1
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Silva WGDP, van Wijngaarden J. Disentangling the Conformational Space and Structural Preferences of Tetrahydrofurfuryl Alcohol Using Rotational Spectroscopy and Computational Chemistry. Chemphyschem 2024; 25:e202400298. [PMID: 38637291 DOI: 10.1002/cphc.202400298] [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: 03/17/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 04/20/2024]
Abstract
The influence of the hydroxymethyl (CH2OH) group on the tetrahydrofuran (THF) ring structure was investigated by disentangling the gas phase conformational landscape of the sugar analogue tetrahydrofurfuryl alcohol (THFA). By combining rotational spectroscopy (6-20 GHz) and quantum chemical calculations, transitions corresponding to two stable conformers of THFA and their 13C isotopologues were observed and assigned in the rotational spectrum. The positions of the C atoms were precisely determined to unambiguously distinguish between nearly isoenergetic pairs of conformers that differ in their ring configurations: envelope (E) versus twist (T). The rotational spectrum confirms that the E ring geometry is favoured when the CH2OH fragment lies gauche (-) to the THF backbone (OCCO ~-60°) whereas the T form is more stable for the gauche (+) alignment of the substituent (OCCO ~+60°). The observed spectral intensities suggest that conformational relaxation of the THF geometry (E↔T) to the more stable form readily occurs within the pairs of g- and g+ conformers which is consistent with the low barriers (1.5-1.7 kJ mol-1) for conversion determined via transition state calculations. Insights into the intramolecular hydrogen bonding and other weak interactions stabilizing the lowest energy structures of THFA were derived and rationalized using non-covalent interaction analyses.
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Affiliation(s)
- Weslley G D P Silva
- I. Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, 50937, Köln, Germany
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2
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Park SM, Kwon CH. Deciphering the conformational preference and ionization dynamics of tetrahydrofuran: Insights from advanced spectroscopic techniques. J Chem Phys 2024; 160:114308. [PMID: 38497473 DOI: 10.1063/5.0186570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
Tetrahydrofuran (THF) has garnered significant attention due to its pivotal role in biological and chemical processes. The diverse array of conformations exhibited by THF profoundly impacts its reactivity and interactions with other molecules. Understanding these conformational preferences is crucial for comprehending its molecular behavior. In this study, we utilize infrared (IR) resonant vacuum ultraviolet photoionization/mass-analyzed threshold ionization (VUV-PI/MATI) mass spectroscopies to capture distinctive vibrational spectra of individual conformers, namely, "twisted" and "bent," within THF. Our conformer-specific vibrational spectra provide valuable insights into the relative populations of these two conformers. The analysis reveals that the twisted (C2) conformer is more stable than the bent (CS) conformer by 17 ± 15 cm-1. By precisely tuning the VUV photon energy to coincide with vibrational excitation via IR absorption, we selectively ionize specific conformers, yielding two-photon IR + VUV-PI/MATI spectra corresponding to the twisted and bent conformers. This investigation conclusively affirms that both the twisted and bent conformers coexist in the neutral state, while only the twisted conformer exists in the cationic state. These findings not only bridge gaps in existing knowledge but also provide profound insights into the behavior of this pivotal molecule in the realms of biology and medicine.
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Affiliation(s)
- Sung Man Park
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Chan Ho Kwon
- Department of Chemistry and Institute for Molecular Science and Fusion Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
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3
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Milešević D, Stimson J, Popat D, Robertson P, Vallance C. Photodissociation dynamics of tetrahydrofuran at 193 nm. Phys Chem Chem Phys 2023; 25:25322-25330. [PMID: 37702573 DOI: 10.1039/d3cp01974h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Tetrahydrofuran (THF), a cyclic ether with the chemical formula C4H8O, can be considered the simplest analog of the deoxyribose backbone component of deoxyribonucleic acid (DNA). As such, it provides a useful model for probing the photochemistry of such biomolecular motifs. We present a velocity-map imaging study into the ultraviolet dissociation of THF at a wavelength of 193 nm. Excitation to the S1 state occurs via a 3s ← n transition involving a lone-pair electron on the oxygen atom, and has been shown by other authors to result in rapid ring opening via cleavage of one of the C-O bonds to form a ring-opened C4H8O diradical, followed by C-C bond cleavage over a longer timescale to form either OCH2 + C3H6 products (Channel 1a), HOCH2 + C2H5 products (Channel 1b), or OCH2CH2 + C2H4 products (Channel 2). The C2H4O products formed via Channel 2 are unstable on the timescale of our experiment and dissociate further to form CH3 and CHO. We also observe a number of minor products resulting from H or H2 loss from the primary photofragments. The speed distributions observed for all photofragments are broad, indicating excitation of a range of rotational and vibrational states of the products. The angular distributions of the photofragments show an interesting speed dependence: the slowest products have almost isotropic angular distributions, but the magnitude of the recoil anisotropy increases monotonically with photofragment speed. The fastest products exhibit highly anisotropic angular distributions, with the recoil anisotropy parameter β approaching its limiting value of -1 (-0.75 for Channel 1 and -0.5 for Channel 2). This behaviour is attributed to the range of timescales over which the diradical intermediate dissociates into the observed photofragments. Rapid dissociation leads to fast photofragments which retain the correlation between the transition dipole moment for the S1 ← S0 excitation (which lies perpendicular to the ring) and the photofragment velocities (which lie predominantly in the plane of the ring). Slow dissociation results in a high degree of energy redistribution into internal modes, slower photofragments, and loss of correlation between the photofragment velocities and the transition dipole. The higher barrier associated with dissociation via Channel 2 suggests somewhat longer lifetimes for the diradical intermediate and is consistent with a corresponding reduction in the maximum observed value for β.
