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Pauls AM, Jamadgni DU, George G, Gitua JN, Thuo MM. Stereo-Structural Fine Tuning of Chromaticity. Angew Chem Int Ed Engl 2024; 63:e202318949. [PMID: 38446671 DOI: 10.1002/anie.202318949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/08/2024]
Abstract
Lanthanoid carboxylates were synthesized and in situ self-assembled to illustrate temperature-driven evolution in chromaticity. Evolution in structure (crystallinity), composition, luminosity, and chromaticity were investigated revealing the coupled role of divergence in order/structure (spatial organization), and composition in tuning observed color. Loss of crystallinity or increase in residual carbon leads to decrease in luminosity even with increase in hue. Comparing Ho and Er congeners shows that the density of accessible transition states relates to shifts in low and high wavelength components of color. This work demonstrates that, just as interface dipoles can lead to change in semiconductor band gap, structure and composition can analogously alter observed color.
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Affiliation(s)
- Alana M Pauls
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC-27606, USA
| | - Dhanush U Jamadgni
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC-27606, USA
| | - Gary George
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO-65211, USA
| | - John N Gitua
- Department of Chemistry, Drake University, 2802 Forest Ave, Des Moines, IA-50311, USA
| | - Martin M Thuo
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC-27606, USA
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2
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Derbali I, Aroule O, Hoffmann G, Thissen R, Alcaraz C, Romanzin C, Zins EL. On the relevance of the electron density analysis for the study of micro-hydration and its impact on the formation of a peptide-like bond. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Song S, Wang L, Su J, Xu Z, Hsu CH, Hua C, Lyu P, Li J, Peng X, Kojima T, Nobusue S, Telychko M, Zheng Y, Chuang FC, Sakaguchi H, Wong MW, Lu J. Manifold dynamic non-covalent interactions for steering molecular assembly and cyclization. Chem Sci 2021; 12:11659-11667. [PMID: 34667560 PMCID: PMC8442717 DOI: 10.1039/d1sc03733a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Deciphering rich non-covalent interactions that govern many chemical and biological processes is crucial for the design of drugs and controlling molecular assemblies and their chemical transformations. However, real-space characterization of these weak interactions in complex molecular architectures at the single bond level has been a longstanding challenge. Here, we employed bond-resolved scanning probe microscopy combined with an exhaustive structural search algorithm and quantum chemistry calculations to elucidate multiple non-covalent interactions that control the cohesive molecular clustering of well-designed precursor molecules and their chemical reactions. The presence of two flexible bromo-triphenyl moieties in the precursor leads to the assembly of distinct non-planar dimer and trimer clusters by manifold non-covalent interactions, including hydrogen bonding, halogen bonding, C-H⋯π and lone pair⋯π interactions. The dynamic nature of weak interactions allows for transforming dimers into energetically more favourable trimers as molecular density increases. The formation of trimers also facilitates thermally-triggered intermolecular Ullmann coupling reactions, while the disassembly of dimers favours intramolecular cyclization, as evidenced by bond-resolved imaging of metalorganic intermediates and final products. The richness of manifold non-covalent interactions offers unprecedented opportunities for controlling the assembly of complex molecular architectures and steering on-surface synthesis of quantum nanostructures.
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Affiliation(s)
- Shaotang Song
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Lulu Wang
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Jie Su
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Zhen Xu
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Chia-Hsiu Hsu
- Department of Physics, National Sun Yat-sen University Kaohsiung 80424 Taiwan
- Physics Division, National Center for Theoretical Sciences Taipei, 10617 Taiwan
| | - Chenqiang Hua
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University Hangzhou People's Republic of China
| | - Pin Lyu
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Jing Li
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Xinnan Peng
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Takahiro Kojima
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Shunpei Nobusue
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Mykola Telychko
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Yi Zheng
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University Hangzhou People's Republic of China
| | - Feng-Chuan Chuang
- Department of Physics, National Sun Yat-sen University Kaohsiung 80424 Taiwan
- Physics Division, National Center for Theoretical Sciences Taipei, 10617 Taiwan
| | - Hiroshi Sakaguchi
- Institute of Advanced Energy, Kyoto University Uji Kyoto 611-0011 Japan
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
| | - Jiong Lu
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543
- Centre for Advanced 2D Materials (CA2DM), National University of Singapore 6 Science Drive 2 Singapore 117546 Singapore
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Anjali BA, Suresh CH. Absorption and emission properties of 5-phenyl tris(8-hydroxyquinolinato) M(III) complexes (M = Al, Ga, In) and correlations with molecular electrostatic potential. J Comput Chem 2020; 41:1497-1508. [PMID: 32289191 DOI: 10.1002/jcc.26193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/09/2020] [Indexed: 11/07/2022]
Abstract
Substituent effect for a series of 5-phenyl tris(8-hydroxyquinolinato) M(III) complexes (Mq3) of aluminum, gallium, and indium are investigated using density functional theory (DFT) for the ground state properties and the time-dependent version of DFT (TDDFT) for their absorption and emission properties. A comparison between the ground state energy of mer and fac isomers of all the complexes revealed that the mer configuration is always more stable than fac. The substituent effect is significantly reflected at the fluorescence maximum (λF ) values whereas the effect is moderate at the absorption maximum (λabs ) values. The molecular electrostatic potential (MESP) at the metal center (VM ) and the most electron rich region indicated by MESP minimum (Vmin ), located at the oxygen of phenoxide ring exhibit excellent correlations with the λF and Stokes shift (λF -λabs ) values. The study suggests the use of Stokes shift as an experimental quantity to measure the excited state substituent effect while the Vmin or VM emerge as theoretical quantities to measure the same.
