1
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Kumawat RL, Sherrill CD. High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs. J Chem Inf Model 2023; 63:3150-3157. [PMID: 37125692 DOI: 10.1021/acs.jcim.3c00428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
High-order quantum chemistry is applied to hydrogen-bonded natural DNA nucleobase pairs [adenine:thymine (A:T) and guanine:cytosine (G:C)] and non-natural Hachimoji nucleobase pairs [isoguanine:1-methylcytosine (B:S) and 2-aminoimidazo[1,2a][1,3,5]triazin-4(1H)-one:6-amino-5-nitropyridin-2-one (P:Z)] to see how the intermolecular interaction energies and their energetic components (electrostatics, exchange-repulsion, induction/polarization, and London dispersion interactions) vary among the base pairs. We examined the Hoogsteen (HG) geometries in addition to the traditional Watson-Crick (WC) geometries. Coupled-cluster theory through perturbative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit and high-order symmetry-adapted perturbation theory (SAPT) at the SAPT2+(3)(CCD)δMP2/aug-cc-pVTZ level are used to estimate highly accurate noncovalent interaction energies. Electrostatic interactions are the most attractive component of the interaction energies, but the sum of induction/polarization and London dispersion is nearly as large, for all base pairs and geometries considered. Interestingly, the non-natural Hachimoji base pairs interact more strongly than the corresponding natural base pairs, by -21.8 (B:S) and -0.3 (P:Z) kcal mol-1 in the WC geometries, according to CCSD(T)/CBS. This is consistent with the H-bond distances being generally shorter in the non-natural base pairs. The natural base pairs are energetically more stabilized in their Hoogsteen geometries than in their WC geometries. The Hoogsteen geometry makes the A:T base pair slightly more stable, by -0.8 kcal mol-1, and it greatly stabilizes the G:C+ base pair, by -15.3 kcal mol-1. The G:C+ stabilization is mainly due to the fact that C has typically added a proton when found in Hoogsteen geometries. By contrast, Hoogsteen geometries are substantially less favorable than WC geometries for non-natural Hachimoji base pairs, by 17.3 (B:S) and 13.8 (P:Z) kcal mol-1.
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Affiliation(s)
- Rameshwar L Kumawat
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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2
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Gašparič L, Poberžnik M, Kokalj A. DFT study of hydrogen bonding between metal hydroxides and organic molecules containing N, O, S, and P heteroatoms: clusters vs. surfaces. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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3
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Sparrow ZM, Ernst BG, Joo PT, Lao KU, DiStasio RA. NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts. J Chem Phys 2021; 155:184303. [PMID: 34773949 DOI: 10.1063/5.0068862] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present NENCI-2021, a benchmark database of ∼8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation-π and anion-π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion-π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (Eint) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The Eint values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) Eint value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent-these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation-π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the Eint values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive Eint values, and maximum errors of ±0.2-0.3 kcal/mol (i.e., ∼±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.
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Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Paul T Joo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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4
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Masumian E, Nowroozi A, Nikparsa P, Zargari F. Theoretical evidence for the resonance-inhibited hydrogen bonding (RIHB) in enol-imine tautomers. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Bella G, Santoro A, Nicolò F, Bruno G, Cordaro M. Do Secondary Electrostatic Interactions Influence Multiple Dihydrogen Bonds? AA-DD Array on an Amine-Borane Aza-Coronand: Theoretical Studies and Synthesis. Chemphyschem 2021; 22:593-605. [PMID: 33432782 DOI: 10.1002/cphc.202000906] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/09/2021] [Indexed: 11/06/2022]
Abstract
Hydrogen bond plays a key role in a wide range of inorganic, organic, as well as biological systems. The understanding on how the chemical environment can affect this kind of interaction is crucial to predict its binding strength and consequently the robustness and the dynamic properties of many supramolecular systems. In this paper a new donor-acceptor complex was synthesized and characterized by SCXRD, showing for the first time in an organic system an AA-DD pattern of a particular hydrogen interaction, called dihydrogen bond. Over 250 functionals were computationally evaluated to select the best method to reproduce the binding interaction geometry of this new pattern. Moreover, a new vector force model was used to split the contribution of primary and secondary electrostatic interactions (SEIs), in order to evaluate how the latter one can modify the binding strength of this unusual hydrogen-hydrogen interaction.
