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Jumai A, Zou GA, Liu GY, Aisa HA. Pyrrolizidine alkaloids from Jacobaea vulgaris Gaertn and theoretical studies on intramolecular interactions. Nat Prod Res 2024; 38:2529-2534. [PMID: 36722688 DOI: 10.1080/14786419.2023.2174533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/03/2023] [Accepted: 01/22/2023] [Indexed: 02/02/2023]
Abstract
Two undescribed pyrrolizidine alkaloids, 13-dehydrosenkirkine (1) and chloromethylretrorsine (2), along with three known analogues, onetine (3), retrorsine (4), and usaramine N-oxide (5), were isolated from Jacobaea vulgaris Gaertn. The structures of the undescribed compounds were elucidated by extensive spectrometric and spectroscopic techniques, including HRESIMS, NMR, calculated 13C-NMR DP4+ analysis and comparison with experimental and calculated ECD spectra. The undescribed compounds were evaluated for their antitumour activity against HT29, HeLa, and HepG2 cells. In addition, the intramolecular interactions and quadrupolar couplings were revealed by investigating the geometrical and electronic properties of three typical otonecine-type PAs in DFT theory.
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Affiliation(s)
- Aikebaier Jumai
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, CAS Key Laboratory of Chemistry of Plant Resources in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Guo-An Zou
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, CAS Key Laboratory of Chemistry of Plant Resources in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ge-Yu Liu
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, CAS Key Laboratory of Chemistry of Plant Resources in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Haji Akber Aisa
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, CAS Key Laboratory of Chemistry of Plant Resources in Arid Regions, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
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2
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Gupta PK, Esser A, Forbert H, Marx D. Toward theoretical terahertz spectroscopy of glassy aqueous solutions: partially frozen solute-solvent couplings of glycine in water. Phys Chem Chem Phys 2019; 21:4975-4987. [PMID: 30758388 DOI: 10.1039/c8cp07489e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular-level understanding of THz spectra of aqueous solutions under ambient conditions has been greatly advanced in recent years. Here, we go beyond previous analyses by performing ab initio molecular dynamics simulations of glycine in water with artificially frozen solute or solvent molecules, respectively, while computing the total THz response as well as its decomposition into mode-specific resonances based on the "supermolecular solvation complex" technique. Clamping the water molecules and keeping glycine moving breaks the coupling of glycine to the structural dynamics of the solvent, however, the polarization and dielectric solvation effects in the static solvation cage are still at work since the full electronic structure of the quenched solvent is taken into account. The complementary approach of fixing glycine reveals both the dynamical and electronic response of the solvation cage at the level of its THz response. Moreover, to quantitatively account for the electronic contribution solely due to solvent embedding, the solute species is "vertically desolvated", thus preserving the fully coupled solute-solvent motion in terms of the solute's structural dynamics in solution, while its electronic structure is no longer subject to solute-solvent polarization and charge transfer effects. When referenced to the free simulation of Gly(aq), this three-fold approach allows us to decompose the THz spectral contributions due to the correlated solute-solvent dynamics into entirely structural and purely electronic effects. Beyond providing hitherto unknown insights, the observed systematic changes of THz spectra in terms of peak shifts and lineshape modulations due to conformational freezing and frozen solvation cages might be useful to investigate the solvation of molecules in highly viscous H-bonding solvents such as ionic liquids and even in cryogenic ices as relevant to polar stratospheric and dark interstellar clouds.
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Affiliation(s)
- Prashant Kumar Gupta
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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3
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Yoo SH, Todorova M, Neugebauer J. Selective Solvent-Induced Stabilization of Polar Oxide Surfaces in an Electrochemical Environment. PHYSICAL REVIEW LETTERS 2018; 120:066101. [PMID: 29481276 DOI: 10.1103/physrevlett.120.066101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/10/2017] [Indexed: 06/08/2023]
Abstract
The impact of an electrochemical environment on the thermodynamic stability of polar oxide surfaces is investigated for the example of ZnO(0001) surfaces immersed in water using density functional theory calculations. We show that solvation effects are highly selective: They have little effect on surfaces showing a metallic character, but largely stabilize semiconducting structures, particularly those that have a high electrostatic penalty in vacuum. The high selectivity is shown to have direct consequences for the surface phase diagram and explains, e.g., why certain surface structures could be observed only in an electrochemical environment.
