangement of the other three priorities from the most electron withdrawing to the least withdrawing (1-2-3) is predicted to be dextrorotatory, the counterclockwise arrangement is predicted to be levorotatory.
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Affiliation(s)
- Hai-Feng Ji
- Department of Chemistry, Drexel University Philadelphia PA 19104 USA +1-215-895-1265 +1-215-895-2562
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12
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Zhang N, Xiong LL, Sun DJ, Zhu M, Zhao ZY, Li H, Chen LX. Anti-infammatory scalemic chromanoids and chromenoids from Rhododendron dauricum. Fitoterapia 2022; 162:105300. [PMID: 36116614 DOI: 10.1016/j.fitote.2022.105300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/04/2022]
Abstract
Four pairs of undescribed chromane and chromene meroterpenoid scalemic mixtures (1a/1b-4a/4b), together with three pairs of known chromane meroterpenoid ones (5a/5b-7a/7b) were isolated from the twigs and leaves of Rhododendron dauricum L. Among them, 1a/1b-3a/3b and 5a/5b-7a/7b were the chromane ones derived from an intramolecular [2 + 2] cyclic addition of their respective chromene precursors, forming a 6/6/6/4 and 6/6/5/4 ring fused scaffold. The absolute configurations of the chiral center at C-15 of 2a/2b were determined by Snatzke's method, and comparing the experimental and calculated electronic circular dichroism (ECD) data. The inhibitory effects of the isolated compounds were tested against lipopolysaccharide (LPS)-induced nitric oxide production in RAW264.7 macrophage cells to evaluate their anti-inflammatory activity. Compounds 4a, 4b and 6a displayed inhibitory effects on nitric oxide (NO) production, and compound 4b exhibited the obvious anti-inflammatory activity, with an IC50 value of 6.91 ± 0.97 μM, by downregulating nuclear factor kappa B (NF-κB) and reducing the expression of inducible nitric oxide synthase (iNOS) in LPS-induced RAW264.7 cells. These results intimated that 4b could be used as a leading compound to develop anti-inflammatory drugs and is worthy of further investigated.
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Affiliation(s)
- Na Zhang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Liang-Liang Xiong
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - De-Juan Sun
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Man Zhu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zi-Yuan Zhao
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
| | - Li-Xia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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13
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Mattiat J, Luber S. Comparison of Length, Velocity, and Symmetric Gauges for the Calculation of Absorption and Electric Circular Dichroism Spectra with Real-Time Time-Dependent Density Functional Theory. J Chem Theory Comput 2022; 18:5513-5526. [PMID: 36041170 DOI: 10.1021/acs.jctc.2c00644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A velocity and symmetric gauge implementation for real-time time-dependent density functional theory (RT-TDDFT) in the CP2K package using a Gaussian and plane wave approach is presented, including the explicit gauge-transformed contributions due to the nonlocal part of pseudopotentials. Absorption spectra of gas-phase α-pinene are calculated in length and velocity gauges in the long-wavelength approximation for the application of a δ pulse in linear and full order. The velocity gauge implementation is also applied to a solvated uracil molecule to showcase its use within periodic boundary conditions (PBC). For the calculation of the expectation value of the electric dipole moment in PBC, both the velocity representation and the modern theory of polarization give equivalent absorption spectra if a distributed reference point is used for the nonlocal term of the velocity operator. The discussion of linear response theory takes place in a unified framework in terms of linear response functions in propagator notation, distinguishing the parts of the linear response functions associated with perturbation and response. To further investigate gauge dependence, electric circular dichroism (ECD) spectra of α-pinene were calculated either as magnetic response to an electric field perturbation, in length or velocity gauge, or as electric response to a magnetic field perturbation in the symmetric gauge. Both approaches, electric and magnetic perturbations, have been found to yield equivalent ECD spectra.
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Affiliation(s)
- Johann Mattiat
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
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14
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Eikås KDR, Beerepoot MTP, Ruud K. A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides. J Phys Chem A 2022; 126:5458-5471. [PMID: 35930395 PMCID: PMC9393892 DOI: 10.1021/acs.jpca.2c02953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and J. Chem. Theory. Comput. 2019, 15, 2847-2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.
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Affiliation(s)
- Karolina Di Remigio Eikås
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Maarten T P Beerepoot
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.,Norwegian Defence Research Establishment, P.O. Box 25, 2027 Kjeller, Norway
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15
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Adnan RH, Madridejos JML, Alotabi AS, Metha GF, Andersson GG. A Review of State of the Art in Phosphine Ligated Gold Clusters and Application in Catalysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105692. [PMID: 35332703 PMCID: PMC9130904 DOI: 10.1002/advs.202105692] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/23/2022] [Indexed: 05/28/2023]
Abstract
Atomically precise gold clusters are highly desirable due to their well-defined structure which allows the study of structure-property relationships. In addition, they have potential in technological applications such as nanoscale catalysis. The structural, chemical, electronic, and optical properties of ligated gold clusters are strongly defined by the metal-ligand interaction and type of ligands. This critical feature renders gold-phosphine clusters unique and distinct from other ligand-protected gold clusters. The use of multidentate phosphines enables preparation of varying core sizes and exotic structures beyond regular polyhedrons. Weak gold-phosphorous (Au-P) bonding is advantageous for ligand exchange and removal for specific applications, such as catalysis, without agglomeration. The aim of this review is to provide a unified view of gold-phosphine clusters and to present an in-depth discussion on recent advances and key developments for these clusters. This review features the unique chemistry, structural, electronic, and optical properties of gold-phosphine clusters. Advanced characterization techniques, including synchrotron-based spectroscopy, have unraveled substantial effects of Au-P interaction on the composition-, structure-, and size-dependent properties. State-of-the-art theoretical calculations that reveal insights into experimental findings are also discussed. Finally, a discussion of the application of gold-phosphine clusters in catalysis is presented.
