1
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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2
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Ferretti A, d’Ischia M, Prampolini G. Benchmarking Cation−π Interactions: Assessment of Density Functional Theory and Möller–Plesset Second-Order Perturbation Theory Calculations with Optimized Basis Sets (mp2mod) for Complexes of Benzene, Phenol, and Catechol with Na+, K+, Rb+, and Cs+. J Phys Chem A 2020; 124:3445-3459. [DOI: 10.1021/acs.jpca.0c02090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Marco d’Ischia
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, I-80126 Napoli, Italy
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3
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Huang XY, You M, Ran GL, Fan HR, Zhang WK. Ester-Derivatized indoles as fluorescent and infrared probes for hydration environments. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1805118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Xin-yue Huang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Min You
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Guang-liu Ran
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Hao-ran Fan
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wen-kai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
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4
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Tarai A, Baruah JB. Different self-assemblies and absorption–emission properties of the picrate salts of aromatic amine or heterocycle linked oximes. NEW J CHEM 2018. [DOI: 10.1039/c7nj04349j] [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
Different sub-assemblies and fluorescence quenching in picrate salts of an aromatic amine and of three different heterocycle tethered aldoximes are described.
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Affiliation(s)
- Arup Tarai
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati-781 039
- India
| | - Jubaraj B. Baruah
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati-781 039
- India
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5
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Kumar S, Singh SK, Vaishnav JK, Hill JG, Das A. Interplay among Electrostatic, Dispersion, and Steric Interactions: Spectroscopy and Quantum Chemical Calculations of π-Hydrogen Bonded Complexes. Chemphyschem 2017; 18:828-838. [PMID: 28124829 DOI: 10.1002/cphc.201601405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/24/2017] [Indexed: 11/07/2022]
Abstract
π-Hydrogen bonding interactions are ubiquitous in both materials and biology. Despite their relatively weak nature, great progress has been made in their investigation by experimental and theoretical methods, but this becomes significantly more complicated when secondary intermolecular interactions are present. In this study, the effect of successive methyl substitution on the supramolecular structure and interaction energy of indole⋅⋅⋅methylated benzene (ind⋅⋅⋅n-mb, n=1-6) complexes is probed through a combination of supersonic jet experiments and benchmark-quality quantum chemical calculations. It is demonstrated that additional secondary interactions introduce a subtle interplay among electrostatic and dispersion forces, as well as steric repulsion, which fine-tunes the overall structural motif. Resonant two-photon ionization and IR-UV double-resonance spectroscopy techniques are used to probe jet-cooled ind⋅⋅⋅n-mb (n=2, 3, 6) complexes, with redshifting of the N-H IR stretching frequency showing that increasing the degree of methyl substitution increases the strength of the primary N-H⋅⋅⋅π interaction. Ab initio harmonic frequency and binding energy calculations confirm this trend for all six complexes. Electronic spectra of the three dimers are broad and structureless, with quantum chemical calculations revealing that this is likely to be due to multiple tilted conformations of each dimer possessing similar stabilization energies.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.,Present address: Department of Dynamics at Surfaces, Max Planck Institute of Biophysical Chemistry, Am Faßberg 11, 37077, Gottingen, Germany
| | - Santosh K Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Jamuna K Vaishnav
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.,Present address: Indian Institute of Technology (IIT) Indore, Khandwa Rd, Simrol, Madhya, Pradesh, 452020, India
| | - J Grant Hill
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
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6
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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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7
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Pagba CV, McCaslin TG, Veglia G, Porcelli F, Yohannan J, Guo Z, McDaniel M, Barry BA. A tyrosine-tryptophan dyad and radical-based charge transfer in a ribonucleotide reductase-inspired maquette. Nat Commun 2015; 6:10010. [PMID: 26627888 PMCID: PMC4686667 DOI: 10.1038/ncomms10010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/23/2015] [Indexed: 01/29/2023] Open
Abstract
In class 1a ribonucleotide reductase (RNR), a substrate-based radical is generated in the α2 subunit by long-distance electron transfer involving an essential tyrosyl radical (Y122O·) in the β2 subunit. The conserved W48 β2 is ∼10 Å from Y122OH; mutations at W48 inactivate RNR. Here, we design a beta hairpin peptide, which contains such an interacting tyrosine–tryptophan dyad. The NMR structure of the peptide establishes that there is no direct hydrogen bond between the phenol and the indole rings. However, electronic coupling between the tyrosine and tryptophan occurs in the peptide. In addition, downshifted ultraviolet resonance Raman (UVRR) frequencies are observed for the radical state, reproducing spectral downshifts observed for β2. The frequency downshifts of the ring and CO bands are consistent with charge transfer from YO· to W or another residue. Such a charge transfer mechanism implies a role for the β2 Y-W dyad in electron transfer. Tyrosine-tryptophan dyads are known to mediate electron transfer reactions in a range of different proteins. Here, the authors study a beta hairpin peptide, probing the tyrosine-tryptophan interaction and showing no hydrogen bonding but rather charge transfer between the tyrosyl radical and tryptophan'.