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Affiliation(s)
- Dennis Milešević
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK.
| | - Joseph Stimson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK.
| | - Divya Popat
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK.
| | - Patrick Robertson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK.
| | - Claire Vallance
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK.
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4
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Charvati E, Sun H. Potential Energy Surfaces Sampled in Cremer-Pople Coordinates and Represented by Common Force Field Functionals for Small Cyclic Molecules. J Phys Chem A 2023; 127:2646-2663. [PMID: 36893434 DOI: 10.1021/acs.jpca.3c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The complex conformations of the cyclic moieties impact the physical and chemical properties of molecules. In this work, we chose 22 molecules of four-, five-, and six-membered rings and performed a thorough conformational sampling using Cremer-Pople coordinates. With consideration of symmetries, we obtained a total of 1504 conformational structures for four-membered, 5576 for five-membered, and 13509 for six-membered rings. All well-known and many less well-known conformers for each molecule were identified. We represented the potential energy surfaces (PESs) by fitting the data to common analytical force field (FF) functional forms. We found that the general features of PESs can be described by the essential FF functional forms; however, the accuracy of representation can be improved remarkably by including the torsion-bond and torsion-angle coupling terms. The best fit yields R-squared (R2) values close to 1.0 and mean absolute errors in energy less than 0.3 kcal/mol.
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Affiliation(s)
- Evangelia Charvati
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Sun
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Ilin DY, Tarazanov SV, Andreychev VV, Lukyanova VA, Druzhinina A, Pimenova SM, Dorofeeva OV. Low-temperature heat capacity and pseudorotation in 2 methyltetrahydrofuran. Phys Chem Chem Phys 2022; 24:5437-5447. [DOI: 10.1039/d1cp05073g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The heat capacity and phase transitions of 2-methyltetrahydrofuran in the temperature range from 7 to 350 K were measured by adiabatic calorimetry. The smoothed molar thermodynamic functions in the condensed...
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6
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Huang S, Pink M, Ngendahimana T, Rajca S, Eaton GR, Eaton SS, Rajca A. Bis-Spiro-Oxetane and Bis-Spiro-Tetrahydrofuran Pyrroline Nitroxide Radicals: Synthesis and Electron Spin Relaxation Studies. J Org Chem 2021; 86:13636-13643. [PMID: 34546727 PMCID: PMC10441184 DOI: 10.1021/acs.joc.1c01670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthesis of bis-spiro-oxetane and bis-spiro-tetrahydrofuran pyrroline nitroxide radicals relies on the Mitsunobu reaction-mediated double cyclizations of N-Boc protected pyrroline tetraols. Structures of the nitroxide radicals are supported by X-ray crystallography. In a trehalose/sucrose matrix at room temperature, the bis-spiro-oxetane nitroxide radical possesses electron spin coherence time, Tm ≈ 0.7 μs. The observed enhanced Tm is most likely associated with strong hydrogen bonding of oxetane moieties to the trehalose/sucrose matrix.
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Affiliation(s)
- Shengdian Huang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304
| | - Maren Pink
- IUMSC, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208-2436
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208-2436
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208-2436
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304
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7
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Milton JR, Jankiewicz BJ, Max JP, Vinueza NR, Kirkpatrick LM, Campbell K, Gallardo VA, Reece JN, Kenttämaa HI. Study on the Gas-Phase Reactivity of Charged Pyridynes. J Org Chem 2021; 86:9979-9993. [PMID: 34242505 DOI: 10.1021/acs.joc.1c00618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reactivities of three isomeric, charged ortho-pyridynes, the 1,2-, 2,3-, and 3,4-didehydropyridinium cations, were examined in the gas phase using Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry. The structures of selected product ions were probed using collision-activated dissociation (CAD) experiments in a linear quadrupole ion trap (LQIT) mass spectrometer. Mechanisms based on quantum chemical calculations are proposed for the formation of all major products. The products of the reactions of the charged ortho-pyridynes in the gas phase were found to closely resemble those formed upon reactions of neutral ortho-arynes in solution, but the mechanisms of these reactions exhibit striking differences. Additionally, no radical reactions were observed for any of the charged ortho-pyridynes examined, in contrast to previous proposals that ortho-benzyne can occasionally react via radical mechanisms. Finally, the relative reactivities of those charged gaseous ortho-pyridynes that yielded similar product distributions were found to be affected mainly by the (calculated) vertical electron affinities of the dehydrocarbon sites, which suggests that the reactivity of these species is controlled by polar effects.
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Affiliation(s)
- Jacob R Milton
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Bartłomiej J Jankiewicz
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States.,Institute of Optoelectronics, Military University of Technology, gen. S. Kaliskiego 2, 00-908 Warsaw, Poland
| | - Joann P Max
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Nelson R Vinueza
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Lindsey M Kirkpatrick
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States.,Ryan White Center for Pediatric Infectious Disease, Indiana University School of Medicine, 705 Riley Hospital Drive, Room 3032, Indianapolis, Indiana 46202, United States
| | - Karinna Campbell
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Vanessa A Gallardo
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Jennifer N Reece
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Hilkka I Kenttämaa
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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8
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Conformations of saturated five-membered heterocycles evaluated by MP2 calculations. Chem Heterocycl Compd (N Y) 2021. [DOI: 10.1007/s10593-020-02855-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Stocka J, Čeponkus J, Šablinskas V, Rodziewicz P. Conformational diversity of the THF molecule in N 2 matrix by means of FTIR matrix isolation experiment and Car-Parrinello molecular dynamics simulations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 238:118425. [PMID: 32413717 DOI: 10.1016/j.saa.2020.118425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/25/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Tetrahydrofuran (THF) is a widely used chemical compound, in particular as a solvent in organic and inorganic synthesis. The THF molecule has also an interesting property, namely, undergoes pseudorotation, similar to the case of the cyclopentane. Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. We study the influence of the molecular environment (N2) on the Cs-C2 equilibrium of tetrahydrofuran in the THF@N2 system utilizing nitrogen matrix isolation infrared spectroscopy. We observe a different ratio between envelope (Cs) and twisted (C2) conformations with respect to a change of the temperature. FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. On the basis of the THF@N2 matrix model, with explicit nitrogen molecules, the anharmonic infrared spectra are generated from the Fourier transformation of the dipole moment autocorrelation function.
