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Deb B, Mahanta H, Baruah NP, Khardewsaw M, Paul AK. On the intramolecular vibrational energy redistribution dynamics of aromatic complexes: A comparative study on C6H6-C6H5Cl, C6H6-C6H3Cl3, C6H6-C6Cl6 and C6H6-C6H5F, C6H6-C6H3F3, C6H6-C6F6. J Chem Phys 2024; 160:024307. [PMID: 38197444 DOI: 10.1063/5.0174748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/17/2023] [Indexed: 01/11/2024] Open
Abstract
Chemical dynamics Simulation studies on benzene dimer (Bz2) and benzene-hexachlorobenzene (Bz-HCB) as performed in the past suggest that the coupling between the monomeric (intramolecular) vibrational modes and modes generated due to the association of two monomers (intermolecular) has to be neither strong nor weak for a fast dissociation of the complex. To find the optimum coupling, four complexes are taken into consideration in this work, namely, benzene-monofluorobenzene, benzene-monochlorobenzene, benzene-trifluorobenzene (Bz-TFB), and benzene-trichlorobenzene. Bz-TFB has the highest rate of dissociation among all seven complexes, including Bz2, Bz-HCB, and Bz-HFB (HFB stands for hexafluorobenzene). The set of vibrational frequencies of Bz-TFB is mainly the reason for this fast dissociation. The mass of chlorine in Bz-HCB is optimized to match its vibrational frequencies similar to those of Bz-TFB, and the dissociation of Bz-HCB becomes faster. The power spectrum of Bz-TFB, Bz-HCB, and Bz-HCB with the modified mass of chlorine is also computed to understand the extent of the said coupling in these complexes.
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Affiliation(s)
- Basudha Deb
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
| | - Himashree Mahanta
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
- Department of Chemistry, Assam Kaziranga University, Koraikhowa, NH-37, Jorhat 785006, India
| | - Netra Prava Baruah
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
| | - Maitjingshai Khardewsaw
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
| | - Amit Kumar Paul
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
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2
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Wang X, Li Q, Scheiner S. Cooperativity between H-bonds and tetrel bonds. Transformation of a noncovalent C⋯N tetrel bond to a covalent bond. Phys Chem Chem Phys 2023; 25:29738-29746. [PMID: 37885414 DOI: 10.1039/d3cp04430k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The dimers and trimers formed by imidazole (IM) and F2TO (T = C, Si, Ge) are studied by ab initio calculations. IM can engage in either a NH⋯O H-bond with F2TO or a T⋯N tetrel bond (TB) with the π-hole above the T atom. The latter is a true noncovalent TB for T = C but is a much shorter and stronger covalent bond with F2SiO or F2GeO. When a second IM is added, the cooperativity emerging from its H-bond with the first IM makes it a stronger nucleophile, leading to two minima with F2CO. The first structure contains a long noncovalent C⋯O TB and there is a much shorter covalent bond in the other, with a small energy barrier separating them. The same sort of double minimum occurs when the two IM units are situated parallel to one another in a stacked geometry.
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Affiliation(s)
- Xin Wang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, P. R. China.
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, P. R. China.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
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3
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Moharana P, Santosh G. Amphiphilic perylene diimide-based fluorescent hemispherical aggregates as probes for metal ions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122696. [PMID: 37043834 DOI: 10.1016/j.saa.2023.122696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 05/14/2023]
Abstract
The self-assembly behaviour of a newly synthesized amphiphilic core-positioned thioester appended with carboxylic acid functionalized perylene diimide derivative is studied in different organic solvents. Fluorescent J-type hemispherical aggregates are formed in THF solution. The effect of added metal ions on these fluorescent aggregates is evaluated using spectroscopic techniques, where we found these probes bind selectively to Fe3+ and Ba2+ ions. Two equivalents of Fe3+ ions bind cooperatively to one equivalent of perylene diimide derivative in the hemispherical aggregates with a binding constant of 1.4×107 M-1 and the limit of detection (LOD) was calculated to be 8.66×10-6 M. The positive cooperative binding effect of Fe3+ ions towards hemispherical aggregates equipped with perylene diimide derivatives leads to supramolecular polymerization. Ba2+ ions showed selectivity and sensitivity towards the fluorescent aggregates in THF by quenching the fluorescence intensity completely. The linear Stern-Volmer plot with a Stern-Volmer constant value of 502.6 M-1 signifies the heavy atom effect of Ba2+ ions, leading to fluorescence quenching. The morphological transformation of the fluorescent J-type hemispherical aggregates in the presence of Fe3+ and Ba2+ was studied in detail using electron microscopy.
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Affiliation(s)
- Prajna Moharana
- Division of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Chennai 600127, India
| | - G Santosh
- Division of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Chennai 600127, India.
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4
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Vasconcellos LC, de Carvalho EFV, Roberto-Neto O. Hydrogen physisorption on the (BeO) n, B 2H 4(Be,Ti), and B 6Ti 3 metal clusters: a computational study of energies and atomic charges. J Mol Model 2023; 29:48. [PMID: 36658290 DOI: 10.1007/s00894-022-05432-0] [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: 04/13/2022] [Accepted: 12/18/2022] [Indexed: 01/21/2023]
Abstract
The equilibrium structures of BeO clusters and Be,Ti-decorated boranes were computed with the ωB97X-D method and the 6-31G + (2d,2p) and aug-cc-pVTZ basis sets to study their intermolecular interactions with hydrogen molecules. Thermochemical and molecular properties such as the harmonic vibrational frequency, dipole and quadrupole moments, and atomic charges are employed to understand the attractive interactions that control the adsorption process. Comparison of molecular properties and atomic charges of the studied compounds before and after H2 molecule adsorption shows that most of the interactions among the BeO clusters and boranes with H2 molecules constitute a combination of dispersion, electrostatic, and weak charge transfer interactions. Calculated values of Hirschfeld atomic charges and ΔEe (in parenthesis) (BeO)4.8H2 (0.028 e and -2.0 kcal.mol-1), (BeO)2.12H2 (0.030 e and -2.8 kcal.mol-1), B6Ti3.10H2 (0.045 e and -15.4 kcal.mol-1), and B6Ti3+.10H2 (0.058 e and -15.3 kcal.mol-1) show qualitative correlation between hydrogen atomic charges and electronic energy of hydrogen interaction. The ωB97X-D/6-31 + G(2d,2p) values of Gibbs free energy at 298.15 K for (BeO)4.8H2 B2H4Ti.4H2 and B6Ti3.10H2 clusters are equal to -5.0, -4.9, and -5.1 kcal.mol-1, respectively, which are within the range of energy parameters of materials that could be employed in hydrogen storage tanks for light vehicles.
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Affiliation(s)
- L C Vasconcellos
- Divisão de Aerotermodinâmica E Hipersônica, Instituto de Estudos Avançados, São José Dos CamposSão Paulo, 12228-001, Brazil
| | - E F V de Carvalho
- Departamento de Física, Universidade Federal Do Maranhão, São LuísMaranhão, 65085-580, Brazil
| | - O Roberto-Neto
- Divisão de Aerotermodinâmica E Hipersônica, Instituto de Estudos Avançados, São José Dos CamposSão Paulo, 12228-001, Brazil.