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Affiliation(s)
- Cynthia V Pagba
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Tyler G McCaslin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Fernando Porcelli
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo 01100, Italy
| | - Jiby Yohannan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zhanjun Guo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Miranda McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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8
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Biswal HS, Bhattacharyya S, Bhattacherjee A, Wategaonkar S. Nature and strength of sulfur-centred hydrogen bonds: laser spectroscopic investigations in the gas phase and quantum-chemical calculations. INT REV PHYS CHEM 2015. [DOI: 10.1080/0144235x.2015.1022946] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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El-Sheshtawy HS, Salman HMA, El-Kemary M. Halogen vs hydrogen bonding in thiazoline-2-thione stabilization with σ- and π-electron acceptors adducts: theoretical and experimental study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:442-449. [PMID: 25238182 DOI: 10.1016/j.saa.2014.08.077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/16/2014] [Accepted: 08/23/2014] [Indexed: 06/03/2023]
Abstract
Molecular charge-transfer complexes (CT) between thiazoline-2-thione (THZ) and different σ- (I2) and π-acceptors (Tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), and 2,3,5,6-tetrachloro-1,4-benzoquinone (CHL)) were investigated. UV-Vis absorption spectroscopy and theoretical calculations using both MP2/aug-cc-pVDZ-PP and B3LYP/6-311++G(d,p) level of theory were corroborated to study the nature of the stabilizing forces for THZ-I2, THZ-DDQ, THZ-TCNE, and THZ-CHL. Halogen bonding (XB) was the stabilizing attractive force in THZ-I2 and THZ-CHL whereas; hydrogen bonding (HB) was dominated in both THZ-TCNE, and THZ-DDQ complexes. Formation constant (K), extinction coefficient (ɛ), thermodynamic parameters such as enthalpy change (ΔH), entropy (ΔS), and Gibbs free energy (ΔG) were measured in different solvents.
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Affiliation(s)
- Hamdy S El-Sheshtawy
- Biotechnology and Fish Processing Department, Faculty of Aquatic and Fisheries Sciences, Kafrelsheikh University, 33516 Kafr ElSheikh, Egypt; Nanochemistry Laboratory, Chemistry Department, Faculty of Science, Kafrelsheikh University, 33516 Kafr ElSheikh, Egypt.
| | - Hassan M A Salman
- Chemistry Department, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Maged El-Kemary
- Nanochemistry Laboratory, Chemistry Department, Faculty of Science, Kafrelsheikh University, 33516 Kafr ElSheikh, Egypt
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10
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Hydrogen Bonds Involving Sulfur: New Insights from ab Initio Calculations and Gas Phase Laser Spectroscopy. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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11
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Bhattacharyya S, Wategaonkar S. ZEKE Photoelectron Spectroscopy of p-Fluorophenol···H2S/H2O Complexes and Dissociation Energy Measurement Using the Birge–Sponer Extrapolation Method. J Phys Chem A 2014; 118:9386-96. [DOI: 10.1021/jp505393p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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12
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León I, Usabiaga I, Millán J, Cocinero EJ, Lesarri A, Fernández JA. Mimicking anesthetic-receptor interactions in jets: the propofol-isopropanol cluster. Phys Chem Chem Phys 2014; 16:16968-75. [PMID: 25005780 DOI: 10.1039/c4cp01702a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of the general anesthetic propofol with an individual residue of threonine in the membrane receptors has been modeled in the gas phase by examining the adduct of propofol with the isopropanol side-chain. We determined the structural preferences of the cluster using a combination of mass-resolved laser spectroscopy and quantum mechanical calculations. The first electronic transition of propofol-isopropanol was recorded with vibrational resolution using resonant two-photon ionization (R2PI) and ion dip IR spectroscopy. The spectra obtained were compared with density-functional calculations (DFT) using the M06-2X functional in order to obtain the cluster's structure. Three isomers have been detected. The results suggest that propofol acts as a Brønsted acid, donating a proton to the isopropanol molecule in a conformation that resembles that of propofol-water, but displaced towards the aromatic ring, due to the interaction with the aliphatic side of isopropanol. The higher affinity of propofol for isopropanol compared to water may correlate with the biological role of propofol at the protein binding site. On the other hand, propofol shows a similar affinity for isopropanol and phenol, which could explain the mobility that propofol experiences inside the GABAA cavity.
