1
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Saparbaev E, Aladinskaia V, Yamaletdinov R, Pereverzev AY, Boyarkin OV. Revealing Single-Bond Anomeric Selectivity in Carbohydrate-Protein Interactions. J Phys Chem Lett 2020; 11:3327-3331. [PMID: 32279507 DOI: 10.1021/acs.jpclett.0c00871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The noncovalent binding of proteins to glycans is amazingly selective to the isoforms of carbohydrates, including α/β anomers that coexist in solution. We isolate in the gas phase and study at the atomic level the simplest model system: noncovalent complexes of monosaccharide α/β-GalNAc and protonated aromatic molecule tyramine. IR/UV cold ion spectroscopy and quantum chemistry calculations jointly solve the structures of the two complexes. Although the onsets of the measured UV absorptions of the complexes differ significantly, the networks of H bonds in both complexes appear identical and do not include the anomeric hydroxyl. The detailed analysis reveals that, through inductive polarization, the α- to β-reorientation of this group nevertheless reduces the length of one remote short intermolecular H-bond by 0.03 Å. Although small, this change substantially strengthens the bond, thus contributing to the anomeric selectivity of the binding.
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Affiliation(s)
- Erik Saparbaev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Viktoriia Aladinskaia
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Ruslan Yamaletdinov
- Nikolaev Institute of Inorganic Chemistry, Novosibirsk, 630090, Russian Federation
| | - Aleksandr Y Pereverzev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Station-6, 1015 Lausanne, Switzerland
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2
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Roy TK, Mani D, Schwaab G, Havenith M. A close competition between O–H⋯O and O–H⋯π hydrogen bonding: IR spectroscopy of anisole–methanol complex in helium nanodroplets. Phys Chem Chem Phys 2020; 22:22408-22416. [DOI: 10.1039/d0cp02589e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anisole forms O–H⋯O as well O–H⋯π bound complexes with methanol.
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Affiliation(s)
- Tarun Kumar Roy
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Devendra Mani
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II
- Ruhr-Universität Bochum
- Bochum
- Germany
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3
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Arathala P, Musah RA. Theoretical Studies of the Gas-Phase Reactions of S-Methyl Methanesulfinothioate (Dimethyl Thiosulfinate) with OH and Cl Radicals: Reaction Mechanisms, Energetics, and Kinetics. J Phys Chem A 2019; 123:8448-8459. [DOI: 10.1021/acs.jpca.9b02435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Parandaman Arathala
- Department of Chemistry, University at Albany—State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Rabi A. Musah
- Department of Chemistry, University at Albany—State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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4
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Makuvaza JT, Kokkin DL, Loman JL, Reid SA. C-H/π and C-H-O Interactions in Concert: A Study of the Anisole-Methane Complex using Resonant Ionization and Velocity Mapped Ion Imaging. J Phys Chem A 2019; 123:2874-2880. [PMID: 30860841 DOI: 10.1021/acs.jpca.9b01020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Noncovalent forces such as hydrogen bonding, halogen bonding, π-π stacking, and C-H/π and C-H/O interactions hold the key to such chemical processes as protein folding, molecular self-assembly, and drug-substrate interactions. Invaluable insight into the nature and strength of these forces continues to come from the study of isolated molecular clusters. In this work, we report on a study of the isolated anisole-methane complex, where both C-H/π and C-H/O interactions are possible, using a combination of theory and experiments that include mass-selected two-color resonant two-photon ionization spectroscopy, two-color appearance potential (2CAP) measurements, and velocity mapped ion imaging (VMI). Using 2CAP and VMI, we derive the binding energies of the complex in ground, excited, and cation radical states. The experimental values from the two methods are in excellent agreement, and they are compared with selected theoretical values calculated using density functional theory and ab initio methods. The optimized ground-state cluster geometry, which is consistent with the experimental observations, shows methane sitting above the ring, interacting with anisole via both C-H/π and C-H/O interactions, and this dual mode of interaction is reflected in a larger ground-state binding energy as compared with the prototypical benzene-methane system.