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Affiliation(s)
- Rohul H. Adnan
- Department of Chemistry, Faculty of ScienceCenter for Hydrogen EnergyUniversiti Teknologi Malaysia (UTM)Johor Bahru81310Malaysia
| | | | - Abdulrahman S. Alotabi
- Flinders Institute for NanoScale Science and TechnologyFlinders UniversityAdelaideSouth Australia5042Australia
- Department of PhysicsFaculty of Science and Arts in BaljurashiAlbaha UniversityBaljurashi65655Saudi Arabia
| | - Gregory F. Metha
- Department of ChemistryUniversity of AdelaideAdelaideSouth Australia5005Australia
| | - Gunther G. Andersson
- Flinders Institute for NanoScale Science and TechnologyFlinders UniversityAdelaideSouth Australia5042Australia
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16
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Niemeyer N, Caricato M, Neugebauer J. Origin invariant electronic circular dichroism in the length dipole gauge without London atomic orbitals. J Chem Phys 2022; 156:154114. [PMID: 35459317 DOI: 10.1063/5.0088922] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present a method for obtaining origin-independent electronic circular dichroism (ECD) in the length-gauge representation LG(OI) without the usage of London atomic orbitals. This approach builds upon the work by Caricato [J. Chem. Phys. 153, 151101 (2020)] and is applied to rotatory strengths and ECD spectra from damped response theory. Numerical results are presented for time-dependent Hartree-Fock and density-functional theory, the second-order algebraic diagrammatic construction method, and linear-response coupled-cluster theory with singles and approximate doubles. We can support the finding that the common choice of placing the gauge origin in the center of mass of a molecule in conventional length-gauge calculations involving chiroptical properties might not be optimal and show that LG(OI) is a valuable alternative for the origin-independent calculation of ECD spectra. We show that, for a limited test set, the convergence of the rotatory strengths calculated with the LG(OI) approach toward the basis-set limit tends to be faster than for the established velocity gauge representation. Relationships between the sum-over-states expression of the optical rotation in the LG(OI) framework and its representation in terms of response functions are analyzed.
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Affiliation(s)
- Niklas Niemeyer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Marco Caricato
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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17
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Parsons T, Balduf T, Cheeseman JR, Caricato M. Basis Set Dependence of Optical Rotation Calculations with Different Choices of Gauge. J Phys Chem A 2022; 126:1861-1870. [PMID: 35271772 DOI: 10.1021/acs.jpca.2c00201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, the basis set dependence of optical rotation (OR) calculations is examined for various choices of gauge/level of theory. The OR is calculated for a set of 50 molecules using B3LYP and CAM-B3LYP and 17 molecules using coupled cluster with single and double excitations (CCSD). The calculations employ the correlation-consistent basis sets, aug-cc-pVζZ with ζ = D, T, Q. An inverse-power extrapolation formula is then utilized to obtain OR values at the complete basis set (CBS) limit. We investigate the basis set convergence for these methods and three choices of gauge: length gauge (with gauge-including atomic orbitals, LG(GIAOs), for DFT), the origin-invariant length gauge [LG(OI)], and the modified velocity gauge (MVG). The results show that all methods converge smoothly to the CBS limit and that the LG(OI) approach has a slightly faster convergence rate than the other choices of gauge. While the DFT methods reach gauge invariance at the CBS limit, CCSD does not. The significant difference between the MVG and LG(OI) results at the CBS limit, 26%, indicates that CCSD is not quite at convergence in the description of electron correlation for this property. On the other hand, gauge invariance at the CBS limit for DFT does not lead to the same OR values for the two density functionals, which is also due to electron correlation incompleteness. A limited comparison to gas-phase experimental OR values for the DFT methods shows that CAM-B3LYP seems more accurate than B3LYP. Overall, this study shows that the LG(OI) approach with the aug-cc-pVTZ basis set for DFT, and with the CBS(DT) extrapolation for CCSD, provides a good cost/accuracy balance.
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Affiliation(s)
- Taylor Parsons
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Ty Balduf
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - James R Cheeseman
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Marco Caricato
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
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18
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Bauman NP, Kowalski K. Coupled Cluster Downfolding Methods: the effect of double commutator terms on the accuracy of ground-state energies. J Chem Phys 2022; 156:094106. [DOI: 10.1063/5.0076260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Karol Kowalski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, United States of America
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19
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Benchmarking study on calculation of specific optical rotation of rigid chiral molecules in solution: 1:1 solute-solvent complex with PCM solvation model. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Meng W, Pi Z, Brigance R, Rossi KA, Schumacher WA, Bostwick JS, Gargalovic PS, Onorato JM, Luk CE, Generaux CN, Wang T, Wexler RR, Finlay HJ. Identification of a Hydroxypyrimidinone Compound ( 21) as a Potent APJ Receptor Agonist for the Potential Treatment of Heart Failure. J Med Chem 2021; 64:18102-18113. [PMID: 34855405 DOI: 10.1021/acs.jmedchem.1c01504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes our continued efforts in the area of small-molecule apelin receptor agonists. Recently disclosed compound 2 showed an acceptable metabolic stability but demonstrated monodemethylation of the dimethoxyphenyl group to generate atropisomer metabolites in vitro. In this article, we extended the structure-activity relationship at the C2 position that led to the identification of potent pyrazole analogues with excellent metabolic stability. Due to the increased polarity at C2, the permeability for these compounds decreased. Further adjustment of the polarity by replacing the N1 2,6-dimethoxyphenyl group with a 2,6-diethylphenyl group and reoptimization for the potency of the C5 pyrroloamides resulted in potent compounds with improved permeability. Compound 21 displayed excellent pharmacokinetic profiles in rat, monkey, and dog models and robust pharmacodynamic efficacy in the rodent heart failure model. Compound 21 also showed an acceptable safety profile in preclinical toxicology studies and was selected as a backup development candidate for the program.