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Affiliation(s)
- Joanna Stocka
- Departament of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Saultekio al. 9, Vilnius 10222, Lithuania
| | - Justinas Čeponkus
- Departament of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Saultekio al. 9, Vilnius 10222, Lithuania
| | - Valdas Šablinskas
- Departament of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Saultekio al. 9, Vilnius 10222, Lithuania
| | - Pawel Rodziewicz
- Institute of Chemistry, Jan Kochanowski University, Swietokrzyska 15G, 25-406 Kielce, Poland.
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10
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Röder A, Skov AB, Boguslavskiy AE, Lausten R, Stolow A. VUV excited-state dynamics of cyclic ethers as a function of ring size. Phys Chem Chem Phys 2020; 22:26241-26254. [DOI: 10.1039/d0cp04292g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ultrafast vacuum ultraviolet (VUV) Rydberg state dynamics of cyclic ethers reflects ring strain.
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Affiliation(s)
- Anja Röder
- Department of Chemistry
- University of Ottawa
- Ottawa
- Canada
- University of Ottawa – National Research Council Joint Centre for Extreme Photonics
| | - Anders B. Skov
- Department of Chemistry
- University of Copenhagen
- 2100 København Ø
- Denmark
| | | | | | - Albert Stolow
- Department of Chemistry
- University of Ottawa
- Ottawa
- Canada
- Department of Physics
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11
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Lee YR, Kim HL, Kwon CH. Determination of the cationic conformational structure of tetrahydrothiophene by one-photon MATI spectroscopy and Franck–Condon fitting. Phys Chem Chem Phys 2020; 22:6184-6191. [DOI: 10.1039/d0cp00073f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study affords more accurate information regarding the pseudorotational PES describing the conformational interconversion of THT.
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Affiliation(s)
- Yu Ran Lee
- Department of Chemistry and Institute for Molecular Science and Fusion Technology
- Kangwon National University
- Chuncheon 24341
- Korea
| | - Hong Lae Kim
- Department of Chemistry and Institute for Molecular Science and Fusion Technology
- Kangwon National University
- Chuncheon 24341
- Korea
| | - Chan Ho Kwon
- Department of Chemistry and Institute for Molecular Science and Fusion Technology
- Kangwon National University
- Chuncheon 24341
- Korea
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12
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Importance of thorough conformational analysis in modelling transition metal-mediated reactions: Case studies on pincer complexes containing phosphine groups. JOURNAL OF SAUDI CHEMICAL SOCIETY 2019. [DOI: 10.1016/j.jscs.2019.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Single-walled carbon nanotubes in tetrahydrofuran solution: microsolvation from first-principles calculations. J Mol Model 2019; 25:206. [PMID: 31256236 DOI: 10.1007/s00894-019-4050-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/24/2019] [Indexed: 10/26/2022]
Abstract
The molecular interactions between the commonly used solvent tetrahydrofuran (THF) and single-walled carbon nanotubes (SWCNT) are studied using density functional theory calculations and Car-Parrinello molecular dynamics simulations. The competitive interplay between THF-THF and THF-SWCNT interactions via C-H⋯O and C-H⋯π hydrogen bonds is analyzed in detail. The binding energies for different global and local energy minima configurations of THF monomers, dimers, trimers, and tetramers on SWCNT(10,0) were determined. The adsorbed species are analyzed in terms of their coordination to the surface via weak hydrogen bonds of the C-H⋯π type and in terms of their ability to form intermolecular C-H⋯O hydrogen bonds, which are responsible for the self-aggregation of THF molecules and a possible dimerization or tetramerization process. A special focus is put on the pseudorotation of the THF molecules at finite temperatures and on the formation of blue-shifting hydrogen bonds.
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14
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Paoloni L, Rampino S, Barone V. Potential-Energy Surfaces for Ring-Puckering Motions of Flexible Cyclic Molecules through Cremer-Pople Coordinates: Computation, Analysis, and Fitting. J Chem Theory Comput 2019; 15:4280-4294. [PMID: 31244128 DOI: 10.1021/acs.jctc.9b00363] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ring-puckering motion in 12 flexible cyclic molecules is investigated by calculation and analysis of two-dimensional potential-energy surfaces (PESs) using the so-called ring-puckering coordinates proposed by Cremer and Pople. The PESs are calculated by means of density-functional theory using a B2PLYP-D3BJ exchange-correlation functional with a maug-cc-pVTZ basis set, and results are compared to the available experimental and theoretical data. Special care is devoted to the aspect of symmetry in such two-dimensional PESs, which are here reported for the first time also for molecules whose planar form has symmetry lower than D5 h or C2 v. The issue of PES fitting and that of solving the nuclear dynamics using ring-puckering coordinates are also addressed. Analytical formulations of the computed PESs using suitable functional forms with a limited set of parameters are provided.