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Affiliation(s)
- James T Makuvaza
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Damian L Kokkin
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - John L Loman
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Scott A Reid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
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5
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Møller KH, Kjaersgaard A, Hansen AS, Du L, Kjaergaard HG. Hybridization of Nitrogen Determines Hydrogen-Bond Acceptor Strength: Gas-Phase Comparison of Redshifts and Equilibrium Constants. J Phys Chem A 2018; 122:3899-3908. [DOI: 10.1021/acs.jpca.8b00541] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristian H. Møller
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Alexander Kjaersgaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Anne S. Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Lin Du
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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6
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Parandaman A, Tangtartharakul CB, Kumar M, Francisco JS, Sinha A. A Computational Study Investigating the Energetics and Kinetics of the HNCO + (CH3)2NH Reaction Catalyzed by a Single Water Molecule. J Phys Chem A 2017; 121:8465-8473. [DOI: 10.1021/acs.jpca.7b08657] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arathala Parandaman
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093, United States
| | - Chanin B. Tangtartharakul
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093, United States
| | - Manoj Kumar
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Joseph S. Francisco
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Amitabha Sinha
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093, United States
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7
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Perez JE, Kumar M, Francisco JS, Sinha A. Oxygenate-Induced Tuning of Aldehyde-Amine Reactivity and Its Atmospheric Implications. J Phys Chem A 2017; 121:1022-1031. [DOI: 10.1021/acs.jpca.6b10845] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Josue E. Perez
- Department
of Chemistry and Biochemistry, University of California—San Diego, La Jolla, California 92093, United States
| | - Manoj Kumar
- Department
of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Joseph S. Francisco
- Department
of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Amitabha Sinha
- Department
of Chemistry and Biochemistry, University of California—San Diego, La Jolla, California 92093, United States
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8
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Malongwe JK, Nachtigallová D, Corrochano P, Klán P. Spectroscopic Properties of Anisole at the Air-Ice Interface: A Combined Experimental-Computational Approach. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5755-5764. [PMID: 27243785 DOI: 10.1021/acs.langmuir.6b01187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A combined experimental and computational approach was used to investigate the spectroscopic properties of anisole in aqueous solutions and at the ice-air interface in the temperature range of 77-298 K. The absorption, diffuse reflectance, and emission spectra of ice samples containing anisole prepared by different techniques, such as slow freezing (frozen aqueous solutions), shock freezing (ice grains), or anisole vapor deposition on ice grains, were measured to evaluate changes in the contaminated ice matrix that occur at different temperatures. It was found that the position of the lowest absorption band of anisole and its tail shift bathochromically by ∼4 nm in frozen samples compared to liquid aqueous solutions. On the other hand, the emission spectra of aqueous anisole solutions were found to fundamentally change upon freezing. While one emission band (∼290 nm) was observed under all circumstances, the second band at ∼350 nm, assigned to an anisole excimer, appeared only at certain temperatures (150-250 K). Its disappearance at lower temperatures is attributed to the formation of crystalline anisole on the ice surface. DFT and ADC(2) calculations were used to interpret the absorption and emission spectra of anisole monomer and dimer associates. Various stable arrangements of the anisole associates were found at the disordered water-air interface in the ground and excited states, but only those with a substantial overlap of the aromatic rings are manifested by the emission band at ∼350 nm.
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Affiliation(s)
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic
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9
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Frey JA, Holzer C, Klopper W, Leutwyler S. Experimental and Theoretical Determination of Dissociation Energies of Dispersion-Dominated Aromatic Molecular Complexes. Chem Rev 2016; 116:5614-41. [DOI: 10.1021/acs.chemrev.5b00652] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jann A. Frey
- Departement
für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Christof Holzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Wim Klopper
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Samuel Leutwyler
- Departement
für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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10
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Ghoshal S, Hazra MK. Impact of OH Radical-Initiated H2CO3 Degradation in the Earth’s Atmosphere via Proton-Coupled Electron Transfer Mechanism. J Phys Chem A 2016; 120:562-75. [DOI: 10.1021/acs.jpca.5b08805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sourav Ghoshal
- Chemical
Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700 064, India
| | - Montu K. Hazra
- Chemical
Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700 064, India
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11
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Bandyopadhyay B, Biswas P, Kumar P. Ammonia as an efficient catalyst for decomposition of carbonic acid: a quantum chemical investigation. Phys Chem Chem Phys 2016; 18:15995-6004. [DOI: 10.1039/c6cp02407f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic structure calculations using M06-2X, MP2 and CCSD(T) methods have been employed to show ammonia as an efficient catalyst for decomposition of carbonic acid.