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5
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Majerz I, Krawczyk MS. Crystal Structure and Chemical Bonds in [Cu II2(Tolf) 4(MeOH) 2]∙2MeOH. Int J Mol Sci 2023; 24:ijms24021745. [PMID: 36675260 PMCID: PMC9864235 DOI: 10.3390/ijms24021745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
A new coordination compound of copper(II) with a tolfenamate ligand of the paddle-wheel-like structure [CuII2(Tolf)4(MeOH)2]∙2MeOH was obtained and structurally characterized. Chemical bonds of Cu(II)∙∙∙Cu(II) and Cu(II)-O were theoretically analyzed and compared with the results for selected similar structures from the CSD database. QTAIM analysis showed that the Cu(II)∙∙∙Cu(II) interaction has a strength comparable to a hydrogen bond, as indicated by the electron density at a critical point. The remaining QTAIM parameters indicate stability of the Cu(II)∙∙∙Cu(II) interaction. Other methods, such as NCI and NBO, also indicate a significant strength of this interaction. Thus, the Cu(II)∙∙∙Cu(II) interaction can be treated as one of the noncovalent interactions that affects the structure of the coordination compound, the packing of molecules in the crystal, and the general properties of the compound.
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6
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Unraveling the Nature of Hydrogen Bonds of "Proton Sponges" Based on Car-Parrinello and Metadynamics Approaches. Int J Mol Sci 2023; 24:ijms24021542. [PMID: 36675059 PMCID: PMC9860969 DOI: 10.3390/ijms24021542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
The nature of intra- and intermolecular non-covalent interactions was studied in four naphthalene derivatives commonly referred to as "proton sponges". Special attention was paid to an intramolecular hydrogen bond present in the protonated form of the compounds. The unsubstituted "proton sponge" served as a reference structure to study the substituent influence on the hydrogen bond (HB) properties. We selected three compounds substituted by methoxy, amino, and nitro groups. The presence of the substituents either retained the parent symmetry or rendered the compounds asymmetric. In order to reveal the non-covalent interaction properties, the Hirshfeld surface (HS) was computed for the crystal structures of the studied compounds. Next, quantum-chemical simulations were performed in vacuo and in the crystalline phase. Car-Parrinello molecular dynamics (CPMD), Path Integral Molecular Dynamics (PIMD), and metadynamics were employed to investigate the time-evolution changes of metric parameters and free energy profile in both phases. Additionally, for selected snapshots obtained from the CPMD trajectories, non-covalent interactions and electronic structure were studied. Quantum theory of atoms in molecules (QTAIM) and the Density Overlap Regions Indicator (DORI) were applied for this purpose. It was found based on Hirshfeld surfaces that, besides intramolecular hydrogen bonds, other non-covalent interactions are present and have a strong impact on the crystal structure organization. The CPMD results obtained in both phases showed frequent proton transfer phenomena. The proton was strongly delocalized in the applied time-scale and temperature, especially in the PIMD framework. The use of metadynamics allowed for tracing the free energy profiles and confirming that the hydrogen bonds present in "proton sponges" are Low-Barrier Hydrogen Bonds (LBHBs). The electronic and topological analysis quantitatively described the temperature dependence and time-evolution changes of the electronic structure. The covalency of the hydrogen bonds was estimated based on QTAIM analysis. It was found that strong hydrogen bonds show greater covalency, which is additionally determined by the proton position in the hydrogen bridge.
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7
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An ab initio study of the structural, vibrational and electronic properties of some tetrel-bonded complexes of methane and tetrafluoromethane. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2023.114021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Different Curcumin-Loaded Delivery Systems for Wound Healing Applications: A Comprehensive Review. Pharmaceutics 2022; 15:pharmaceutics15010038. [PMID: 36678665 PMCID: PMC9862251 DOI: 10.3390/pharmaceutics15010038] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Curcumin or turmeric is the active constituent of Curcuma longa L. It has marvelous medicinal applications in many diseases. When the skin integrity is compromised due to either acute or chronic wounds, the body initiates several steps leading to tissue healing and skin barrier function restoration. Curcumin has very strong antibacterial and antifungal activities with powerful wound healing ability owing to its antioxidant activity. Nevertheless, its poor oral bioavailability, low water solubility and rapid metabolism limit its medical use. Tailoring suitable drug delivery systems for carrying curcumin improves its pharmaceutical and pharmacological effects. This review summarizes the most recent reported curcumin-loaded delivery systems for wound healing purposes, chiefly hydrogels, films, wafers, and sponges. In addition, curcumin nanoformulations such as nanohydrogels, nanoparticles and nanofibers are also presented, which offer better solubility, bioavailability, and sustained release to augment curcumin wound healing effects through stimulating the different healing phases by the aid of the small carrier.
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9
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Zhang YL, Li B. Reliability of Computing van der Waals Bond Lengths of Some Rare Gas Diatomics. Int J Mol Sci 2022; 23:ijms232213944. [PMID: 36430420 PMCID: PMC9696166 DOI: 10.3390/ijms232213944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
When the bond lengths of 11 molecules containing van der Waals bonds are optimized by 572 methods and 20 basis sets, it is found that the best mean absolute deviations (MADs) of density-functional theory (DFT) methods are 0.005 Å (shown by APFD/6-311++G**), 0.007 Å (B2PLYPD3(Full)/aug-cc-pVQZ), and 0.010 Å (revDSDPBEP86/aug-cc-pVQZ), while the best MADs of ab initio methods are 0.008 Å (BD(T)/aug-cc-pVTZ) and 0.016 Å (MP4/aug-cc-pVQZ). Moreover, the best MADs calculated by 54 selected methods in combination with 60 other basis sets (such as 6-311++G, 6-31++G(3d'f,3p'd), and UGBS1V++) are not better. Therefore, these bond lengths can be calculated with extremely high accuracy by some special methods and basis sets, and CCSD(T) is also not as good as expected because its best MAD is only 0.023 Å (CCSD(T)/aug-cc-pVQZ).
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10
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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11
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Mahmoudi G, García-Santos I, Pittelkow M, Kamounah FS, Zangrando E, Babashkina MG, Frontera A, Safin DA. The tetrel bonding role in supramolecular aggregation of lead(II) acetate and a thiosemicarbazide derivative. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:685-694. [PMID: 35975834 DOI: 10.1107/s2052520622005789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
A new PbII coordination complex [PbL(OAc)], which was readily synthesized from a mixture of Pb(OAc)2·3H2O and 1-(pyridin-2-yl)benzylidene-4-phenylthiosemicarbazide (HL) is reported. The crystal structure analysis of [PbL(OAc)] showed that the PbII cation is N,N',S-chelated by the tridentate pincer-type ligand L and by the oxygen atoms of the acetate anion. In addition, the metal centre forms Pb...O and Pb...S tetrel bonds with an adjacent complex molecule, yielding a 1D zigzag polymeric chain, which is reinforced by N-H...O hydrogen bonds and π...π interactions. These chains are interlinked by C-H...py non-covalent interactions, realized between one of the acetate hydrogen atoms and the pyridine rings. According to the Hirshfeld surface analysis, the crystal packing is mainly characterized by intermolecular H...H, H...C and H...O contacts, followed by H...N, H...S, C...C, C...N, Pb...H, Pb...O and Pb...S contacts. The FTIR and 1H NMR spectra of [PbL(OAc)] testify to the deprotonation of the parent ligand HL, while the acetate ligand exhibits an anisobidentate coordination mode as established by means of single-crystal X-ray diffraction and FTIR spectroscopy. Lastly, theoretical calculations at the PBE0-D3/def2-TZVP level of theory have been used to analyze and characterize the Pb...O and Pb...S tetrel bonds observed in the crystal of [PbL(OAc)], using a combination of QTAIM (Quantum Theory of Atoms in Molecules) and NCIPlot (Non-Covalent Interaction Plot) computational tools.