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Affiliation(s)
- Lorenzo Paoloni
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| | - Sergio Rampino
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| | - Vincenzo Barone
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
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15
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Plazinski W, Gaweda K, Plazinska A. Relation between the NMR data and the pseudorotational free-energy profile for oxolane. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The conformation of five-membered furanose rings is a crucial issue for the structural analysis of many biologically-relevant molecules, including DNA and RNA. Oxolane can be treated as a prototypical furanose, composed only of saturated unsubstituted ring. In spite of its structural simplicity, providing the accurate quantitative description of the oxolane conformational features remains a great challenge for both the experimental and theoretical techniques. Here we show the method of recovering the free-energy profiles describing the conformational equilibrium in the oxolane ring (i.e. pseudorotation) based on the experimentally-inferred NMR data ([Formula: see text] coupling constants). The results remain in agreement with the quantum-mechanical-based molecular dynamics simulations and emphasize the large contributions of all ring conformers, even those located at the free-energy barriers. This includes the significant populations of limiting 3T2/2T3 and OE/EO shapes. Our findings provide another example of a poor applicability of the two-state model, which is routinely applied to analyze the NMR data in terms of population of different ring conformers.
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Affiliation(s)
- Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Kraków, Poland
| | - Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Kraków, Poland
| | - Anita Plazinska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, ul. W. Chodzki 4A, PL-20093 Lublin, Poland
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16
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Gaweda K, Plazinski W. The systematic influence of solvent on the conformational features of furanosides. Org Biomol Chem 2019; 17:2479-2485. [PMID: 30756110 DOI: 10.1039/c9ob00043g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The endo- and exo-anomeric effects are the two most recognizable stereoelectronic effects exhibited by carbohydrates. Their presence relies on the interactions between ring substituent(s) and ring oxygen atoms. Here, we report the finding of a new effect that partially controls the conformational properties of furanose rings and can be ascribed to the influence of the solvent on the electronic structure of a molecule. In contrast to anomeric effects, it is not dependent on either presence or absence of ring substituents. Its origins lie in a solvent-induced flux of atomic charges that involves atoms forming the furanose ring. This systematically changes the energy of the whole molecular system and alters the ring-distortion free energies by ∼2.5-6.5 kJ mol-1, favoring the geometries close to the twist 3T2/2T3 conformers and disfavoring the envelope OE/EO-like shapes. This intriguing effect has never been reported before, although it is expected to exist in all furanose rings. Along with more recognized stereoelectronic effects, this phenomenon contributes to a wide applicability of the two-state (north vs. south) model of pseudorotation in furanosides and, in the case of extremely flexible furanose rings, may change the preferred conformation type in comparison with the gas-phase-oriented predictions.
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Affiliation(s)
- Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow, Poland.
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17
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Tautomeric and epimeric equilibria of aldo- and ketohexoses studied by the MD simulations and QM calculations. Carbohydr Res 2019; 474:8-15. [DOI: 10.1016/j.carres.2019.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 11/17/2022]
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18
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Nester K, Gaweda K, Plazinski W. A GROMOS Force Field for Furanose-Based Carbohydrates. J Chem Theory Comput 2019; 15:1168-1186. [DOI: 10.1021/acs.jctc.8b00838] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
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19
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Stortz CA, Sarotti AM. Exhaustive exploration of the conformational landscape of mono- and disubstituted five-membered rings by DFT and MP2 calculations. RSC Adv 2019; 9:24134-24145. [PMID: 35527879 PMCID: PMC9069843 DOI: 10.1039/c9ra03524a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/18/2019] [Indexed: 11/21/2022] Open
Abstract
The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set. Our results showed that the conformational preference of these compounds was governed mainly by the specific characteristics of the substituents, with a minor influence of the level of theory employed. After a detailed analysis of the computational data, we found an interesting preference of the electronegative substituents to take pseudo-axial positions, whereas alkyl groups preferred adopting the pseudo-equatorial locations. Such preferences were pronounced with MP2 and M06-2X and underestimated by B3LYP. Despite each level of theory affording different landscapes in many cases, as a general trend, we noticed that M06-2X afforded much higher correlation with the MP2 results than B3LYP. The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set.![]()
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Affiliation(s)
- Carlos A. Stortz
- Universidad de Buenos Aires
- Facultad de Ciencias Exactas
- Departamento de Química Orgánica
- Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR)
- 1428 Buenos Aires
| | - Ariel M. Sarotti
- Instituto de Química Rosario (CONICET)
- Facultad de Ciencias Bioquímicas y Farmacéuticas
- Universidad Nacional de Rosario
- Rosario 2000
- Argentina
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20
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Xie F, Ng X, Seifert NA, Thomas J, Jäger W, Xu Y. Rotational spectroscopy of chiral tetrahydro-2-furoic acid: Conformational landscape, conversion, and abundances. J Chem Phys 2018; 149:224306. [DOI: 10.1063/1.5063683] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Fan Xie
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Xiaoqian Ng
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Nathan A. Seifert
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Javix Thomas
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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21
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Knochenmuss R, Sinha RK, Poblotzki A, Den T, Leutwyler S. Intermolecular dissociation energies of hydrogen-bonded 1-naphthol complexes. J Chem Phys 2018; 149:204311. [DOI: 10.1063/1.5055720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Richard Knochenmuss
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Rajeev K. Sinha
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Anja Poblotzki
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Takuya Den
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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22
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Telfah H, Reza MA, Alam J, Paul AC, Liu J. Direct Observation of Tetrahydrofuranyl and Tetrahydropyranyl Peroxy Radicals via Cavity Ring-Down Spectroscopy. J Phys Chem Lett 2018; 9:4475-4480. [PMID: 30037233 DOI: 10.1021/acs.jpclett.8b01721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Room-temperature cavity ring-down (CRD) spectra of the à ← X̃ electronic transition of tetrahydrofuranyl peroxy (THFOO•) and tetrahydropyranyl peroxy (THPOO•) radicals were recorded. The peroxy radicals were produced by Cl-initiated oxidation of tetrahydrofuran and tetrahydropyran. Quantum chemical calculations of the lowest-energy conformers of all regioisomers of these two peroxy radicals have been carried out to aid the spectral simulation. Conformational identification and vibrational assignment were achieved by comparing the experimentally obtained spectra to the simulated ones. The absence of α-THPOO• absorption peaks in the CRD spectrum is attributed to ring opening due to its weak Cα'O bond.