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Affiliation(s)
- Su-Hyun Yoo
- Department of Computational Materials Design, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Str. 1, D-40237 Düsseldorf, Germany
| | - Mira Todorova
- Department of Computational Materials Design, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Str. 1, D-40237 Düsseldorf, Germany
| | - Jörg Neugebauer
- Department of Computational Materials Design, Max-Planck-Institut für Eisenforschung GmbH, Max-Planck-Str. 1, D-40237 Düsseldorf, Germany
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4
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Ghosh MK, Choi TH, Choi CH. Conformers of Zwitterionic Glycine in Aqueous Phase. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Manik Kumer Ghosh
- Department of Chemical and Environmental Sciences; Materials & Surface Science Institute, University of Limerick; Limerick Ireland
| | - Tae Hoon Choi
- Department of Chemistry; University of Pittsburgh; Pittsburgh Pennsylvania 15260 USA
| | - Cheol Ho Choi
- Department of Chemistry and Green-Nano Materials Research Center, College of Natural Sciences; Kyungpook National University; Daegu 702-701 South Korea
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5
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Fisicaro G, Genovese L, Andreussi O, Mandal S, Nair NN, Marzari N, Goedecker S. Soft-Sphere Continuum Solvation in Electronic-Structure Calculations. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00375] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Giuseppe Fisicaro
- Department
of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Luigi Genovese
- Laboratoire
de simulation atomistique (L_Sim), SP2M, INAC, CEA-UJF, F-38054 Grenoble, France
| | - Oliviero Andreussi
- Institute
of Computational Science, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6904 Lugano, Switzerland
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne, Switzerland
| | - Sagarmoy Mandal
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N. Nair
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nicola Marzari
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne, Switzerland
| | - Stefan Goedecker
- Department
of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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6
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7
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Andreussi O, Dabo I, Marzari N. Revised self-consistent continuum solvation in electronic-structure calculations. J Chem Phys 2012; 136:064102. [DOI: 10.1063/1.3676407] [Citation(s) in RCA: 323] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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8
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Symmetric versus asymmetric discretization of the integral equations in polarizable continuum solvation models. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.04.092] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Anisimov VM, Cavasotto CN. Hydration Free Energies Using Semiempirical Quantum Mechanical Hamiltonians and a Continuum Solvent Model with Multiple Atomic-Type Parameters. J Phys Chem B 2011; 115:7896-905. [DOI: 10.1021/jp203885n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Victor M. Anisimov
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin Street, Houston, Texas 77030, United States
| | - Claudio N. Cavasotto
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin Street, Houston, Texas 77030, United States
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10
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Sun J, Bousquet D, Forbert H, Marx D. Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics. J Chem Phys 2010; 133:114508. [DOI: 10.1063/1.3481576] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Lipparini F, Scalmani G, Mennucci B, Cancès E, Caricato M, Frisch MJ. A variational formulation of the polarizable continuum model. J Chem Phys 2010; 133:014106. [DOI: 10.1063/1.3454683] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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12
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Nagarajan S, Rajadas J, Malar EP. Density functional theory analysis and spectral studies on amyloid peptide Aβ(28–35) and its mutants A30G and A30I. J Struct Biol 2010; 170:439-50. [DOI: 10.1016/j.jsb.2010.02.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 02/18/2010] [Accepted: 02/19/2010] [Indexed: 11/25/2022]
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13
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Sánchez VM, Sued M, Scherlis DA. First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent. J Chem Phys 2009; 131:174108. [DOI: 10.1063/1.3254385] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Su P, Li H. Continuous and smooth potential energy surface for conductorlike screening solvation model using fixed points with variable areas. J Chem Phys 2009; 130:074109. [PMID: 19239286 DOI: 10.1063/1.3077917] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rigorously continuous and smooth potential energy surfaces, as well as exact analytic gradients, are obtained for a conductorlike screening solvation model (CPCM, a variant of the general COSMO) with Hartree-Fock (RHF, ROHF, UHF, and MCSCF) and density functional theory (R-DFT, RO-DFT, and U-DFT) methods using a new tessellation scheme, fixed points with variable areas (FIXPVA). In FIXPVA, spheres centered at atoms are used to define the molecular cavity and surface. The surface of each sphere is divided into 60, 240, or 960 tesserae, which have positions fixed relative to the sphere center and areas scaled by switching functions of their distances to neighboring spheres. Analytic derivatives of the positions and areas of the surface tesserae with respect to atomic coordinates can be obtained and used to evaluate the solvation energy gradients. Due to the accurate analytic gradients and smooth potential energy surface, geometry optimization processes using these methods are stable and convergent.