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Affiliation(s)
- Wei Meng
- Departments of Discovery Chemistry, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Zulan Pi
- Departments of Discovery Chemistry, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Robert Brigance
- Departments of Discovery Chemistry, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Karen A Rossi
- Computer-Assisted Drug Design, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - William A Schumacher
- Cardiovascular Drug Discovery Biology, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Jeffrey S Bostwick
- Cardiovascular Drug Discovery Biology, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Peter S Gargalovic
- Cardiovascular Drug Discovery Biology, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Joelle M Onorato
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Chiuwa E Luk
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Claudia N Generaux
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Tao Wang
- Leads Discovery and Optimization, Research and Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Ruth R Wexler
- Departments of Discovery Chemistry, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
| | - Heather J Finlay
- Departments of Discovery Chemistry, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States
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21
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Sarala S, Geetha S, Muthu S, Irfan A. Theoretical investigation on influence of protic and aprotic solvents effect and structural (Monomer, Dimer), Van-der Waals and Hirshfeld surface analysis for clonidine molecule. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Martin AT, Nichols SM, Murphy VL, Kahr B. Chiroptical anisotropy of crystals and molecules. Chem Commun (Camb) 2021; 57:8107-8120. [PMID: 34322691 DOI: 10.1039/d1cc00991e] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Optical activity, a foundational part of chemistry, is not restricted to chiral molecules although generations have been instructed otherwise. A more inclusive view of optical activity is valuable because it clarifies structure-property relationships however, this view only comes into focus in measurements of oriented molecules, commonly found in crystals. Unfortunately, measurements of optical rotatory dispersion or circular dichroism in anisotropic single crystals have challenged scientists for more than two centuries. New polarimetric methods for unpacking the optical activity of crystals in general directions are still needed. Such methods are reviewed as well as some of the 'nourishment' they provide, thereby inviting to new researchers. Methods for fitting intensity measurements in terms of the constitutive tensor that manifests as the differential refraction and absorption of circularly polarized light, are described, and examples are illustrated. Single oriented molecules, as opposed to single oriented crystals, can be treated computationally. Structure-property correlations for such achiral molecules with comparatively simple electronic structures are considered as a heuristic foundation for the response of crystals that may be subject to measurement.
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Affiliation(s)
- Alexander T Martin
- Department of Chemistry and Molecular Design Institute, New York University, New York City, NY 10003, USA.
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23
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Ghosh S, Herink G, Perri A, Preda F, Manzoni C, Polli D, Cerullo G. Broadband Optical Activity Spectroscopy with Interferometric Fourier-Transform Balanced Detection. ACS PHOTONICS 2021; 8:2234-2242. [PMID: 34476287 PMCID: PMC8377715 DOI: 10.1021/acsphotonics.0c01866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 06/13/2023]
Abstract
Spectrally resolved measurements of optical activity, such as circular dichroism (CD) and optical rotatory dispersion (ORD), are powerful tools to study chiroptical properties of (bio)molecular and nanoplasmonic systems. The wider utilization of these techniques, however, has been impeded by the bulky and slow design of conventional spectropolarimeters, which have been limited to a narrowband scanning approach for more than 50 years. In this work, we demonstrate broadband measurements of optical activity by combining a balanced detection scheme with interferometric Fourier-transform spectroscopy. The setup utilizes a linearly polarized light field that creates an orthogonally polarized weak chiral free-induction-decay field, along with a phase-locked achiral transmitted signal, which serves as the local oscillator for heterodyne amplification. By scanning the delay between the two fields with a birefringent common-path interferometer and recording their interferogram with a balanced detector that measures polarization rotation, broadband CD and ORD spectra are retrieved simultaneously with a Fourier transform. Using an incoherent thermal light source, we achieve state-of-the-art sensitivity for CD and ORD across a broad wavelength range in a remarkably simple setup. We further demonstrate the potential of our technique for highly sensitive measurements of glucose concentration and the real-time monitoring of ground-state chemical reactions. The setup also accepts broadband pulses and will be suitable for broadband transient optical activity spectroscopy and broadband optical activity imaging.
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Affiliation(s)
- Soumen Ghosh
- Dipartimento
di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Georg Herink
- Experimental
Physics VIII, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Antonio Perri
- Dipartimento
di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
- NIREOS
S.R.L., Via G. Durando
39, 20158 Milano, Italy
| | - Fabrizio Preda
- Dipartimento
di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
- NIREOS
S.R.L., Via G. Durando
39, 20158 Milano, Italy
| | - Cristian Manzoni
- Istituto
di Fotonica e Nanotecnologie (IFN)−CNR, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Dario Polli
- Dipartimento
di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
- NIREOS
S.R.L., Via G. Durando
39, 20158 Milano, Italy
- Istituto
di Fotonica e Nanotecnologie (IFN)−CNR, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Giulio Cerullo
- Dipartimento
di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
- NIREOS
S.R.L., Via G. Durando
39, 20158 Milano, Italy
- Istituto
di Fotonica e Nanotecnologie (IFN)−CNR, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
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24
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Caricato M, Balduf T. Origin invariant full optical rotation tensor in the length dipole gauge without London atomic orbitals. J Chem Phys 2021; 155:024118. [PMID: 34266245 DOI: 10.1063/5.0053450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present an origin-invariant approach to compute the full optical rotation tensor (Buckingham/Dunn tensor) in the length dipole gauge without recourse to London atomic orbitals, called LG(OI). The LG(OI) approach is simpler and less computationally demanding than the more common length gauge (LG)-London and modified velocity gauge (MVG) approaches, and it can be used with any approximate wave function or density functional method. We report an implementation at the coupled cluster with single and double excitations level (CCSD), for which we present the first simulations of the origin-invariant Buckingham/Dunn tensor in the LG. We compare LG(OI) and MVG results on a series of 22 organic molecules, showing good linear correlation between the approaches, although for small tensor elements, they provide values of opposite sign. We also attempt to decouple the effects of electron correlation and basis set incompleteness on the choice of gauge for specific rotation calculations on simple test systems. The simulations show a smooth convergence of the LG(OI) and MVG results with the basis set size toward the complete basis set limit. However, these preliminary results indicate that CCSD may not be close to a complete description of the electron correlation effects on this property even for small molecules and that basis set incompleteness may be a less important cause of discrepancy between choices of gauge than electron correlation incompleteness.