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Affiliation(s)
- Biman Bandyopadhyay
- Department of Chemistry
- Malaviya National Institute of Technology Jaipur
- Jaipur – 302017
- India
| | - Partha Biswas
- Department of Chemistry
- Scottish Church College
- Kolkata-700006
- India
| | - Pradeep Kumar
- Department of Chemistry
- Malaviya National Institute of Technology Jaipur
- Jaipur – 302017
- India
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12
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Louie MK, Francisco JS, Verdicchio M, Klippenstein SJ, Sinha A. Dimethylamine Addition to Formaldehyde Catalyzed by a Single Water Molecule: A Facile Route for Atmospheric Carbinolamine Formation and Potential Promoter of Aerosol Growth. J Phys Chem A 2015; 120:1358-68. [DOI: 10.1021/acs.jpca.5b04887] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matthew K. Louie
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093-0314, United States
| | - Joseph S. Francisco
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Marco Verdicchio
- Argonne National
Laboratory, Chemical Sciences and Engineering Division, Argonne, Illinois 60439-4837, United States
| | - Stephen J. Klippenstein
- Argonne National
Laboratory, Chemical Sciences and Engineering Division, Argonne, Illinois 60439-4837, United States
| | - Amitabha Sinha
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093-0314, United States
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13
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Louie MK, Francisco JS, Verdicchio M, Klippenstein SJ, Sinha A. Hydrolysis of Ketene Catalyzed by Formic Acid: Modification of Reaction Mechanism, Energetics, and Kinetics with Organic Acid Catalysis. J Phys Chem A 2015; 119:4347-57. [DOI: 10.1021/jp5076725] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew K. Louie
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093-0314, United States
| | - Joseph S. Francisco
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Marco Verdicchio
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439-4837, United States
| | - Stephen J. Klippenstein
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439-4837, United States
| | - Amitabha Sinha
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093-0314, United States
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14
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Heger M, Altnöder J, Poblotzki A, Suhm MA. To π or not to π – how does methanol dock onto anisole? Phys Chem Chem Phys 2015; 17:13045-52. [DOI: 10.1039/c5cp01545f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Supersonic jet spectroscopy reveals that methanol opts against aromatic docking onto anisole despite a very close competition.
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Affiliation(s)
- Matthias Heger
- Institut für Physikalische Chemie
- Georg-August-Universität Göttingen
- D-37077 Göttingen
- Germany
| | - Jonas Altnöder
- Institut für Physikalische Chemie
- Georg-August-Universität Göttingen
- D-37077 Göttingen
- Germany
| | - Anja Poblotzki
- Institut für Physikalische Chemie
- Georg-August-Universität Göttingen
- D-37077 Göttingen
- Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Georg-August-Universität Göttingen
- D-37077 Göttingen
- Germany
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15
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Ghoshal S, Hazra MK. H2CO3→ CO2+ H2O decomposition in the presence of H2O, HCOOH, CH3COOH, H2SO4and HO2radical: instability of the gas-phase H2CO3molecule in the troposphere and lower stratosphere. RSC Adv 2015. [DOI: 10.1039/c4ra13233e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Carbonic acid decomposition of potential atmospheric significance.
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Affiliation(s)
- Sourav Ghoshal
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata-700 064
- India
| | - Montu K. Hazra
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata-700 064
- India
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16
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Puzzarini C, Biczysko M. Microsolvation of 2-thiouracil: molecular structure and spectroscopic parameters of the thiouracil-water complex. J Phys Chem A 2014; 119:5386-95. [PMID: 25474644 DOI: 10.1021/jp510511d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
State-of-the-art quantum-chemical computations have been employed to accurately determine the equilibrium structure and interaction energy of the 2-thiouracil-water complex, thus extending available reference data for biomolecule solvation patterns. The coupled-cluster level of theory in conjunction with a triple-ζ basis set has been considered together with extrapolation to the basis set limit, performed by employing second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections. On the basis of the comparison of experiment and theory for 2-thiouracil [ Puzzarini et al. Phys. Chem. Chem. Phys. 2013 , 15 , 16965 - 16975 ], structural changes due to water complexation have been pointed out. Molecular and spectroscopic properties of the 2-thiouracil-water complex have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the accurate determination of the molecular dipole moment and of the spectroscopic parameters required for predicting the rotational spectrum.
