1
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Nikulshin PV, Makarov AY, Koskin IP, Becker CS, Kazantsev MS, Beckmann J, Balmohammadi Y, Grabowsky S, Mebs S, Naumova OV, Protasov DY, Svit KA, Irtegova IG, Radiush EA, Bagryanskaya IY, Shundrin LA, Zibarev AV. 1,2,3,4-Tetrafluorobiphenylene: A Prototype Janus-Headed Scaffold for Ambipolar Materials. Chempluschem 2024; 89:e202300692. [PMID: 38052725 DOI: 10.1002/cplu.202300692] [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: 11/26/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
The title compound was synthesized by Ullmann cross-coupling in low yield as the first representative of [n]phenylene containing hydrocarbon and fluorocarbon rings. Stille/Suzuki-Miyaura cross-coupling reactions, as well as substitution of fluorine in suitable starting compounds, failed to give the same product. The geometric and electronic structures of the title compound were studied by X-ray diffraction, cyclic voltammetry and density functional theory calculations, together with Hirshfeld surface and reduced density gradient analyses. The crystal structure features head-to-tail π-stacking and other fluorine-related secondary bonding interactions. From the nucleus-independent chemical shifts descriptor, the four-membered ring of the title compound is antiaromatic, and the six-membered rings are aromatic. The Janus molecule is highly polarized; and the six-membered fluoro- and hydrocarbon rings are Lewis π-acidic and π-basic, respectively. The electrochemically-generated radical cation of the title compound is long-lived as characterized by electron paramagnetic resonance, whereas the radical anion is unstable in solution. The title compound reveals electrical properties of an insulator. On expanding its molecular scaffold towards partially fluorinated [n]phenylenes (n≥2), the properties presumably can be transformed into those of semiconductors. In this context, the title compound is suggested as a prototype scaffold for ambipolar materials for organic electronics and spintronics.
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Affiliation(s)
- Pavel V Nikulshin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Current address: Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Alexander Yu Makarov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Igor P Koskin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Christina S Becker
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Maxim S Kazantsev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Jens Beckmann
- Institute for Inorganic Chemistry and Crystallography, University of Bremen, 28359, Bremen, Germany
| | - Yaser Balmohammadi
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Stefan Mebs
- Institute for Experimental Physics, Free University of Berlin, 14195, Berlin, Germany
| | - Olga V Naumova
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Dmitry Yu Protasov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Kirill A Svit
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina G Irtegova
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Ekaterina A Radiush
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina Yu Bagryanskaya
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Leonid A Shundrin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Andrey V Zibarev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
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2
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Varadwaj PR. Halogen Bond via an Electrophilic π-Hole on Halogen in Molecules: Does It Exist? Int J Mol Sci 2024; 25:4587. [PMID: 38731806 PMCID: PMC11083155 DOI: 10.3390/ijms25094587] [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: 02/29/2024] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 05/13/2024] Open
Abstract
This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δginter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan;
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
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3
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Nolan D, Chin TR, Eamsureya M, Oppenheim S, Paley O, Alves C, Parks G. Modeling the behavior of monoclonal antibodies on hydrophobic interaction chromatography resins. BIORESOUR BIOPROCESS 2024; 11:25. [PMID: 38647931 PMCID: PMC10991917 DOI: 10.1186/s40643-024-00738-8] [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: 11/06/2023] [Accepted: 02/01/2024] [Indexed: 04/25/2024] Open
Abstract
Monoclonal antibodies (mAbs) require a high level of purity for regulatory approval and safe administration. High-molecular weight (HMW) species are a common impurity associated with mAb therapies. Hydrophobic interaction chromatography (HIC) resins are often used to remove these HMW impurities. Determination of a suitable HIC resin can be a time and resource-intensive process. In this study, we modeled the chromatographic behavior of seven mAbs across 13 HIC resins using measurements of surface hydrophobicity, surface charge, and thermal stability for mAbs, and hydrophobicity and zeta-potential for HIC resins with high fit quality (adjusted R2 > 0.80). We identified zeta-potential as a novel key modeling parameter. When using these models to select a HIC resin for HMW clearance of a test mAb, we were able to achieve 60% HMW clearance and 89% recovery. These models can be used to expedite the downstream process development for mAbs in an industry setting.