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Affiliation(s)
- Marco Caricato
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, USA
| | - Ty Balduf
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, USA
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25
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Balduf T, Caricato M. Gauge Dependence of the S̃ Molecular Orbital Space Decomposition of Optical Rotation. J Phys Chem A 2021; 125:4976-4985. [PMID: 34086473 DOI: 10.1021/acs.jpca.1c01653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The measurement of optical rotation (OR) is a foundational technique for the detection and characterization of chiral molecules, but it is poorly understood how the observed property relates to the structure of the molecule. Over the years, several schemes have been developed to decompose the OR into more chemically intuitive contributions. In this paper, we introduce two alternative formulations of our previously developed S̃ molecular orbital space decomposition. These new expressions use the modified velocity gauge-magnetic (MVG-M) and -electric (MVG-E) definitions of OR, rather than the length gauge-magnetic (LG-M) definition used in the original paper. Comparing these formulations across a small set of previously studied chiral molecules, we find that these different definitions produce consistent physical interpretations of the OR. These results demonstrate that the S̃ methodology for investigations of structure-property relationships in chiral molecules is insensitive to the choice of gauge.
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Affiliation(s)
- Ty Balduf
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Marco Caricato
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
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26
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Pearce KC, Fuentes RG, Calderon S, Marolikar R, Kingston DGI, Crawford TD. Structure Elucidation and Confirmation of Phloroglucinols from the Roots of Garcinia dauphinensis by Comparison of Experimental and Calculated ECD Spectra and Specific Rotations. JOURNAL OF NATURAL PRODUCTS 2021; 84:1163-1174. [PMID: 33823109 DOI: 10.1021/acs.jnatprod.0c01208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Eight phloroglucinols from Garcinia dauphinensis were recently reported to have good to moderate antiplasmodial and anticancer activities, consistent with other phloroglucinol derivatives isolated from natural sources. Chiroptical properties were previously calculated and compared to experimental data for compound 2 as a means to deduce its absolute configuration. Tentative assignments for the remaining compounds were also reported based on these data. In order to arrive at stereochemical assignments for phloroglucinols 1 and 3-8, ECD spectra and specific rotations were computed for all stereoisomers of each compound. Molecular orbital analyses were also carried out for the most energetically favorable conformers of each compound. Absolute configurations are reported for all eight phloroglucinols for the first time.
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Affiliation(s)
- Kirk C Pearce
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rolly G Fuentes
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
- Division of Natural Sciences and Mathematics, University of the Philippines Visayas Tacloban College, 6500 Tacloban City, Philippines
| | - Susana Calderon
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rageshwari Marolikar
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - David G I Kingston
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - T Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Molecular Sciences Software Institute, 1880 Pratt Drive, Suite 1100, Blacksburg, Virginia 24060, United States
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27
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D'Cunha R, Crawford TD. Modeling Complex Solvent Effects on the Optical Rotation of Chiral Molecules: A Combined Molecular Dynamics and Density Functional Theory Study. J Phys Chem A 2021; 125:3095-3108. [PMID: 33829790 DOI: 10.1021/acs.jpca.1c00803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The challenge of assigning the absolute stereochemical configuration to a chiral compound can be overcome via accurate ab initio predictions of optical rotation, a sensitive molecular property that is further complicated by solvent effects. The solvent's "chiral imprint"-the transfer of the chirality from the solute to the surrounding achiral solvent-is explored here using conformational averaging and time-dependent density-functional theory. These complex solvent effects are taken into account via simple averaging over a molecular dynamics trajectory together with the explicit quantum mechanical consideration of the solvent molecules within the solute's cybotactic region and implicit modeling of the bulk solvent. We consider several axes along which the system's optical rotation varies, including the sampling of the dynamical trajectory, the quality of the one-electron basis set, and the use of continuum solvent models to account for bulk effects.