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Affiliation(s)
- Hamzeh Telfah
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| | - Md Asmaul Reza
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| | - Jahangir Alam
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| | - Anam C Paul
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| | - Jinjun Liu
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
- Conn Center for Renewable Energy Research , University of Louisville , Louisville , Kentucky 40292 , United States
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23
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Jin S, Hu Y, Wang P, Zhan H, Lu Q, Liu F, Sheng L. Hydrogen bonding and dominant conformations of hydrated sugar analogue complexes using tetrahydrofurfuryl alcohol as the model sugar molecule. Phys Chem Chem Phys 2018; 20:7351-7360. [DOI: 10.1039/c7cp07935d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water molecules, which serve as both hydrogen bond donors and acceptors, have been found to influence the conformational landscape of gas-phase phenyl-β-d-glucopyranoside.
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Affiliation(s)
- Shan Jin
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Pengchao Wang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Huaqi Zhan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Qiao Lu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Fuyi Liu
- National Synchrotron Radiation Laboratory
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Liusi Sheng
- National Synchrotron Radiation Laboratory
- University of Science and Technology of China
- Hefei
- P. R. China
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24
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Würmel J, Simmie JM. H-Atom Abstraction Reactions by Ground-State Ozone from Saturated Oxygenates. J Phys Chem A 2017; 121:8053-8060. [DOI: 10.1021/acs.jpca.7b07760] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Würmel
- Galway Mayo Institute of Technology, Galway H91 T8NW, Ireland
| | - J. M. Simmie
- School
of Chemistry, National University of Ireland, Galway H91 TK33, Ireland
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25
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Wang P, Hu Y, Zhan H, Chen J, Jin S, Song W, Li Y. Vibrational spectroscopy of the mass-selected tetrahydrofurfuryl alcohol monomers and its dimers in gas phase using IR depletion and VUV single photon ionization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 185:63-68. [PMID: 28544895 DOI: 10.1016/j.saa.2017.04.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/22/2017] [Accepted: 04/30/2017] [Indexed: 06/07/2023]
Abstract
Tetrahydrofurfuryl alcohol (THFA, C5H10O2) is a close chemical analog of the sugar rings present in the phosphate-deoxyribose backbone structure of the nucleic acids. In present report, the infrared (IR) spectra of the size-selected THFA monomer and its dimer have been investigated in a pulsed supersonic jet using infrared-vacuum ultraviolet (VUV) ionization. Herein, the laser light at 118nm wavelength served as the source of "soft" ionization in a time-of-flight mass spectrometer. The IR features for the monomers located at 3622cm-1 can be assigned to the intramolecular hydrogen bonding stretch vibrations mainly referring to A and C conformers. Compared with the monomer, however, characteristic peaks for the dimer centered at 3415 and 3453cm-1, red shifted 207 and 169cm-1, respectively, were associated with the intermolecular hydrogen bonding stretch vibrations. Combined with the quantum-chemical calculations, the dimer in the gas phase preferred cyclic AC conformer stabled by forming two strong intermolecular hydrogen bonds, which shown the high hydrogen bond selectivity in the cluster. The conclusions drawn from the role played in the conformational flexibility by the hydroxyl and ether groups may be extended to other biomolecules.
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Affiliation(s)
- Pengchao Wang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China.
| | - Huaqi Zhan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Jiaxin Chen
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Shan Jin
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Wentao Song
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Yujian Li
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
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26
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Erdmann E, Bacchus-Montabonel MC, Łabuda M. Modelling charge transfer processes in C 2+-tetrahydrofuran collision for ion-induced radiation damage in DNA building blocks. Phys Chem Chem Phys 2017; 19:19722-19732. [PMID: 28540940 DOI: 10.1039/c7cp02100c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Investigations of collision-induced processes involving carbon ions and molecules of biological interest, in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest in accurate calculations to understand fundamental processes occurring in ion-molecule collision systems has been growing recently. In this context, the charge transfer process in the collision of C2+(1s22s2) ions with the heterocyclic sugar moiety building block tetrahydrofuran (THF) was studied in order to interpret the mechanisms occurring at the molecular level. The molecular structure properties of THF were obtained by means of ab initio quantum chemistry methods. The role of the conformational structure and the orientation of the THF molecule in collision with C2+ ions are particularly discussed. Anisotropic effects of the process dynamics in the collision energy ranging from eV to keV by means of semiclassical treatment are also presented and compared to previous experimental and theoretical investigations. A detailed analysis of the obtained cross sections points out an increase in these values by three orders of magnitude by a change of the THF symmetry from C2v to Cs in collision with C2+, which determines a more efficient charge transfer in this case.
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Affiliation(s)
- Ewa Erdmann
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
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27
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Dampc M, Mielewska B, Siggel-King MR, King GC, Zubek M. A study of the photoelectron spectra of α-tetrahydrofurfuryl alcohol over the outer valence energy region (9–25 eV). Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Park SM, Lee YR, Kang DW, Kim HL, Kwon CH. Conformational structures of the tetrahydrofuran cation determined using one-photon mass-analyzed threshold ionization spectroscopy. Phys Chem Chem Phys 2017; 19:30362-30369. [DOI: 10.1039/c7cp05646j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One-photon vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy was used to characterize the essential conformations of tetrahydrofuran (THF) and thus determine the stereochemistry of the furanose ring constituting the backbones of DNA and RNA.
