1
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Mo Y, Danovich D, Shaik S. The roles of charge transfer and polarization in non-covalent interactions: a perspective from ab initio valence bond methods. J Mol Model 2022; 28:274. [PMID: 36006511 DOI: 10.1007/s00894-022-05187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH‧‧‧HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH3, H2O and NMe3 partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO2 (X = Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H∙∙∙H-C interactions in alkane dimers and graphene sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.
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Affiliation(s)
- Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA.
| | - David Danovich
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel.
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2
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Alić J, Biljan I, Štefanić Z, Šekutor M. Preparation and characterization of non-aromatic ether self-assemblies on a HOPG surface. NANOTECHNOLOGY 2022; 33:355603. [PMID: 35545006 DOI: 10.1088/1361-6528/ac6e72] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
On-surface self-assemblies of aromatic organic molecules have been widely investigated, but the characterization of analogous self-assemblies consisting of fully sp3-hybridized molecules remains challenging. The possible on-surface orientations of alkyl molecules not exclusively comprised of long alkyl chains are difficult to distinguish because of their inherently low symmetry and non-planar nature. Here, we present a detailed study of diamondoid ethers, structurally rigid and fully saturated molecules, which form uniform 2D monolayers on a highly oriented pyrolytic graphite (HOPG) surface. Using scanning tunneling microscopy, various computational tools, and x-ray structural analysis, we identified the most favorable on-surface orientations of these rigid ethers and accounted for the forces driving the self-organization process. The influence of the oxygen atom and London dispersion interactions were found to be responsible for the formation of the observed highly ordered 2D ether assemblies. Our findings provide insight into the on-surface properties and behavior of non-aromatic organic compounds and broaden our understanding of the phenomena characteristic of monolayers consisting of non-planar molecules.
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Affiliation(s)
- Jasna Alić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia
| | - Ivana Biljan
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Zoran Štefanić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia
| | - Marina Šekutor
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia
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3
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Maley SM, Steagall R, Lief GR, Buck RM, Yang Q, Sydora OL, Bischof SM, Ess DH. Computational Evaluation and Design of Polyethylene Zirconocene Catalysts with Noncovalent Dispersion Interactions. Organometallics 2022. [DOI: 10.1021/acs.organomet.1c00670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Steven M. Maley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Robert Steagall
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Graham R. Lief
- Research and Technology, Chevron Phillips Chemical Company LP, Highways 60 & 123, Bartlesville, Oklahoma 74003, United States
| | - Richard M. Buck
- Research and Technology, Chevron Phillips Chemical Company LP, Highways 60 & 123, Bartlesville, Oklahoma 74003, United States
| | - Qing Yang
- Research and Technology, Chevron Phillips Chemical Company LP, Highways 60 & 123, Bartlesville, Oklahoma 74003, United States
| | - Orson L. Sydora
- Research and Technology, Chevron Phillips Chemical Company LP, 1862, Kingwood Drive, Kingwood, Texas 77339, United States
| | - Steven M. Bischof
- Research and Technology, Chevron Phillips Chemical Company LP, 1862, Kingwood Drive, Kingwood, Texas 77339, United States
| | - Daniel H. Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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4
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Chen L, Dang J, Du J, Wang C, Mo Y. Hydrogen and Halogen Bonding in Homogeneous External Electric Fields: Modulating the Bond Strengths. Chemistry 2021; 27:14042-14050. [PMID: 34319620 DOI: 10.1002/chem.202102284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 12/28/2022]
Abstract
Recent years have witnessed various fascinating phenomena arising from the interactions of noncovalent bonds with homogeneous external electric fields (EEFs). Here we performed a computational study to interpret the sensitivity of intrinsic bond strengths to EEFs in terms of steric effect and orbital interactions. The block-localized wavefunction (BLW) method, which combines the advantages of both ab initio valence bond (VB) theory and molecular orbital (MO) theory, and the subsequent energy decomposition (BLW-ED) approach were adopted. The sensitivity was monitored and analyzed using the induced energy term, which is the variation in each energy component along the EEF strength. Systems with single or multiple hydrogen (H) or halogen (X) bond(s) were also examined. It was found that the X-bond strength change to EEFs mainly stems from the covalency change, while generally the steric effect rules the response of H-bonds to EEFs. Furthermore, X-bonds are more sensitive to EEFs, with the key difference between H- and X-bonds lying in the charge transfer interaction. Since phenylboronic acid has been experimentally used as a smart linker in EEFs, switchable sensitivity was scrutinized with the example of the phenylboronic acid dimer, which exhibits two conformations with either antiparallel or parallel H-bonds, thereby, opposite or consistent responses to EEFs. Among the studied systems, the quadruple X-bonds in molecular capsules exhibit remarkable sensitivity, with its interaction energy increased by -95.2 kJ mol-1 at the EEF strength 0.005 a.u.