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Affiliation(s)
- Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, PO Box 55181-83111, Maragheh, Iran
| | - Isabel García-Santos
- Departamento de Química Inorgánica, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Maria G Babashkina
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, 640020 Kurgan, Russian Federation
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca, Spain
| | - Damir A Safin
- Advanced Materials for Industry and Biomedicine Laboratory, Kurgan State University, Sovetskaya Str. 63/4, 640020 Kurgan, Russian Federation
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Moharana P, Santosh G. Organogels Fabricated from Self-Assembled Nanotubes Containing Core Substituted Perylene Diimide Derivative. ACS OMEGA 2022; 7:21932-21938. [PMID: 35785309 PMCID: PMC9245106 DOI: 10.1021/acsomega.2c02210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/31/2022] [Indexed: 05/27/2023]
Abstract
Perylene-based organogels are well-known for their applications as sensors and optoelectronic materials. Among them, core-substituted perylene diimide-based organogels are rarely explored. Herein, the hierarchical self-assembly mechanism of a newly synthesized, amide-linked core-substituted perylene diimide derivative, which formed organogels in organic solvents like toluene and methyl cyclohexane (MCH), is discussed. These organogels are composed of one-dimensional molecular aggregates like nanofibers and nanotubes. Organogels composed of nanofibers are very frequent. On the contrary, for the first time, we have encountered a perylene diimide-based organogel consisting of self-assembled nanotubes. The molecular interactions, molecular packing, and rheological properties of this organogel are also discussed.
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Lambert EC, Williams AE, Fortenberry RC, Hammer NI. Probing halogen bonding interactions between heptafluoro-2-iodopropane and three azabenzenes with Raman spectroscopy and density functional theory. Phys Chem Chem Phys 2022; 24:11713-11720. [PMID: 35506511 DOI: 10.1039/d2cp00463a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The potential formation of halogen bonded complexes between a donor, heptafluoro-2-iodopropane (HFP), and the three acceptor heterocyclic azines (azabenzenes: pyridine, pyrimidine, and pyridazine) is investigated herein through normal mode analysis via Raman spectroscopy, density functional theory, and natural electron configuration analysis. Theoretical Raman spectra of the halogen bonded complexes are in good agreement with experimental data providing insight into the Raman spectra of these complexes. The exhibited shifts in vibrational frequency of as high as 8 cm-1 for each complex demonstrate, in conjunction with NEC analysis, significant evidence of charge transfer from the halogen bond acceptor to donor. Here, an interesting charge flow mechanism is proposed involving the donated nitrogen lone pair electrons pushing the dissociated fluorine atoms back to their respective atoms. This mechanism provides further insight into the formation and fundamental nature of halogen bonding and its effects on neighboring atoms. The present findings provide novel and deeper characterization of halogen bonding with applications in supramolecular and organometallic chemistry.
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Affiliation(s)
- Ethan C Lambert
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA.
| | - Ashley E Williams
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA. .,University of Mississippi Medical Center, School of Medicine, Office of Student Affairs, 2500 N. State Street, Jackson, MS, 39216, USA
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA.
| | - Nathan I Hammer
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA.
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14
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Mollazadeh S, Babaei S, Ostadhassan M, Yazdian-Robati R. Concentration-dependent assembly of Bovine serum albumin molecules in the doxorubicin loading process: Molecular dynamics simulation. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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Juraskova V, Celerse F, Laplaza R, Corminboeuf C. Assessing the persistence of chalcogen bonds in solution with neural network potentials. J Chem Phys 2022; 156:154112. [DOI: 10.1063/5.0085153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on Density Functional Theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications have centered on solid-state materials or fairly simple molecules made of a limited number of elements. Herein, we focus on the persistence and strength of chalcogen bonds involving a benzotelluradiazole in condensed phase. While the tellurium-containing heteroaromatic molecules are known to exhibit pronounced interactions with anions and lone pairs of different atoms, the relevance of competing intermolecular interactions, notably with the solvent, is complicated to monitor experimentally but also challenging to model at an accurate electronic structure level. Here, we train direct and baselined NNPs to reproduce hybrid DFT energies and forces in order to identify what are the most prevalent non-covalent interactions occurring in a solute-Cl$^-$-THF mixture. The simulations in explicit solvent highlight competition with chalcogen bonds formed with the solvent and the short-range directionality of the interaction with direct consequences for the molecular properties in the solution. The comparison with other potentials (e.g., AMOEBA, direct NNP and continuum solvent model) also demonstrates that baselined NNPs offer a reliable picture of the non-covalent interaction interplay occurring in solution.
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16
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Schneider H. Noncovalent interactions: A brief account of a long history. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Lebedeva NS, Koifman OI. Supramolecular Systems Based on Macrocyclic Compounds with Proteins: Application Prospects. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022010071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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18
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Majumdar D, Frontera A, Gomila RM, Das S, Bankura K. Synthesis, spectroscopic findings and crystal engineering of Pb(ii)-Salen coordination polymers, and supramolecular architectures engineered by σ-hole/spodium/tetrel bonds: a combined experimental and theoretical investigation. RSC Adv 2022; 12:6352-6363. [PMID: 35424552 PMCID: PMC8982041 DOI: 10.1039/d1ra09346k] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
Spontaneous self-assembly is one of the available synthetic routes to achieve structurally versatile and unique crystal complexes with selected metal-ligand combinations in the spirit of pseudohalides. In this endeavour, we designed a novel 1D coordination polymer (CP), [(Cd)(Pb)(L)(η1-NCS)(η1-SCN)] n (1), using a compartmental Salen ligand (H3L) in the presence of NaSCN. The characterization of the CP was accomplished using several spectroscopic techniques: MALDI-TOF, PXRD, SEM, EDX mapping, and single-crystal X-ray crystallography. The CP crystallizes in the monoclinic space group P21/c with Z = 4. SCXRD reveals Cd(ii) and Pb(ii) metal ions fulfilled distorted square pyramidal and hemi-directed coordination spheres. Cd(ii) is placed in the inner N2O2 and heavier Pb(ii) in the outer O4 compartments of the de-protonated form of the ligand [L]2-. Supramolecular interactions in the intricate crystal structure produced attractive molecular architectures of the compound. The flexible aliphatic -OH pendent group coordinates with the Pb(ii) ions. This unique binding further elevates the supramolecular crystal topographies. The supramolecular interactions were authenticated by Hirshfeld surface analysis (HSA). The observation of the recurring unconventional tetrel bonds was rationalized by DFT calculations and surface plots of molecular electrostatic potential (MEP). In the 1D polymeric chain in the complex, the O-atom of the -OH groups shows a tetrel bonding interaction with the Pb atom. We have found that the combination of QTAIM/NCI and QTAIM/ELF plots helps reveal the nature of these contacts. Moreover, the QTAIM/ELF plot determines the donor-acceptor interaction between the O-atom and the Pb atom, establishing the σ-hole. Agreeably, the σ-hole interaction also helps Pb(ii) serve as a Lewis acid in the complex. Finally, spodium and tetrel bonds are formed, possible thanks to a hemi-directional coordination sphere of the Pb atoms in the polymer described.