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Affiliation(s)
- Sung Man Park
- Department of Chemistry
- College of Natural Sciences and Institute for Molecular Science and Fusion Technology
- Kangwon National University
- Chuncheon 24341
- Korea
| | - Yu Ran Lee
- Department of Chemistry
- College of Natural Sciences and Institute for Molecular Science and Fusion Technology
- Kangwon National University
- Chuncheon 24341
- Korea
| | - Do Won Kang
- Department of Chemistry
- College of Natural Sciences and Institute for Molecular Science and Fusion Technology
- Kangwon National University
- Chuncheon 24341
- Korea
| | - Hong Lae Kim
- Department of Chemistry
- College of Natural Sciences and Institute for Molecular Science and Fusion Technology
- Kangwon National University
- Chuncheon 24341
- Korea
| | - Chan Ho Kwon
- Department of Chemistry
- College of Natural Sciences and Institute for Molecular Science and Fusion Technology
- Kangwon National University
- Chuncheon 24341
- Korea
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29
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Vorobyov I, Anisimov VM, Greene S, Venable RM, Moser A, Pastor RW, MacKerell AD. Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers. J Chem Theory Comput 2015; 3:1120-33. [PMID: 26627431 DOI: 10.1021/ct600350s] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers. Initiation of the optimization process involved validation of the aliphatic parameters based on linear alkanes and cyclic alkanes. Results showed the transfer to cyclohexane to yield satisfactory agreement with target data; however, in the case of cyclopentane direct transfer of the Lennard-Jones parameters was not sufficient due to ring strain, requiring additional optimization of these parameters for this molecule. Parameters for the ethers were then developed starting with the available aliphatic parameters, with the nonbond parameters for the oxygens optimized to reproduce both gas- and condensed-phase properties. Nonbond parameters for the polarizable model include the use of an anisotropic electrostatic model on the oxygens. Parameter optimization emphasized the development of transferable parameters between the ethers of a given class. The ether models are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties, and the resulting parameters are transferable to test molecules. The presented force field will allow for simulation studies of ethers in condensed phase and provides a basis for ongoing developments in both additive and polarizable force fields for biological molecules.
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Affiliation(s)
- Igor Vorobyov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Victor M Anisimov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shannon Greene
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard M Venable
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Adam Moser
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard W Pastor
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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30
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Goracci G, Arbe A, Alegría A, Lohstroh W, Su Y, Colmenero J. Dynamics of tetrahydrofuran as minority component in a mixture with poly(2-(dimethylamino)ethyl methacrylate): A neutron scattering and dielectric spectroscopy investigation. J Chem Phys 2015; 143:094505. [PMID: 26342375 DOI: 10.1063/1.4929906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have investigated a mixture of poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) and tetrahydrofuran (THF) (70 wt. % PDMAEMA/30 wt. % THF) by combining dielectric spectroscopy and quasielastic neutron scattering (QENS) on a labelled sample, focusing on the dynamics of the THF molecules. Two independent processes have been identified. The "fast" one has been qualified as due to an internal motion of the THF ring leading to hydrogen displacements of about 3 Å with rather broadly distributed activation energies. The "slow" process is characterized by an Arrhenius-like temperature dependence of the characteristic time which persists over more than 9 orders of magnitude in time. The QENS results evidence the confined nature of this process, determining a size of about 8 Å for the volume within which THF hydrogens' motions are restricted. In a complementary way, we have also investigated the structural features of the sample. This study suggests that THF molecules are well dispersed among side-groups nano-domains in the polymer matrix, ruling out a significant presence of clusters of solvent. Such a good dispersion, together with a rich mobility of the local environment, would prevent cooperativity effects to develop for the structural relaxation of solvent molecules, frustrating thereby the emergence of Vogel-Fulcher-like behavior, at least in the whole temperature interval investigated.
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Affiliation(s)
- G Goracci
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU)-Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - A Arbe
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU)-Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - A Alegría
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU)-Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - W Lohstroh
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstraße 1, D-85748 Garching, Germany
| | - Y Su
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching, Germany
| | - J Colmenero
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU)-Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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Vanommeslaeghe K, Yang M, MacKerell AD. Robustness in the fitting of molecular mechanics parameters. J Comput Chem 2015; 36:1083-101. [PMID: 25826578 PMCID: PMC4412823 DOI: 10.1002/jcc.23897] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/28/2015] [Accepted: 02/21/2015] [Indexed: 12/21/2022]
Abstract
Automated methods for force field parametrization have attracted renewed interest of the community, but the robustness issues associated with the often ill-conditioned nature of parameter optimization have been vastly underappreciated in the recent literature. For this reason, this article offers a detailed description of the origin and nature of these issues. This includes a discussion of the restrained electrostatic potential fit (RESP) charge model, which does contain explicit robustness-enhancing measures albeit not in the context of bonded parameters, and which forms an inspiration for the present work. It is also discussed how all the bonded parameters in a Class I force field can be simultaneously fit using the linear least squares (LLS) procedure, and a novel restraining strategy is presented that overcomes robustness issues in the LLS fitting of bonded parameters while minimally impacting the fitted values of well-behaved parameters. Two variants of this methodology are then validated through a number of case studies, including the fitting of bond-charge increments, which illustrates the method's potential for robustly solving general LLS problems beyond force field parametrization.
