1
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Masumian E, Boese AD. Benchmarking Swaths of Intermolecular Interaction Components with Symmetry-Adapted Perturbation Theory. J Chem Theory Comput 2024; 20:30-48. [PMID: 38117939 PMCID: PMC10782453 DOI: 10.1021/acs.jctc.3c00801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
A benchmark database for interaction energy components of various noncovalent interactions (NCIs) along their dissociation curve is one of the essential needs in theoretical chemistry, especially for the development of force fields and machine-learning methods. We utilize DFT-SAPT or SAPT(DFT) as one of the most accurate methods to generate an extensive stock of the energy components, including dispersion energies extrapolated to the complete basis set limit (CBS). Precise analyses of the created data, and benchmarking the total interaction energies against the best available CCSD(T)/CBS values, reveal different aspects of the methodology and the nature of NCIs. For example, error cancellation effects between the S2 approximation and nonexact xc-potentials occur, and large charge transfer energies in some systems, including heavy atoms, can explain the lower accuracy of DFT-SAPT. This method is perfect for neutral complexes containing light nonmetals, while other systems with heavier atoms should be treated carefully. In the last part, a representative data set for all NCIs is extracted from the original data.
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Affiliation(s)
- Ehsan Masumian
- Physical and Theoretical Chemistry,
Department of Chemistry, University of Graz, 8010 Graz, Austria
| | - A. Daniel Boese
- Physical and Theoretical Chemistry,
Department of Chemistry, University of Graz, 8010 Graz, Austria
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2
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Jansen G, Schulz S, van der Vight F. Effects of Dispersion and Charge‐Transfer Interactions on Structures of Heavy Chalcogenide Compounds: A Quantum Chemical Case Study for (Et2Bi)2Te. Chempluschem 2022; 87:e202100487. [DOI: 10.1002/cplu.202100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/03/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Georg Jansen
- Universitat Duisburg-Essen Chemistry Universitätsstr. 5-7 45141 Essen GERMANY
| | - Stephan Schulz
- University of Duisburg-Essen: Universitat Duisburg-Essen Chemistry Universitätsstr. 5-7 45141 Essen GERMANY
| | - Felix van der Vight
- University of Duisburg-Essen: Universitat Duisburg-Essen Chemistry Universitätsstr. 5-7 45141 Essen GERMANY
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3
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Decomposition of the interaction energy of several flavonoids with Escherichia coli DNA Gyr using the SAPT (DFT) method: The relation between the interaction energy components, ligand structure, and biological activity. Biochim Biophys Acta Gen Subj 2022; 1866:130111. [DOI: 10.1016/j.bbagen.2022.130111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/19/2022] [Accepted: 02/07/2022] [Indexed: 12/28/2022]
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4
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Ibrahim MAA, Moussa NAM, Soliman MES, Moustafa MF, Al-Fahemi JH, El-Mageed HRA. On the Potentiality of X-T-X 3 Compounds (T = C, Si, and Ge, and X = F, Cl, and Br) as Tetrel- and Halogen-Bond Donors. ACS OMEGA 2021; 6:19330-19341. [PMID: 34337270 PMCID: PMC8320108 DOI: 10.1021/acsomega.1c03183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/08/2021] [Indexed: 05/08/2023]
Abstract
The versatility of the X-T-X3 compounds (where T = C, Si, and Ge, and X = F, Cl, and Br) to participate in tetrel- and halogen-bonding interactions was settled out, at the MP2/aug-cc-pVTZ level of theory, within a series of configurations for (X-T-X3)2 homodimers. The electrostatic potential computations ensured the remarkable ability of the investigated X-T-X3 monomers to participate in σ-hole halogen and tetrel interactions. The energetic findings significantly unveil the favorability of the tetrel···tetrel directional configuration with considerable negative binding energies over tetrel···halogen, type III halogen···halogen, and type II halogen···halogen analogs. Quantum theory of atoms in molecules and noncovalent interaction analyses were accomplished to disclose the nature of the tetrel- and halogen-bonding interactions within designed configurations, giving good correlations between the total electron densities and binding energies. Further insight into the binding energy physical meanings was invoked through using symmetry-adapted perturbation theory-based energy decomposition analysis, featuring the dispersion term as the most prominent force beyond the examined interactions. The theoretical results were supported by versatile crystal structures which were characterized by the same type of interactions. Presumably, the obtained findings would be considered as a solid underpinning for future supramolecular chemistry, materials science, and crystal engineering studies, as well as a fundamental linchpin for a better understanding of the biological activities of chemicals.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mahmoud E. S. Soliman