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Affiliation(s)
- Giovanni Bella
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Antonio Santoro
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Francesco Nicolò
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Giuseppe Bruno
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Massimiliano Cordaro
- Department of chemical, biological, pharmaceutical and environmental sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166, Messina, Italy
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6
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Loreau J, Kalugina YN, Faure A, van der Avoird A, Lique F. Potential energy surface and bound states of the H 2O-HF complex. J Chem Phys 2020; 153:214301. [PMID: 33291892 DOI: 10.1063/5.0030064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present the first global five-dimensional potential energy surface for the H2O-HF dimer, a prototypical hydrogen bonded complex. Large scale ab initio calculations were carried out using the explicitly correlated coupled cluster approach with single- and double-excitations together with non-iterative perturbative treatment of triple excitations with the augmented correlation-consistent triple zeta basis sets, in which the water and hydrogen fluoride monomers were frozen at their vibrationally averaged geometries. The ab initio data points were fitted to obtain a global potential energy surface for the complex. The equilibrium geometry of the complex corresponds to the formation of a hydrogen bond with water acting as a proton acceptor and a binding energy of De = 3059 cm-1 (8.75 kcal/mol). The energies and wavefunctions of the lowest bound states of the complex were computed using a variational approach, and the dissociation energies of both ortho-H2O-HF (D0 = 2089.4 cm-1 or 5.97 kcal/mol) and para-H2O-HF (D0 = 2079.6 cm-1 or 5.95 kcal/mol) were obtained. The rotational constant of the complex was found to be in good agreement with the available experimental data.
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Affiliation(s)
- Jérôme Loreau
- KU Leuven, Department of Chemistry, B-3001 Leuven, Belgium
| | - Yulia N Kalugina
- Department of Optics and Spectroscopy, Tomsk State University, 36 Lenin Ave., Tomsk 634050, Russia
| | - Alexandre Faure
- Université Grenoble Alpes, CNRS, IPAG, F-38000 Grenoble, France
| | - Ad van der Avoird
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - François Lique
- LOMC-UMR 6294, Normandie Université, Université du Havre and CNRS, 25 rue Philippe Lebon, BP 1123, 76 063 Le Havre Cedex, France
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7
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Yang L, Ji H, Liu X, Lu W. Ring-Stacking Water Clusters: Morphology and Stabilities. ChemistryOpen 2019; 8:210-218. [PMID: 30815330 PMCID: PMC6376211 DOI: 10.1002/open.201800284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/16/2019] [Indexed: 12/12/2022] Open
Abstract
The structures and interaction energies of water clusters with ring stacking motifs are studied by using ab initio calculations. The structures of the water clusters are constructed by stacking either single rings or multi-rings of tetramer, pentamer, and hexamer. We found that, in the single-ring-stacking motif, the most stable isomers exhibit an alternative clockwise-anticlockwise stacking pattern. We also show that four-layer single-ring-stacking isomers are not energetically favorable in comparison with those of two-layer multi-ring-stacking isomers. The relative stability of the isomers is also analyzed in terms of H-bond strength and elastic distortions of the water molecules.
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Affiliation(s)
- Liu Yang
- Center for Quantum Sciences and School of PhysicsNortheast Normal UniversityChangchun130117China
| | - Hanyang Ji
- Center for Quantum Sciences and School of PhysicsNortheast Normal UniversityChangchun130117China
| | - Xiaojie Liu
- Center for Quantum Sciences and School of PhysicsNortheast Normal UniversityChangchun130117China
- Center for Advanced Optoelectronic Functional Materials Research and Key Laboratory of UV Light-Emitting Materials and Technology of Ministry of EducationsNortheast Normal UniversityChangchun130024China
| | - Wen‐Cai Lu
- State Key Laboratory of Theoretical and Computational Chemistry Institute of Theoretical ChemistryJilin University ChangchunJilin130021PR China
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8
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Loboda OA, Dolgonos GA, Boese AD. Towards hybrid density functional calculations of molecular crystals via fragment-based methods. J Chem Phys 2018; 149:124104. [DOI: 10.1063/1.5046908] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Oleksandr A. Loboda
- Institute of Chemistry, University of Graz, Heinrichstrasse 28/IV, A-8010 Graz, Austria
| | - Grygoriy A. Dolgonos
- Institute of Chemistry, University of Graz, Heinrichstrasse 28/IV, A-8010 Graz, Austria
| | - A. Daniel Boese
- Institute of Chemistry, University of Graz, Heinrichstrasse 28/IV, A-8010 Graz, Austria
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9
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Sirianni DA, Alenaizan A, Cheney DL, Sherrill CD. Assessment of Density Functional Methods for Geometry Optimization of Bimolecular van der Waals Complexes. J Chem Theory Comput 2018; 14:3004-3013. [PMID: 29763302 DOI: 10.1021/acs.jctc.8b00114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We explore the suitability of three popular density functionals (B97-D3, B3LYP-D3, M05-2X) for producing accurate equilibrium geometries of van der Waals (vdW) complexes with diverse binding motifs. For these functionals, optimizations using Dunning's aug-cc-pVDZ basis set best combine accuracy and a reasonable computational expense. Each DFT/aug-cc-pVDZ combination produces optimized equilibrium geometries for 21 small vdW complexes of organic molecules (up to four non-hydrogen atoms total) that agree with high-level CCSD(T)/CBS reference geometries to within ±0.1 Å for the averages of the center-of-mass displacement and the mean least root-mean-squared displacement. The DFT/aug-cc-pVDZ combinations are also able to reproduce the optimal center-of-mass displacements interpolated from CCSD(T)/CBS radial potential energy surfaces in both NBC7x and HBC6 test sets to within ±0.1 Å. We therefore conclude that each of these denisty functional methods, together with the aug-cc-pVDZ basis set, is suitable for producing equilibrium geometries of generic nonbonded complexes.