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Affiliation(s)
- Iker León
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco-UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain.
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13
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Chen YC, Wen CC, Liau I, Hsieh YZ, Hsu HY. Oligonucleotides as ‘bio-solvent’ for in situ extraction and functionalisation of carbon nanoparticles. J Mater Chem B 2014; 2:4100-4107. [DOI: 10.1039/c4tb00314d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We used ssDNA oligonucleotides as a ‘bio-solvent’ for CNP extraction and in situ functionalisation, developing efficient, eco-friendly, biocompatible fluorescence probes.
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Affiliation(s)
- Yu-Cheng Chen
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao-Tung University
- Hsinchu 30010, Taiwan
| | - Cheng-Che Wen
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao-Tung University
- Hsinchu 30010, Taiwan
| | - Ian Liau
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao-Tung University
- Hsinchu 30010, Taiwan
| | - You-Zung Hsieh
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao-Tung University
- Hsinchu 30010, Taiwan
| | - Hsin-Yun Hsu
- Department of Applied Chemistry and Institute of Molecular Science
- National Chiao-Tung University
- Hsinchu 30010, Taiwan
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14
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Kumar S, Das A. Effect of acceptor heteroatoms on π-hydrogen bonding interactions: a study of indole···thiophene heterodimer in a supersonic jet. J Chem Phys 2013; 137:094309. [PMID: 22957571 DOI: 10.1063/1.4748818] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Resonant two photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques combined with quantum chemistry calculations have been used to determine the structure of indole···thiophene dimer observed in a supersonic jet. With the help of combined experimental and theoretical IR spectra it has been found that the observed dimer has a N-H···π hydrogen bonded slanted T-shaped structure. The present study demonstrates the effect of heteroatoms present in the acceptors on the strength of the π-hydrogen bonding interactions. It was concluded by Sherrill and co-workers from their theoretical study of benzene···pyridine dimer that aromatic rings containing heteroatoms are poorest π-hydrogen bond acceptors [E. G. Hohenstein and C. D. Sherrill, J. Phys. Chem. A 113, 878 (2009)]. But the current spectroscopic investigation exhibits that five membered aromatic heterocycles are favorable π-hydrogen bond acceptors. In this study, it has also been shown that thiophene is a better π-hydrogen bond acceptor than furan. The present work has immense biological significance as indole is the chromophore of tryptophan residue in the proteins and thiophene derivatives have potential therapeutic applications. Thus, understanding the binding motif between indole and thiophene in the heterodimer studied in this work may help in designing efficient drugs.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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15
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Kumar S, Mukherjee A, Das A. Structure of Indole···Imidazole Heterodimer in a Supersonic Jet: A Gas Phase Study on the Interaction between the Aromatic Side Chains of Tryptophan and Histidine Residues in Proteins. J Phys Chem A 2012; 116:11573-80. [DOI: 10.1021/jp309167a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation
Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra,
India
| | - Ankita Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation
Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra,
India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation
Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra,
India
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16
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León I, Millán J, Castaño F, Fernández JA. A Spectroscopic and Computational Study of Propofol Dimers and Their Hydrated Clusters. Chemphyschem 2012; 13:3819-26. [DOI: 10.1002/cphc.201200633] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Indexed: 11/09/2022]
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17
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Thiourea-catalysed ring opening of episulfonium ions with indole derivatives by means of stabilizing non-covalent interactions. Nat Chem 2012; 4:817-24. [PMID: 23000995 PMCID: PMC3457659 DOI: 10.1038/nchem.1450] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 07/31/2012] [Indexed: 02/03/2023]
Abstract
Small organic and metal-containing molecules (molecular mass <1,000) can catalyse synthetically useful reactions with the high levels of stereoselectivity typically associated with macromolecular enzymatic catalysts. Whereas enzymes are generally understood to accelerate reactions and impart selectivity as they stabilize specific transition structures through networks of cooperative interactions, enantioselectivity with chiral, small-molecule catalysts is rationalized typically by the steric destabilization of all but one dominant pathway. However, it is increasingly apparent that stabilizing effects also play an important role in small-molecule catalysis, although the mechanistic characterization of such systems is rare. Here, we show that arylpyrrolidino amido thiourea catalysts catalyse the enantioselective nucleophilic ring opening of episulfonium ions by indoles. Evidence is provided for the selective transition-state stabilization of the major pathway by the thiourea catalyst in the rate- and selectivity-determining step. Enantioselectivity is achieved through a network of attractive anion binding, cation-π and hydrogen-bond interactions between the catalyst and the reacting components in the transition-structure assembly.