- Molecular
Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Mahmoud F. Moustafa
- Department
of Biology, College of Science, King Khalid
University, Abha 9004, Saudi Arabia
- Department
of Botany and Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Jabir H. Al-Fahemi
- Chemistry
Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - H. R. Abd El-Mageed
- Micro-Analysis,
Environmental Research and Community Affairs Center (MAESC), Faculty
of Science, Beni-Suef University, Beni-Suef 62511, Egypt
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5
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Mao L, Hu Y, Tu Q, Jiang WL, Zhao XL, Wang W, Yuan D, Wen J, Shi X. Highly efficient synthesis of non-planar macrocycles possessing intriguing self-assembling behaviors and ethene/ethyne capture properties. Nat Commun 2020; 11:5806. [PMID: 33199747 PMCID: PMC7669899 DOI: 10.1038/s41467-020-19677-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/21/2020] [Indexed: 01/24/2023] Open
Abstract
It has been a challenging topic and perpetual task to design and synthesize covalent macrocycles with characteristic self-assembling behaviors and excellent host-guest properties in supramolecular chemistry. Herein, we present a family of macrocyclic diphenylamine[n]arenes (DPA[n]s, n = 3-7) consisting of methyldiphenylamine units through a facile one-pot synthesis strategy. Unlike many other reported macrocyclic arenes, the resultant non-planar DPA[n]s feature intrinsic π-π stacking interactions, interesting self-assembling behaviors and ethene/ethyne capture properties. Specifically, strong multiple intermolecular edge-to-face aromatic interactions in DPA[3] have been systematically investigated both in solid and solution states. The intriguing findings on the intermolecular edge-to-face stacking interaction mode in the macrocycle would further highlight the importance of noncovalent π-π interaction in supramolecular self-assembly. This study will also shed light on the macrocyclic and supramolecular chemistry and, we expect, will provide a direction for design and synthesis of covalent macrocycles in this area.
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Affiliation(s)
- Lijun Mao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663N. Zhongshan Road, 200062, Shanghai, People's Republic of China
| | - Yang Hu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663N. Zhongshan Road, 200062, Shanghai, People's Republic of China
| | - Qian Tu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663N. Zhongshan Road, 200062, Shanghai, People's Republic of China
| | - Wei-Ling Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663N. Zhongshan Road, 200062, Shanghai, People's Republic of China
| | - Xiao-Li Zhao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663N. Zhongshan Road, 200062, Shanghai, People's Republic of China
| | - Wenjing Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 350002, Fujian, Fuzhou, People's Republic of China
| | - Daqiang Yuan
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 350002, Fujian, Fuzhou, People's Republic of China
| | - Jin Wen
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610, Prague 6, Czech Republic
| | - Xueliang Shi
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663N. Zhongshan Road, 200062, Shanghai, People's Republic of China.
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6
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Andersson CD, Mishra BK, Forsgren N, Ekström F, Linusson A. Physical Mechanisms Governing Substituent Effects on Arene-Arene Interactions in a Protein Milieu. J Phys Chem B 2020; 124:6529-6539. [PMID: 32610016 PMCID: PMC7467712 DOI: 10.1021/acs.jpcb.0c03778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/26/2020] [Indexed: 11/28/2022]
Abstract
Arene-arene interactions play important roles in protein-ligand complex formation. Here, we investigate the characteristics of arene-arene interactions between small organic molecules and aromatic amino acids in protein interiors. The study is based on X-ray crystallographic data and quantum mechanical calculations using the enzyme acetylcholinesterase and selected inhibitory ligands as a model system. It is shown that the arene substituents of the inhibitors dictate the strength of the interaction and the geometry of the resulting complexes. Importantly, the calculated interaction energies correlate well with the measured inhibitor potency. Non-hydrogen substituents strengthened all interaction types in the protein milieu, in keeping with results for benzene dimer model systems. The interaction energies were dispersion-dominated, but substituents that induced local dipole moments increased the electrostatic contribution and thus yielded more strongly bound complexes. These findings provide fundamental insights into the physical mechanisms governing arene-arene interactions in the protein milieu and thus into molecular recognition between proteins and small molecules.