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Affiliation(s)
- Cristina Puzzarini
- †Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Malgorzata Biczysko
- ‡Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,§Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
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17
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Ghoshal S, Hazra MK. Autocatalytic isomerizations of the two most stable conformers of carbonic acid in vapor phase: double hydrogen transfer in carbonic acid homodimers. J Phys Chem A 2014; 118:4620-30. [PMID: 24878165 DOI: 10.1021/jp5024873] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cis-cis [(cc)] and cis-trans [(ct)] conformers of carbonic acid (H2CO3) are known as the two most stable conformers based on the different orientations of two OH functional groups present in the molecule. To explain the interconversion of the (cc)-conformer to its (ct)-conformer, the rotation of one of the two indistinguishable OH functional groups present in the (cc)-conformer has been shown until now as the effective isomerization mechanism. Moreover, the (ct)-conformer, which is slightly energetically disfavored over the (cc)-conformer, has been considered as the starting point for the decomposition of H2CO3 into CO2 and H2O molecules. Experimentally, on the other hand, the infrared (IR) and Raman spectroscopy of the crystalline H2CO3 polymorphs suggest that the most possible basic building blocks of H2CO3 polymorphs consist of only and exclusively the (cc)-conformers. However, the sublimations of these crystalline H2CO3 polymorphs result both the (cc)- and (ct)-conformers in the vapor phase with the (cc)-conformer being the major species. In this article, we first report the high level ab initio calculations investigating the energetics of the autocatlytic isomerization mechanism between the two most stable conformers of carbonic acid in the vapor phase. The calculations have been performed at the MP2 level of theory in conjunction with aug-cc-pVDZ, aug-cc-pVTZ, and 6-311++G(3df,3pd) basis sets. The results of the present study specifically and strongly suggest that double hydrogen transfer within the eight-membered cyclic doubly hydrogen-bonded (H-bonded) ring interface of the H2CO3 homodimer formed between two (cc)-conformers is ultimately the starting mechanism for the isomerization of the (cc)-conformer to its (ct)-conformer, especially, during the sublimation of the H2CO3 polymorphs, which result in the vapor phase concentration of the (cc)-conformer at the highest levels.
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Affiliation(s)
- Sourav Ghoshal
- Chemical Sciences Division, Saha Institute of Nuclear Physics , 1/AF Bidhannagar, Kolkata-700 064, India
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18
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Fornaro T, Biczysko M, Monti S, Barone V. Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers. Phys Chem Chem Phys 2014; 16:10112-28. [PMID: 24531740 PMCID: PMC4612423 DOI: 10.1039/c3cp54724h] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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19
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Hazra MK, Francisco JS, Sinha A. Hydrolysis of Glyoxal in Water-Restricted Environments: Formation of Organic Aerosol Precursors through Formic Acid Catalysis. J Phys Chem A 2014; 118:4095-105. [DOI: 10.1021/jp502126m] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Montu K. Hazra
- Chemical
Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Joseph S. Francisco
- Department
of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Amitabha Sinha
- Department
of Chemistry and Biochemistry, University of California—San Diego, La Jolla, California 92093-0314, United States
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20
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Ghoshal S, Hazra MK. New Mechanism for Autocatalytic Decomposition of H2CO3 in the Vapor Phase. J Phys Chem A 2014; 118:2385-92. [DOI: 10.1021/jp412239e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sourav Ghoshal
- Chemical
Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Montu K. Hazra
- Chemical
Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
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21
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Ultraviolet and infrared spectroscopy of neutral and ionic non-covalent diastereomeric complexes in the gas phase. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2013. [DOI: 10.1007/s12210-013-0241-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Buchanan EG, Gord JR, Zwier TS. Solvent Effects on Vibronic Coupling in a Flexible Bichromophore: Electronic Localization and Energy Transfer induced by a Single Water Molecule. J Phys Chem Lett 2013; 4:1644-1648. [PMID: 26282972 DOI: 10.1021/jz400641p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Size and conformation-specific ultraviolet and infrared spectra are used to probe the effects of binding a single water molecule on the close-lying excited states present in a model flexible bichromophore, 1,2-diphenoxyethane (DPOE). The water molecule binds to DPOE asymmetrically, thereby localizing the two electronically excited states on one or the other ring, producing a S1/S2 splitting of 190 cm(-1). Electronic localization is reflected clearly in the OH stretch transitions in the excited states. Since the S2 origin is imbedded in vibronic levels of the S1 manifold, its OH stretch spectrum reflects the vibronic coupling between these levels, producing four OH stretch transitions that are a sum of contributions from S2-localized and S1-localized excited states. The single solvent water molecule thus plays multiple roles, localizing the electronic excitation in the bichromophore, inducing electronic energy transfer between the two rings, and reporting on the state mixing via its OH stretch absorptions.