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Affiliation(s)
- Peifeng Su
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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15
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Anisimov VM, Bugaenko VL. QM/QM docking method based on the variational finite localized molecular orbital approximation. J Comput Chem 2009; 30:784-98. [DOI: 10.1002/jcc.21100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Brancato G, Rega N, Barone V. A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations. J Chem Phys 2008; 128:144501. [DOI: 10.1063/1.2897759] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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17
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Gale JD, Rohl AL. An efficient technique for the prediction of solvent-dependent morphology: the COSMIC method. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927020701713902] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Scherlis DA, Fattebert JL, Gygi F, Cococcioni M, Marzari N. A unified electrostatic and cavitation model for first-principles molecular dynamics in solution. J Chem Phys 2007; 124:74103. [PMID: 16497026 DOI: 10.1063/1.2168456] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.
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Affiliation(s)
- Damián A Scherlis
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, 02139, USA.
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19
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Jesus AJL, Tomé LIN, Eusébio MES, Rosado MTS, Redinha JS. Hydration of Cyclohexylamines: CPCM Calculation of Hydration Gibbs Energy of the Conformers. J Phys Chem A 2007; 111:3432-7. [PMID: 17417830 DOI: 10.1021/jp070243e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work presents a theoretical study on the hydration of cyclohexylamine and isomers of cyclohexyldiamine. All possible conformers were fully optimized in solution using the conductor-like polarizable continuum model (CPCM) and density functional theory. Values of the Gibbs energy of solvation, its respective contributions (electrostatic, nonelectrostatic and conformational change), and the relative Gibbs energy of the conformers in aqueous solution and gas phase are reported. From these values and the Boltzmann populations of the conformers in both phases, the weighted mean values of DeltaG(solv) for the compounds are calculated. Three structural features were found to be important for the hydration of these compounds: the distance between the two NH2 groups (proximity disfavors hydration), their position relative to the ring (equatorial is preferred over axial), and the orientation of the nitrogen lone-pairs (gauche is more favorable to hydration than trans). In the particular case of vicinal cyclohexyldiamines, in addition to these two factors, the relative orientation of one group to the other should also be taken into account.
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Affiliation(s)
- A J Lopes Jesus
- Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal.
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20
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Ziegler T, Autschbach J. Theoretical methods of potential use for studies of inorganic reaction mechanisms. Chem Rev 2005; 105:2695-722. [PMID: 15941226 DOI: 10.1021/cr0307188] [Citation(s) in RCA: 367] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tom Ziegler
- Department of Chemistry, University of Calgary, Canada.
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21
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Affiliation(s)
- Jacopo Tomasi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
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22
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Leung K, Rempe SB. Ab initio molecular dynamics study of glycine intramolecular proton transfer in water. J Chem Phys 2005; 122:184506. [PMID: 15918728 DOI: 10.1063/1.1885445] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use ab initio molecular-dynamics simulations to quantify structural and thermodynamic properties of a model proton transfer reaction that converts a neutral glycine molecule, stable in the gas phase, to the zwitterion that predominates in aqueous solution. We compute the potential of mean force associated with the direct intramolecular proton transfer event in glycine. Structural analyses show that the average hydration number (N(w)) of glycine is not constant along the reaction coordinate, but rather progresses from N(w) = 5 in the neutral molecule to N(w) = 8 for the zwitterion. We report the free-energy difference between the neutral and charged glycine molecules, and the free-energy barrier to proton transfer. Finally, we identify the approximations inherent in our method and estimate the corresponding corrections to our reported thermodynamic predictions.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415 and 0310, Albuquerque, New Mexico 87185, USA.