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Affiliation(s)
- Dhrubajyoti Majumdar
- Department of Chemistry, Tamralipta Mahavidyalaya Tamluk 721636 West Bengal India .,Department of Chemistry, Indian Institute of Technology (Indian School of Mines) Dhanbad Jharkhand 826004 India
| | - A Frontera
- Department de Quimica, Universitat de les Illes Balears Cra. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Rosa M Gomila
- Department de Quimica, Universitat de les Illes Balears Cra. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Sourav Das
- Department of Basic Sciences, Chemistry Discipline, Institute of Infrastructure Technology Research and Management Near Khokhara Circle, Maninagar East Ahmedabad-380026 Gujarat India
| | - Kalipada Bankura
- Department of Chemistry, Tamralipta Mahavidyalaya Tamluk 721636 West Bengal India
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19
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Malonaldehyde-like Systems: BeF2 Clusters—A Subtle Balance between Hydrogen Bonds, Beryllium Bonds, and Resonance. SCI 2022. [DOI: 10.3390/sci4010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The stability of malonaldehyde is governed by intramolecular hydrogen bonds (IMHBs) as well as in malonaldehyde-like systems where oxygen is replaced by N or S at any of the basic sites. As beryllium bonds have been shown to strongly cooperate with hydrogen bonds, this work explores at the high level ab initio G4 level of theory the effect of including this non-covalent interaction in the system through its association with BeF2. Although malonaldehyde follows the expected trends, where the formation of a pseudocyclic form is favored also when IMHB and Be bonds are present, the subtle balance between both non-covalent interactions leads to some surprising results when other heteroatoms are involved, to the point that interaction energies can be much larger than expected or even cyclization is not favored. A complete analysis using different computational tools gives an answer to those cases escaping the predictable trends.
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20
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Jezierska A, Panek JJ, Błaziak K, Raczyński K, Koll A. Exploring Intra- and Intermolecular Interactions in Selected N-Oxides-The Role of Hydrogen Bonds. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030792. [PMID: 35164056 PMCID: PMC8846293 DOI: 10.3390/molecules27030792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/30/2022]
Abstract
Intra- and intermolecular interactions have been explored in selected N-oxide derivatives: 2-(N,N-dimethylamino-N-oxymethyl)-4,6-dimethylphenyl (1) and 5,5’-dibromo-3-diethylaminomethyl-2,2’-biphenol N-oxide (2). Both compounds possess intramolecular hydrogen bonding, which is classified as moderate in 1 and strong in 2, and resonance-assisted in both cases. Density Functional Theory (DFT) in its classical formulation as well as Time-Dependent extension (TD-DFT) were employed to study proton transfer phenomena. The simulations were performed in the gas phase and with implicit and explicit solvation models. The obtained structures of the studied N-oxides were compared with experimental data available. The proton reaction path was investigated using scan with an optimization method, and water molecule reorientation in the monohydrate of 1 was found upon the proton scan progress. It was found that spontaneous proton transfer phenomenon cannot occur in the electronic ground state of the compound 1. An opposite situation was noticed for the compound 2. The changes of nucleophilicity and electrophilicity upon the bridged proton migration were analyzed on the basis of Fukui functions in the case of 1. The interaction energy decomposition of dimers and microsolvation models was investigated using Symmetry-Adapted Perturbation Theory (SAPT). The simulations were performed in both phases to introduce polar environment influence on the interaction energies. The SAPT study showed rather minor role of induction in the formation of homodimers. However, it is worth noticing that the same induction term is responsible for the preference of water molecules’ interaction with N-oxide hydrogen bond acceptor atoms in the microsolvation study. The Natural Bond Orbital (NBO) analysis was performed for the complexes with water to investigate the charge flow upon the polar environment introduction. Finally, the TD-DFT was applied for isolated molecules as well as for microsolvation models showing that the presence of solvent affects excited states, especially when the N-oxide acceptor atom is microsolvated.
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Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (J.J.P.); (K.R.)
- Correspondence: ; Tel.: +48-71-3757-224; Fax: +48-71-3282-348
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (J.J.P.); (K.R.)
| | - Kacper Błaziak
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 01-224 Warsaw, Poland;
- Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 01-224 Warsaw, Poland
| | - Kamil Raczyński
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (J.J.P.); (K.R.)
| | - Aleksander Koll
- Non-Public Medical School in Wrocław, ul. Nowowiejska 69, 50-340 Wrocław, Poland;
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21
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Rezaei Z, Solimannejad M, Atashzar SM, Esrafili MD. Systematic study of cooperative interplay between single-electron pnicogen bond and halogen bond in X3C···PH2Y···ClY (X=H, CH3; Y=CN, NC) complexes in two different minima configuration. Mol Phys 2021. [DOI: 10.1080/00268976.2021.2014588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Zahra Rezaei
- Faculty of Sciences, Quantum Chemistry Group, Department of Chemistry, Arak University, Arak, Iran
| | - Mohammad Solimannejad
- Faculty of Sciences, Quantum Chemistry Group, Department of Chemistry, Arak University, Arak, Iran
| | | | - Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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22
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Badorrek J, Walter M. Computational study on noncovalent interactions between (n, n) single-walled carbon nanotubes and simple lignin model-compounds. J Comput Chem 2021; 43:340-348. [PMID: 34893979 DOI: 10.1002/jcc.26794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/10/2022]
Abstract
Composites of carbon nanotubes (CNTs) and lignin are promising and potentially cheap precursors of-to this day-expensive carbon fibers. Since the control of the CNT-lignin interface is crucial to maximize fiber performance, it is imperative to understand the fundamental noncovalent interactions between lignin and CNT. In the present study a density functional theory study is conducted to investigate the fundamental noncovalent interaction strength between metallic (n, n) single-walled CNT (SWCNT) and simple lignin model molecules. In particular, the respective adsorption energies are used to gauge the strength of interaction classes (ππ interaction, CHπ hydrogen bonding and OH-related hydrogen bonding. From the data, substituent-dependent interaction trends as well as class- and curvature-dependent interaction trends are derived. Overall, we find that most of the interaction strength trends appear to be strongly influenced by geometry: flat orientation of the test molecules relative to the (n, n) SWCNT surface and small (n, n) SWCNT curvature-that is, large diameter enhances the CHπ and ππ interactions.
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Affiliation(s)
- Jan Badorrek
- Freiburger Materialforschungszentrum, Freiburg im Breisgau, Germany
| | - Michael Walter
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), Universität Freiburg, Freiburg im Breisgau, Germany.,Cluster of Excellence livMatS @ FIT, Freiburg im Breisgau, Germany.,Fraunhofer IWM, Freiburg im Breisgau, Germany
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23
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Sharma P, Dutta D, Gomila RM, Frontera A, Barcelo-Oliver M, Verma AK, Bhattacharyya MK. Benzoato bridged dinuclear Mn(II) and Cu(II) compounds involving guest chlorobenzoates and dimeric paddle wheel supramolecular assemblies: Antiproliferative evaluation and theoretical studies. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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24
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Experimental and Computational Validation of Structural Features and BSA Binding Tendency of 5‐Hydroxy‐5‐trifluoromethyl‐3‐arylpyrazolines**. ChemistrySelect 2021. [DOI: 10.1002/slct.202102669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces. Molecules 2021; 26:molecules26185642. [PMID: 34577113 PMCID: PMC8468954 DOI: 10.3390/molecules26185642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/04/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller-Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers' stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm-1-1700 cm-1 and 2300 cm-1-3400 cm-1 in the gas phase and 600 cm-1-1800 cm-1 and 2200 cm-1-3400 cm-1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm-1-1700 cm-1 and 2300 cm-1-3300 cm-1 for the gas phase and one broad absorption region in the solid state between 700 cm-1 and 3100 cm-1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.
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Jezierska A, Błaziak K, Klahm S, Lüchow A, Panek JJ. Non-Covalent Forces in Naphthazarin-Cooperativity or Competition in the Light of Theoretical Approaches. Int J Mol Sci 2021; 22:ijms22158033. [PMID: 34360798 PMCID: PMC8348774 DOI: 10.3390/ijms22158033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/27/2022] Open
Abstract
Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.
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Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland;
- Correspondence: (A.J.); (K.B.)
| | - Kacper Błaziak
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 01-224 Warsaw, Poland
- Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 01-224 Warsaw, Poland
- Correspondence: (A.J.); (K.B.)
| | - Sebastian Klahm
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany; (S.K.); (A.L.)
| | - Arne Lüchow
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany; (S.K.); (A.L.)