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Affiliation(s)
- Bai A Anjali
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-NIIST Campus, Trivandrum, India
| | - Cherumuttathu H Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-NIIST Campus, Trivandrum, India
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Zins EL. Microhydration of a Carbonyl Group: How does the Molecular Electrostatic Potential (MESP) Impact the Formation of (H 2O) n:(R 2C═O)Complexes? J Phys Chem A 2020; 124:1720-1734. [PMID: 32049521 DOI: 10.1021/acs.jpca.9b09992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presence of a carbonyl group in a molecule usually leads to the identification of a π-hole on the molecular electrostatic potential (MESP) of the species. How does this electrophilic site influence the formation of microhydrated complexes? To address this point, a panel of R2CO solutes with various MESPs was selected, and we identified the structures and properties of several complexes containing one, two, three and six water molecules. The following solutes were considered in the present study: H2CO, F2CO, Cl2CO,(NC)2CO and H2C═CO. Geometry optimizations and frequency calculations were carried out at the LC-ωPBE/6-311++G(d,p) level, with the GD3BJ empirical correction for dispersion. For a number of n water molecules around the R2CO solute, the structure and the features of the most stable (H2O)n:(R2CO) complexes are highly dependent on the MESP of the isolated R2CO solute. The formation of pi-hole bondings appears to play a decisive role in the initiation of a three-dimensional organization of water molecules around the solute.
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Affiliation(s)
- Emilie-Laure Zins
- De la Molécule aux Nano-Objets: Réactivité, Interactions Spectroscopies, MONARIS, CNRS, Sorbonne Université, 75005, Paris, France
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Kalai C, Alikhani ME, Zins EL. The molecular electrostatic potential analysis of solutes and water clusters: a straightforward tool to predict the geometry of the most stable micro-hydrated complexes of β-propiolactone and formamide. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2345-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Kakekhani A, Roling LT, Kulkarni A, Latimer AA, Abroshan H, Schumann J, AlJama H, Siahrostami S, Ismail-Beigi S, Abild-Pedersen F, Nørskov JK. Nature of Lone-Pair–Surface Bonds and Their Scaling Relations. Inorg Chem 2018; 57:7222-7238. [DOI: 10.1021/acs.inorgchem.8b00902] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arvin Kakekhani
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Luke T. Roling
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ambarish Kulkarni
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Allegra A. Latimer
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Hadi Abroshan
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Julia Schumann
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Hassan AlJama
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Samira Siahrostami
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Sohrab Ismail-Beigi
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, United States
| | - Frank Abild-Pedersen
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jens K. Nørskov
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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9
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D'Ascenzo L, Leonarski F, Vicens Q, Auffinger P. 'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response. Nucleic Acids Res 2016; 44:5944-56. [PMID: 27151194 PMCID: PMC4937326 DOI: 10.1093/nar/gkw388] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/28/2016] [Indexed: 01/09/2023] Open
Abstract
Since the work of Alexander Rich, who solved the first Z-DNA crystal structure, we have known that d(CpG) steps can adopt a particular structure that leads to forming left-handed helices. However, it is still largely unrecognized that other sequences can adopt ‘left-handed’ conformations in DNA and RNA, in double as well as single stranded contexts. These ‘Z-like’ steps involve the coexistence of several rare structural features: a C2’-endo puckering, a syn nucleotide and a lone pair–π stacking between a ribose O4’ atom and a nucleobase. This particular arrangement induces a conformational stress in the RNA backbone, which limits the occurrence of Z-like steps to ≈0.1% of all dinucleotide steps in the PDB. Here, we report over 600 instances of Z-like steps, which are located within r(UNCG) tetraloops but also in small and large RNAs including riboswitches, ribozymes and ribosomes. Given their complexity, Z-like steps are probably associated with slow folding kinetics and once formed could lock a fold through the formation of unique long-range contacts. Proteins involved in immunologic response also specifically recognize/induce these peculiar folds. Thus, characterizing the conformational features of these motifs could be a key to understanding the immune response at a structural level.
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Affiliation(s)
- Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France
| | - Filip Leonarski
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Quentin Vicens
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg 67084, France
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Kumar A, Gadre SR. Exploring the Gradient Paths and Zero Flux Surfaces of Molecular Electrostatic Potential. J Chem Theory Comput 2016; 12:1705-13. [PMID: 26881455 DOI: 10.1021/acs.jctc.6b00073] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The gradient vector field of molecular electrostatic potential, ∇V(r), has remained relatively unexplored in molecular quantum mechanics. The present article explores the conceptual as well as practical aspects of this vector field. A three-dimensional atomic partition of molecular space has been achieved on the basis of zero flux surfaces (ZFSs) of ∇V(r). Such ZFSs may completely enclose some of the atoms in the molecule, unlike what is observed in density-based atomic partitioning. The demonstration of this phenomenon is elucidated through typical examples, e.g., N2, CO, H2O, H2CO, OF(•), :CH2, and NH3BF3, where the electronegative atoms or group of atoms (group electronegativity) exhibits a closed ZFS of ∇V(r) around them. The present article determines an explicit reason for this phenomenon and also provides a necessary and sufficient condition for such a closed ZFS of ∇V(r) to exist. It also describes how the potential-based picture of atoms in molecules differs from its electron density-based analogue. This work further illustrates the manifestation of anisotropy in the gradient paths of MESP of some molecular systems, with respect to CO, (•)OH, H2O, and H2CO, and points to its potential in understanding the reactivity patterns of the interacting molecules.
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Affiliation(s)
- Anmol Kumar
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
| | - Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
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