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Affiliation(s)
- Ruhee D'Cunha
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - T Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.,Molecular Sciences Software Institute, 1880 Pratt Drive, Suite 1100, Blacksburg, Virginia 24060, United States
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28
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Galeano Carrano RS, Provasi PF, Ferraro MB, Alkorta I, Elguero J, Sauer SPA. A Density Functional Theory Study of Optical Rotation in Some Aziridine and Oxirane Derivatives. Chemphyschem 2021; 22:764-774. [PMID: 33528071 DOI: 10.1002/cphc.202001010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/01/2021] [Indexed: 12/25/2022]
Abstract
We present time-dependent density functional theory (TDDFT) calculations of the electronic optical rotation (ORP) for seven oxirane and two aziridine derivatives in the gas phase and in solution and compare the results with the available experimental values. For seven of the studied molecules it is the first time that their optical rotation was studied theoretically and we have therefore investigated the influence of several settings in the TDDFT calculations on the results. This includes the choice of the one-electron basis set, the exchange-correlation functional or the particular polarizable continuum model (PCM). We can confirm that polarized quadruple zeta basis sets augmented with diffuse functions are necessary for converged results and find that the aug-pc-3 basis set is a viable alternative to the frequently employed aug-cc-pVQZ basis set. Based on our study, we cannot recommend the generalized gradient functional KT3 for calculations of the ORP in these compounds, whereas the hybrid functional PBE0 gives results quite similar to the long-range correct CAM-B3LYP functional. Finally, we observe large differences in the solvent effects predicted by the integral equation formalism of PCM and the SMD variant of PCM. For the majority of solute/solvent combinations in this study, we find that the SMD model in combination with the PBE0 functional and the aug-pc-3 basis set gives the best agreement with the experimental values.
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Affiliation(s)
- Ramiro S Galeano Carrano
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Patricio F Provasi
- Department of Physics, IMIT, Northeastern University, CONICET, Corrientes, Argentina
| | - Marta B Ferraro
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Buenos Aires, Argentina
| | - Ibon Alkorta
- Instituto de Química Médica (C.S.I.C.), Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (C.S.I.C.), Madrid, Spain
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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29
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Zhang K, Balduf T, Caricato M. Full optical rotation tensor at coupled cluster with single and double excitations level in the modified velocity gauge. Chirality 2021; 33:303-314. [PMID: 33826196 DOI: 10.1002/chir.23310] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/11/2021] [Accepted: 03/06/2021] [Indexed: 11/07/2022]
Abstract
This work presents the first simulations of the full optical rotation (OR) tensor at coupled cluster with single and double excitations (CCSD) level in the modified velocity gauge (MVG) formalism. The CCSD-MVG OR tensor is origin independent, and each tensor element can in principle be related directly to experimental measurements on oriented systems. We compare the CCSD results with those from two density functionals, B3LYP and CAM-B3LYP, on a test set of 22 chiral molecules. The results show that the functionals consistently overestimate the CCSD results for the individual tensor components and for the trace (which is related to the isotropic OR), by 10%-20% with CAM-B3LYP and 20%-30% with B3LYP. The data show that the contribution of the electric dipole-magnetic dipole polarizability tensor to the OR tensor is on average twice as large as that of the electric dipole-electric quadrupole polarizability tensor. The difficult case of (1S,4S)-(-)-norbornenone also reveals that the evaluation of the former polarizability tensor is more sensitive than the latter. We attribute the better agreement of CAM-B3LYP with CCSD to the ability of this functional to better reproduce electron delocalization compared with B3LYP, consistent with previous reports on isotropic OR. The CCSD-MVG approach allows the computation of reference data of the full OR tensor, which may be used to test more computationally efficient approximate methods that can be employed to study realistic models of optically active materials.
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Affiliation(s)
- Kaihua Zhang
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Ty Balduf
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Marco Caricato
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
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30
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Makkonen E, Rossi TP, Larsen AH, Lopez-Acevedo O, Rinke P, Kuisma M, Chen X. Real-time time-dependent density functional theory implementation of electronic circular dichroism applied to nanoscale metal-organic clusters. J Chem Phys 2021; 154:114102. [PMID: 33752382 DOI: 10.1063/5.0038904] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Electronic circular dichroism (ECD) is a powerful spectroscopy method for investigating chiral properties at the molecular level. ECD calculations with the commonly used linear-response time-dependent density functional theory (LR-TDDFT) framework can be prohibitively costly for large systems. To alleviate this problem, we present here an ECD implementation within the projector augmented-wave method in a real-time-propagation TDDFT framework in the open-source GPAW code. Our implementation supports both local atomic basis sets and real-space finite-difference representations of wave functions. We benchmark our implementation against an existing LR-TDDFT implementation in GPAW for small chiral molecules. We then demonstrate the efficiency of our local atomic basis set implementation for a large hybrid nanocluster and discuss the chiroptical properties of the cluster.
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Affiliation(s)
- Esko Makkonen
- Department of Applied Physics, Aalto University, Espoo, Finland
| | - Tuomas P Rossi
- Department of Applied Physics, Aalto University, Espoo, Finland
| | | | - Olga Lopez-Acevedo
- Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Patrick Rinke
- Department of Applied Physics, Aalto University, Espoo, Finland
| | - Mikael Kuisma
- Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Xi Chen
- Department of Applied Physics, Aalto University, Espoo, Finland
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31
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Nikerov DS, Ashatkina MA, Shiryaev VA, Tkachenko IM, Rybakov VB, Reznikov AN, Klimochkin YN. Synthesis of non-racemic dihydrofurans via Ni(II)-catalyzed asymmetric Michael addition. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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32
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D'Cunha R, Crawford TD. PNO++: Perturbed Pair Natural Orbitals for Coupled Cluster Linear Response Theory. J Chem Theory Comput 2021; 17:290-301. [PMID: 33351627 DOI: 10.1021/acs.jctc.0c01086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reduced-scaling methods are needed to make accurate and systematically improvable coupled cluster linear response methods for the calculation of molecular properties tractable for large molecules. In this paper, we examine the perturbed pair natural orbital-based PNO++ approach that creates an orbital space optimized for response properties derived from a lower-cost field-perturbed density matrix. We analyze truncation errors in correlation energies, dynamic polarizabilities, and specific rotations from a coupled cluster singles and doubles (CCSD) reference. We find that incorporating a fixed number of orbitals from the pair natural orbital (PNO) space into the PNO++ method-a new method presented here, the "combined PNO++" approach-recovers accuracy in the CCSD correlation energy while preserving the well-behaved convergence behavior of the PNO++ method for linear response properties.