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Affiliation(s)
| | - Brijesh Kumar Mishra
- International
Institute of Information Technology, Bangalore, Karnataka 560003, India
| | - Nina Forsgren
- CBRN
Defense and Security, Swedish Defense Research
Agency, SE-90621 Umeå, Sweden
| | - Fredrik Ekström
- CBRN
Defense and Security, Swedish Defense Research
Agency, SE-90621 Umeå, Sweden
| | - Anna Linusson
- Department
of Chemistry, Umeå University, SE-90187 Umeå, Sweden
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7
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Tekin A. Towards the crystal structure of thymine: An intermolecular force field development and parallel global cluster optimizations. J Chem Phys 2019; 151:244302. [DOI: 10.1063/1.5131754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
- Research Institute for Fundamental Sciences (TÜBİTAK-TBAE), 41470 Gebze, Kocaeli, Turkey
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8
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Shirkov L, Makarewicz J. Theoretical study of the complexes of dichlorobenzene isomers with argon. II. SAPT analysis of the intermolecular interaction. J Chem Phys 2019; 150:074302. [PMID: 30795670 DOI: 10.1063/1.5053802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The interaction of argon with dichlorobenzene isomers (DCB-Ar) has been analyzed with the help of the symmetry-adapted perturbation theory based on the density functional description of monomer properties (DFT-SAPT). The global potential energy surface (PES) of these complexes determined from the DFT-SAPT interaction energy (Eint) values has been compared to the CCSD(T) (coupled cluster method including single and double excitations with perturbative triple excitations) PES reported in the companion Paper I [J. Makarewicz and L. Shirkov, J. Chem. Phys. 150, 074301 (2019)]. The equilibrium structures and the binding energies found using DFT-SAPT and CCSD(T) methods combined with adequate basis sets are in good agreement. Besides DCB-Ar, we confirmed that DFT-SAPT gives accurate values of these quantities for other complexes containing an aromatic molecule and Ar. However, DFT-SAPT PES of DCB-Ar is flatter than the corresponding CCSD(T) one. As a result, the intermolecular vibrational energies are systematically underestimated. The analytical form of the important interrelations between SAPT components of Eint, established previously by us [J. Makarewicz and L. Shirkov, J. Chem. Phys. 144, 204115 (2016)], has been approved for the DCB-Ar complexes. Simplified SAPT models based on these relations have been employed to explain physical reasons for differences in the structures and the binding energies of DCB-Ar isomers. It is shown that the equilibrium distance of Ar to DCB plane and the binding energy are determined mainly by dispersion energy. The shift of Ar toward Cl is caused by both exchange and dispersion terms.
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Affiliation(s)
- Leonid Shirkov
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Jan Makarewicz
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
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9
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Al-Hamdani YS, Tkatchenko A. Understanding non-covalent interactions in larger molecular complexes from first principles. J Chem Phys 2019; 150:010901. [PMID: 30621423 PMCID: PMC6910608 DOI: 10.1063/1.5075487] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/05/2018] [Indexed: 01/02/2023] Open
Abstract
Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non-covalent interactions to date has been mainly developed in the tens-of-atoms molecular regime. This falls considerably short of the scales at which we would like to understand energy trends, structural properties, and temperature dependencies in materials where non-covalent interactions have an appreciable role. However, as more reference information is obtained beyond moderately sized molecular systems, our understanding is improving and we stand to gain pertinent insights by tackling more complex systems, such as supramolecular complexes, molecular crystals, and other soft materials. In addition, accurate reference information is needed to provide the drive for extending the predictive power of more efficient workhorse methods, such as density functional approximations that also approximate van der Waals dispersion interactions. In this perspective, we discuss the first-principles approaches that have been used to obtain reference interaction energies for beyond modestly sized molecular complexes. The methods include quantum Monte Carlo, symmetry-adapted perturbation theory, non-canonical coupled cluster theory, and approaches based on the random-phase approximation. By considering the approximations that underpin each method, the most accurate theoretical references for supramolecular complexes and molecular crystals to date are ascertained. With these, we also assess a handful of widely used exchange-correlation functionals in density functional theory. The discussion culminates in a framework for putting into perspective the accuracy of high-level wavefunction-based methods and identifying future challenges.
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Affiliation(s)
- Yasmine S Al-Hamdani
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
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10
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Stöhr M, Van Voorhis T, Tkatchenko A. Theory and practice of modeling van der Waals interactions in electronic-structure calculations. Chem Soc Rev 2019; 48:4118-4154. [PMID: 31190037 DOI: 10.1039/c9cs00060g] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules and materials. vdW forces arise from the interaction of quantum-mechanical fluctuations in the electronic charge density. Within (semi-)local density functional approximations or Hartree-Fock theory such interactions are neglected altogether. Non-covalent vdW interactions, however, are ubiquitous in nature and play a key role for the understanding and accurate description of the stability, dynamics, structure, and response properties in a plethora of systems. During the last decade, many promising methods have been developed for modeling vdW interactions in electronic-structure calculations. These methods include vdW-inclusive Density Functional Theory and correlated post-Hartree-Fock approaches. Here, we focus on the methods within the framework of Density Functional Theory, including non-local van der Waals density functionals, interatomic dispersion models within many-body and pairwise formulation, and random phase approximation-based approaches. This review aims to guide the reader through the theoretical foundations of these methods in a tutorial-style manner and, in particular, highlight practical aspects such as the applicability and the advantages and shortcomings of current vdW-inclusive approaches. In addition, we give an overview of complementary experimental approaches, and discuss tools for the qualitative understanding of non-covalent interactions as well as energy decomposition techniques. Besides representing a reference for the current state-of-the-art, this work is thus also designed as a concise and detailed introduction to vdW-inclusive electronic structure calculations for a general and broad audience.