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland;
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27
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Calabrese C, Temelso B, Usabiaga I, Seifert NA, Basterretxea FJ, Prampolini G, Shields GC, Pate BH, Evangelisti L, Cocinero EJ. The Role of Non-Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane. Angew Chem Int Ed Engl 2021; 60:16894-16899. [PMID: 34028158 PMCID: PMC8362204 DOI: 10.1002/anie.202103900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/27/2021] [Indexed: 01/30/2023]
Abstract
The role of non-covalent interactions (NCIs) has broadened with the inclusion of new types of interactions and a plethora of weak donor/acceptor partners. This work illustrates the potential of chirped-pulse Fourier transform microwave technique, which has revolutionized the field of rotational spectroscopy. In particular, it has been exploited to reveal the role of NCIs' in the molecular self-aggregation of difluoromethane where a pentamer, two hexamers and a heptamer were detected. The development of a new automated assignment program and a sophisticated computational screening protocol was essential for identifying the homoclusters in conditions of spectral congestion. The major role of dispersion forces leads to less directional interactions and more distorted structures than those found in polar clusters, although a detailed analysis demonstrates that the dominant interaction energy is the pairwise interaction. The tetramer cluster is identified as a structural unit in larger clusters, representing the maximum expression of bond between dimers.
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Affiliation(s)
- Camilla Calabrese
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
- Instituto Biofisika (UPV/EHU, CSIC)48940LeioaSpain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)48940LeioaSpain
| | - Berhane Temelso
- George Mason UniversityInformation Technology ServicesFairfaxVA22030USA
| | - Imanol Usabiaga
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
- Instituto Biofisika (UPV/EHU, CSIC)48940LeioaSpain
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bolognavia S. Alberto 16348100RavennaItaly
| | - Nathan A. Seifert
- Department of ChemistryUniversity of VirginiaMcCormick RoadCharlottesvilleVA22903USA
| | - Francisco J. Basterretxea
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR)Area della Ricercavia G. Moruzzi 156124PisaItaly
| | | | - Brooks H. Pate
- Department of ChemistryUniversity of VirginiaMcCormick RoadCharlottesvilleVA22903USA
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”Università degli Studi di Bolognavia S. Alberto 16348100RavennaItaly
| | - Emilio J. Cocinero
- Departament of Physical ChemistryUniversity of the Basque Country (UPV/EHU)Barrio Sarriena, S/N48940LeioaSpain
- Instituto Biofisika (UPV/EHU, CSIC)48940LeioaSpain
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28
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Calabrese C, Temelso B, Usabiaga I, Seifert NA, Basterretxea FJ, Prampolini G, Shields GC, Pate BH, Evangelisti L, Cocinero EJ. The Role of Non‐Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Camilla Calabrese
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Instituto Biofisika (UPV/EHU, CSIC) 48940 Leioa Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) 48940 Leioa Spain
| | - Berhane Temelso
- George Mason University Information Technology Services Fairfax VA 22030 USA
| | - Imanol Usabiaga
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Instituto Biofisika (UPV/EHU, CSIC) 48940 Leioa Spain
- Dipartimento di Chimica “Giacomo Ciamician” Università degli Studi di Bologna via S. Alberto 163 48100 Ravenna Italy
| | - Nathan A. Seifert
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22903 USA
| | - Francisco J. Basterretxea
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR) Area della Ricerca via G. Moruzzi 1 56124 Pisa Italy
| | | | - Brooks H. Pate
- Department of Chemistry University of Virginia McCormick Road Charlottesville VA 22903 USA
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician” Università degli Studi di Bologna via S. Alberto 163 48100 Ravenna Italy
| | - Emilio J. Cocinero
- Departament of Physical Chemistry University of the Basque Country (UPV/EHU) Barrio Sarriena, S/N 48940 Leioa Spain
- Instituto Biofisika (UPV/EHU, CSIC) 48940 Leioa Spain
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29
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Mahanta H, Paul AK. Unimolecular Dissociation of C 6H 6-C 6Cl 6 Complex and Effect of Mode-Mode Coupling. J Phys Chem A 2021; 125:5870-5877. [PMID: 34192876 DOI: 10.1021/acs.jpca.1c01851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The unimolecular dissociation dynamics of the C6H6-C6Cl6 (Bz-HCB) complex is studied with initial excitation of all vibrational modes for a temperature range of 1000-2000 K and with mode-specific excitations at 1500 K. The results are compared with those of the C6H6-C6F6 [Bz- HFB] complex. When all modes of Bz-HCB are initially excited, the rate of dissociation is slower with respect to Bz-HFB. However, the rate of dissociation is faster when simulations with nonrandom excitation of the specific vibrational modes are performed. The rate of dissociation of Bz-HCB is found to become slower when a few intramolecular modes are excited along with all inter-fragment modes compared to the simulation when only inter-fragment modes of the same complex are excited. Such an energy-transfer dynamics is absent if both intramolecular and inter-fragment modes are not initially excited. Thus, a "stimulated" resonance energy-transfer dynamics is observed in Bz-HCB dissociation dynamics.
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Affiliation(s)
- Himashree Mahanta
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India
| | - Amit K Paul
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India
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Mahmoudi G, Zangrando E, Miroslaw B, Gurbanov AV, Babashkina MG, Frontera A, Safin DA. Spodium bonding and other non-covalent interactions assisted supramolecular aggregation in a new mercury(II) complex of a nicotinohydrazide derivative. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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31
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A matrix isolation and Ab initio study on C2H6…HCN complex: An unusual example of hydrogen bonding. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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32
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Shiryaev AA, Burkhanova TM, Mitoraj MP, Kukulka M, Sagan F, Mahmoudi G, Babashkina MG, Bolte M, Safin DA. Supramolecular structures of Ni II and Cu II with the sterically demanding Schiff base dyes driven by cooperative action of preagostic and other non-covalent interactions. IUCRJ 2021; 8:351-361. [PMID: 33953922 PMCID: PMC8086159 DOI: 10.1107/s2052252521000610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
This work reports on synthesis and extensive experimental and theoretical investigations on photophysical, structural and thermal properties of the NiII and CuII discrete mononuclear homoleptic complexes [Ni(L I,II)2] and [Cu(L I,II)2] fabricated from the Schiff base dyes o-HOC6H4-CH=N-cyclo-C6H11 (HL I) and o-HOC10H6-CH=N-cyclo-C6H11 (HL II), containing the sterically crowding cyclo-hexyl units. The six-membered metallocycles adopt a clearly defined envelope conformation in [Ni(L II)2], while they are much more planar in the structures of [Ni(L I)2] and [Cu(L I,II)2]. It has been demonstrated by in-depth bonding analyses based on the ETS-NOCV and Interacting Quantum Atoms energy-decomposition schemes that application of the bulky substituents, containing several C-H groups, has led to the formation of a set of classical and unintuitive intra- and inter-molecular interactions. All together they are responsible for the high stability of [Ni(L I,II)2] and [Cu(L I,II)2]. More specifically, London dispersion dominated intramolecular C-H⋯O, C-H⋯N and C-H⋯H-C hydrogen bonds are recognized and, importantly, the attractive, chiefly the Coulomb driven, preagostic (not repulsive anagostic) C-H⋯Ni/Cu interactions have been discovered despite their relatively long distances (∼2.8-3.1 Å). All the complexes are further stabilized by the extremely efficient intermolecular C-H⋯π(benzene) and C-H⋯π(chelate) interactions, where both the charge-delocalization and London dispersion constituents appear to be crucial for the crystal packing of the obtained complexes. All the complexes were found to be photoluminescent in CH2Cl2, with [Cu(L II)2] exhibiting the most pronounced emission - the time-dependent density-functional-theory computations revealed that it is mostly caused by metal-to-ligand charge-transfer transitions.