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Affiliation(s)
- Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - Mingjun Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
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32
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Xie M, Matsuda Y, Fujii A. Infrared Spectroscopic Investigation of Photoionization-Induced Acidic C–H Bonds in Cyclic Ethers. J Phys Chem A 2015; 119:5668-75. [DOI: 10.1021/acs.jpca.5b03406] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Min Xie
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba,
Aoba-ku, Sendai, 980-8578 Miyagi, Japan
| | - Yoshiyuki Matsuda
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba,
Aoba-ku, Sendai, 980-8578 Miyagi, Japan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba,
Aoba-ku, Sendai, 980-8578 Miyagi, Japan
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33
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Sandbeck DJS, Kuntz CM, Luu C, Mondor RA, Ottaviano JG, Rayer AV, Sumon KZ, East ALL. Challenges in Predicting ΔrxnG in Solution: The Mechanism of Ether-Catalyzed Hydroboration of Alkenes. J Phys Chem A 2014; 118:11768-79. [DOI: 10.1021/jp507793v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel J. S. Sandbeck
- Department of Chemistry and
Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S
0A2, Canada
| | - Colin M. Kuntz
- Department of Chemistry and
Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S
0A2, Canada
| | - Christine Luu
- Department of Chemistry and
Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S
0A2, Canada
| | - Rachelle A. Mondor
- Department of Chemistry and
Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S
0A2, Canada
| | - John G. Ottaviano
- Department of Chemistry and
Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S
0A2, Canada
| | - Aravind V. Rayer
- Department of Industrial Systems Engineering, University of Regina, 3737 Wascana Parkway, Regina, SK S4S
0A2, Canada
| | - Kazi Z. Sumon
- Department of Industrial Systems Engineering, University of Regina, 3737 Wascana Parkway, Regina, SK S4S
0A2, Canada
| | - Allan L. L. East
- Department of Chemistry and
Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S
0A2, Canada
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34
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Ford TA. The evolution of the structural, vibrational and electronic properties of the cyclic ethers – on ring size. An ab initio study. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.03.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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35
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Begum S, Subramanian R. Reaction of chlorine radical with tetrahydrofuran: a theoretical investigation on mechanism and reactivity in gas phase. J Mol Model 2014; 20:2262. [PMID: 24867438 DOI: 10.1007/s00894-014-2262-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/23/2014] [Indexed: 10/25/2022]
Abstract
Reaction of chlorine (Cl) radical with heterocyclic saturated ether, tetrahydrofuran has been studied. The detailed reactivity and mechanism of this reaction is analyzed using hybrid density functional theory (DFT), B3LYP and BB1K methods, and aug-cc-pVTZ basis set. To explore the mechanism of the reaction of tetrahydrofuran with Cl radical, four possible sites of hydrogen atom (H) abstraction pathways in tetrahydrofuran were analyzed. The barrier height and rate constants are calculated for the four H-abstraction channels. The BB1K calculated rate constant for α-axial H-abstraction is comparable with the experimentally determined rate constant. It reflects that α-axial H-abstraction is the main degradation pathway of tetrahydrofuran with Cl radical. DFT-based reactivity descriptors are also calculated and these values describe α-axial H-abstraction as the main reaction channel.
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Affiliation(s)
- Samiyara Begum
- Department of Chemistry, Indian Institute of Technology, Patna, India, 800013
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36
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Shojaei SHR, Morini F, Deleuze MS. Photoelectron and electron momentum spectroscopy of tetrahydrofuran from a molecular dynamical perspective. J Phys Chem A 2013; 117:1918-29. [PMID: 23387306 DOI: 10.1021/jp310722a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The results of experimental studies of the valence electronic structure of tetrahydrofuran employing He I photoelectron spectroscopy as well as Electron Momentum Spectroscopy (EMS) have been reinterpreted on the basis of Molecular Dynamical simulations employing the classical MM3 force field and large-scale quantum mechanical simulations employing Born-Oppenheimer Molecular Dynamics in conjunction with the dispersion corrected ωB97XD exchange-correlation functional. Analysis of the produced atomic trajectories demonstrates the importance of thermal deviations from the lowest energy path for pseudorotation, in the form of considerable variations of the ring-puckering amplitude. These deviations are found to have a significant influence on several outer-valence electron momentum distributions, as well as on the He I photoelectron spectrum.
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Affiliation(s)
- S H Reza Shojaei
- Research Group of Theoretical Chemistry and Molecular Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
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37
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Chertkov AV, Shestakova AK, Chertkov VA. Synthesis and NMR spectra of tetrahydrofuran-2-13C. Chem Heterocycl Compd (N Y) 2012. [DOI: 10.1007/s10593-012-1008-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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38
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Szlachcic P, Kolek P, Uchacz T, Stadnicka K. Molecular and crystal structure of selected compounds containing 8,11-dioxa[4.3.3]propellane moiety. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2011.11.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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PAKIARI AH, FAKHRAEE S. ELECTRON DENSITY ANALYSIS OF WEAK VAN DER WAALS COMPLEXES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633606002490] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nature of weak van der Waals interactions in different complexes of some atmospheric molecules such as CO 2, N 2 O , and N 2 was examined. Ab initio calculation was carried out at MP2 level of theory using Dunning's aug-cc-pVTZ basis set. Bader's theory of atoms in molecules (AIM) was employed to analyze electron density and to characterize the nature and properties of van der Waals interactions. A set of criteria, having been proposed in the context of AIM theory, was examined for these complexes. In spite of the parameter kinetics energy, per electron density is expected to be greater than unity for closed-shell interactions; we obtained values less than unity for many of these polyatomic systems. A set of limitations has also been outlined for the values of two AIM quantities: total energy density, H(r), and Laplacian of electron density, ∇2ρ, which correspond to different bond natures.