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Affiliation(s)
- Martin Stöhr
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg.
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11
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Mishra BK, Venkatnarayan R. Substituents’ influence on the C–H···π interaction in the T-shaped benzene dimer. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2249-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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12
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Heßelmann A. DFT-SAPT Intermolecular Interaction Energies Employing Exact-Exchange Kohn–Sham Response Methods. J Chem Theory Comput 2018; 14:1943-1959. [DOI: 10.1021/acs.jctc.7b01233] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andreas Heßelmann
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstrasse 3, D-91058 Erlangen, Germany
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13
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Calvo F, Yurtsever E, Tekin A. Physisorption of H 2 on Fullerenes and the Solvation of C 60 by Hydrogen Clusters at Finite Temperature: A Theoretical Assessment. J Phys Chem A 2018; 122:2792-2800. [PMID: 29451795 DOI: 10.1021/acs.jpca.8b00163] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction between hydrogen and carbonaceous nanostructures is of fundamental interest in various areas of physical chemistry. In this contribution we have revisited the physisorption of hydrogen molecules and H2 clusters on fullerenes, following a first-principles approach in which the interaction is quantitatively evaluated for the C20 system using high-level electronic structure methods. Relative to coupled cluster data at the level of single, double, and perturbative triple excitations taken as a benchmark, the results for rotationally averaged physisorbed H2 show a good performance of MP2 variants and symmetry-adapted perturbation theory, but significant deviations and basis set convergence issues are found for dispersion-corrected density functional theory. These electronic structure data are fitted to produce effective coarse-grained potentials for use in larger systems such as C60-H2. Using path-integral molecular dynamics, the potentials are also applied to parahydrogen clusters solvated around fullerenes, across the regime where the first solvation shell becomes complete and as a function of increasing temperature. For C60 our findings indicate a sensible dependence of the critical solvation size on the underlying potential. As the temperature is increased, a competition is found between the surface and radial expansions of the solvation shell, with one molecule popping away at intermediate temperatures but getting reinserted at even higher temperatures.
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Affiliation(s)
- F Calvo
- LiPhy , Université Grenoble Alpes and CNRS UMR 5588 , 140 Avenue de la Physique , 38402 St Martin d'Hères , France
| | - E Yurtsever
- Koç University , Chemistry Department , Rumeli Feneri Yolu , 34450 Sariyer, Istanbul , Turkey
| | - A Tekin
- Informatics Institute , Istanbul Technical University , 34469 Maslak, Istanbul , Turkey
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14
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Bamdad M, Farrokhpour H, Najafi B, Ashrafizaadeh M. Energy decomposition analysis of the intermolecular interaction energy between different gas molecules (H2, O2, H2O, N2, CO2, H2S, and CO) and selected Li+-doped graphitic molecules: DF-SAPT (DFT) calculations. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2224-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Karatosun A, Çankaya M, Tekin A. Symmetry-adapted perturbation theory potential for the adenine dimer. Phys Chem Chem Phys 2018; 20:26303-26314. [DOI: 10.1039/c8cp03798a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A new ab initio intermolecular interaction potential for the adenine dimer has been developed.
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Affiliation(s)
- Armağan Karatosun
- Informatics Institute, Istanbul Technical University
- 34469 Maslak
- Turkey
| | - Mehmet Çankaya
- Informatics Institute, Istanbul Technical University
- 34469 Maslak
- Turkey
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University
- 34469 Maslak
- Turkey
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16
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Shirkov L, Sladek V. Benchmark CCSD-SAPT study of rare gas dimers with comparison to MP-SAPT and DFT-SAPT. J Chem Phys 2017; 147:174103. [DOI: 10.1063/1.4997569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Leonid Shirkov
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Vladimir Sladek
- Institute of Chemistry–Centre for Glycomics, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia
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17
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Manukyan A, Tekin A. The intermolecular dimer potential for guanine. J Chem Phys 2017; 147:154311. [DOI: 10.1063/1.4998792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Artür Manukyan
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
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18
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Sedlak R, Řezáč J. Empirical D3 Dispersion as a Replacement for ab Initio Dispersion Terms in Density Functional Theory-Based Symmetry-Adapted Perturbation Theory. J Chem Theory Comput 2017; 13:1638-1646. [DOI: 10.1021/acs.jctc.6b01198] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert Sedlak
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
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19
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Bernhard D, Dietrich F, Fatima M, Perez C, Poblotzki A, Jansen G, Suhm MA, Schnell M, Gerhards M. Multi-spectroscopic and theoretical analyses on the diphenyl ether–tert-butyl alcohol complex in the electronic ground and electronically excited state. Phys Chem Chem Phys 2017; 19:18076-18088. [DOI: 10.1039/c7cp02967e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multi-spectroscopic and theoretical investigations on the isolated diphenyl ether–tert-butyl alcohol complex – an ideal benchmark system for theory with strongly competing OH–O and OH–π binding motifs.