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Affiliation(s)
- Li Chen
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Jingshuang Dang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Juan Du
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience & Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC 27401, USA
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5
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DFT study on binding of single and double methane with aromatic hydrocarbons and graphene: stabilizing CH…HC interactions between two methane molecules. Struct Chem 2020. [DOI: 10.1007/s11224-020-01657-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Lin X, Wu W, Mo Y. A theoretical perspective of the agostic effect in early transition metal compounds. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213401] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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7
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Śliwa P, Mitoraj MP, Sagan F, Handzlik J. Formation of active species from ruthenium alkylidene catalysts-an insight from computational perspective. J Mol Model 2019; 25:331. [PMID: 31701244 DOI: 10.1007/s00894-019-4202-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/03/2019] [Indexed: 10/25/2022]
Abstract
Ruthenium alkylidene complexes are commonly used as olefin metathesis catalysts. Initiation of the catalytic process requires formation of a 14-electron active ruthenium species via dissociation of a respective ligand. In the present work, this initiation step has been computationally studied for the Grubbs-type catalysts (H2IMes)(PCy3)(Cl)2Ru=CHPh, (H2IMes)(PCy3)(Cl)2Ru=CH-CH=CMe2 and (H2IMes)(3-Br-py)2(Cl)2Ru=CHPh, and the Hoveyda-Grubbs-type catalysts (H2IMes)(Cl)2Ru=CH(o-OiPrC6H4), (H2IMes)(Cl)2Ru=CH(5-NO2-2-OiPrC6H3), and (H2IMes)(Cl)2Ru=CH(2-OiPr-3-PhC6H3), using density functional theory (DFT). Additionally, the extended-transition-state combined with the natural orbitals for the chemical valence (ETS-NOCV) and the interacting quantum atoms (IQA) energy decomposition methods were applied. The computationally determined activity order within both families of the catalysts and the activation parameters are in agreement with reported experimental data. The significance of solvent simulation and the basis set superposition error (BSSE) correction is discussed. ETS-NOCV demonstrates that the bond between the dissociating ligand and the Ru-based fragment is largely ionic followed by the charge delocalizations: σ(Ru-P) and π(Ru-P) and the secondary CH…Cl, CH…π, and CH…HC interactions. In the case of transition state structures, the majority of stabilization stems from London dispersion forces exerted by the efficient CH…Cl, CH…π, and CH…HC interactions. Interestingly, the height of the electronic dissociation barriers is, however, directly connected with the prevalent (unfavourable) changes in the electrostatic and orbital interaction contributions despite the favourable relief in Pauli repulsion and geometry reorganization terms during the activation process. According to the IQA results, the isopropoxy group in the Hoveyda-Grubbs-type catalysts is an efficient donor of intra-molecular interactions which are important for the activity of these catalysts.
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Affiliation(s)
- Paweł Śliwa
- Faculty of Chemical Engineering and Technology, Cracow University of Technology, ul. Warszawska 24, 31-155, Kraków, Poland
| | - Mariusz P Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387, Kraków, Poland.
| | - Filip Sagan
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387, Kraków, Poland
| | - Jarosław Handzlik
- Faculty of Chemical Engineering and Technology, Cracow University of Technology, ul. Warszawska 24, 31-155, Kraków, Poland.