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Affiliation(s)
- Douglas Nolan
- Takeda Pharmaceuticals America Inc, Lexington, MA, 02421, USA.
| | - Thomas R Chin
- Takeda Pharmaceuticals America Inc, Lexington, MA, 02421, USA
| | - Mick Eamsureya
- Eurofins Lancaster Laboratories Professional Scientific Services, LLC, Lancaster, PA, 17601, USA
| | | | - Olga Paley
- Takeda Pharmaceuticals America Inc, Lexington, MA, 02421, USA
| | - Christina Alves
- Takeda Pharmaceuticals America Inc, Lexington, MA, 02421, USA
| | - George Parks
- Takeda Pharmaceuticals America Inc, Lexington, MA, 02421, USA
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4
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Li Y, Castillo HD, Dobscha JR, Morgan AR, Tait SL, Flood AH. Breaking Radial Dipole Symmetry in Planar Macrocycles Modulates Edge-to-Edge Packing and Disrupts Cofacial Stacking. Chemistry 2024; 30:e202302946. [PMID: 37950681 DOI: 10.1002/chem.202302946] [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: 09/09/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Dipolar interactions are ever-present in supramolecular architectures, though their impact is typically revealed by making dipoles stronger. While it is also possible to assess the role of dipoles by altering their orientations by using synthetic design, doing so without altering the molecular shape is not straightforward. We have now done this by flipping one triazole unit in a rigid macrocycle, tricarb. The macrocycle is composed of three carbazoles (2 Debye) and three triazoles (5 Debye) defining an array of dipoles aligned radially but organized alternately in and out. These dipoles are believed to dictate edge-to-edge tiling and face-to-face stacking. We modified our synthesis to prepare isosteric macrocycles with the orientation of one triazole dipole rotated 40°. The new dipole orientation guides edge-to-edge contacts to reorder the stability of two surface-bound 2D polymorphs. The impact on dipole-enhanced π stacking, however, was unexpected. Our stacking model identified an unchanged set of short-range (3.4 Å) anti-parallel dipole contacts. Despite this situation, the reduction in self-association was attributed to long-range (~6.4 Å) dipolar repulsions between π-stacked macrocycles. This work highlights our ability to control the build-up and symmetry of macrocyclic skeletons by synthetic design, and the work needed to further our understanding of how dipoles control self-assembly.
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Affiliation(s)
- Yan Li
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Henry D Castillo
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - James R Dobscha
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Amanda R Morgan
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Steven L Tait
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Amar H Flood
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, 47405, USA
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5
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Anjalikrishna PK, Suresh CH. Utilization of the through-space effect to design donor-acceptor systems of pyrrole, indole, isoindole, azulene and aniline. Phys Chem Chem Phys 2024; 26:1340-1351. [PMID: 38108385 DOI: 10.1039/d3cp03393g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Molecular electrostatic potential (MESP) topology analysis reveals the underlying phenomenon of the through-space effect (TSE), which imparts electron donor-acceptor properties to a wide range of chemical systems, including derivatives of pyrrole, indole, isoindole, azulene, and aniline. The TSE is inherent in pyrrole owing to the strong polarization of electron density (PoED) from the formally positively charged N-center to the C3C4 bonding region. The N → C3C4 directional nature of the TSE has been effectively employed to design molecules with high electronic polarization, such as bipyrroles, polypyrroles, phenyl pyrroles, multi-pyrrolyl systems and N-doped nanographenes. In core-expanded structures, the direction of electron flow from pyrrole units towards the core leads to highly electron-rich systems, while the opposite arrangement results in highly electron-deficient systems. Similarly, the MESP analysis reveals the presence of the TSE in azulene, indole, isoindole, and aniline. Oligomeric chains of these systems are designed in such a way that the direction of electron flow is consistent across each monomer, leading to substantial electronic polarization between the first and last monomer units. Notably, these designed systems exhibit strong donor-acceptor characteristics despite the absence of explicit donor and acceptor moieties, which is supported by FMO analysis, APT charge analysis, NMR data and λmax data. Among the systems studied, the TSEs of many experimentally known systems (bipyrroles, phenyl pyrroles, hexapyrrolylbenzene, octapyrrolylnaphthalene, decapyrrolylcorannulene, polyindoles, polyazulenes, etc.) are unraveled for the first time, while numerous new systems (polypyrroles, polyisoindoles, and amino-substituted benzene polymers) are predicted to be promising materials for the creation of donor-acceptor systems. These findings demonstrate the potential of the TSE in molecular design and provide new avenues for creating functional materials.