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Affiliation(s)
- Dominic Bernhard
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - Fabian Dietrich
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - Mariyam Fatima
- Max-Planck-Institut für Struktur und Dynamik der Materie
- D-22761 Hamburg
- Germany
| | - Cristobal Perez
- Max-Planck-Institut für Struktur und Dynamik der Materie
- D-22761 Hamburg
- Germany
| | - Anja Poblotzki
- Institut für Physikalische Chemie
- Universität Göttingen
- D-37077 Göttingen
- Germany
| | - Georg Jansen
- Fakultät für Chemie
- Universität Duisburg-Essen
- D-45117 Essen
- Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Universität Göttingen
- D-37077 Göttingen
- Germany
| | - Melanie Schnell
- Max-Planck-Institut für Struktur und Dynamik der Materie
- D-22761 Hamburg
- Germany
| | - Markus Gerhards
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
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20
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Makarewicz J, Shirkov L. Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components. J Chem Phys 2016; 144:204115. [PMID: 27250287 DOI: 10.1063/1.4950955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.
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Affiliation(s)
- Jan Makarewicz
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Leonid Shirkov
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
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21
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Řezáč J, Hobza P. Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications. Chem Rev 2016; 116:5038-71. [DOI: 10.1021/acs.chemrev.5b00526] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
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22
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Berg L, Mishra BK, Andersson CD, Ekström F, Linusson A. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes. Chemistry 2016; 22:2672-81. [DOI: 10.1002/chem.201503973] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Lotta Berg
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
| | | | | | - Fredrik Ekström
- CBRN Defense and Security; Swedish Defense Research Agency; 906 21 Umeå Sweden
| | - Anna Linusson
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
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23
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Chen YT, Hui K, Chai JD. The van der Waals interactions in rare-gas dimers: the role of interparticle interactions. Phys Chem Chem Phys 2016; 18:3011-22. [DOI: 10.1039/c5cp06317e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the potential energy curves of rare-gas dimers with various ranges and strengths of interparticle interactions (nuclear–electron, electron–electron, and nuclear–nuclear interactions).
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Affiliation(s)
- Yu-Ting Chen
- Department of Physics
- National Taiwan University
- Taipei 10617
- Taiwan
| | - Kerwin Hui
- Department of Physics
- National Taiwan University
- Taipei 10617
- Taiwan
| | - Jeng-Da Chai
- Department of Physics
- National Taiwan University
- Taipei 10617
- Taiwan
- Center for Theoretical Sciences and Center for Quantum Science and Engineering
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24
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Gilday LC, Robinson SW, Barendt TA, Langton MJ, Mullaney BR, Beer PD. Halogen Bonding in Supramolecular Chemistry. Chem Rev 2015; 115:7118-95. [DOI: 10.1021/cr500674c] [Citation(s) in RCA: 913] [Impact Index Per Article: 101.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lydia C. Gilday
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sean W. Robinson
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Timothy A. Barendt
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Matthew J. Langton
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin R. Mullaney
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Paul D. Beer
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
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25
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Yourdkhani S, Korona T, Hadipour NL. Structure and Energetics of Complexes of B12N12 with Hydrogen Halides—SAPT(DFT) and MP2 Study. J Phys Chem A 2015; 119:6446-67. [DOI: 10.1021/acs.jpca.5b01756] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sirous Yourdkhani
- Department
of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
- Faculty
of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Tatiana Korona
- Faculty
of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Nasser L. Hadipour
- Department
of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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26
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Liu Y, Liu Y, Gallo AA, Knierim KD, Taylor ER, Tzeng N. Performances of DFT methods implemented in G09 for simulations of the dispersion-dominated CH-π in ligand–protein complex: A case study with glycerol-GDH. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.12.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Shirkov L, Makarewicz J. Does DFT-SAPT method provide spectroscopic accuracy? J Chem Phys 2015; 142:064102. [DOI: 10.1063/1.4907204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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28
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Riley KE, Ford CL, Demouchet K. Comparison of hydrogen bonds, halogen bonds, C H⋯π interactions, and C X⋯π interactions using high-level ab initio methods. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.040] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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29
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Sharma B, Srivastava HK, Gayatri G, Sastry GN. Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions. J Comput Chem 2015; 36:529-38. [DOI: 10.1002/jcc.23827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Bhaskar Sharma
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
| | - Hemant Kumar Srivastava
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
| | - Gaddamanugu Gayatri
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
| | - Garikapati Narahari Sastry
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
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30
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Manukyan A, Tekin A. First principles potential for the cytosine dimer. Phys Chem Chem Phys 2015; 17:14685-701. [DOI: 10.1039/c5cp00553a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new first principles potential for the cytosine dimer.