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Affiliation(s)
- Alexey A. Shiryaev
- University of Tyumen, Volodarskogo Street 6, Tyumen, 625003, Russian Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University named after the First President of Russia B. N. Yeltsin, Mira Street 19, Ekaterinburg, 620002, Russian Federation
| | - Tatyana M. Burkhanova
- University of Tyumen, Volodarskogo Street 6, Tyumen, 625003, Russian Federation
- Kurgan State University, Sovetskaya Street 63/4, 640020, Russian Federation
| | - Mariusz P. Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Kraków, 30-387, Poland
| | - Mercedes Kukulka
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Kraków, 30-387, Poland
| | - Filip Sagan
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Kraków, 30-387, Poland
| | - Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, PO Box 55181-83111, Maragheh, Iran
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Place L. Pasteur 1, Louvain-la-Neuve, 1348, Belgium
| | - Michael Bolte
- Institut für Anorganische Chemie, J.-W.-Goethe-Universität, Frankfurt/Main, Germany
| | - Damir A. Safin
- University of Tyumen, Volodarskogo Street 6, Tyumen, 625003, Russian Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University named after the First President of Russia B. N. Yeltsin, Mira Street 19, Ekaterinburg, 620002, Russian Federation
- Kurgan State University, Sovetskaya Street 63/4, 640020, Russian Federation
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Bhattacharyya S, Ghosh S, Wategaonkar S. O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives. Phys Chem Chem Phys 2021; 23:5718-5739. [PMID: 33662068 DOI: 10.1039/d0cp01589j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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Donchev AG, Taube AG, Decolvenaere E, Hargus C, McGibbon RT, Law KH, Gregersen BA, Li JL, Palmo K, Siva K, Bergdorf M, Klepeis JL, Shaw DE. Quantum chemical benchmark databases of gold-standard dimer interaction energies. Sci Data 2021; 8:55. [PMID: 33568655 PMCID: PMC7876112 DOI: 10.1038/s41597-021-00833-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Advances in computational chemistry create an ongoing need for larger and higher-quality datasets that characterize noncovalent molecular interactions. We present three benchmark collections of quantum mechanical data, covering approximately 3,700 distinct types of interacting molecule pairs. The first collection, which we refer to as DES370K, contains interaction energies for more than 370,000 dimer geometries. These were computed using the coupled-cluster method with single, double, and perturbative triple excitations [CCSD(T)], which is widely regarded as the gold-standard method in electronic structure theory. Our second benchmark collection, a core representative subset of DES370K called DES15K, is intended for more computationally demanding applications of the data. Finally, DES5M, our third collection, comprises interaction energies for nearly 5,000,000 dimer geometries; these were calculated using SNS-MP2, a machine learning approach that provides results with accuracy comparable to that of our coupled-cluster training data. These datasets may prove useful in the development of density functionals, empirically corrected wavefunction-based approaches, semi-empirical methods, force fields, and models trained using machine learning methods.
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Affiliation(s)
| | | | | | - Cory Hargus
- D. E. Shaw Research, New York, NY, 10036, USA
| | | | - Ka-Hei Law
- D. E. Shaw Research, New York, NY, 10036, USA
| | | | - Je-Luen Li
- D. E. Shaw Research, New York, NY, 10036, USA
| | - Kim Palmo
- D. E. Shaw Research, New York, NY, 10036, USA
| | | | | | | | - David E Shaw
- D. E. Shaw Research, New York, NY, 10036, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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Mahmoudi G, Abedi M, Lawrence SE, Zangrando E, Babashkina MG, Klein A, Frontera A, Safin DA. Tetrel Bonding and Other Non-Covalent Interactions Assisted Supramolecular Aggregation in a New Pb(II) Complex of an Isonicotinohydrazide. Molecules 2020; 25:molecules25184056. [PMID: 32899863 PMCID: PMC7571010 DOI: 10.3390/molecules25184056] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/31/2022] Open
Abstract
A new supramolecular Pb(II) complex [PbL(NO2)]n was synthesized from Pb(NO3)2, N’-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide (HL) and NaNO2. [PbL(NO2)]n is constructed from discrete [PbL(NO2)] units with an almost ideal N2O3 square pyramidal coordination environment around Pb(II). The ligand L− is coordinated through the 2-pyridyl N-atom, one aza N-atom, and the carbonyl O-atom. The nitrite ligand binds in a κ2-O,O coordination mode through both O-atoms. The Pb(II) center exhibits a hemidirected coordination geometry with a pronounced coordination gap, which allows a close approach of two additional N-atoms arising from the N=C(O) N-atom of an adjacent molecule and from the 4-pyridyl N-atom from the another adjacent molecule, yielding a N4O3 coordination, constructed from two Pb–N and three Pb–O covalent bonds, and two Pb⋯N tetrel bonds. Dimeric units in the structure of [PbL(NO2)]n are formed by the Pb⋯N=C(O) tetrel bonds and intermolecular electrostatically enforced π+⋯π− stacking interactions between the 2- and 4-pyridyl rings and further stabilized by C–H⋯π intermolecular interactions, formed by one of the methyl H-atoms and the 4-pyridyl ring. These dimers are embedded in a 2D network representing a simplified uninodal 3-connected fes (Shubnikov plane net) topology defined by the point symbol (4∙82). The Hirshfeld surface analysis of [PbL(NO2)] revealed that the intermolecular H⋯X (X = H, C, N, O) contacts occupy an overwhelming majority of the molecular surface of the [PbL(NO2)] coordination unit. Furthermore, the structure is characterized by intermolecular C⋯C and C⋯N interactions, corresponding to the intermolecular π⋯π stacking interactions. Notably, intermolecular Pb⋯N and, most interestingly, Pb⋯H interactions are remarkable contributors to the molecular surface of [PbL(NO2)]. While the former contacts are due to the Pb⋯N tetrel bonds, the latter contacts are mainly due to the interaction with the methyl H-atoms in the π⋯π stacked [PbL(NO2)] molecules. Molecular electrostatic potential (MEP) surface calculations showed marked electrostatic contributions to both the Pb⋯N tetrel bonds and the dimer forming π+⋯π− stacking interactions. Quantum theory of atoms in molecules (QTAIM) analyses underlined the tetrel bonding character of the Pb⋯N interactions. The manifold non-covalent interactions found in this supramolecular assembly are the result of the proper combination of the polyfunctional multidentate pyridine-hydrazide ligand and the small nitrito auxiliary ligand.
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Affiliation(s)
- Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh P.O. Box 55181-83111, Iran
- Correspondence: (G.M.); (A.K.); (D.A.S.)
| | - Marjan Abedi
- Department of Chemistry, Faculty of Science, University of Mohaghegh Ardabili, Ardabil P.O. Box 56199-11367, Iran;
| | - Simon E. Lawrence
- School of Chemistry, Analytical and Biological Chemistry Research Facility, Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, T12 K8AF Cork, Ireland;
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy;
| | - Maria G. Babashkina
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, D-50939 Köln, Germany;
| | - Axel Klein
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, D-50939 Köln, Germany;
- Correspondence: (G.M.); (A.K.); (D.A.S.)
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 5.7, 7122 Palma de Mallorca Baleares, Spain;
| | - Damir A. Safin
- Institute of Chemistry, University of Tyumen, Volodarskogo Str. 6, 625003 Tyumen, Russia
- West-Siberian Interregional Scientific and Educational Center, 625003 Tyumen, Russia
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University named after the First President of Russia B.N. Eltsin, Mira Str. 19, 620002 Ekaterinburg, Russia
- Correspondence: (G.M.); (A.K.); (D.A.S.)