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8
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He X, Zhao L, Zhou Z, Zhang S, Pan H, Chen J, Xu J. Near unity charge separation efficiency leads to pure ultraviolet emission in few layer graphene nanosheets. NANOTECHNOLOGY 2019; 30:295201. [PMID: 30812023 DOI: 10.1088/1361-6528/ab0afe] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Two-dimensional materials with van der Waals structure attract intense interest due to their high performance in ultrathin optoelectronic devices. In particular, the high efficiency charge separation between the two-dimensional materials can significantly improve the photo-response of a given device. Here we report the discovery of pure ultraviolet (UV) emission from few layer graphene nanosheets (GNS). Near unity charge separation efficiency is key to pure UV emission. The dynamics of an excited electron were analyzed using femtosecond transient absorption techniques. Electron transfer is observed from surface defect states induced by oxygen-containing functional groups to intrinsic sp2 domain states in few layer GNS. Moreover, a solar blind response device based on few layer GNS with a high on-off ratio was successfully fabricated.
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Affiliation(s)
- Xiaoxiao He
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, People's Republic of China
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9
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Rasouli S, Moghbeli MR, Nikkhah SJ. A deep insight into the polystyrene chain in cyclohexane at theta temperature: molecular dynamics simulation and quantum chemical calculations. J Mol Model 2019; 25:195. [DOI: 10.1007/s00894-019-4078-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
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10
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Nguyen HT, Truong TN. Nature of interlayer carbon–carbon covalent bonding in graphene-based materials. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2458-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Mitoraj MP, Babashkina MG, Robeyns K, Sagan F, Szczepanik DW, Seredina YV, Garcia Y, Safin DA. Chameleon-like Nature of Anagostic Interactions and Its Impact on Metalloaromaticity in Square-Planar Nickel Complexes. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mariusz P. Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
- Institute of Chemistry, University of Tyumen, Perekopskaya Street 15a, 625003 Tyumen, Russian Federation
| | - Koen Robeyns
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
| | - Filip Sagan
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Dariusz W. Szczepanik
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Cracow, Poland
| | - Yulia V. Seredina
- Institute of Chemistry, University of Tyumen, Perekopskaya Street 15a, 625003 Tyumen, Russian Federation
| | - Yann Garcia
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
| | - Damir A. Safin
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, 1348 Louvain-la-Neuve, Belgium
- Institute of Chemistry, University of Tyumen, Perekopskaya Street 15a, 625003 Tyumen, Russian Federation
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12
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Brovarets’ OO, Hovorun DM. Key microstructural mechanisms of the 2-aminopurine mutagenicity: Results of extensive quantum-chemical research. J Biomol Struct Dyn 2019; 37:2716-2732. [DOI: 10.1080/07391102.2018.1495577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2-h Akademika Hlushkova Ave, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2-h Akademika Hlushkova Ave, Kyiv, Ukraine
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13
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Mitoraj MP, Sagan F, Babashkina MG, Isaev AY, Chichigina YM, Safin DA. N
-Thiophosphorylthioureas RNHC(S)NHP(S)(Oi
Pr)2
as an Excellent Platform for Studying the Synergy between Hydrogen-Hydrogen Bonding and Other Families of Non-Covalent Interactions. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mariusz P. Mitoraj
- Department of Theoretical Chemistry; Faculty of Chemistry; Jagiellonian University; Gronostajowa 2 30-387 Cracow Poland
| | - Filip Sagan
- Department of Theoretical Chemistry; Faculty of Chemistry; Jagiellonian University; Gronostajowa 2 30-387 Cracow Poland
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences; Université catholique de Louvain; Place L. Pasteur 1 1348 Louvain-la-Neuve Belgium
| | - Alexey Y. Isaev
- Institute of Chemistry; University of Tyumen; Perekopskaya Str. 15a 625003 Tyumen Russian Federation
| | - Yana M. Chichigina
- Institute of Chemistry; University of Tyumen; Perekopskaya Str. 15a 625003 Tyumen Russian Federation