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18
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Kumar S, Pande V, Das A. π-Hydrogen Bonding Wins over Conventional Hydrogen Bonding Interaction: A Jet-Cooled Study of Indole···Furan Heterodimer. J Phys Chem A 2012; 116:1368-74. [DOI: 10.1021/jp211366z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Vedant Pande
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education & Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
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19
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Raju RK, Bloom JWG, An Y, Wheeler SE. Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry. Chemphyschem 2011; 12:3116-30. [PMID: 21928437 DOI: 10.1002/cphc.201100542] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 02/01/2023]
Abstract
Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.
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Affiliation(s)
- Rajesh K Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
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20
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Hohenstein EG, Jaeger HM, Carrell EJ, Tschumper GS, Sherrill CD. Accurate Interaction Energies for Problematic Dispersion-Bound Complexes: Homogeneous Dimers of NCCN, P2, and PCCP. J Chem Theory Comput 2011; 7:2842-51. [PMID: 26605475 DOI: 10.1021/ct200374m] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
All intermolecular interactions involve London dispersion forces. The accurate treatment of dispersion is essential for the computation of realistic interaction potentials. In general, the most reliable method for computing intermolecular interactions is coupled-cluster singles and doubles with perturbative triples [CCSD(T)] in conjunction with a sufficiently flexible Gaussian atomic orbital basis set, a combination which is not routinely applicable due to its excessive computational demands (CPU time, memory, storage). Recently, many theoretical methods have been developed that attempt to account for dispersion in a more efficient manner. It is well-known that dispersion interactions are more difficult to compute in some systems than others; for example, π-π dispersion is notoriously difficult, while alkane-alkane dispersion is relatively simple to compute. In this work, numerous theoretical methods are tested for their ability to compute reliable interaction energies in particularly challenging systems, namely, the P2, PCCP, and NCCN dimers. Symmetry-adapted perturbation theory (SAPT) is applied to these dimers to demonstrate their sensitivity to the treatment of dispersion. Due to the small size of these systems, highly accurate CCSD(T) potential energy curves could be estimated at the complete basis set limit. Numerous theoretical methods are tested against the reliable CCSD(T) benchmarks. Methods using a treatment of dispersion that relies on time-dependent density functional theory (TDDFT) response functions are found to be the most reliable.