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Affiliation(s)
- A. H. PAKIARI
- Chemistry Department, College of Sciences, Shiraz University, Shiraz, 71454, Iran
| | - S. FAKHRAEE
- Chemistry Department, College of Sciences, Shiraz University, Shiraz, 71454, Iran
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40
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Kim IP, Perepelitsyna EO, Shestakov AF, Shul’ga YM, Kunitsa AA. Radiation telomerization of tetrafluoroethylene in tetrahydrofuran. HIGH ENERGY CHEMISTRY 2011. [DOI: 10.1134/s0018143911060117] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Biswal HS, Wategaonkar S. OH···X (X = O, S) hydrogen bonding in thetrahydrofuran and tetrahydrothiophene. J Chem Phys 2011; 135:134306. [DOI: 10.1063/1.3645107] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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42
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Zubek M, Dampc M, Linert I, Neumann T. Electronic states of tetrahydrofuran molecules studied by electron collisions. J Chem Phys 2011; 135:134317. [DOI: 10.1063/1.3646511] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Nazarski RB, Pasternak B, Leśniak S. Three-component conformational equilibria of some flexible pyrrolidin-2-(thi)ones in solution by NMR data (δC, δH, and nJHH) and their DFT predictions: a confrontation of different approaches. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.06.095] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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44
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Blochowicz T, Lusceac SA, Gutfreund P, Schramm S, Stühn B. Two Glass Transitions and Secondary Relaxations of Methyltetrahydrofuran in a Binary Mixture. J Phys Chem B 2011; 115:1623-37. [DOI: 10.1021/jp110506z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- T. Blochowicz
- Institut für Festkörperphysik, TU-Darmstadt, 64289 Darmstadt, Germany
| | - S. A. Lusceac
- Institut für Festkörperphysik, TU-Darmstadt, 64289 Darmstadt, Germany
| | - P. Gutfreund
- Institut Laue-Langevin, 38042 Grenoble Cedex, France
| | - S. Schramm
- Institut für Festkörperphysik, TU-Darmstadt, 64289 Darmstadt, Germany
| | - B. Stühn
- Institut für Festkörperphysik, TU-Darmstadt, 64289 Darmstadt, Germany
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45
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Duflot D, Flament JP, Heinesch J, Hubin-Franskin MJ. The K-shell spectra of tetrahydrofuran studied by electron energy loss spectroscopy and abinitio calculations. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.06.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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46
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Platinum(II) complexes with thiourea derivatives containing oxygen, sulfur or selenium in a heterocyclic ring: computational studies and cytotoxic properties. TRANSIT METAL CHEM 2010. [DOI: 10.1007/s11243-010-9375-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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47
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Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, MacKerell AD. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 2010; 31:671-90. [PMID: 19575467 PMCID: PMC2888302 DOI: 10.1002/jcc.21367] [Citation(s) in RCA: 2966] [Impact Index Per Article: 211.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.
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Affiliation(s)
- K. Vanommeslaeghe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - E. Hatcher
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - C. Acharya
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - S. Kundu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - S. Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - J. Shim
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - E. Darian
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - O. Guvench
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - P. Lopes
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - I. Vorobyov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - A. D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
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48
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Lee SH. Dynamics of multi-channel dissociation of tetrahydrofuran photoexcited at 193 nm: distributions of kinetic energy, angular anisotropies and branching ratios. Phys Chem Chem Phys 2010; 12:2655-63. [DOI: 10.1039/b921219a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Aroulanda C, Lafon O, Lesot P. Enantiodiscrimination of Flexible Cyclic Solutes Using NMR Spectroscopy in Polypeptide Chiral Mesophases: Investigation of cis-Decalin and THF. J Phys Chem B 2009; 113:10628-40. [DOI: 10.1021/jp902233m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Christie Aroulanda
- Méthodologie RMN, UMR CNRS-UHP 7036, Institut Jean Barriol, Faculté des Sciences, Nancy-Université, BP 70239, 54506 Vandoeuvre-lès-Nancy cedex, France, Unité de catalyse et de chimie du solide (UCCS), UMR CNRS 8181, Ecole Nationale Supérieure de Chimie de Lille, Université de Lille 1, Bât. C7, BP 90108, 59652 Villeneuve d’Ascq cedex, France, and Laboratoire de Chimie Structurale Organique, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris Sud 11, Bât. 410, 91405 Orsay cedex, France
| | - Olivier Lafon
- Méthodologie RMN, UMR CNRS-UHP 7036, Institut Jean Barriol, Faculté des Sciences, Nancy-Université, BP 70239, 54506 Vandoeuvre-lès-Nancy cedex, France, Unité de catalyse et de chimie du solide (UCCS), UMR CNRS 8181, Ecole Nationale Supérieure de Chimie de Lille, Université de Lille 1, Bât. C7, BP 90108, 59652 Villeneuve d’Ascq cedex, France, and Laboratoire de Chimie Structurale Organique, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris Sud 11, Bât. 410, 91405 Orsay cedex, France
| | - Philippe Lesot
- Méthodologie RMN, UMR CNRS-UHP 7036, Institut Jean Barriol, Faculté des Sciences, Nancy-Université, BP 70239, 54506 Vandoeuvre-lès-Nancy cedex, France, Unité de catalyse et de chimie du solide (UCCS), UMR CNRS 8181, Ecole Nationale Supérieure de Chimie de Lille, Université de Lille 1, Bât. C7, BP 90108, 59652 Villeneuve d’Ascq cedex, France, and Laboratoire de Chimie Structurale Organique, RMN en Milieu Orienté, ICMMO, UMR CNRS 8182, Université Paris Sud 11, Bât. 410, 91405 Orsay cedex, France
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50
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Dampc M, Mielewska B, Siggel-King MR, King GC, Zubek M. Threshold photoelectron spectra of tetrahydrofuran over the energy range 9–29eV. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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