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Affiliation(s)
- Artür Manukyan
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
| | - Adem Tekin
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
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31
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Singh MK, Rajaraman G. Can CH⋅⋅⋅π Interactions Be Used To Design Single-Chain Magnets? Chemistry 2014; 21:980-3. [DOI: 10.1002/chem.201404853] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 11/11/2022]
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32
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Gadre SR, Yeole SD, Sahu N. Quantum chemical investigations on molecular clusters. Chem Rev 2014; 114:12132-73. [PMID: 25341561 DOI: 10.1021/cr4006632] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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33
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Mishra BK, Deshmukh MM, Venkatnarayan R. C-H···π interactions and the nature of the donor carbon atom. J Org Chem 2014; 79:8599-606. [PMID: 25157745 DOI: 10.1021/jo501251s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The influence of multiple substituents (F, CH3, NO2, CN, Cl, OH and NH2) on the C-H···π interaction in benzene-ethylene complex was investigated using the estimated CCSD(T) method and complete basis set limit. The results were compared with our earlier reported complexes of benzene-acetylene and benzene-methane, thus completing the sp, sp(2) and sp(3) series of C-H donors. The stabilization energy values for multiple fluoro-substituted benzene-ethylene complexes are found to be very close to those of the multiple fluoro-substituted benzene-methane complexes. Expectedly, the stabilization energies for the multiple methyl-substituted benzene-ethylene complexes lie between those of the multiple methyl-substituted benzene-methane and benzene-acetylene complexes. Energy decomposition analysis using the DFT-SAPT method predicts the dispersion energy to be dominant, similar to the benzene-methane complexes. For the symmetrically disubstituted complexes (-OH, -Cl, -NH2, -CN and -NO2), additional C-H···X interaction was observed, possibly due to the angular orientation of the ethylene molecule. Multidimensional correlation analysis between the electrostatic, dispersion and exchange-repulsion with the C-H···π interaction distance (r), Hammett constant (σ) and the molar refractivity (MR) revealed strong correlation between dispersion energy and the C-H···π interaction distance (r) as well as molar refractivity (MR).
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Affiliation(s)
- Brijesh Kumar Mishra
- International Institute of Information Technology Bangalore , Bangalore 560100, Karnataka, India
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34
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Hatz R, Hänninen V, Halonen L. Dispersion Interactions in Small Zinc, Cadmium, and Mercury Clusters. J Phys Chem A 2014; 118:5734-40. [DOI: 10.1021/jp505023g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard Hatz
- Laboratory
of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55
(A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
| | - Vesa Hänninen
- Laboratory
of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55
(A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
| | - Lauri Halonen
- Laboratory
of Physical Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55
(A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
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35
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Ni J, Wang YG, Wang HH, Xu L, Zhao YQ, Pan YZ, Zhang JJ. Thermo- and mechanical-grinding-triggered color and luminescence switches of the diimine-platinum(II) complex with 4-bromo-2,2'-bipyridine. Dalton Trans 2014; 43:352-60. [PMID: 24108349 DOI: 10.1039/c3dt51936h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The square-planar diimine-platinum(II) complex, Pt(4-Brbpy)(C≡CC6H5)2 (1) (4-Brbpy = 4-bromo-2,2'-bipyridine), was prepared and characterized. Solid-state 1 exhibits reversible thermo- and mechanical-grinding-triggered color and luminescence changes. When crystalline 1·2(CH2Cl2) or 1·2(CHCl3) are heated or ground, the original bright yellow-green emission centered at 525 (549, sh) nm changed to 637 and 690 nm, corresponding to thermo- and mechanochromic response shifts of approximately 88-112 nm and 141-165 nm, respectively. Meanwhile the crystalline state changes into an amorphous phase in both processes. Once the amorphous sample absorbs organic vapors, it can be reverted to the original crystalline state, along with red luminescence turning back to yellow-green emission. The reversibility of thermo- and mechanical-grinding-triggered chromic luminescence properties has been dynamically monitored by emission spectra and X-ray diffraction patterns. The dramatic thermo- and mechanical-grinding-triggered emission red shifts are most likely due to the conversion of the (3)MLCT/(3)LLCT emission state into the (3)MMLCT triplet state.