| | - Damir A. Safin
- Institute of Condensed Matter and Nanosciences; Université catholique de Louvain; Place L. Pasteur 1 1348 Louvain-la-Neuve Belgium
- Institute of Chemistry; University of Tyumen; Perekopskaya Str. 15a 625003 Tyumen Russian Federation
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14
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Wang C, Danovich D, Shaik S, Wu W, Mo Y. Attraction between electrophilic caps: A counterintuitive case of noncovalent interactions. J Comput Chem 2018; 40:1015-1022. [DOI: 10.1002/jcc.25566] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/03/2018] [Accepted: 07/29/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Changwei Wang
- School of Chemistry & Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - David Danovich
- Institute of ChemistryThe Hebrew University Jerusalem 91904 Israel
| | - Sason Shaik
- Institute of ChemistryThe Hebrew University Jerusalem 91904 Israel
| | - Wei Wu
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical EngineeringXiamen University Xiamen 360015 China
| | - Yirong Mo
- Department of ChemistryWestern Michigan University Kalamazoo Michigan 49008
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15
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Cabaleiro-Lago EM, Rodríguez-Otero J. On the Nature of σ-σ, σ-π, and π-π Stacking in Extended Systems. ACS OMEGA 2018; 3:9348-9359. [PMID: 31459068 PMCID: PMC6645327 DOI: 10.1021/acsomega.8b01339] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/27/2018] [Indexed: 05/30/2023]
Abstract
Stacking interactions have been evaluated, employing computational methods, in dimers formed by analogous aliphatic and aromatic species of increasing size. Changes in stability as the systems become larger are mostly controlled by the balance of increasing repulsion and dispersion contributions, while electrostatics plays a secondary but relevant role. The interaction energy increases as the size of the system grows, but it does much faster in π-π dimers than in σ-π complexes and more remarkably than in σ-σ dimers. The main factor behind the larger stability of aromatic dimers compared to complexes containing aliphatic molecules is related to changes in the properties of the aromatic systems due to electron delocalization leading to larger dispersion contributions. Besides, an extra stabilization in π-π complexes is due to the softening of the repulsive wall in aromatic species that allows the molecules to come closer.
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Affiliation(s)
- Enrique M. Cabaleiro-Lago
- Facultade
de Ciencias (Dpto. de Química Física), Universidade de Santiago de Compostela, Campus de Lugo. Avda. Alfonso X El Sabio s/n, 27002 Lugo, Galicia, Spain
| | - Jesús Rodríguez-Otero
- CIQUS
and Facultade de Química (Dpto. de Química Física), Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Galicia, Spain
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16
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Gryn’ova G, Corminboeuf C. Steric "attraction": not by dispersion alone. Beilstein J Org Chem 2018; 14:1482-1490. [PMID: 30013675 PMCID: PMC6037011 DOI: 10.3762/bjoc.14.125] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/02/2018] [Indexed: 12/23/2022] Open
Abstract
Non-covalent interactions between neutral, sterically hindered organic molecules generally involve a strong stabilizing contribution from dispersion forces that in many systems turns the 'steric repulsion' into a 'steric attraction'. In addition to London dispersion, such systems benefit from electrostatic stabilization, which arises from a short-range effect of charge penetration and gets bigger with increasing steric bulk. In the present work, we quantify this contribution for a diverse set of molecular cores, ranging from unsubstituted benzene and cyclohexane to their derivatives carrying tert-butyl, phenyl, cyclohexyl and adamantyl substituents. While the importance of electrostatic interactions in the dimers of sp2-rich (e.g., π-conjugated) cores is well appreciated, less polarizable assemblies of sp3-rich systems with multiple short-range CH···HC contacts between the bulky cyclohexyl and adamantyl moieties are also significantly influenced by electrostatics. Charge penetration is drastically larger in absolute terms for the sp2-rich cores, but still has a non-negligible effect on the sp3-rich dimers, investigated herein, both in terms of their energetics and equilibrium interaction distances. These results emphasize the importance of this electrostatic effect, which has so far been less recognized in aliphatic systems compared to London dispersion, and are therefore likely to have implications for the development of force fields and methods for crystal structure prediction.