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Affiliation(s)
- Edward G Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Heather M Jaeger
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677, United States
| | - Emily J Carrell
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677, United States
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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Kumar S, Biswas P, Kaul I, Das A. Competition between Hydrogen Bonding and Dispersion Interactions in the Indole···Pyridine Dimer and (Indole)2···Pyridine Trimer Studied in a Supersonic Jet. J Phys Chem A 2011; 115:7461-72. [DOI: 10.1021/jp202658r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Partha Biswas
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Indu Kaul
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune-411008, Maharashtra, India
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22
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Čajan M, Trávníček Z. Structural (X-ray), spectral (FT-IR and Raman) and quantum chemical investigations of a series of 6-benzylaminopurine derivatives. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.03.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1167] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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25
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Biswal HS, Gloaguen E, Mons M, Bhattacharyya S, Shirhatti PR, Wategaonkar S. Structure of the Indole−Benzene Dimer Revisited. J Phys Chem A 2011; 115:9485-92. [DOI: 10.1021/jp1119684] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Himansu S. Biswal
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
| | - Pranav R. Shirhatti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
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26
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Hohenstein EG, Sherrill CD. Density fitting of intramonomer correlation effects in symmetry-adapted perturbation theory. J Chem Phys 2010; 133:014101. [PMID: 20614953 DOI: 10.1063/1.3451077] [Citation(s) in RCA: 204] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Symmetry-adapted perturbation theory (SAPT) offers insight into the nature of intermolecular interactions. In addition, accurate energies can be obtained from the wave function-based variant of SAPT provided that intramonomer electron correlation effects are included. We apply density-fitting (DF) approximations to the intramonomer correlation corrections in SAPT. The introduction of this approximation leads to an improvement in the computational cost of SAPT by reducing the scaling of certain SAPT terms, reducing the amount of disk I/O, and avoiding the explicit computation of certain types of MO integrals. We have implemented all the intramonomer correlation corrections to SAPT through second-order under the DF approximation. Additionally, leading third-order terms are also implemented. The accuracy of this truncation of SAPT is tested against the S22 test set of Hobza and co-workers [Phys. Chem. Chem. Phys. 8, 1985 (2006)]. When the intramonomer corrections to dispersion are included in SAPT, a mean absolute deviation of 0.3-0.4 kcal mol(-1) is observed for the S22 test set when using an aug-cc-pVDZ basis. The computations on the adenine-thymine complexes in the S22 test set with an aug-cc-pVDZ basis represent the largest SAPT computations to date that include this degree of intramonomer correlation. Computations of this size can now be performed routinely with our newly developed DF-SAPT program.
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Affiliation(s)
- Edward G Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Hohenstein EG, Sherrill CD. Density fitting and Cholesky decomposition approximations in symmetry-adapted perturbation theory: Implementation and application to probe the nature of π-π interactions in linear acenes. J Chem Phys 2010. [DOI: 10.1063/1.3426316] [Citation(s) in RCA: 231] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Geng Y, Takatani T, Hohenstein EG, Sherrill CD. Accurately Characterizing the π−π Interaction Energies of Indole−Benzene Complexes. J Phys Chem A 2010; 114:3576-82. [DOI: 10.1021/jp9099495] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yue Geng
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280
| | - Tait Takatani
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280
| | - Edward G. Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280
| | - C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280
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Biswal HS, Wategaonkar S. Sulfur, not too far behind O, N, and C: SH...pi hydrogen bond. J Phys Chem A 2010; 113:12774-82. [PMID: 19831375 DOI: 10.1021/jp907747w] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report hydrogen-bonded complexes of H(2)S with indole and 3-methyl indole stabilized by the S-H...pi interaction. It is interesting to discover that although sulfur and its hydrides are known as poor hydrogen-bond donor/acceptors, sulfur is not too far behind oxygen, nitrogen, and carbon in regard to forming the pi-type hydrogen bonds. This report also extends the scope of our earlier studies from sigma-type hydrogen-bonded complexes of sulfur (O-H...S and N-H...S sigma-type hydrogen-bonded complexes) to pi-type hydrogen-bonded complexes of sulfur (S-H...pi pi-type hydrogen-bonded complexes). The experiments were carried out using the supersonic jet expansion technique, and the complexes were probed using laser-induced spectroscopy such as laser-induced fluorescence (LIF), resonant two-photon inonization (R2PI), and fluorescence dip infrared spectroscopy (FDIRS). The FDIR spectroscopy revealed that while there was no shift in the N-H stretch, the S-H stretch was red shifted by about 21 cm(-1). For the H(2)O complexes of indole and 3-methylindole, however, there was a significant red shift in the N-H stretch. These observations suggest that H(2)O forms a NH...O type complex, whereas H(2)S prefers to form a SH...pi type complex. The experimental results were complemented by ab initio calculations and energy decomposition analysis. The binding energies for both the sigma-type and pi-type hydrogen-bonded M.L complexes (M = indole and 3-methylindole; L = H(2)O and H(2)S) were calculated by extrapolating MP2 interaction energies to the complete basis set limit. The calculated M.H(2)S (sigma-type) interaction energy (2.74 kcal/mol) was considerably smaller than that of the M.H(2)S pi-type hydrogen-bonded complex (4.89 kcal/mol), which is exactly opposite of the trend found for the M.H(2)O complexes. This is consistent with the experimental observations. Comparison of the S-H...pi interaction with the other type of X-H...pi (X = C, N, and O) shows that the S-H...pi interaction is the strongest among them. In all of the pi-type HB complexes, the dispersion energy component has significant contribution to the total binding energy.