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Affiliation(s)
- Dominic A Sirianni
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
| | - Asem Alenaizan
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
| | - Daniel L Cheney
- Molecular Structure and Design , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , 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 30332-0400 , United States
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10
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Abstract
Even though (H2O)2 and (HF)2 are arguably the most thoroughly characterized prototypes for hydrogen bonding, their heterogeneous analogue H2O···HF has received relatively little attention. Here we report that the experimental dissociation energy ( D0) of this important paradigm for heterogeneous hydrogen bonding is too large by 2 kcal mol-1 or 30% relative to our computed value of 6.3 kcal mol-1. For reference, computational procedures similar to those employed here to compute D0 (large basis set CCSD(T) computations with anharmonic corrections from second-order vibrational perturbation theory) provide results within 0.1 kcal mol-1 of the experimental values for (H2O)2 and (HF)2. Near the CCSD(T) complete basis set limit, the electronic dissociation energy for H2O···HF is ∼4 kcal mol-1 larger than those for (H2O)2 and (HF)2 (∼9 kcal mol-1 for the heterogeneous dimer vs ∼5 kcal mol-1 for the homogeneous dimers). Results reported here from symmetry-adapted perturbation theory computations suggest that this large difference is primarily due to the induction contribution to the interaction energy.
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Affiliation(s)
- Thomas More Sexton
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677-1848 , United States
| | - J Coleman Howard
- Department of Chemistry , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677-1848 , United States
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11
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Quiñonero D. Sigma-hole carbon-bonding interactions in carbon-carbon double bonds: an unnoticed contact. Phys Chem Chem Phys 2018; 19:15530-15540. [PMID: 28581553 DOI: 10.1039/c7cp01780d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this manuscript, we combine high-level ab initio calculations on some small complexes and a CSD survey to analyze the existence of unprecedented noncovalent carbon bonds in X2C[double bond, length as m-dash]CH2Y systems (Y = electron-rich atom or group). The methylene group is usually seen as a weak hydrogen bond donor when interacting with an electron-rich atom. However, we demonstrate that when the electron-rich atom is located equidistant from the two H atoms and along the C[double bond, length as m-dash]C bond a σ-hole noncovalent carbon-bonding interaction is established, instead of a bifurcated hydrogen bond, as derived from Atoms-in-Molecules (AIM) and Natural bond orbital (NBO) analyses. The physical nature of the interaction has been analyzed using the Symmetry Adapted Perturbation Theory (SAPT) method. The results indicate that electrostatics is very important followed by either the induction or dispersion terms in anionic and neutral complexes, respectively. In addition the CSD analysis reveals the existence of such interactions, giving reliability to our calculations, which are much more numerous for neutral than for anionic Y systems.
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Affiliation(s)
- D Quiñonero
- Department de Química, Universitat de les Illes Balears, Crta. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain.
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12
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Zhu T, de Silva P, Van Voorhis T. Self-Attractive Hartree Decomposition: Partitioning Electron Density into Smooth Localized Fragments. J Chem Theory Comput 2017; 14:92-103. [DOI: 10.1021/acs.jctc.7b00931] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tianyu Zhu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Piotr de Silva
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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13
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Sirianni DA, Burns LA, Sherrill CD. Comparison of Explicitly Correlated Methods for Computing High-Accuracy Benchmark Energies for Noncovalent Interactions. J Chem Theory Comput 2016; 13:86-99. [DOI: 10.1021/acs.jctc.6b00797] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dominic A. Sirianni
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry,
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Lori A. Burns
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry,
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C. David Sherrill
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry,
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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14
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Sobczyk L, Chudoba D, Tolstoy PM, Filarowski A. Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding. Molecules 2016; 21:E1657. [PMID: 27918442 PMCID: PMC6273268 DOI: 10.3390/molecules21121657] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 11/16/2022] Open
Abstract
A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed.
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Affiliation(s)
- Lucjan Sobczyk
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland.
| | - Dorota Chudoba
- Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznan, Poland.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.
| | - Peter M Tolstoy
- Center for Magnetic Resonance, St. Petersburg State University, St. Petersburg 198504, Russia.
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str., 50-383 Wrocław, Poland.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.