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Affiliation(s)
- Ganna Gryn’ova
- Institut des Sciences et Ingénierie Chimiques, École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Clémence Corminboeuf
- Institut des Sciences et Ingénierie Chimiques, École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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17
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Rosado Piquer L, Sánchez RR, Sañudo EC, Echeverría J. Understanding the Molecule-Electrode Interface for Molecular Spintronic Devices: A Computational and Experimental Study. Molecules 2018; 23:molecules23061441. [PMID: 29899309 PMCID: PMC6100063 DOI: 10.3390/molecules23061441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/28/2018] [Accepted: 05/28/2018] [Indexed: 11/16/2022] Open
Abstract
A triple-decker SYML-Dy2 single-molecule magnet (SMM) was synthetized and grafted onto the surface of iron oxide nanoparticles (IO-NPs) coated by an oleic acid monolayer. The magnetism of the SYML-Dy2 complex, and the hybrid system, NP-Dy2, were studied by a superconducting quantum interference device (SQUID). Density functional theory (DFT) calculations were carried out to study both the energetics of the interaction between SYML-Dy2 complex to the organic capping, and the assembly presented by the oleic acid chains.
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Affiliation(s)
- Lidia Rosado Piquer
- Departament de Química Inorgànica, Secció de Química Inorgànica; C/Martí i Franqués 1-11, 08028 Barcelona, Spain.
- Institut de Nanociència i Nanotecnologia (IN2UB), C/Martí i Franqués 1-11, 08028 Barcelona, Spain.
| | - Raquel Royo Sánchez
- Departament de Química Inorgànica, Secció de Química Inorgànica; C/Martí i Franqués 1-11, 08028 Barcelona, Spain.
| | - E Carolina Sañudo
- Departament de Química Inorgànica, Secció de Química Inorgànica; C/Martí i Franqués 1-11, 08028 Barcelona, Spain.
- Institut de Nanociència i Nanotecnologia (IN2UB), C/Martí i Franqués 1-11, 08028 Barcelona, Spain.
| | - Jorge Echeverría
- Departament de Química Inorgànica, Secció de Química Inorgànica; C/Martí i Franqués 1-11, 08028 Barcelona, Spain.
- Institut de Química Teòrica i Computacional (IQTC-UB), Universitat Barcelona, Martí i Franqués 1-11, 08028 Barcelona, Spain.
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18
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Echeverría J. Intermolecular Carbonyl···Carbonyl Interactions in Transition-Metal Complexes. Inorg Chem 2018; 57:5429-5437. [PMID: 29664621 DOI: 10.1021/acs.inorgchem.8b00392] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We performed a comprehensive analysis of intermolecular carbonyl-carbonyl interactions in transition-metal complexes. Those interactions can be classified in two main types depending on the organometallic or organic nature of the donor carbonyl: M-CO···CO and R-CO···CO, respectively. By means of a combined structural and computational study we unraveled their geometrical features and strength. Moreover, electronic structure, natural bond orbitals, energy decomposition analysis, and quantum theory of atoms in molecules calculations were performed to try to understand their nature. Remarkably, we discovered that these carbonyl-carbonyl contacts have several features of the n → π* interaction. The charge transfer from an oxygen lone pair to an empty antibonding π orbital of the acceptor carbonyl is also accompanied by an electrostatic Oδ-···Cδ+ interaction. To the best of our knowledge this is the first report of an intermolecular n → π* interaction in metal complexes. These results might be significant, for instance, for the catalytic activation of carbonyl-containing small molecules with metal compounds or in the design of hybrid organic-inorganic materials, metal-organic frameworks, and other extended structures.