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Affiliation(s)
- Jun Ni
- Chemistry College, Dalian University of Technology, Dalian 116024, China.
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36
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Riley KE, Hobza P. The relative roles of electrostatics and dispersion in the stabilization of halogen bonds. Phys Chem Chem Phys 2014; 15:17742-51. [PMID: 24067893 DOI: 10.1039/c3cp52768a] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this work we highlight recent work aimed at the characterization of halogen bonds. Here we discuss the origins of the σ-hole, the modulation of halogen bond strength by changing of neighboring chemical groups (i.e. halogen bond tuning), the performance of various computational methods in treating halogen bonds, and the strength and character of the halogen bond, the dihalogen bond, and two hydrogen bonds in bromomethanol dimers (which serve as model complexes) are compared. Symmetry adapted perturbation theory analysis of halogen bonding complexes indicates that halogen bonds strongly depend on both dispersion and electrostatics. The electrostatic interaction that occurs between the halogen σ-hole and the electronegative halogen bond donor is responsible for the high degree of directionality exhibited by halogen bonds. Because these noncovalent interactions have a strong dispersion component, it is important that the computational method used to treat a halogen bonding system be chosen very carefully, with correlated methods (such as CCSD(T)) being optimal. It is also noted here that most forcefield-based molecular mechanics methods do not describe the halogen σ-hole, and thus are not suitable for treating systems with halogen bonds. Recent attempts to improve the molecular mechanics description of halogen bonds are also discussed.
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Affiliation(s)
- Kevin E Riley
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, Box 22, New Orleans, LA 70125, USA.
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37
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Roles of electrostatic interaction and dispersion in CH···CH, CH···π, and π···π ethylene dimers. J Mol Model 2014; 20:2185. [DOI: 10.1007/s00894-014-2185-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/17/2014] [Indexed: 11/29/2022]
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38
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de Lara-Castells MP, Stoll H, Mitrushchenkov AO. Assessing the Performance of Dispersionless and Dispersion-Accounting Methods: Helium Interaction with Cluster Models of the TiO2(110) Surface. J Phys Chem A 2014; 118:6367-84. [DOI: 10.1021/jp412765t] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Hermann Stoll
- Institut für Theoretische Chemie, Universität Stuttgart, D-70550 Stuttgart, Germany
| | - Alexander O. Mitrushchenkov
- Laboratoire Modélisation et Simulation Multi Echelle, MSME
UMR 8208 CNRS, Université Paris-Est, 5 bd Descartes, 77454 Marne-la-Vallée, France
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39
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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40
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Ulrich NW, Seifert NA, Dorris RE, Peebles RA, Pate BH, Peebles SA. Benzene⋯acetylene: a structural investigation of the prototypical CH⋯π interaction. Phys Chem Chem Phys 2014; 16:8886-94. [DOI: 10.1039/c4cp00845f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The benzene⋯acetylene dimer is a symmetric top with μ = 0.438(11) D and H⋯π = 2.4921(1) Å.