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Affiliation(s)
- Himansu S Biswal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005.
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Lopes PEM, Lamoureux G, Mackerell AD. Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. J Comput Chem 2009; 30:1821-38. [PMID: 19090564 DOI: 10.1002/jcc.21183] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the nitrogen-containing heteroaromatic compounds pyridine, pyrimidine, pyrrole, imidazole, indole, and purine. Initial parameters for the six-membered rings were based on benzene with nonbond parameter optimization focused on the nitrogen atoms and adjacent carbons and attached hydrogens. In the case of five-member rings, parameters were first developed for imidazole and transferred to pyrrole. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data were used for the determination of initial electrostatic parameters, the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones (LJ) parameters, through computations of the interactions of dimers of model compounds, model compound-water interactions, and interactions of rare gases with model compounds. The absolute values of the LJ parameters were determined targeting experimental heats of vaporization, molecular volumes, heats of sublimation, crystal lattice parameters, and free energies of hydration. Final scaling of the polarizabilities from the gas-phase values by 0.85 was determined by reproduction of the dielectric constants of pyridine and pyrrole. The developed parameter set was extensively validated against additional experimental data such as diffusion constants, heat capacities, and isothermal compressibilities, including data as a function of temperature.
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Affiliation(s)
- Pedro E M Lopes
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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31
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Affiliation(s)
- Himansu S. Biswal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005
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32
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Melša P, Čajan M, Havlas Z, Mazal C. Substituent Effect on exo Stereoselectivity in the 1,3-Dipolar Cycloaddition Reaction of Tulipalin A with Nitrile Ylides. J Org Chem 2008; 73:3032-9. [DOI: 10.1021/jo702563n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Petr Melša
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Department of Inorganic Chemistry, Faculty of Science, Palacký University, Křížkovského 10, 771 47 Olomouc, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Michal Čajan
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Department of Inorganic Chemistry, Faculty of Science, Palacký University, Křížkovského 10, 771 47 Olomouc, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Zdeněk Havlas
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Department of Inorganic Chemistry, Faculty of Science, Palacký University, Křížkovského 10, 771 47 Olomouc, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Ctibor Mazal
- Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Department of Inorganic Chemistry, Faculty of Science, Palacký University, Křížkovského 10, 771 47 Olomouc, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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Tuttle T, Thiel W. OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application. Phys Chem Chem Phys 2008; 10:2159-66. [DOI: 10.1039/b718795e] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Garcia-Raso A, Albertí FM, Fiol JJ, Tasada A, Barceló-Oliver M, Molins E, Escudero D, Frontera A, Quiñonero D, Deyà PM. Anion−π Interactions in Bisadenine Derivatives: A Combined Crystallographic and Theoretical Study. Inorg Chem 2007; 46:10724-35. [DOI: 10.1021/ic701555n] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Angel Garcia-Raso
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
| | - Francisca M. Albertí
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
| | - Juan J. Fiol
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
| | - Andres Tasada
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
| | - Miquel Barceló-Oliver
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
| | - Elies Molins
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
| | - Daniel Escudero
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
| | - David Quiñonero
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
| | - Pere M. Deyà
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain and Institut de Ciència de Materials de Barcelona (CSIC), Campus de la UAB, E-08193 Cerdanyola (Barcelona), Spain
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Profant V, Poterya V, Fárník M, Slavíček P, Buck U. Fragmentation Dynamics of Size-Selected Pyrrole Clusters Prepared by Electron Impact Ionization: Forming a Solvated Dimer Ion Core. J Phys Chem A 2007; 111:12477-86. [DOI: 10.1021/jp0751561] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Václav Profant
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