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Affiliation(s)
- Evan G Buchanan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Joseph R Gord
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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23
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Hazra MK, Francisco JS, Sinha A. Gas Phase Hydrolysis of Formaldehyde To Form Methanediol: Impact of Formic Acid Catalysis. J Phys Chem A 2013; 117:11704-10. [DOI: 10.1021/jp4008043] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Montu K. Hazra
- Chemical Sciences
Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar,
Kolkata-700064, India
| | - Joseph S. Francisco
- Department
of Chemistry, Purdue University, West Lafayette,
Indiana 47907-2084,
United States
| | - Amitabha Sinha
- Department
of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
92093-0314, United States
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24
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Ciavardini A, Rondino F, Paladini A, Speranza M, Fornarini S, Satta M, Piccirillo S. The effect of fluorine substitution on chiral recognition: interplay of CH⋯π, OH⋯π and CH⋯F interactions in gas-phase complexes of 1-aryl-1-ethanol with butan-2-ol. Phys Chem Chem Phys 2013; 15:19360-70. [DOI: 10.1039/c3cp53215a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Bloom JWG, Raju RK, Wheeler SE. Physical Nature of Substituent Effects in XH/π Interactions. J Chem Theory Comput 2012; 8:3167-74. [DOI: 10.1021/ct300520n] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacob W. G. Bloom
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Rajesh K. Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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26
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Hazra MK, Francisco JS, Sinha A. Computational study of hydrogen-bonded complexes of HOCO with acids: HOCO⋯HCOOH, HOCO⋯H2SO4, and HOCO⋯H2CO3. J Chem Phys 2012; 137:064319. [DOI: 10.1063/1.4742817] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Hazra MK, Sinha A. Formic Acid Catalyzed Hydrolysis of SO3 in the Gas Phase: A Barrierless Mechanism for Sulfuric Acid Production of Potential Atmospheric Importance. J Am Chem Soc 2011; 133:17444-53. [DOI: 10.1021/ja207393v] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Montu K. Hazra
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0314, United States
| | - Amitabha Sinha
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0314, United States
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28
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Matisz G, Kelterer AM, Fabian WMF, Kunsági-Máté S. Coordination of Methanol Clusters to Benzene: A Computational Study. J Phys Chem A 2011; 115:10556-64. [DOI: 10.1021/jp206248w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gergely Matisz
- Department of General and Physical Chemistry, University of Pécs, Pécs, H-7624, Hungary
- Institute of Chemistry, Karl-Franzens University Graz, Heinrichstr. 28, Graz, A-8010, Austria
| | - Anne-Marie Kelterer
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/I, A-8010 Graz, Austria
| | - Walter M. F. Fabian
- Institute of Chemistry, Karl-Franzens University Graz, Heinrichstr. 28, Graz, A-8010, Austria
| | - Sándor Kunsági-Máté
- Department of General and Physical Chemistry, University of Pécs, Pécs, H-7624, Hungary
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29
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Malyshev DA, Pfaff DA, Ippoliti SI, Hwang GT, Dwyer TJ, Romesberg FE. Solution structure, mechanism of replication, and optimization of an unnatural base pair. Chemistry 2011; 16:12650-9. [PMID: 20859962 DOI: 10.1002/chem.201000959] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
As part of an ongoing effort to expand the genetic alphabet for in vitro and eventual in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs and evaluated their replication in DNA. Collectively, the results have led us to propose that these base pairs, which lack stabilizing edge-on interactions, are replicated by means of a unique intercalative mechanism. Here, we report the synthesis and characterization of three novel derivatives of the nucleotide analogue dMMO2, which forms an unnatural base pair with the nucleotide analogue d5SICS. Replacing the para-methyl substituent of dMMO2 with an annulated furan ring (yielding dFMO) has a dramatically negative effect on replication, while replacing it with a methoxy (dDMO) or with a thiomethyl group (dTMO) improves replication in both steady-state assays and during PCR amplification. Thus, dTMO-d5SICS, and especially dDMO-d5SICS, represent significant progress toward the expansion of the genetic alphabet. To elucidate the structure-activity relationships governing unnatural base pair replication, we determined the solution structure of duplex DNA containing the parental dMMO2-d5SICS pair, and also used this structure to generate models of the derivative base pairs. The results strongly support the intercalative mechanism of replication, reveal a surprisingly high level of specificity that may be achieved by optimizing packing interactions, and should prove invaluable for the further optimization of the unnatural base pair.