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15
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Chan B, Karton A, Raghavachari K, Radom L. Restricted-Open-Shell G4(MP2)-Type Procedures. J Phys Chem A 2016; 120:9299-9304. [DOI: 10.1021/acs.jpca.6b09361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bun Chan
- Graduate
School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
| | - Amir Karton
- School
of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Krishnan Raghavachari
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Leo Radom
- School
of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
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16
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Richard RM, Marshall MS, Dolgounitcheva O, Ortiz JV, Brédas JL, Marom N, Sherrill CD. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules I. Reference Data at the CCSD(T) Complete Basis Set Limit. J Chem Theory Comput 2016; 12:595-604. [PMID: 26731487 DOI: 10.1021/acs.jctc.5b00875] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In designing organic materials for electronics applications, particularly for organic photovoltaics (OPV), the ionization potential (IP) of the donor and the electron affinity (EA) of the acceptor play key roles. This makes OPV design an appealing application for computational chemistry since IPs and EAs are readily calculable from most electronic structure methods. Unfortunately reliable, high-accuracy wave function methods, such as coupled cluster theory with single, double, and perturbative triples [CCSD(T)] in the complete basis set (CBS) limit are too expensive for routine applications to this problem for any but the smallest of systems. One solution is to calibrate approximate, less computationally expensive methods against a database of high-accuracy IP/EA values; however, to our knowledge, no such database exists for systems related to OPV design. The present work is the first of a multipart study whose overarching goal is to determine which computational methods can be used to reliably compute IPs and EAs of electron acceptors. This part introduces a database of 24 known organic electron acceptors and provides high-accuracy vertical IP and EA values expected to be within ±0.03 eV of the true non-relativistic, vertical CCSD(T)/CBS limit. Convergence of IP and EA values toward the CBS limit is studied systematically for the Hartree-Fock, MP2 correlation, and beyond-MP2 coupled cluster contributions to the focal point estimates.
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Affiliation(s)
- Ryan M Richard
- 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 30332-0400, United States
| | - Michael S Marshall
- 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 30332-0400, United States
| | - O Dolgounitcheva
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849-5312, United States
| | - J V Ortiz
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849-5312, United States
| | - Jean-Luc Brédas
- Solar & Photovoltaics Engineering Research Center, Physical Science and Engineering Division King Abdullah University of Science and Technology , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Noa Marom
- Department of Physics, Tulane University , New Orleans, Louisiana 70118-5645, 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 30332-0400, United States
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17
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Scholz F, Unkrig W, Eiden P, Schmidt MA, Garsuch A, Krossing I. Synthesis, Spectroscopic Characterization, Crystal Structures, Energetics, and Thermal Stabilities of Li[AlX
4
] (X = Cl, Br): Investigation and Performance of Their Electrolyte Solutions. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Franziska Scholz
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany, http://portal.uni‐freiburg.de/molchem
| | - Wiebke Unkrig
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany, http://portal.uni‐freiburg.de/molchem
| | - Philipp Eiden
- BASF SE, Carl‐Bosch‐Str. 38, 67056 Ludwigshafen am Rhein
| | | | - Arnd Garsuch
- BASF SE, Carl‐Bosch‐Str. 38, 67056 Ludwigshafen am Rhein
| | - Ingo Krossing
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany, http://portal.uni‐freiburg.de/molchem
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18
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Boese AD. Density Functional Theory and Hydrogen Bonds: Are We There Yet? Chemphyschem 2015; 16:978-85. [DOI: 10.1002/cphc.201402786] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/12/2014] [Indexed: 11/12/2022]
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19
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Affiliation(s)
- A. Daniel Boese
- Department of Chemistry, University of Potsdam, Potsdam, Germany
- Department of Chemistry, University of Graz, Graz, Austria
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20
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Böhrer H, Trapp N, Himmel D, Schleep M, Krossing I. From unsuccessful H2-activation with FLPs containing B(Ohfip)3 to a systematic evaluation of the Lewis acidity of 33 Lewis acids based on fluoride, chloride, hydride and methyl ion affinities. Dalton Trans 2015; 44:7489-99. [DOI: 10.1039/c4dt02822h] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From hard to soft: The ion affinities of a large set of 33 Lewis acids towards hard and soft bases were examined with a unified isodesmic approach.