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Affiliation(s)
- Ruhee D'Cunha
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - T Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.,Molecular Sciences Software Institute, 1880 Pratt Drive, Suite 1100, Blacksburg, Virginia 24060, United States
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33
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A Unified Strategy for the Chemically Intuitive Interpretation of Molecular Optical Response Properties. J Chem Theory Comput 2020; 16:7709-7720. [DOI: 10.1021/acs.jctc.0c00990] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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34
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Assignment of protonated R-homocitrate in extracted FeMo-cofactor of nitrogenase via vibrational circular dichroism spectroscopies. Commun Chem 2020; 3:145. [PMID: 34337161 PMCID: PMC8323615 DOI: 10.1038/s42004-020-00392-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Protonation of FeMo-cofactor is important for the process of substrate hydrogenation. Its structure has been clarified as Δ-Mo*Fe7S9C(R-homocit*)(cys)(Hhis) for the efforts of nearly 30 years, while it remains controversial whether FeMo-cofactor is protonated or deprotonated with chelated ≡C-O(H) homocitrate. We have used protonated molybdenum(V) lactates 1 and its enantiomer as model compounds for R-homocitrate in FeMo-cofactor of nitrogenase. Vibrational circular dichroism (VCD) spectrum of 1 at 1051 cm-1 is attributed to ≡C-OH vibration, and molybdenum(VI) R-lactate at 1086 cm-1 is assigned as ≡C-O α-alkoxy vibration. These vibrations set up labels for the protonation state of coordinated α-hydroxycarboxylates. The characteristic VCD band of NMF-extracted FeMo-cofactor is assigned to ν(C-OH), which is based on the comparison of molybdenum(VI) R-homocitrate. Density Functional Theory calculations are in consistent with these assignments. To the best of our knowledge, this is the first time that protonated R-homocitrate in FeMo-cofactor is confirmed by VCD spectra.
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35
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Caricato M. Origin invariant optical rotation in the length dipole gauge without London atomic orbitals. J Chem Phys 2020; 153:151101. [PMID: 33092358 DOI: 10.1063/5.0028849] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present an approach to perform origin invariant optical rotation calculations in the length dipole gauge without recourse to London atomic orbitals, called origin invariant length gauge [LG(OI)]. The LG(OI) approach works with any approximate wave function or density functional method, but here we focus on the implementation with the coupled cluster (CC) with single and double excitations method because of the lack of production-level alternatives. Preliminary numerical tests show the efficacy of the LG(OI) procedure and indicate that putting the origin in the center of mass of a molecule may not be an optimal choice for conventional CC-LG calculations.
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Affiliation(s)
- Marco Caricato
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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36
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Tafelska-Kaczmarek A, Kołodziejska R, Kwit M, Stasiak B, Wypij M, Golińska P. Synthesis, Absolute Configuration, Antibacterial, and Antifungal Activities of Novel Benzofuryl β-Amino Alcohols. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E4080. [PMID: 32937873 PMCID: PMC7560283 DOI: 10.3390/ma13184080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/29/2022]
Abstract
A series of new benzofuryl α-azole ketones was synthesized and reduced by asymmetric transfer hydrogenation (ATH). Novel benzofuryl β-amino alcohols bearing an imidazolyl and triazolyl substituents were obtained with excellent enantioselectivity (96-99%). The absolute configuration (R) of the products was confirmed by means of electronic circular dichroism (ECD) spectroscopy supported by theoretical calculations. Selected benzofuryl α-azole ketones were also successfully asymmetrically bioreduced by fungi of Saccharomyces cerevisiae and Aureobasidium pullulans species. Racemic and chiral β-amino alcohols, as well as benzofuryl α-amino and α-bromo ketones were evaluated for their antibacterial and antifungal activities. From among the synthesized β-amino alcohols, the highest antimicrobial activity was found for (R)-1-(3,5-dimethylbenzofuran-2-yl)-2-(1H-imidazol-1-yl)ethan-1-ol against S. aureus ATCC 25923 (MIC = 64, MBC = 96 μg mL-1) and (R)-1-(3,5-dimethylbenzofuran-2-yl)-2-(1H-1,2,4-triazol-1-yl)ethan-1-ol against yeasts of M. furfur DSM 6170 (MIC = MBC = 64 μg mL-1). In turn, from among the tested ketones, 1-(benzofuran-2-yl)-2-bromoethanones (1-4) were found to be the most active against M. furfur DSM 6170 (MIC = MBC = 1.5 μg mL-1) (MIC-minimal inhibitory concentration, MBC-minimal biocidal concentration).
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Affiliation(s)
- Agnieszka Tafelska-Kaczmarek
- Department of Organic Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Street, 87-100 Toruń, Poland
| | - Renata Kołodziejska
- Department of Medical Biology and Biochemistry, Faculty of Medicine, Nicolaus Copernicus University in Toruń, Collegium Medicum in Bydgoszcz, 24 Karłowicz Street, 85-092 Bydgoszcz, Poland;
| | - Marcin Kwit
- Faculty of Chemistry, Adam Mickiewicz University, 8 Uniwersytetu Poznańskiego Street, 61-614 Poznań, Poland; (M.K.); (B.S.)
| | - Bartosz Stasiak
- Faculty of Chemistry, Adam Mickiewicz University, 8 Uniwersytetu Poznańskiego Street, 61-614 Poznań, Poland; (M.K.); (B.S.)
| | - Magdalena Wypij
- Department of Microbiology, Faculty of Biology and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 1 Lwowska Street, 87-100 Toruń, Poland; (M.W.); (P.G.)
| | - Patrycja Golińska
- Department of Microbiology, Faculty of Biology and Veterinary Sciences, Nicolaus Copernicus University in Toruń, 1 Lwowska Street, 87-100 Toruń, Poland; (M.W.); (P.G.)