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Østrøm I, Ortolan AO, Caramori GF, Mascal M, Muñoz‐Castro A, Parreira RLT. In Silico
Design of Cylindrophanes: The Role of Functional Groups in a Fluoride Selective Host. Chemphyschem 2020; 21:1989-2005. [DOI: 10.1002/cphc.202000321] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/23/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ina Østrøm
- Departamento de Química Universidade Federal de Santa Catarina Campus Universitário Trindade, CP 476 Florianópolis SC, 88040-900 Brazil
| | - Alexandre O. Ortolan
- Departamento de Química Universidade Federal de Santa Catarina Campus Universitário Trindade, CP 476 Florianópolis SC, 88040-900 Brazil
| | - Giovanni F. Caramori
- Departamento de Química Universidade Federal de Santa Catarina Campus Universitário Trindade, CP 476 Florianópolis SC, 88040-900 Brazil
| | - Mark Mascal
- Department of Chemistry University of California Davis 1 Shields Avenue Davis CA 95616 USA
| | - Alvaro Muñoz‐Castro
- Laboratorio de Química Inorgánica y Materiales Moleculares, Facultad de Ingeniería Universidad Autonoma de Chile Llano Subercaseaux 2801 San Miguel, Santiago Chile
| | - Renato L. T. Parreira
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas Universidade de Franca 14404-600 Franca, SP Brazil
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37
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Campetella M, De Mitri N, Prampolini G. Automated parameterization of quantum-mechanically derived force-fields including explicit sigma holes: A pathway to energetic and structural features of halogen bonds in gas and condensed phase. J Chem Phys 2020; 153:044106. [PMID: 32752684 DOI: 10.1063/5.0014280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In classical molecular dynamics, general purpose atomistic force-fields (FFs) often deliver inaccurate results when dealing with halogen bonds (XBs), notwithstanding their crucial role in many fields of science, ranging from material design to drug development. Given the large dimensions of the systems of interest, it would be therefore desirable to increase the FF accuracy maintaining the simplicity of the standard Lennard-Jones (LJ) plus point charge description to avoid an excessive computational cost. A simple yet effective strategy consists in introducing a number of virtual sites able to mimic the so-called "explicit σ-hole." In this work, we present an automated FF parameterization strategy based on a global optimization of both LJ and charge parameters with respect to accurate quantum mechanical data, purposely computed for the system under investigation. As a test case, we report on two homologue series, characterized either by weak or strong XBs, namely, the di-halogenated methanes and the mono-, di-, and tri-substituted acetonitriles, taking into consideration Cl, Br, and I substituents. The resulting quantum mechanically derived FFs are validated for each compound in the gas and in the condensed phase by comparing them to general purpose and specific FFs without virtual sites and to highly accurate reference quantum mechanical data. The results strongly support the adoption of the specific FFs with virtual sites, which overcome the other investigated models in representing both gas phase energetics and the structural patterns of the liquid phase structure related to the presence of XBs.
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Affiliation(s)
- Marco Campetella
- Institut des Nanosciences de Paris, Sorbonne Université, CNRS, UMR7588, F-75252 Paris, France
| | - Nicola De Mitri
- Enthought Ltd., Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, United Kingdom
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici (ICCOM), CNR Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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38
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Novel lanthanide(III) complex [LaL2(NO3) (H2O)2]·5H2O with 2-pyridine carboxaldehyde isonicotinoyl hydrazine exhibiting a 3D supramolecular topology 3,6T49. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128151] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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39
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Nguyen BD, Chen GP, Agee MM, Burow AM, Tang MP, Furche F. Divergence of Many-Body Perturbation Theory for Noncovalent Interactions of Large Molecules. J Chem Theory Comput 2020; 16:2258-2273. [DOI: 10.1021/acs.jctc.9b01176] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Brian D. Nguyen
- University of California, Irvine, Department of Chemistry, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Guo P. Chen
- University of California, Irvine, Department of Chemistry, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Matthew M. Agee
- University of California, Irvine, Department of Chemistry, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Asbjörn M. Burow
- University of California, Irvine, Department of Chemistry, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Matthew P. Tang
- University of California, Irvine, Department of Chemistry, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Filipp Furche
- University of California, Irvine, Department of Chemistry, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
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40
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Akbari Afkhami F, Mahmoudi G, Qu F, Gupta A, Köse M, Zangrando E, Zubkov FI, Alkorta I, Safin DA. Supramolecular lead(ii) architectures engineered by tetrel bonds. CrystEngComm 2020. [DOI: 10.1039/d0ce00102c] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The structures, including tetrel bonding, of PbII coordination compounds assembled from N′-(pyridin-2-ylmethylene)picolinohydrazide, N′-(pyridin-2-ylmethylene)nicotinohydrazide and N′-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide ligands are discussed.
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Affiliation(s)
| | - Ghodrat Mahmoudi
- Department of Chemistry
- Faculty of Science
- University of Maragheh
- Maragheh
- Iran
| | - Fengrui Qu
- Department of Chemistry
- The University of Alabama
- Tuscaloosa
- USA
| | - Arunava Gupta
- Department of Chemistry
- The University of Alabama
- Tuscaloosa
- USA
| | - Muhammet Köse
- Chemistry Department
- Kahramanmaraş Sütçü Imam University
- Kahmaranmaraş
- Turkey
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- Trieste
- Italy
| | - Fedor I. Zubkov
- Organic Chemistry Department
- Faculty of Science
- Peoples' Friendship University of Russia (RUDN University)
- Moscow
- Russian Federation
| | - Ibon Alkorta
- Instituto de Quimica Medica (CSIC)
- 28006-Madrid
- Spain
| | - Damir A. Safin
- University of Tyumen
- 625003 Tyumen
- Russian Federation
- West-Siberian interregional scientific and educational center
- Russia
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41
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Mahmoudi G, Lawrence SE, Cisterna J, Cárdenas A, Brito I, Frontera A, Safin DA. A new spodium bond driven coordination polymer constructed from mercury(ii) azide and 1,2-bis(pyridin-2-ylmethylene)hydrazine. NEW J CHEM 2020. [DOI: 10.1039/d0nj04444j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this manuscript, the synthesis and X-ray characterization of a new spodium bond driven coordination polymer constructed from mercury(ii) azide and 1,2-bis(pyridin-2-ylmethylene)hydrazine are reported.
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Affiliation(s)
- Ghodrat Mahmoudi
- Department of Chemistry
- Faculty of Science
- University of Maragheh
- Maragheh
- Iran
| | - Simon E. Lawrence
- School of Chemistry, Analytical and Biological Chemistry Research Facility
- Synthesis and Solid State Pharmaceutical Centre
- University College Cork
- Cork
- UK
| | - Jonathan Cisterna
- Departamento de Química
- Facultad de Ciencias Básicas
- Universidad de Antofagasta
- Antofagasta
- Chile
| | - Alejandro Cárdenas
- Departamento de Física
- Facultad de Ciencias Básicas
- Universidad de Antofagasta
- Antofagasta
- Chile
| | - Iván Brito
- Departamento de Química
- Facultad de Ciencias Básicas
- Universidad de Antofagasta
- Antofagasta
- Chile
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Damir A. Safin
- University of Tyumen
- 625003 Tyumen
- Russian Federation
- West-Siberian Interregional Scientific and Educational Center
- Russian Federation
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42
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Mahmoudi G, Masoudiasl A, Babashkina MG, Frontera A, Doert T, White JM, Zangrando E, Zubkov FI, Safin DA. On the importance of π-hole spodium bonding in tricoordinated HgII complexes. Dalton Trans 2020; 49:17547-17551. [DOI: 10.1039/d0dt03938a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and X-ray characterization of two new tri-coordinated Hg complexes where the planar Hg atom participates in π-hole spodium bonding.