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Affiliation(s)
- Hannes Böhrer
- Albert-Ludwigs-Universität Freiburg
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF)
- 79104 Freiburg
- Germany
| | - Nils Trapp
- Albert-Ludwigs-Universität Freiburg
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF)
- 79104 Freiburg
- Germany
| | - Daniel Himmel
- Albert-Ludwigs-Universität Freiburg
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF)
- 79104 Freiburg
- Germany
| | - Mario Schleep
- Albert-Ludwigs-Universität Freiburg
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF)
- 79104 Freiburg
- Germany
| | - Ingo Krossing
- Albert-Ludwigs-Universität Freiburg
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF)
- 79104 Freiburg
- Germany
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21
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Rahaman O, Doren DJ, Di Toro DM. Quantum mechanical estimation of Abraham hydrogen bond parameters using 1:1 donor-acceptor complexes. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Obaidur Rahaman
- Department of Chemistry and Biochemistry; University of Delaware; Newark DE 19716 USA
- Institut de Biologie Physico-Chimique; Paris 75005 France
| | - Douglas J. Doren
- Department of Chemistry and Biochemistry; University of Delaware; Newark DE 19716 USA
| | - Dominic M. Di Toro
- Department of Civil and Environmental Engineering; University of Delaware; Newark DE 19716 USA
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22
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Hopkins WS, Hasan M, Burt M, Marta RA, Fillion E, McMahon TB. Persistent Intramolecular C–H···X (X = O or S) Hydrogen-Bonding in Benzyl Meldrum’s Acid Derivatives. J Phys Chem A 2014; 118:3795-3803. [DOI: 10.1021/jp5029245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- W. Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada, N2L 3G1
| | - Moaraj Hasan
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada, N2L 3G1
| | - Michael Burt
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada, N2L 3G1
| | - Rick A. Marta
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada, N2L 3G1
| | - Eric Fillion
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada, N2L 3G1
| | - Terry B. McMahon
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada, N2L 3G1
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23
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Kalescky R, Kraka E, Cremer D. Accurate determination of the binding energy of the formic acid dimer: The importance of geometry relaxation. J Chem Phys 2014; 140:084315. [DOI: 10.1063/1.4866696] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Scholz F, Himmel D, Eisele L, Unkrig W, Krossing I. The Superacid HBr/AlBr3: Protonation of Benzene and Ordered Crystal Structure of [C6H7]+[Al2Br7]−. Angew Chem Int Ed Engl 2014; 53:1689-92. [DOI: 10.1002/anie.201308120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Indexed: 11/08/2022]
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25
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Scholz F, Himmel D, Eisele L, Unkrig W, Krossing I. Die Supersäure HBr/AlBr3: Protonierung von Benzol und ausgeordnete Kristallstruktur von [C6H7]+[Al2Br7]−. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Burns LA, Marshall MS, Sherrill CD. Comparing Counterpoise-Corrected, Uncorrected, and Averaged Binding Energies for Benchmarking Noncovalent Interactions. J Chem Theory Comput 2013; 10:49-57. [PMID: 26579890 DOI: 10.1021/ct400149j] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lori A Burns
- 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 30332-0400, United States
| | - Michael S Marshall
- 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 30332-0400, 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 30332-0400, United States
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27
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Tentscher PR, Arey JS. On the Nature of Interactions of Radicals with Polar Molecules. J Phys Chem A 2013; 117:12560-8. [DOI: 10.1021/jp407041e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter R. Tentscher
- Environmental
Chemistry Modeling Laboratory, Swiss Federal Institute of Technology Lausanne
, 1015
Lausanne, Switzerland
| | - J. Samuel Arey
- Environmental
Chemistry Modeling Laboratory, Swiss Federal Institute of Technology Lausanne
, 1015
Lausanne, Switzerland
- Department
of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology
, 8600
Dübendorf, Switzerland
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28
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Boese AD. Assessment of Coupled Cluster Theory and more Approximate Methods for Hydrogen Bonded Systems. J Chem Theory Comput 2013; 9:4403-13. [DOI: 10.1021/ct400558w] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Daniel Boese
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam, Germany
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29
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Kozuch S, Martin JML. Spin-component-scaled double hybrids: An extensive search for the best fifth-rung functionals blending DFT and perturbation theory. J Comput Chem 2013; 34:2327-44. [DOI: 10.1002/jcc.23391] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 06/25/2013] [Accepted: 06/28/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Sebastian Kozuch
- Department of Organic Chemistry; Weizmann Institute of Science; IL-76100; Rechovot; Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry; Weizmann Institute of Science; IL-76100; Rechovot; Israel
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30