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Affiliation(s)
- Jorge Echeverría
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional IQTC-UB , Universitat de Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
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19
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Jaroš A, Badri Z, Bora PL, Bonab EF, Marek R, Straka M, Foroutan-Nejad C. How Does a Container Affect Acidity of its Content: Charge-Depletion Bonding Inside Fullerenes. Chemistry 2018; 24:4245-4249. [DOI: 10.1002/chem.201706017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Adam Jaroš
- Institute of Organic Chemistry and Biochemistry, of the; Czech Academy of Sciences; Flemingovo nám. 2. 16610 Prague Czech Republic
| | - Zahra Badri
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
| | - Pankaj Lochan Bora
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
- Department of Chemistry, Faculty of Science; Masaryk University; 62500 Brno Czech Republic
| | - Esmaeil Farajpour Bonab
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
- Department of Chemistry, Faculty of Science; Masaryk University; 62500 Brno Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
- Department of Chemistry, Faculty of Science; Masaryk University; 62500 Brno Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, of the; Czech Academy of Sciences; Flemingovo nám. 2. 16610 Prague Czech Republic
| | - Cina Foroutan-Nejad
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
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20
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Shi J, Xia T, Wang C, Yuan K, Zhang J. Ultra-low friction mechanism of highly sp3-hybridized amorphous carbon controlled by interfacial molecule adsorption. Phys Chem Chem Phys 2018; 20:22445-22454. [DOI: 10.1039/c8cp00859k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The friction behaviors of highly sp3-hybridized carbon films, including ultra-nanocrystalline diamond and diamond-like carbon materials, strongly depend on atmospheres.
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Affiliation(s)
- Jing Shi
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
- China
| | - Tiandong Xia
- School of Materials Science & Engineering
- Lanzhou University of Technology
- Lanzhou 730050
- China
| | - Chengbing Wang
- School of Materials Science & Engineering
- Shaanxi University of Science and Technology
- Xi'an 710021
- China
| | - Kun Yuan
- College of Chemical Engineering & Technology
- Tianshui Normal University
- Tianshui 741001
- China
- Institute for Chemical Physics & Department of Chemistry
| | - Junyan Zhang
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou 730000
- China
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21
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Echeverría J. The silane-methane dimer revisited: more than a dispersion-bound system? Phys Chem Chem Phys 2017; 19:32663-32669. [PMID: 29192909 DOI: 10.1039/c7cp07241d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present here a comprehensive computational and theoretical analysis of the silane-methane dimer with the goal of understanding the origin of the interactions that hold it together and the factors that affect its strength. Several interaction topologies have been analysed and the associated interaction energies have been evaluated at the CCSD(T)/aug-cc-pVTZ level of theory. Next, substitution effects have been studied on several silane and methane derivatives. The molecular electrostatic potential (MEP) maps of the molecules involved in the interactions have been built to try to correlate the interaction energies with the maximum/minimum EP values (Vs). Furthermore, we have performed an energy decomposition analysis to gain deeper insight into the physical nature of the interactions and to unravel whether dispersion is the primary component of the attraction. Finally, we complete the theoretical analysis with the study of several experimental crystal structures in which there are silylmethyl short contacts.
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Affiliation(s)
- Jorge Echeverría
- Departament de Química Inorgànica i Orgànica (Secció Inorgànica) and Institut de Química Teòrica i Computacional IQTC-UB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.
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22
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Ebeling D, Šekutor M, Stiefermann M, Tschakert J, Dahl JEP, Carlson RMK, Schirmeisen A, Schreiner PR. London Dispersion Directs On-Surface Self-Assembly of [121]Tetramantane Molecules. ACS NANO 2017; 11:9459-9466. [PMID: 28846392 DOI: 10.1021/acsnano.7b05204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
London dispersion (LD) acts between all atoms and molecules in nature, but the role of LD interactions in the self-assembly of molecular layers is still poorly understood. In this study, direct visualization of single molecules using atomic force microscopy with CO-functionalized tips revealed the exact adsorption structures of bulky and highly polarizable [121]tetramantane molecules on Au(111) and Cu(111) surfaces. We determined the absolute molecular orientations of the completely sp3-hybridized tetramantanes on metal surfaces. Moreover, we demonstrate how LD drives this on-surface self-assembly of [121]tetramantane hydrocarbons, resulting in the formation of a highly ordered 2D lattice. Our experimental findings were underpinned by a systematic computational study, which allowed us to quantify the energies associated with LD interactions and to analyze intermolecular close contacts and attractions in detail.