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Affiliation(s)
- Ghodrat Mahmoudi
- Department of Chemistry
- Faculty of Science
- University of Maragheh
- Maragheh
- Iran
| | - Ardavan Masoudiasl
- Department of Chemistry
- Faculty of Science
- University of Maragheh
- Maragheh
- Iran
| | - Maria G. Babashkina
- Institute of Condensed Matter and Nanosciences
- Université Catholique de Louvain
- 1348 Louvain-la-Neuve
- Belgium
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares)
- Spain
| | - Thomas Doert
- Department of Chemistry and Food Chemistry
- Dresden University of Technology
- 01069 Dresden
- Germany
| | - Jonathan M. White
- BIO-21 Molecular Science and Biotechnology
- University of Melbourne
- Parkville
- Australia
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- Trieste
- Italy
| | - Fedor I. Zubkov
- Organic Chemistry Department
- Faculty of Science
- Peoples Friendship University of Russia (RUDN University)
- Moscow
- Russian Federation
| | - Damir A. Safin
- University of Tyumen
- 625003 Tyumen
- Russian Federation
- West-Siberian interregional scientific and educational center
- Russian Federation
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Schouder C, Chatterley AS, Calvo F, Christiansen L, Stapelfeldt H. Structure determination of the tetracene dimer in helium nanodroplets using femtosecond strong-field ionization. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:044301. [PMID: 31463336 PMCID: PMC6711753 DOI: 10.1063/1.5118005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/09/2019] [Indexed: 05/29/2023]
Abstract
Dimers of tetracene molecules are formed inside helium nanodroplets and identified through covariance analysis of the emission directions of kinetic tetracene cations stemming from femtosecond laser-induced Coulomb explosion. Next, the dimers are aligned in either one or three dimensions under field-free conditions by a nonresonant, moderately intense laser pulse. The experimental angular covariance maps of the tetracene ions are compared to calculated covariance maps for seven different dimer conformations and found to be consistent with four of these. Additional measurements of the alignment-dependent strong-field ionization yield of the dimer narrow the possible conformations down to either a slipped-parallel or parallel-slightly rotated structure. According to our quantum chemistry calculations, these are the two most stable gas-phase conformations of the dimer and one of them is favorable for singlet fission.
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Affiliation(s)
- Constant Schouder
- Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Adam S Chatterley
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Florent Calvo
- Université Grenoble Alpes CNRS, LIPHY, F-38000 Grenoble, France
| | - Lars Christiansen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Henrik Stapelfeldt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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44
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Cacelli I, Lipparini F, Greff da Silveira L, Jacobs M, Livotto PR, Prampolini G. Accurate interaction energies by spin component scaled Möller-Plesset second order perturbation theory calculations with optimized basis sets (SCS-MP2mod): Development and application to aromatic heterocycles. J Chem Phys 2019; 150:234113. [DOI: 10.1063/1.5094288] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Ivo Cacelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Leandro Greff da Silveira
- Instituto de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Matheus Jacobs
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany
- IRIS Adelrshof, Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, 12489 Berlin, Germany
| | - Paolo Roberto Livotto
- Instituto de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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Seeking the best model for non-covalent interactions within the crystal structure of meloxicam. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bayach I, D'Aleó A, Trouillas P. Tuning Optical Properties of Chalcone Derivatives: A Computational Study. J Phys Chem A 2019; 123:194-201. [PMID: 30565921 DOI: 10.1021/acs.jpca.8b08529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformational feature of noncovalent complexes of two borondifluoride chalcone derivatives was assessed using DFT-D2. The corresponding optical properties were analyzed based on time-dependent density functional theory calculations. As already described in such complexes, the π-stacking interaction existing between both fragments allowed formation of a new absorption band corresponding to the S0 → S1 transition. However, this band appears very close to the most intense band corresponding the S0 → S2 transition.
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Affiliation(s)
- Imene Bayach
- Chemistry Department, College of Science , King Faisal Univzersity , Al Hufüf, 31982 Al-Ahsa , Saudi Arabia
| | - Anthony D'Aleó
- Aix Marseille University, CNRS , CINaM UMR 7325 , Campus de Luminy, 13007 Marseille , France
| | - Patrick Trouillas
- INSERM U1248 IPPRITT , Univ. Limoges , 87032 Limoges , France.,RCPTM, Fac. Sciences , Palacký University , Šlechtitelů 27 , 78371 Olomouc , Czech Republic
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48
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Ohno K, Kodaya Y, Yamakado H. Quantum chemical exploration of formaldehyde clusters (H 2 CO) n (n = 2-4). J Comput Chem 2018; 39:1498-1507. [PMID: 29607516 DOI: 10.1002/jcc.25220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/13/2018] [Accepted: 03/17/2018] [Indexed: 01/25/2023]
Abstract
Global exploration of equilibrium structures and interconversion pathways on the quantum chemical potential energy surface (PES) is performed for (H2 CO)n (n = 2-4) by using the Scaled Hypersphere Search-Anharmonic Downward Distortion Following (SHS-ADDF) method. Density functional theoretical (DFT) calculations with empirical dispersion corrections (D3) yielded comparable results for formaldehyde dimer in comparison with recent detailed studies at CCSD(T) levels. Based on DFT-D3 calculations, trimer and tetramer structures and their stabilities were studied. For tetramer, a highly symmetrical S4 structure was found as the most stable form in good accordance with experimentally determined tetramer unit in the formaldehyde crystal. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Kaigan 3-9-15, Minato-ku, Tokyo, 108-0022, Japan.,Department of Chemistry Graduate School of Science, Tohoku University, Aramaki Aza-Aoba 6-3, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Yoshitomo Kodaya
- Graduate School of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
| | - Hideo Yamakado
- Faculty of Systems Engineering, Wakayama University, Sakaedani 930, Wakayama, Wakayama, 640-8510, Japan
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Jacobs M, Greff Da Silveira L, Prampolini G, Livotto PR, Cacelli I. Interaction Energy Landscapes of Aromatic Heterocycles through a Reliable yet Affordable Computational Approach. J Chem Theory Comput 2018; 14:543-556. [DOI: 10.1021/acs.jctc.7b00602] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Matheus Jacobs
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Leandro Greff Da Silveira
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
- Departamento
de Ciências Exatas e da Terra, Universidade Regional Integrada do Alto Uruguay e da Missões (URI), Avenida Assis Brasil 709, CEP 98400-00 Frederico Westphalen, Brazil
| | - Giacomo Prampolini
- Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Paolo Roberto Livotto
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Ivo Cacelli
- Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi
3, I-56124 Pisa, Italy
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Thirman J, Engelage E, Huber SM, Head-Gordon M. Characterizing the interplay of Pauli repulsion, electrostatics, dispersion and charge transfer in halogen bonding with energy decomposition analysis. Phys Chem Chem Phys 2018; 20:905-915. [DOI: 10.1039/c7cp06959f] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Variational energy decomposition analysis establishes charge-transfer as the origin of halogen bond strength differences that go against electrostatics.
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Affiliation(s)
- Jonathan Thirman
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley
- Berkeley
- USA
| | - Elric Engelage
- Organische Chemie I, Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum
- D-44801 Bochum
- Germany
| | - Stefan M. Huber
- Organische Chemie I, Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum
- D-44801 Bochum
- Germany
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley
- Berkeley
- USA
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