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Tentscher PR, Arey JS. Binding in Radical-Solvent Binary Complexes: Benchmark Energies and Performance of Approximate Methods. J Chem Theory Comput 2013; 9:1568-79. [DOI: 10.1021/ct300846m] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter R. Tentscher
- Environmental
Chemistry Modeling
Laboratory, EPFL, Lausanne, Switzerland
| | - J. Samuel Arey
- Environmental
Chemistry Modeling
Laboratory, EPFL, Lausanne, Switzerland
- Swiss Federal Institute of Aquatic
Science and Technology (Eawag), Dübendorf, Switzerland
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31
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Sivey JD, Arey JS, Tentscher PR, Roberts AL. Reactivity of BrCl, Br₂, BrOCl, Br₂O, and HOBr toward dimethenamid in solutions of bromide + aqueous free chlorine. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:1330-1338. [PMID: 23323704 DOI: 10.1021/es302730h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
HOBr, formed via oxidation of bromide by free available chlorine (FAC), is frequently assumed to be the sole species responsible for generating brominated disinfection byproducts (DBPs). Our studies reveal that BrCl, Br(2), BrOCl, and Br(2)O can also serve as brominating agents of the herbicide dimethenamid in solutions of bromide to which FAC was added. Conditions affecting bromine speciation (pH, total free bromine concentration ([HOBr](T)), [Cl(-)], and [FAC](o)) were systematically varied, and rates of dimethenamid bromination were measured. Reaction orders in [HOBr](T) ranged from 1.09 (±0.17) to 1.67 (±0.16), reaching a maximum near the pK(a) of HOBr. This complex dependence on [HOBr](T) implicates Br(2)O as an active brominating agent. That bromination rates increased with increasing [Cl(-)], [FAC](o) (at constant [HOBr](T)), and excess bromide (where [Br(-)](o)>[FAC](o)) implicate BrCl, BrOCl, and Br(2), respectively, as brominating agents. As equilibrium constants for the formation of Br(2)O and BrOCl (aq) have not been previously reported, we have calculated these values (and their gas-phase analogues) using benchmark-quality quantum chemical methods [CCSD(T) up to CCSDTQ calculations plus solvation effects]. The results allow us to compute bromine speciation and hence second-order rate constants. Intrinsic brominating reactivity increased in the order: HOBr ≪ Br(2)O < BrOCl ≈ Br(2) < BrCl. Our results indicate that species other than HOBr can influence bromination rates under conditions typical of drinking water and wastewater chlorination.
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Affiliation(s)
- John D Sivey
- Department of Geography and Environmental Engineering, Johns Hopkins University, 313 Ames Hall 3400 North Charles Street Baltimore, Maryland 21218, United States
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32
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Boese AD, Kirchner M, Echeverria GA, Boese R. Ethyl Acetate: X‐ray, Solvent and Computed Structures. Chemphyschem 2012; 14:799-804. [DOI: 10.1002/cphc.201200724] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Indexed: 11/10/2022]
Affiliation(s)
- A. Daniel Boese
- Department of Chemistry, Humboldt‐Universität zu Berlin, Unter den Linden 6, 10099 Berlin (Germany)
| | - Michael Kirchner
- Faculty of Chemistry, Universität Duisburg‐Essen, 45117 Essen (Germany)
| | - Gustavo A. Echeverria
- Departamento de Física, Facultad de Ciencias Exactas and Facultad de Ingeniería, Universidad Nacional de La Plata, C. C. 67, 1900 La Plata (Argentina)
| | - Roland Boese
- Faculty of Chemistry, Universität Duisburg‐Essen, 45117 Essen (Germany)
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33
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Boese AD, Codorniu-Hernández E. Cross-talk between amino acid residues and flavonoid derivatives: insights into their chemical recognition. Phys Chem Chem Phys 2012; 14:15682-92. [PMID: 23086511 DOI: 10.1039/c2cp42174g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Currently, there is a general consensus that flavonoids exert their antioxidant activity through their ability to interact with a broad range of proteins, enzymes and transcription factors rather than acting as conventional hydrogen-donating antioxidants. For this, the effect of different chemical groups of the conjugated flavonoid metabolites is apparently playing a pivotal role. Yet, many questions concerning the relevant molecular mechanisms still remain open. It is therefore crucial to gain a deeper insight into the amino acid residue-flavonoid interaction. Here we show extensive theoretical thermodynamic data and structural characteristics of the interaction of chalcone, genistein, epigallocatechin gallate, and quercetin and some of its metabolites with amino acid residues. By correlating (a) the binding energies of flavonoids-amino acid residues, (b) the hydrophobicity of amino acids, and (c) the abundance of amino acid residues in the binding sites of proteins, we can conclude that flavonoids appear to be strongly bonded to only few charged hydrophilic amino acids in the protein pockets, and rather weakly bonded to the majority of amino acid residues in the binding sites. This finding strongly impacts the understanding of the chemical recognition of flavonoids and their metabolites in their interaction with proteins and would contribute to a better design of further experimental studies. Particularly, the amino acids Phe, Leu, Ile and Trp seem to play a crucial role in the dynamics of flavonoid ligands in the binding sites of proteins.
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Affiliation(s)
- A Daniel Boese
- Department of Chemistry, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany.