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Affiliation(s)
- Nathan W. Ulrich
- Eastern Illinois University
- Department of Chemistry
- Charleston, USA
| | - Nathan A. Seifert
- University of Virginia
- Department of Chemistry and Biochemistry
- Charlottesville, USA
| | - Rachel E. Dorris
- Eastern Illinois University
- Department of Chemistry
- Charleston, USA
| | | | - Brooks H. Pate
- University of Virginia
- Department of Chemistry and Biochemistry
- Charlottesville, USA
| | - Sean A. Peebles
- Eastern Illinois University
- Department of Chemistry
- Charleston, USA
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41
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Maranzana A, Giordana A, Indarto A, Tonachini G, Barone V, Causà M, Pavone M. Density functional theory study of the interaction of vinyl radical, ethyne, and ethene with benzene, aimed to define an affordable computational level to investigate stability trends in large van der Waals complexes. J Chem Phys 2013; 139:244306. [DOI: 10.1063/1.4846295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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42
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Jansen G. Symmetry‐adapted perturbation theory based on density functional theory for noncovalent interactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1164] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Georg Jansen
- Theoretical Organic Chemistry, Department of ChemistryUniversity Duisburg‐EssenEssenGermany
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43
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Ansorg K, Tafipolsky M, Engels B. Cation−π Interactions: Accurate Intermolecular Potential from Symmetry-Adapted Perturbation Theory. J Phys Chem B 2013; 117:10093-102. [DOI: 10.1021/jp403578r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kay Ansorg
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Maxim Tafipolsky
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Campus Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg,
Germany
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44
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Simeon TM, Ratner MA, Schatz GC. Nature of noncovalent interactions in catenane supramolecular complexes: calibrating the MM3 force field with ab initio, DFT, and SAPT methods. J Phys Chem A 2013; 117:7918-27. [PMID: 23941280 DOI: 10.1021/jp400051b] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H···O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the [3]catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3. Symmetry adapted perturbation theory (DFT-SAPT) provides the highest level of theory considered, and we use the DFT-SAPT results both to calibrate the other electronic structure methods, and the empirical potential MM3 force field that is often used to describe larger catenane and rotaxane structures where [C-H···O] hydrogen-bonding and π-π stacking interactions play a role. Our results indicate that the MM3 calculated complexation energies agree qualitatively with the energetic ordering from DFT-SAPT calculations with an aug-cc-pVTZ basis, both for structures dominated by [C-H···O] hydrogen-bonding and π-π stacking interactions. When the DFT-SAPT energies are decomposed into components, we find that electrostatic interactions dominate the [C-H···O] hydrogen-bonding interactions, while dispersion makes a significant contribution to π-π stacking. Another important conclusion is that DFT-D3 based on M06 or M06-2X provides interaction energies that are in near-quantitative agreement with DFT-SAPT. DFT results without the D3 correction have important differences compared to DFT-SAPT, while HF and even MP2 results are in poor agreement with DFT-SAPT.
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Affiliation(s)
- Tomekia M Simeon
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.
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45
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Karthikeyan S, Ramanathan V, Mishra BK. Influence of the Substituents on the CH...π Interaction: Benzene–Methane Complex. J Phys Chem A 2013; 117:6687-94. [DOI: 10.1021/jp404972f] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- S. Karthikeyan
- Department of Chemistry, Sungkyunkwan University, Suwon, South Korea
| | - V. Ramanathan
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
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46
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47
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Böning M, Stuhlmann B, Engler G, Busker M, Häber T, Tekin A, Jansen G, Kleinermanns K. Towards a Spectroscopic and Theoretical Identification of the Isolated Building Blocks of the Benzene–Acetylene Cocrystal. Chemphyschem 2012. [DOI: 10.1002/cphc.201200701] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Markus Böning
- Institut für Physikalische Chemie, Heinrich‐Heine Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf (Germany)
| | - Benjamin Stuhlmann
- Institut für Physikalische Chemie, Heinrich‐Heine Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf (Germany)
| | - Gernot Engler
- Institut für Physikalische Chemie, Heinrich‐Heine Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf (Germany)
| | - Matthias Busker
- Institut für Physikalische Chemie, Heinrich‐Heine Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf (Germany)
| | - Thomas Häber
- Institut für Physikalische Chemie, Heinrich‐Heine Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf (Germany)
- Current address: Karlsruher Institut für Technologie (KIT), Engler‐Bunte‐Institut, Bereich Verbrennungstechnik, Engler‐Bunte‐Ring 1, 76131 Karlsruhe (Germany)
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul (Turkey)
| | - Georg Jansen
- Fakultät für Chemie, Universität Duisburg‐Essen, Universitätsstr. 5, 45117 Essen (Germany)
| | - Karl Kleinermanns
- Institut für Physikalische Chemie, Heinrich‐Heine Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf (Germany)
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48
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Jantimapornkij P, Jundee P, Uttamapinant N, Pianwanit S, Karpfen A. AH⋯π hydrogen bonding to acetylene and benzene: The role of intramolecular coupling. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Sameera WMC, Pantazis DA. A Hierarchy of Methods for the Energetically Accurate Modeling of Isomerism in Monosaccharides. J Chem Theory Comput 2012; 8:2630-45. [PMID: 26592108 DOI: 10.1021/ct3002305] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- W. M. C. Sameera
- Institut Català d’Investigació
Química, Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an
der Ruhr, Germany
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50
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Kuchenbecker D, Jansen G. Intermolecular Interactions in Weak Donor-Acceptor Complexes from Symmetry-Adapted Perturbation and Coupled-Cluster Theory: Tetracyanoethylene-Benzene and Tetracyanoethylene-p-Xylene. Chemphyschem 2012; 13:2769-76. [DOI: 10.1002/cphc.201200164] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/23/2012] [Indexed: 11/12/2022]
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