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Affiliation(s)
- Denis A Malyshev
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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30
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Rondino F, Paladini A, Ciavardini A, Casavola A, Catone D, Satta M, Barth HD, Giardini A, Speranza M, Piccirillo S. Chiral recognition between 1-(4-fluorophenyl)ethanol and 2-butanol: higher binding energy of homochiral complexes in the gas phase. Phys Chem Chem Phys 2011; 13:818-24. [DOI: 10.1039/c0cp01401j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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31
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Toledo EJ, Custodio R, Ramalho TC, Porto MEG, Magriotis ZM. Electrical field effects on dipole moment, structure and energetic of (H2O)n (2⩽n⩽15) cluster. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.08.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Solomonov BN, Sedov IA, Akhmadiyarov AA. Gibbs energy of cooperative hydrogen-bonding interactions in aqueous solutions of amines and pyridines. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Pasquini M, Schiccheri N, Becucci M, Pietraperzia G. High resolution electronic spectroscopy on deuterated anisole. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2008.10.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Inter-molecular vibrational frequencies of doubly hydrogen-bonded complexes involving 2-pyridone: Reliability of few selected theoretical level of calculations. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.03.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Lin T, Zhang W, Wang L. Complex Formation between Anisole and Boron Trifluoride: Structural and Binding Properties. J Phys Chem A 2008; 112:13600-8. [DOI: 10.1021/jp805748b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tao Lin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China, and Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901
| | - Weijiang Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China, and Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901
| | - Lichang Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China, and Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901
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36
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Pawlukojć A, Prager M, Dobrowolska WS, Bator G, Sobczyk L, Ivanov A, Rols S, Grech E, Nowicka-Scheibe J, Unruh T. The structure, methyl rotation reflected in inelastic and quasielastic neutron scattering and vibrational spectra of 1,2,3,5-tetramethoxybenzene and its 2:1 complex with 1,2,4,5-tetracyanobenzene. J Chem Phys 2008; 129:154506. [PMID: 19045208 DOI: 10.1063/1.2990650] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
X-ray diffraction studies show that molecules of the 1,2,3,5-tetramethoxybenzene (TMOB)(2) x 1,2,4,5-tetracyanobenzene complex form ...CCDCCDCC... columns with the short distances between molecular planes of C and D molecules equal to 3.186 A. The vibrational spectra recorded by using the inelastic neutron scattering, Raman, IR, and quasielastic neutron scattering (QENS) techniques aided by density functional theory calculations for the isolated molecules and the crystalline state enabled all four inequivalent librational modes, ascribed to the methoxy groups, to be analyzed. A rather good consistency was found between the experimental frequencies and those calculated for the crystal. The consistency was also achieved between the experimental structure of molecules and the theoretically reproduced one. A close similarity of the structures of the TMOB molecule isolated and in the complex is taken as a sign of dominating intramolecular interaction. The QENS spectra contain three Lorentzians of relative intensities of 1:1:2. Thus the two most strongly hindered of the four inequivalent methoxy groups in the crystalline lattice are characterized by rather similar barrier heights in good agreement with the packing analysis.
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37
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Toledo EJ, Ramalho TC, Magriotis ZM. Influence of magnetic field on physical–chemical properties of the liquid water: Insights from experimental and theoretical models. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.01.010] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Kim DY, Singh NJ, Lee JW, Kim KS. Solvent-Driven Structural Changes in Anion−π Complexes. J Chem Theory Comput 2008; 4:1162-9. [DOI: 10.1021/ct8001283] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dong Young Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - N. Jiten Singh
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Jung Woo Lee
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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39
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The role of dispersion correction to DFT for modelling weakly bound molecular complexes in the ground and excited electronic states. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.02.036] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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40
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Kumar A, Kołaski M, Kim KS. Ground state structures and excited state dynamics of pyrrole-water complexes: Ab initio excited state molecular dynamics simulations. J Chem Phys 2008; 128:034304. [DOI: 10.1063/1.2822276] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Brameld KA, Kuhn B, Reuter DC, Stahl M. Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis. J Chem Inf Model 2008; 48:1-24. [PMID: 18183967 DOI: 10.1021/ci7002494] [Citation(s) in RCA: 276] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Based on torsion angle distributions of frequently occurring substructures, conformation preferences of druglike molecules are presented, accompanied by a review of the relevant literature. First, the relevance of the Cambridge Structural Database (CSD) for drug design is demonstrated by comparing substructures present in compounds entering clinical trials with those found in the CSD and protein-bound ligands in the Protein Data Bank (PDB). Next, we briefly highlight preferred conformations of elementary acyclic systems, followed by a discussion of sulfonamide conformations. Due to their central role in medicinal chemistry, we discuss properties of aryl ring substituents in depth, including biaryl systems and systems of two aryl rings connected by two acyclic bonds. For a subset of torsion motifs, we also compare torsion angle histograms derived from CSD structures with those derived from ligands in the PDB. Furthermore, selected properties of some six- and seven-membered ring systems are discussed. The article closes with a section on attractive sulfur-oxygen contacts.