| | - Viktoriya Poterya
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
| | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, Institute of Chemical Technology, Technická 5, Prague 6, Czech Republic
| | - Udo Buck
- Max-Planck-Institut für Dynamik und Selbstorganization, Bunsenstrasse 10, D-37073 Göttingen, Germany
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Mukhutdinov EA, Mukhutdinov AA, Kovalenko VI, Sol’yashinova OA. Quantum-chemical predictions of the formation of H-bonds between the N-phenyl-N’-isopropyl-p-phenylenediamine and N,N’-diphenyl-p-phenylenediamine molecules. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2007. [DOI: 10.1134/s0036024407050172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Chervenkov S, Karaminkov R, Braun JE, Neusser HJ, Panja SS, Chakraborty T. Specific and nonspecific interactions in a molecule with flexible side chain: 2-phenylethanol and its 1:1 complex with argon studied by high-resolution UV spectroscopy. J Chem Phys 2006; 124:234302. [PMID: 16821913 DOI: 10.1063/1.2202831] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using high-resolution resonance-enhanced two-photon ionization spectroscopy in combination with genetic-algorithm-based computer-aided rotational fit analysis and ab initio quantum chemistry calculations we determined the conformational structure and transition moment orientation in 2-phenylethanol and its 1:1 clusters with argon. The results clearly demonstrate that the gauche structure of 2-phenylethanol, which is stabilized by the intramolecular pi-hydrogen bond between the folded side chain and the benzene ring, is the most abundant in the cold molecular beam. In this conformer the transition moment is rotated by 18 degrees from the short axis of the aromatic ring. Two distinct 1:1 complexes of 2-phenylethanol with argon in a cis- and trans-configuration with respect to the side chain have been found. Employing the Kraitchman [Am. J. Phys. 21, 17 (1953)] analysis we have found that the structure of the 2-phenylethanol moiety and the orientation of the transition moment do not change after the complexation with argon within the experimental accuracy. From the measured band intensities we conclude that in addition to the dispersion interaction of the argon atom with the aromatic ring a hydrogen-bond-type interaction with the terminal -OH group of the side chain stabilizes the cis-structure of the 1:1 complex of 2-phenylethanol with argon.
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Affiliation(s)
- S Chervenkov
- Physikalische und Theoretische Chemie, Technische Universität München, Lichtenbergstrasse 4, D-85748 Garching, 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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Liu Y, Yang EC, Chen Y, Guo DS, Ding F. Molecular Selective Binding of Pyridinium Guest Ions by Water-Soluble Calix[4]arenes. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500354] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Quiñonero D, Garau C, Frontera A, Ballester P, Costa A, Deyà PM. Structure and Binding Energy of Anion−π and Cation−π Complexes: A Comparison of MP2, RI-MP2, DFT, and DF-DFT Methods. J Phys Chem A 2005; 109:4632-7. [PMID: 16833802 DOI: 10.1021/jp044616c] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several complexes of benzene with cations, hexafluorobenzene with anions, 1,3,5-trifluorobenzene with cations and anions, and s-triazine with cations and anions have been evaluated and compared at the MP2 and resolution of the identity MP2 (RI-MP2) levels. The RI-MP2 method is considerably faster than the MP2 and the interaction energies and equilibrium distances are almost identical for both methods. A similar result is found when comparing DFT and density fitting DFT (DF-DFT) levels. Therefore RI-MP2 and DF-DFT methods are well suited for the study of ion-pi interactions.
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Affiliation(s)
- David Quiñonero
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain
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Grimme S. Accurate description of van der Waals complexes by density functional theory including empirical corrections. J Comput Chem 2005; 25:1463-73. [PMID: 15224390 DOI: 10.1002/jcc.20078] [Citation(s) in RCA: 2977] [Impact Index Per Article: 156.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT-D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R(-6). The use of pure, gradient-corrected density functionals (BLYP and PBE), together with the resolution-of-the-identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The "double counting" of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene. H2O and four H-bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT-D-BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT-D data may either be used to calibrate much simpler (e.g., force-field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies.
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Affiliation(s)
- Stefan Grimme
- Organisch-Chemisches Institut der Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany.