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34
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Chan B, Gill PMW, Radom L. Performance of Gradient-Corrected and Hybrid Density Functional Theory: Role of the Underlying Local Density Approximation and the Gradient Correction. J Chem Theory Comput 2012; 8:4899-906. [DOI: 10.1021/ct300603d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Bun Chan
- School of
Chemistry and ARC
Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Peter M. W. Gill
- Research School of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Leo Radom
- School of
Chemistry and ARC
Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
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35
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Kang R, Lai W, Yao J, Shaik S, Chen H. How Accurate Can a Local Coupled Cluster Approach Be in Computing the Activation Energies of Late-Transition-Metal-Catalyzed Reactions with Au, Pt, and Ir? J Chem Theory Comput 2012; 8:3119-27. [PMID: 26605723 DOI: 10.1021/ct3003942] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To improve the accuracy of local coupled cluster (LCC) methods in computing activation energies, we propose herein a new computational scheme. Its applications to various types of late-transition-metal-catalyzed reactions involving Au, Pt, and Ir indicate that the new corrective approach for LCC methods can downsize the mean unsigned deviation and maximum deviation, from the CCSD(T)/CBS reference, to about 0.3 and 0.9 kcal/mol. Using this method, we also calibrated the performance of popular density functionals, with respect to the same test set of reactions. It is concluded that the best functional is the general-purpose double hybrid functional B2GP-PLYP. Other well-performing functionals include the "kinetic" functionals M06-2X and BMK, which have a large percentage of HF exchange, and general-purpose functionals like PBE0 and wB97X. Comparatively, general-purpose functionals like PBE0 and TPSSh perform much better than the tested "kinetic" functionals for Pt-/Ir-catalyzed reactions, while the opposite is true for Au-catalyzed reactions. In contrast, wB97X performs more uniformly in these two classes of reactions. These findings hint that even within the scope of late transition metals, different types of reactions may require different types of optimal DFT methods. Empirical dispersion correction of DFT was found to have a small or no effect on the studied reactions barriers.
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Affiliation(s)
- Runhua Kang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China, Beijing, 100872, China
| | - Jiannian Yao
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, 91904 Jerusalem, Israel
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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36
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Himmel D, Goll SK, Leito I, Krossing I. Bulk Gas-Phase Acidity. Chemistry 2012; 18:9333-40. [DOI: 10.1002/chem.201104025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Indexed: 11/07/2022]
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37
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Deglmann P, Schenk S. Thermodynamics of chemical reactions with COSMO-RS: the extreme case of charge separation or recombination. J Comput Chem 2012; 33:1304-20. [PMID: 22430261 DOI: 10.1002/jcc.22961] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 02/03/2012] [Accepted: 02/07/2012] [Indexed: 11/09/2022]
Abstract
Many technically relevant chemical processes in the condensed phase involve as elementary reactive steps the formation of ions from neutral species or, as the opposite, recombination of ions. Such reactions that generate or annihilate charge defy the standard gas phase quantum chemical treatment, and also continuum solvation models are only partially able to account for the right amount of stabilization in solution. In this work, for such types of reaction, a solvation treatment involving the COSMO-RS method is assessed, which leads to improved results, i.e., errors of only around 10 kJ/mol for both protic and aprotic solvents. The examples discussed here comprise protolysis reactions and organo halide heterolysis, for both of which a comparison with reliable experimental data is possible. It is observed that for protolysis, the quality of results does not strongly depend on the quantum chemical method used for energy calculation. In contrast, in the case of heterolytic carbon-chlorine bond cleavage, clearly better results are obtained for higher correlated (coupled cluster) methods or the density functional M06-2X, which is well known for its accuracy if applied to organic chemistry. This hints at least that the right answer is obtained for the right reason and not due to a compensation of errors from gas phase thermodynamics with those from the solvation treatment. Problems encountered with certain critical solvents or upon decomposing Gibbs free energies into heats or entropies of reaction are found to relate mostly to the parameterization of the H-bonding term within COSMO-RS.
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Affiliation(s)
- Peter Deglmann
- BASF SE, Polymer Physics and Analytics, Carl-Bosch-Str. 38, 67056 Ludwigshafen, Germany.
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38
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Baburin IA, Leoni S. The energy landscapes of zeolitic imidazolate frameworks (ZIFs): towards quantifying the presence of substituents on the imidazole ring. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm15629f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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39
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Marshall MS, Burns LA, Sherrill CD. Basis set convergence of the coupled-cluster correction, δMP2CCSD(T): Best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases. J Chem Phys 2011; 135:194102. [DOI: 10.1063/1.3659142] [Citation(s) in RCA: 263] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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40
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DeKock RL, Brandsen BM, Strikwerda JR. Theoretical study of formation of ion pairs in (NH3·HCl)(H2O)6 and (NH3·HF)(H2O)6. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1032-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Mutter ST, Platts JA. Density Functional Theory Studies of Interactions of Ruthenium–Arene Complexes with Base Pair Steps. J Phys Chem A 2011; 115:11293-302. [DOI: 10.1021/jp2049487] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Shaun T. Mutter
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - James A. Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
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42
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Bates DM, Smith JR, Tschumper GS. Efficient and Accurate Methods for the Geometry Optimization of Water Clusters: Application of Analytic Gradients for the Two-Body:Many-Body QM:QM Fragmentation Method to (H2O)n, n = 3–10. J Chem Theory Comput 2011; 7:2753-60. [DOI: 10.1021/ct200176t] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Desiree M. Bates
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Joshua R. Smith
- 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
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43
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Skelton AA, Wesolowski DJ, Cummings PT. Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:8700-8709. [PMID: 21648451 DOI: 10.1021/la2005826] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.