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Affiliation(s)
- Ken A Brameld
- Discovery Chemistry, Roche Palo Alto LLC, Palo Alto, California, USA
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42
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Pasquini M, Schiccheri N, Piani G, Pietraperzia G, Becucci M, Biczysko M, Pavone M, Barone V. Isotopomeric Conformational Changes in the Anisole−Water Complex: New Insights from HR-UV Spectroscopy and Theoretical Studies. J Phys Chem A 2007; 111:12363-71. [DOI: 10.1021/jp0757558] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Massimiliano Pasquini
- LENS and Dipartimento di Chimica, Università di Firenze, via N. Carrara 1, Polo Scientifico, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Comp. Univ. M. S. Angelo, via Cintia, 80126 Napoli, Italy
| | - Nicola Schiccheri
- LENS and Dipartimento di Chimica, Università di Firenze, via N. Carrara 1, Polo Scientifico, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Comp. Univ. M. S. Angelo, via Cintia, 80126 Napoli, Italy
| | - Giovanni Piani
- LENS and Dipartimento di Chimica, Università di Firenze, via N. Carrara 1, Polo Scientifico, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Comp. Univ. M. S. Angelo, via Cintia, 80126 Napoli, Italy
| | - Giangaetano Pietraperzia
- LENS and Dipartimento di Chimica, Università di Firenze, via N. Carrara 1, Polo Scientifico, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Comp. Univ. M. S. Angelo, via Cintia, 80126 Napoli, Italy
| | - Maurizio Becucci
- LENS and Dipartimento di Chimica, Università di Firenze, via N. Carrara 1, Polo Scientifico, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Comp. Univ. M. S. Angelo, via Cintia, 80126 Napoli, Italy
| | - Malgorzata Biczysko
- LENS and Dipartimento di Chimica, Università di Firenze, via N. Carrara 1, Polo Scientifico, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Comp. Univ. M. S. Angelo, via Cintia, 80126 Napoli, Italy
| | - Michele Pavone
- LENS and Dipartimento di Chimica, Università di Firenze, via N. Carrara 1, Polo Scientifico, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Comp. Univ. M. S. Angelo, via Cintia, 80126 Napoli, Italy
| | - Vincenzo Barone
- LENS and Dipartimento di Chimica, Università di Firenze, via N. Carrara 1, Polo Scientifico, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Comp. Univ. M. S. Angelo, via Cintia, 80126 Napoli, Italy
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43
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Biczysko M, Piani G, Pasquini M, Schiccheri N, Pietraperzia G, Becucci M, Pavone M, Barone V. On the properties of microsolvated molecules in the ground (S0) and excited (S1) states: The anisole-ammonia 1:1 complex. J Chem Phys 2007; 127:144303. [DOI: 10.1063/1.2767265] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Matsuda S, Leconte AM, Romesberg FE. Minor groove hydrogen bonds and the replication of unnatural base pairs. J Am Chem Soc 2007; 129:5551-7. [PMID: 17411040 PMCID: PMC2527036 DOI: 10.1021/ja068282b] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
As part of an effort to expand the genetic alphabet, we examined the synthesis of DNA with six different unnatural nucleotides bearing methoxy-derivatized nucleobase analogues. Different nucleobase substitution patterns were used to systematically alter the nucleobase electronics, sterics, and hydrogen-bonding potential. We determined the ability of the Klenow fragment of E. coli DNA polymerase I to synthesize and extend the different unnatural base pairs and mispairs under steady-state conditions. Unlike other hydrogen-bond acceptors examined in the past, the methoxy groups do not facilitate mispairing, implying that they are not recognized by any of the hydrogen-bond donors of the natural nucleobases; however, they do facilitate replication. The more efficient replication results largely from an increase in the rate of extension of primers terminating at the unnatural base pair and, interestingly, requires that the methoxy group be at the ortho position where it is positioned in the developing minor groove and can form a functionally important hydrogen bond with the polymerase. Thus, ortho methoxy groups should be generally useful for the effort to expand the genetic alphabet.
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45
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Parthipan G, Thenappan T. Studies on molecular interactions and fluid structure of anisole with 2-ethyl-1-hexanol and decyl alcohol. J Mol Liq 2007. [DOI: 10.1016/j.molliq.2006.05.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Szydłowska I, Nosenko Y, Brutschy B, Tarakeshwar P, Herbich J. Supersonic jet studies of solvation effects on the spectroscopy and photophysics of 4-diethylaminopyridine. Phys Chem Chem Phys 2007; 9:4981-91. [PMID: 17851594 DOI: 10.1039/b705532c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We present the results of spectroscopic and photophysical investigations of 4-diethylaminopyridine (DEAP) and its 1 : 1 complexes with a number of protic solvents such as water and various alcohols of different acidity isolated under supersonic jet conditions. While a double resonance vibrational spectroscopic method was employed to investigate the size and geometrical structure of jet-cooled clusters, laser-induced fluorescence spectroscopy was used to examine the changes of photophysics induced by complexation of DEAP with solvent molecule(s). The results obtained from ab initio calculations enable the assignment of geometries and of the vibrational spectra of the clusters in the OH-stretch region. The comparison of the experimental and calculated vibrational spectra indicates that the solvent molecule is hydrogen-bonded to the pyridine nitrogen atom. Dual luminescence is observed only for the complexes with alcohols of relatively strong acidity.