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23
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Alezra V, Bernardinelli G, Corminboeuf C, Frey U, Kündig EP, Merbach AE, Saudan CM, Viton F, Weber J. [CpRu((R)-Binop-F)(H2O)][SbF6], a new fluxional chiral Lewis acid catalyst: synthesis, dynamic nmr, asymmetric catalysis, and theoretical studies. J Am Chem Soc 2004; 126:4843-53. [PMID: 15080688 DOI: 10.1021/ja0374123] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The C(2)-symmetric electron-poor ligand (R)-BINOP-F (4) was prepared by reaction of (R)-BINOL with bis(pentafluorophenyl)-phosphorus bromide in the presence of triethylamine. The iodo complex [CpRu((R)-BINOP-F)(I)] ((R)-6) was obtained by substitution of two carbonyl ligands by (R)-4 in the in situ-prepared [CpRu(CO)(2)H] complex followed by reaction with iodoform. Complex 6 was reacted with [Ag(SbF(6))] in acetone to yield [CpRu((R)-BINOP-F)(acetone)][SbF(6)] ((R)-7). X-ray structures were obtained for both (R)-6 and (R)-7. The chiral one-point binding Lewis acid [CpRu((R)-BINOP-F)][SbF(6)] derived from either (R)-7 or the corresponding aquo complex (R)-8 activates methacrolein and catalyzes the Diels-Alder reaction with cyclopentadiene to give the [4 + 2] cycloadduct with an exo/endo ratio of 99:1 and an ee of 92% of the exo product. Addition occurs predominantly to the methacrolein C(alpha)-Re face. In solution, water in (R)-8 exchanges readily. Moreover, a second exchange process renders the diastereotopic BINOP-F phosphorus atoms equivalent. These processes were studied by the application of variable-temperature (1)H, (31)P, and (17)O NMR spectroscopy, variable-pressure (31)P and(17)O NMR spectroscopy, and, using a simpler model complex, density functional theory (DFT) calculations. The results point to a dissociative mechanism of the aquo ligand and a pendular motion of the BINOP-F ligand. NMR experiments show an energy barrier of 50.7 kJ mol(-1) (12.2 kcal mol(-1)) for the inversion of the pseudo-chirality at the ruthenium center.
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Affiliation(s)
- Valérie Alezra
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
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24
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Ito M, Re S, Tokiwa H. Ab Initio Molecular Orbital Investigation of a Precursor in Ethylene Biosynthesis: Proton Transfer in a Cluster of 1-Aminocyclopropane-1-carboxylic Acid and Water. J Phys Chem A 2004. [DOI: 10.1021/jp031146y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mika Ito
- Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan, and Department of Theoretical Studies, Institute for Molecular Science, 38 Myodaiji, Okazaki 444-8585, Japan
| | - Suyong Re
- Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan, and Department of Theoretical Studies, Institute for Molecular Science, 38 Myodaiji, Okazaki 444-8585, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan, and Department of Theoretical Studies, Institute for Molecular Science, 38 Myodaiji, Okazaki 444-8585, Japan
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25
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Li H, Jensen JH. Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: New energy gradients and molecular surface tessellation. J Comput Chem 2004; 25:1449-62. [PMID: 15224389 DOI: 10.1002/jcc.20072] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
New equations are derived and implemented for efficient and accurate computation of solvation energy derivatives for the conductor-like polarizable continuum model (C-PCM) and the isotropic integral equation formalism polarizable continuum model (IEF-PCM). Two new molecular surface tessellation procedures GEPOL-RT and GEPOL-AS that generate near continuous potential energy surfaces are proposed for PCM geometry optimization. The combined use of these new techniques leads to efficient and convergent geometry optimizations with the PCMs.
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Affiliation(s)
- Hui Li
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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26
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Balta B, Aviyente V. Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer. J Comput Chem 2003; 24:1789-802. [PMID: 12964198 DOI: 10.1002/jcc.10341] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The relative stabilities of glycine tautomers involved in the intramolecular proton transfer are investigated computationally by considering glycine-water complexes containing up to five water molecules. The supermolecule results are compared with continuum calculations. Specific solute-solvent interactions and solvent induced changes in the solute wave function are considered using the natural bond orbitals (NBO) method. The stabilization of the zwitterion upon solvation is explained by the changes in the wave functions localized on the forming and breaking bonds as well as by the different interaction energies in the zwitterionic and neutral clusters. Only the neutral species exist in mono- and dihydrated clusters and in the gas phase. In the smaller clusters, zwitterions are mainly stabilized by conformational effects, whereas in larger clusters, in particular when glycine is solvated on both sides of its heavy atom backbone, polarization effects dominate the stability of a given tautomer. Generally, the strength of the solute-solvent interactions is governed by the intermolecular charge transfer interactions. As the solvation progresses, the hypothetical gaseous zwitterion is better solvated than the gaseous neutral, making zwitterion to neutral tautomerization progressively less exothermic for clusters containing up to three water molecules, and endothermic for larger clusters. The neutral isomer does not exist for some solvent arrangements with five water molecules. Only solvent arrangements in which water molecules do not interact with the reactive proton are considered. Hence, the experimentally observed double well potential energy surface may be due to such an interaction or to a different reaction mechanism.
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Affiliation(s)
- Bülent Balta
- Chemistry Department, Boğaziçi University, 80815 Bebek/Istanbul, Turkey
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