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37
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de Wergifosse M, Seibert J, Grimme S. Simplified time-dependent density functional theory (sTD-DFT) for molecular optical rotation. J Chem Phys 2020; 153:084116. [DOI: 10.1063/5.0020543] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marc de Wergifosse
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Jakob Seibert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
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38
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Mądry T, Czapik A, Kwit M. Point-to-Axial Chirality Transmission: A Highly Sensitive Triaryl Chirality Probe for Stereochemical Assignments of Amines. J Org Chem 2020; 85:10413-10431. [PMID: 32806087 PMCID: PMC7458434 DOI: 10.1021/acs.joc.0c00734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Indexed: 01/17/2023]
Abstract
A readily available stereodynamic and the electronic circular dichroism (ECD)-silent 2,5-di(1-naphthyl)-terephthalaldehyde-based probe has been applied for chirality sensing of primary amines. The chiral amine (the inductor) forces a change in the structure of the chromophore system through the point-to-axial chirality transmission mechanism. As a result, efficient induction of optical activity in the chromophoric system is observed. The butterflylike structure of the probe, with the terminal aryl groups acting as changeable "wings", allowed for the generation of exciton Cotton effects in the region of 1Bb electronic transition in the naphthalene chromophores. The sign of the exciton couplets observed for inductor-reporter systems might be correlated with an absolute configuration of the inductor, whereas the linear relationship between amplitudes of the specific Cotton effect and enantiomeric excess of the parent amine gives potentiality for quantitative chirality sensing. Despite the structural simplicity, the probe turned out to be unprecedentedly highly sensitive to even subtle differences in the inductor structure (i.e., O vs CH2).
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Affiliation(s)
- Tomasz Mądry
- Department
of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61 614 Poznan, Poland
| | - Agnieszka Czapik
- Department
of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61 614 Poznan, Poland
| | - Marcin Kwit
- Department
of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61 614 Poznan, Poland
- Center
for Advanced Technologies, Adam Mickiewicz
University, Uniwersytetu
Poznanskiego 10, 61 614 Poznan, Poland
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39
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Li X, Govind N, Isborn C, DePrince AE, Lopata K. Real-Time Time-Dependent Electronic Structure Theory. Chem Rev 2020; 120:9951-9993. [DOI: 10.1021/acs.chemrev.0c00223] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christine Isborn
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Kenneth Lopata
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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40
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Aharon T, Caricato M. Compact Basis Sets for Optical Rotation Calculations. J Chem Theory Comput 2020; 16:4408-4415. [DOI: 10.1021/acs.jctc.0c00446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tal Aharon
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Marco Caricato
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
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41
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Saito F, Gerbig D, Becker J, Schreiner PR. Absolute Configuration of trans-Perhydroazulene. Org Lett 2020; 22:3895-3899. [DOI: 10.1021/acs.orglett.0c01184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fumito Saito
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Dennis Gerbig
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Jonathan Becker
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R. Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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42
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Padula D, Mazzeo G, Santoro E, Scafato P, Belviso S, Superchi S. Amplification of the chiroptical response of UV-transparent amines and alcohols by N-phthalimide derivatization enabling absolute configuration determination through ECD computational analysis. Org Biomol Chem 2020; 18:2094-2102. [PMID: 32107518 DOI: 10.1039/d0ob00052c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The stereoselective transformation of chiral UV-transparent amines and alcohols to phthalimides has proved to be a simple and efficient method to enhance the chiroptical response of these substrates allowing their reliable absolute configuration determination by computational analysis of ECD spectra. Such a transformation also leads to a significant reduction in the molecular conformational flexibility thus simplifying the conformational analysis required by the computational treatment. The method described herein thus allows the absolute configuration assignment to these challenging substrates to be much easier and reliable.
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Affiliation(s)
- Daniele Padula
- Dipartimento di Scienze, Università della Basilicata, via dell'Ateneo Lucano, 85100, Potenza, Italy.
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43
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Ozcelik A, Pereira-Cameselle R, Poklar Ulrih N, Petrovic AG, Alonso-Gómez JL. Chiroptical Sensing: A Conceptual Introduction. SENSORS (BASEL, SWITZERLAND) 2020; 20:E974. [PMID: 32059394 PMCID: PMC7071115 DOI: 10.3390/s20040974] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 12/21/2022]
Abstract
Chiroptical responses have been an essential tool over the last decades for chemical structural elucidation due to their exceptional sensitivity to geometry and intermolecular interactions. In recent times, there has been an increasing interest in the search for more efficient sensing by the rational design of tailored chiroptical systems. In this review article, advances made in chiroptical systems towards their implementation in sensing applications are summarized. Strategies to generate chiroptical responses are illustrated. Theoretical approaches to assist in the design of these systems are discussed. The development of efficient chiroptical reporters in different states of matter, essential for the implementation in sensing devises, is reviewed. In the last part, remarkable examples of chiroptical sensing applications are highlighted.
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Affiliation(s)
- Ani Ozcelik
- Department of Organic Chemistry, University of Vigo, 36310 Vigo, Spain; (A.O.); (R.P.-C.)
| | | | - Natasa Poklar Ulrih
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Kongresni trg 12, 1000 Ljubljana, Slovenia;
| | - Ana G. Petrovic
- Department of Biological & Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA
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44
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Osadchuk I, Borovkov V, Aav R, Clot E. Benchmarking computational methods and influence of guest conformation on chirogenesis in zinc porphyrin complexes. Phys Chem Chem Phys 2020; 22:11025-11037. [DOI: 10.1039/d0cp00965b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different computational methods and influence of the guest conformation and solvent effect to analyze chirogenesis in zinc porphyrins by several chiral compounds have been investigated.