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Affiliation(s)
- Izabela Szydłowska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
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47
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Kusaka R, Inokuchi Y, Ebata T. Laser spectroscopic study on the conformations and the hydrated structures of benzo-18-crown-6-ether and dibenzo-18-crown-6-ether in supersonic jets. Phys Chem Chem Phys 2007; 9:4452-9. [PMID: 17690770 DOI: 10.1039/b704750a] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The laser-induced fluorescence spectra of jet-cooled benzo-18-crown-6 (B18C6) and dibenzo-18-crown-6 (DB18C6) exhibit a number of vibronic bands in the 35 000-37 000 cm(-1) region. We attribute these bands to monomers and hydrated clusters by fluorescence-detected IR-UV and UV-UV double resonance spectroscopy. We found four and two conformers for bare B18C6 and DB18C6, and the hydration of one water molecule reduces the number of isomers to three and one for B18C6-(H(2)O)(1) and DB18C6-(H(2)O)(1), respectively. The IR-UV spectra of B18C6-(H(2)O)(1) and DB18C6-(H(2)O)(1) suggest that all isomers of the monohydrated clusters have a double proton-donor type (bidentate) hydration. That is, the water molecule is bonded to B18C6 or DB18C6 via two O-H[dot dot dot]O hydrogen bonds. The blue shift of the electronic origin of the monohydrated clusters and the quantum chemical calculation suggest that the water molecule in B18C6-(H(2)O)(1) and DB18C6-(H(2)O)(1) prefers to be bonded to the ether oxygen atoms near the benzene ring.
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Affiliation(s)
- Ryoji Kusaka
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
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48
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Becucci M, Pietraperzia G, Pasquini M, Piani G, Zoppi A, Chelli R, Castellucci E, Demtroeder W. A study on the anisole-water complex by molecular beam-electronic spectroscopy and molecular mechanics calculations. J Chem Phys 2006; 120:5601-7. [PMID: 15267436 DOI: 10.1063/1.1648635] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
An experimental and theoretical study is made on the anisole-water complex. It is the first van der Waals complex studied by high resolution electronic spectroscopy in which the water is seen acting as an acid. Vibronically and rotationally resolved electronic spectroscopy experiments and molecular mechanics calculations are used to elucidate the structure of the complex in the ground and first electronic excited state. Some internal dynamics in the system is revealed by high resolution spectroscopy.
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Affiliation(s)
- M Becucci
- LENS and Dipartimento di Chimica, Polo Scientifico di Sesto Fiorentino, Universita di Firenze, I-50019 Sesto Fiorentino (Firenze), Italy.
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49
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Vaupel S, Brutschy B, Tarakeshwar P, Kim KS. Characterization of Weak NH−π Intermolecular Interactions of Ammonia with Various Substituted π-Systems. J Am Chem Soc 2006; 128:5416-26. [PMID: 16620113 DOI: 10.1021/ja056454j] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among the several weak intermolecular interactions pervading chemistry and biology, the NH-pi interaction is one of the most widely known. Nevertheless its weak nature makes it one of the most poorly understood and characterized interactions. The present study details the results obtained on gas-phase complexes of ammonia with various substituted pi systems using both laser vibrational spectroscopy and ab initio calculations. The spectroscopic measurements carried out by applying one-color resonant two-photon ionization (R2PI) and IR-vibrational predissociation spectroscopy in the region of the NH stretches yield the first experimental NH stretching shifts of ammonia upon its interaction with various kinds of pi-systems. The experiments were complemented by ab initio calculations and energy decompositions, carried out at the second-order Møller-Plesset (MP2) level of theory. The observed complexes show characteristic vibrational spectra which are very similar to the calculated ones, thereby allowing an in-depth analysis of the interaction forces and energies. The interaction energy of the conformers responsible for the observed vibrational spectra has the maximum contribution from dispersion energies. This implies that polarizabilities of the pi-electron systems play a very important role in governing the nature and geometry of the NH-pi interaction. The larger polarizability of ammonia as compared to water and the tendency to maximize the dispersion energy implies that the characteristics of the NH-pi interactions are markedly different from that of the corresponding OH-pi interactions.
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Affiliation(s)
- Sascha Vaupel
- Institut für Physikalische und Theoretische Chemie, J. W. Goethe-Universität Frankfurt, Marie-Curie-Str. 11, D-60439 Frankfurt/Main, Germany
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Hobza P, Zahradník R, Müller-Dethlefs K. The World of Non-Covalent Interactions: 2006. ACTA ACUST UNITED AC 2006. [DOI: 10.1135/cccc20060443] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.
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