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Affiliation(s)
- Daniel Ebeling
- Institute of Applied Physics, Justus-Liebig University , Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Marina Šekutor
- Institute of Organic Chemistry, Justus-Liebig University , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Marvin Stiefermann
- Institute of Applied Physics, Justus-Liebig University , Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Jalmar Tschakert
- Institute of Applied Physics, Justus-Liebig University , Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Jeremy E P Dahl
- Stanford Institute for Materials and Energy Sciences , Stanford, California 94305, United States
| | - Robert M K Carlson
- Stanford Institute for Materials and Energy Sciences , Stanford, California 94305, United States
| | - André Schirmeisen
- Institute of Applied Physics, Justus-Liebig University , Heinrich-Buff-Ring 16, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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23
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Novák M, Marek R, Foroutan-Nejad C. Anti-Electrostatic CH-Ion Bonding in Decorated Graphanes. Chemistry 2017; 23:14931-14936. [DOI: 10.1002/chem.201703459] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Martin Novák
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- Department of Chemistry, Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Cina Foroutan-Nejad
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
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24
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Cabaleiro-Lago EM, Rodríguez-Otero J. σ-σ, σ-π, and π-π Stacking Interactions between Six-Membered Cyclic Systems. Dispersion Dominates and Electrostatics Commands. ChemistrySelect 2017. [DOI: 10.1002/slct.201700671] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Enrique M. Cabaleiro-Lago
- Facultade de Ciencias (Dpto. de Química Física); Universidade de Santiago de Compostela; Avda. Alfonso X El Sabio s/n 27002 Lugo, Galicia Spain
| | - Jesús Rodríguez-Otero
- CIQUS and Facultade de Química (Dpto. de Química Física); Universidade de Santiago de Compostela; 15782 Santiago de Compostela, Galicia Spain)
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25
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Wang C, Danovich D, Shaik S, Mo Y. A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds. J Chem Theory Comput 2017; 13:1626-1637. [DOI: 10.1021/acs.jctc.6b01133] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Changwei Wang
- Department
of Chemistry, School of Science, China University of Petroleum (East China), Changjiangxi Road 66, 266580 Tsingtao, China
| | - David Danovich
- Institute
of Chemistry and Lise Meitner Minerva Center for Computational Quantum
Chemistry, The Hebrew University, Jerusalem 91904, Israel
| | - Sason Shaik
- Institute
of Chemistry and Lise Meitner Minerva Center for Computational Quantum
Chemistry, The Hebrew University, Jerusalem 91904, Israel
| | - Yirong Mo
- Department
of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
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26
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Yuan K, Zhao RS, Zheng JJ, Zheng H, Nagase S, Zhao SD, Liu YZ, Zhao X. Van Der Waals heterogeneous layer-layer carbon nanostructures involving π···H-C-C-H···π···H-C-C-H stacking based on graphene and graphane sheets. J Comput Chem 2017; 38:730-739. [DOI: 10.1002/jcc.24743] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Kun Yuan
- Institute for Chemical Physics & Department of Chemistry; School of Science, State Key Laboratory of Electrical Insulation and Power Equipment, School of Mechanical Engineering, Xi'an Jiaotong University; Xi'an 710049 China
- College of Chemical engineering & Technology; Department of Chemistry, Tianshui Normal University; Tianshui 741001 China
- Fukui Institute for Fundamental Chemistry, Kyoto University; Kyoto 606-8103 Japan
| | - Rui-Sheng Zhao
- Institute for Chemical Physics & Department of Chemistry; School of Science, State Key Laboratory of Electrical Insulation and Power Equipment, School of Mechanical Engineering, Xi'an Jiaotong University; Xi'an 710049 China
| | - Jia-Jia Zheng
- Institute for Chemical Physics & Department of Chemistry; School of Science, State Key Laboratory of Electrical Insulation and Power Equipment, School of Mechanical Engineering, Xi'an Jiaotong University; Xi'an 710049 China
- Fukui Institute for Fundamental Chemistry, Kyoto University; Kyoto 606-8103 Japan
| | - Hong Zheng
- Institute for Chemical Physics & Department of Chemistry; School of Science, State Key Laboratory of Electrical Insulation and Power Equipment, School of Mechanical Engineering, Xi'an Jiaotong University; Xi'an 710049 China
- Fukui Institute for Fundamental Chemistry, Kyoto University; Kyoto 606-8103 Japan
| | - Shigeru Nagase
- Fukui Institute for Fundamental Chemistry, Kyoto University; Kyoto 606-8103 Japan
| | - Sheng-Dun Zhao