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Affiliation(s)
- A A Skelton
- Department of Chemical Engineering, Vanderbilt University, Nashville, Tennessee, United States.
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44
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Chen YF, Dannenberg JJ. The effect of polarization on multiple hydrogen-bond formation in models of self-assembling materials. J Comput Chem 2011; 32:2890-5. [PMID: 21717481 DOI: 10.1002/jcc.21870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/01/2011] [Accepted: 05/23/2011] [Indexed: 01/27/2023]
Abstract
We report density functional theory calculations at the B3LYP/D95(d,p) level on several different cyclic H-bonding dimers, where the monomers of each are connected by a pair of N-H···O=C H-bonding interactions, and the H-bonding donors and acceptors on each monomer are separated by polarizable spacers. Depending on the structures, the individual H-bonds vary in strength (enthalpy) by over a factor of four, from 2.41 to 10.99 kcal/mol. We attribute most of the variation in interaction energies to differences in the extent of polarization due to each of the H-bonds, which can either combine constructively or destructively. The dipole-dipole interactions between the pair of H-bonds also contribute somewhat to the relative stabilities. The relevance of these results to the design of self-assembling materials is discussed.
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Affiliation(s)
- Yung-Fou Chen
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065, USA
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45
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Himmel D, Goll SK, Leito I, Krossing I. Anchor Points for the Unified Brønsted Acidity Scale: The rCCC Model for the Calculation of Standard Gibbs Energies of Proton Solvation in Eleven Representative Liquid Media. Chemistry 2011; 17:5808-26. [DOI: 10.1002/chem.201003164] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Indexed: 11/10/2022]
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46
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Friedrich J, Perlt E, Roatsch M, Spickermann C, Kirchner B. Coupled Cluster in Condensed Phase. Part I: Static Quantum Chemical Calculations of Hydrogen Fluoride Clusters. J Chem Theory Comput 2011; 7:843-51. [DOI: 10.1021/ct100131c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joachim Friedrich
- Institute for Chemistry, Chemnitz University of Technology, Strasse der Nationen 62, 09111 Chemnitz, Germany
| | - Eva Perlt
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103 Leipzig, Germany
| | - Martin Roatsch
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103 Leipzig, Germany
| | - Christian Spickermann
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103 Leipzig, Germany
| | - Barbara Kirchner
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103 Leipzig, Germany
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47
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Gai XS, Coutifaris BA, Brewer SH, Fenlon EE. A direct comparison of azide and nitrile vibrational probes. Phys Chem Chem Phys 2011; 13:5926-30. [PMID: 21336362 DOI: 10.1039/c0cp02774j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The synthesis of 2'-azido-5-cyano-2'-deoxyuridine, N(3)CNdU (1), from trityl-protected 2'-amino-2'-deoxyuridine was accomplished in four steps with a 12.5% overall yield. The IR absorption positions and profiles of the azide and nitrile group of N(3)CNdU were investigated in 14 different solvents and water/DMSO solvent mixtures. The azide probe was superior to the nitrile probe in terms of its extinction coefficient, which is 2-4 times larger. However, the nitrile IR absorbance profile is generally less complicated by accidental Fermi resonance. The IR frequencies of both probes undergo a substantial red shift upon going from water to aprotic solvents such as THF or DMSO. DFT calculations supported the hypothesis that the molecular origin of the higher observed frequency in water is primarily due to hydrogen bonds between the probes and water molecules.
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Affiliation(s)
- Xin Sonia Gai
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003, USA
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48
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Riley KE, Hobza P. Noncovalent interactions in biochemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.8] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin E. Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
- Department of Physical Chemistry, Palacky University, Olomouc, Czech Republic
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49
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Hujo W, Grimme S. Comparison of the performance of dispersion-corrected density functional theory for weak hydrogen bonds. Phys Chem Chem Phys 2011; 13:13942-50. [DOI: 10.1039/c1cp20591a] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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50
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Kozuch S, Martin JML. DSD-PBEP86: in search of the best double-hybrid DFT with spin-component scaled MP2 and dispersion corrections. Phys Chem Chem Phys 2011; 13:20104-7. [DOI: 10.1039/c1cp22592h] [Citation(s) in RCA: 318] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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