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Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and Biotechnology
- Tallinn University of Technology
- Tallinn 12618
- Estonia
- ICGM, University of Montpellier
| | - Victor Borovkov
- Department of Chemistry and Biotechnology
- Tallinn University of Technology
- Tallinn 12618
- Estonia
- College of Chemistry and Materials Science
| | - Riina Aav
- Department of Chemistry and Biotechnology
- Tallinn University of Technology
- Tallinn 12618
- Estonia
| | - Eric Clot
- ICGM, University of Montpellier
- CNRS
- ENSCM
- Montpellier
- France
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45
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A molecular orbital selection approach for fast calculations of specific rotation with density functional theory. Chirality 2019; 32:243-253. [DOI: 10.1002/chir.23158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 11/07/2022]
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46
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Mattiat J, Luber S. Vibrational (resonance) Raman optical activity with real time time dependent density functional theory. J Chem Phys 2019; 151:234110. [DOI: 10.1063/1.5132294] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Johann Mattiat
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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47
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Gendron F, Moore Ii B, Cador O, Pointillart F, Autschbach J, Le Guennic B. Ab Initio Study of Circular Dichroism and Circularly Polarized Luminescence of Spin-Allowed and Spin-Forbidden Transitions: From Organic Ketones to Lanthanide Complexes. J Chem Theory Comput 2019; 15:4140-4155. [PMID: 31125219 DOI: 10.1021/acs.jctc.9b00286] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complete and restricted active space self-consistent field (CAS-/RAS-SCF) wave function methods are applied for the calculation of circular dichroism (CD) and circularly polarized luminescence (CPL) of a series of molecules comprising four organic ketones, the chiral cobalt(III) complex [Co(en)3]3+, and the europium(III) complex [Eu(DPA)3]3-. The ab initio results are in good agreement with the experimental data and previous results obtained with Kohn-Sham density functional theory in the case of the spin-allowed transitions. CD and CPL properties are calculated ab initio for the spin-forbidden transitions of both a transition metal and a lanthanide complex.
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Affiliation(s)
- Frédéric Gendron
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Barry Moore Ii
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Olivier Cador
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Fabrice Pointillart
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Jochen Autschbach
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Boris Le Guennic
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
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48
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Mancinelli M, Franzini R, Renzetti A, Marotta E, Villani C, Mazzanti A. Determination of the absolute configuration of conformationally flexible molecules by simulation of chiro-optical spectra: a case study. RSC Adv 2019; 9:18165-18175. [PMID: 35515261 PMCID: PMC9064610 DOI: 10.1039/c9ra03526e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/01/2019] [Indexed: 11/24/2022] Open
Abstract
The assignment of the absolute configuration (AC) of two conformational flexible organic molecules by means of TD-DFT simulation of the electronic circular dichroism (ECD) spectra is presented. The factors leading to a reliable assignment were evaluated in the various steps of the process. The effects of different functionals and basis sets in the geometry optimization step is very limited in terms of the resulting optimized geometries, whereas the inclusion of the solvent in the calculations has a much larger effect on the correct evaluation of the conformational ratio. B3LYP and M06-2x were found to be the most accurate functionals for geometry optimization. CAM-B3LYP and ωB97X-D provided the best results in the TD-DFT simulations.
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Affiliation(s)
- Michele Mancinelli
- Department of Industrial Chemistry "Toso Montanari", University of Bologna Viale Risorgimento 4 40136-Bologna Italy
| | - Roberta Franzini
- Dipartimento di Chimica e Tecnologie Del Farmaco, Sapienza Università di Roma P.le A. Moro 5 00185 Roma Italy
| | - Andrea Renzetti
- Faculty of Education, Room 426, University of the Ryukyus 1 Senbaru, Nishihara Okinawa 903-0213 Japan
| | - Emanuela Marotta
- Department of Industrial Chemistry "Toso Montanari", University of Bologna Viale Risorgimento 4 40136-Bologna Italy
| | - Claudio Villani
- Dipartimento di Chimica e Tecnologie Del Farmaco, Sapienza Università di Roma P.le A. Moro 5 00185 Roma Italy
| | - Andrea Mazzanti
- Department of Industrial Chemistry "Toso Montanari", University of Bologna Viale Risorgimento 4 40136-Bologna Italy
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49
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Peyton BG, Crawford TD. Basis Set Superposition Errors in the Many-Body Expansion of Molecular Properties. J Phys Chem A 2019; 123:4500-4511. [DOI: 10.1021/acs.jpca.9b03864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Benjamin G. Peyton
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - T. Daniel Crawford
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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50
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Daramola O, Cullen J. Identifying absolute configurations of PCB atropisomers by comparison of their experimental specific rotations with their DFT calculated values. CAN J CHEM 2019. [DOI: 10.1139/cjc-2018-0458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nineteen enantiomer pairs of polychlorinated biphenyls (PCBs) with three or four chloro substituents about the central carbon–carbon bond form a stable subclass of compounds whose biological effects vary with their chirality. Optical rotations for this group of PCBs were determined from density functional calculations employing extended atomic orbital gauge invariant basis sets. A comparison of these results with the experimental ones found from the literature for 10 of the pairs enabled the identification of their absolute configurations as analytes in gas chromatography studies.
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Affiliation(s)
- Oluwadamilola Daramola
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB R3T 2N2, Canada
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB R3T 2N2, Canada
| | - John Cullen
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB R3T 2N2, Canada
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, MB R3T 2N2, Canada
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