- Institute for Chemical Physics & Department of Chemistry; School of Science, State Key Laboratory of Electrical Insulation and Power Equipment, School of Mechanical Engineering, Xi'an Jiaotong University; Xi'an 710049 China
| | - Yan-Zhi Liu
- College of Chemical engineering & Technology; Department of Chemistry, Tianshui Normal University; Tianshui 741001 China
| | - Xiang Zhao
- Institute for Chemical Physics & Department of Chemistry; School of Science, State Key Laboratory of Electrical Insulation and Power Equipment, School of Mechanical Engineering, Xi'an Jiaotong University; Xi'an 710049 China
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27
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Sharma C, Joy J, Nethaji M, Jemmis ED, Awasthi SK. Synthetic, Crystallographic, and Computational Studies of Extensively Hydrogen Bonded Bilayers in Thermally Stable Adamantane Hydroperoxides. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Chiranjeev Sharma
- Chemical Biology Laboratory; Department of Chemistry; University of Delhi; Delhi 110007 India
| | - Jyothish Joy
- Department of Chemistry; Indian Institute of Science Education and Research; Thiruvananthapuram 695016 Kerala India
| | - Munirathinam Nethaji
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Eluvathingal D. Jemmis
- Department of Inorganic and Physical Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Satish Kumar Awasthi
- Chemical Biology Laboratory; Department of Chemistry; University of Delhi; Delhi 110007 India
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28
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Novák M, Foroutan-Nejad C, Marek R. Modulating Electron Sharing in Ion-π-Receptors via Substitution and External Electric Field: A Route toward Bond Strengthening. J Chem Theory Comput 2016; 12:3788-95. [DOI: 10.1021/acs.jctc.6b00586] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Novák
- CEITEC −
Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-625 00 Brno, Czech Republic
| | - Cina Foroutan-Nejad
- CEITEC −
Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-625 00 Brno, Czech Republic
| | - Radek Marek
- CEITEC −
Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-625 00 Brno, Czech Republic
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29
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Wagner JP, Schreiner PR. London’sche Dispersionswechselwirkungen in der Molekülchemie - eine Neubetrachtung sterischer Effekte. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503476] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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30
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Wagner JP, Schreiner PR. London dispersion in molecular chemistry--reconsidering steric effects. Angew Chem Int Ed Engl 2015; 54:12274-96. [PMID: 26262562 DOI: 10.1002/anie.201503476] [Citation(s) in RCA: 633] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 12/15/2022]
Abstract
London dispersion, which constitutes the attractive part of the famous van der Waals potential, has long been underappreciated in molecular chemistry as an important element of structural stability, and thus affects chemical reactivity and catalysis. This negligence is due to the common notion that dispersion is weak, which is only true for one pair of interacting atoms. For increasingly larger structures, the overall dispersion contribution grows rapidly and can amount to tens of kcal mol(-1) . This Review collects and emphasizes the importance of inter- and intramolecular dispersion for molecules consisting mostly of first row atoms. The synergy of experiment and theory has now reached a stage where dispersion effects can be examined in fine detail. This forces us to reconsider our perception of steric hindrance and stereoelectronic effects. The quantitation of dispersion energy donors will improve our ability to design sophisticated molecular structures and much better catalysts.
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Affiliation(s)
- J Philipp Wagner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen (Germany)
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen (Germany).
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31
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Umadevi D, Narahari Sastry G. Graphane versus graphene: a computational investigation of the interaction of nucleobases, aminoacids, heterocycles, small molecules (CO2, H2O, NH3, CH4, H2), metal ions and onium ions. Phys Chem Chem Phys 2015; 17:30260-9. [DOI: 10.1039/c5cp05094d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We compared the binding affinity of graphane and graphene with various molecules and ions.
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Affiliation(s)
- Deivasigamani Umadevi
- Centre for Molecular Modeling
- CSIR – Indian Institute of Chemical Technology
- Hyderabad - 500 607
- India
| | - G. Narahari Sastry
- Centre for Molecular Modeling
- CSIR – Indian Institute of Chemical Technology
- Hyderabad - 500 607
- India
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