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Belau L, Haas Y, Rettig W. Dual Emission of 4-(1H-Pyrrol-1-yl)benzonitrile Clusters with Acetonitrile in a Supersonic Jet and Its Absence in Phenylpyrrole Clusters. J Phys Chem A 2004. [DOI: 10.1021/jp037547v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leonid Belau
- Department of Physical Chemistry and the Farkas Center for Light Induced Processes, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yehuda Haas
- Department of Physical Chemistry and the Farkas Center for Light Induced Processes, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Wolfgang Rettig
- Humboldt University of Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
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Jurečka P, Šponer J, Hobza P. Potential Energy Surface of the Cytosine Dimer: MP2 Complete Basis Set Limit Interaction Energies, CCSD(T) Correction Term, and Comparison with the AMBER Force Field. J Phys Chem B 2004. [DOI: 10.1021/jp049956c] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jurecka P, Hobza P. True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine...cytosine, adenine...thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison with experiment. J Am Chem Soc 2004; 125:15608-13. [PMID: 14664608 DOI: 10.1021/ja036611j] [Citation(s) in RCA: 311] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Planar H-bonded and stacked structures of guanine...cytosine (G.C), adenine...thymine (A...T), 9-methylguanine...1-methylcytosine (mG...mC), and 9-methyladenine...1-methylthymine (mA...mT) were optimized at the RI-MP2 level using the TZVPP ([5s3p2d1f/3s2p1d]) basis set. Planar H-bonded structures of G...C, mG...mC, and A...T correspond to the Watson-Crick (WC) arrangement, in contrast to mA...mT for which the Hoogsteen (H) structure is found. Stabilization energies for all structures were determined as the sum of the complete basis set limit of MP2 energies and a (DeltaE(CCSD(T)) - DeltaE(MP2)) correction term evaluated with the cc-pVDZ(0.25,0.15) basis set. The complete basis set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and X = T and Q. This procedure is required since the convergency of the MP2 interaction energy for the present complexes is rather slow, and it is thus important to include the extrapolation to the complete basis set limit. For the MP2/aug-cc-pVQZ level of theory, stabilization energies for all complexes studied are already very close to the complete basis set limit. The much cheaper D-->T extrapolation provided a complete basis set limit close (by less than 0.7 kcal/mol) to the more accurate T-->Q term, and the D-->T extrapolation can be recommended for evaluation of complete basis set limits of more extended complexes (e.g. larger motifs of DNA). The convergency of the (DeltaE(CCSD(T)) - DeltaE(MP2)) term is known to be faster than that of the MP2 or CCSD(T) correlation energy itself, and the cc-pVDZ(0.25,0.15) basis set provides reasonable values for planar H-bonded as well as stacked structures. Inclusion of the CCSD(T) correction is essential for obtaining reliable relative values for planar H-bonding and stacking interactions; neglecting the CCSD(T) correction results in very considerable errors between 2.5 and 3.4 kcal/mol. Final stabilization energies (kcal/mol) for the base pairs studied are very substantial (A...T WC, 15.4; mA...mT H, 16.3; A...T stacked, 11.6; mA...mT stacked, 13.1; G...C WC, 28.8; mG...mC WC, 28.5; G...C stacked, 16.9; mG...mC stacked, 18.0), much larger than published previously. On the basis of comparison with experimental data, we conclude that our values represent the lower boundary of the true stabilization energies. On the basis of error analysis, we expect the present H-bonding energies to be fairly close to the true values, while stacked energies are still expected to be about 10% too low. The stacking energy for the mG...mC pair is considerably lower than the respective H-bonding energy, but it is larger than the mA...mT H-bonding energy. This conclusion could significantly change the present view on the importance of specific H-bonding interactions and nonspecific stacking interactions in nature, for instance, in DNA. Present stabilization energies for H-bonding and stacking energies represent the most accurate and reliable values and can be considered as new reference data.
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Affiliation(s)
- Petr Jurecka
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, 182 23 Prague 8, Czech Republic
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Braun JE, Neusser HJ. Mass-Analyzed Threshold Ionization of the trans-1-Naphthol−Water Complex: Assignment of Vibrational Modes, Ionization Energy, and Binding Energy. J Phys Chem A 2003. [DOI: 10.1021/jp0304677] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. E. Braun
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, Lichtenbergstr. 4, D - 85748 Garching, Germany
| | - H. J. Neusser
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, Lichtenbergstr. 4, D - 85748 Garching, Germany
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