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Affiliation(s)
- Puthannur K Anjalikrishna
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, 695019, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Cherumuttathu H Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, 695019, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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6
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Richaud AD, Mandal S, Das A, Roche SP. Tunable CH/π Interactions within a Tryptophan Zipper Motif to Stabilize the Fold of Long β-Hairpin Peptides. ACS Chem Biol 2023; 18:2555-2563. [PMID: 37976523 DOI: 10.1021/acschembio.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The tryptophan zipper (Trpzip) is an iconic folding motif of β-hairpin peptides capitalizing on two pairs of cross-strand tryptophans, each stabilized by an aromatic-aromatic stacking in an edge-to-face (EtF) geometry. Yet, the origins and the contribution of this EtF packing to the unique Trpzip stability remain poorly understood. To address this question of structure-stability relationship, a library of Trpzip hairpins was developed by incorporating readily accessible nonproteinogenic tryptophans of varying electron densities. We found that each EtF geometry was, in fact, stabilized by an intricate combination of XH/π interactions. By tuning the π-electron density of Trpface rings, CH/π interactions are strengthened to gain additional stability. On the contrary, our DFT calculations support the notion that Trpedge modulations are challenging due to their simultaneous paradoxical engagement as H-bond donors in CH/π and acceptors in NH/π interactions.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Sourav Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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7
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Gong Z, Smith A, Farah AO, Dickerson SD, González-Montiel GA, Laddusaw JM, Cheong PHY, Wiskur SL. Investigating Substituent Interactions with Cationic Catalysts. J Org Chem 2023. [PMID: 37993265 DOI: 10.1021/acs.joc.3c01721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Rates of isothiourea catalyzed silylation and acylation reactions were measured for substrates with various electronic substituents at the aryl group. Through these measurements, the intermolecular interactions between cationic catalyst intermediates and different aryl groups were explored. These studies were performed to understand how changes in the catalyst structure affected electrostatic intermolecular interactions. Three different catalysts (N-methylimidazole and two isothioureas) were employed that varied in their ability to delocalize their cationic nature. The results show that more delocalization on the catalyst reduces the sensitivity to the electronics on the aryl group. Surprisingly, the isothiourea with a fused benzene ring provided additional points of interaction with groups that contained lone-pairs, significantly affecting the overall rate. This work helps explore the interactions that dominate in these types of catalytic systems, to aid in future organocatalysis development. Density functional theory (DFT) studies further confirmed isothiourea/aryl ring interaction with the alcohol substrate in the acylation process, which confirmed these hypotheses. Electron rich or lone-pair bearing functional groups stabilize the cationic catalyst core, thereby stabilizing the transition states and accelerating the reaction. It was also discovered that in one case, the formation of a stable substrate dimer was responsible for its lower reactivity.
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Affiliation(s)
- Ziyuan Gong
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, GSRC 109, Columbia, South Carolina 29206, United States
| | - Alberto Smith
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, GSRC 109, Columbia, South Carolina 29206, United States
| | - Abdikani Omar Farah
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Shelby D Dickerson
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, GSRC 109, Columbia, South Carolina 29206, United States
| | - Gisela A González-Montiel
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Jacqueline M Laddusaw
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Paul Ha-Yeon Cheong
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Sheryl L Wiskur
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, GSRC 109, Columbia, South Carolina 29206, United States
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8
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Carter-Fenk K, Liu M, Pujal L, Loipersberger M, Tsanai M, Vernon RM, Forman-Kay JD, Head-Gordon M, Heidar-Zadeh F, Head-Gordon T. The Energetic Origins of Pi-Pi Contacts in Proteins. J Am Chem Soc 2023; 145. [PMID: 37917924 PMCID: PMC10655088 DOI: 10.1021/jacs.3c09198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein's stability and structure. Pi-pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi-pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi-pi contact motifs. We find that neutral pi-pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter-Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi-pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi-pi contacts in polar media and like typical ion-pi interactions in nonpolar environments. Like-charged pairs such as arginine-arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi-pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.
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Affiliation(s)
- Kevin Carter-Fenk
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Meili Liu
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Leila Pujal
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Matthias Loipersberger
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Maria Tsanai
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Robert M. Vernon
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Julie D. Forman-Kay
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Martin Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Farnaz Heidar-Zadeh
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
- Center
for Molecular Modeling (CMM), Ghent University, 9052 Zwijnaarde, Belgium
| | - Teresa Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
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9
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Roos G, Murray JS. Intramolecular Repulsion Visible Through the Electrostatic Potential in Disulfides: Analysis via Varying Iso-density Envelopes. J Phys Chem A 2023; 127:8354-8364. [PMID: 37768140 DOI: 10.1021/acs.jpca.3c04691] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
For a series of diethyl disulfide conformations, the nearly touching contours of the electrostatic potential plotted on iso-density molecular surfaces allow the assessment of intramolecular repulsion. The electrostatic potential is plotted on varying iso-density envelopes to find the nearly touching contours for which (a) the surface electrostatic potential does not show overlap between atoms or functional groups and (b) the typical features are visible (σ-hole, lone pair, hydrogen VS,max). When these nearly touching contours X are closer to the nuclei, the more electron density is excluded from the iso-density envelopes and the smaller are the volumes corresponding to these envelopes. Both the contours X and the corresponding volumes are found to correlate with relative conformational energy, reflecting the degree of intramolecular repulsion present in the various diethyl disulfides. Quantitative estimates of intramolecular repulsion can be made based on relationships between the nearly touching contour X vs relative energy and volume (of the nearly touching contour X) vs relative energy, obtained for series of diethyl disulfide conformers. These relations were used to analyze intramolecular repulsion in a set of disulfides broader than diethyl disulfide conformers. We have shown that the approach of varying electronic density contours can be used in the study of repulsive intramolecular interactions, hereby extending earlier work involving attractive intermolecular interactions.
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Affiliation(s)
- Goedele Roos
- CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle,Univ. Lille, F-59000 Lille, France
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148 United States
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10
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Sun J, Decato DA, Bryantsev VS, John EA, Berryman OB. The interplay between hydrogen and halogen bonding: substituent effects and their role in the hydrogen bond enhanced halogen bond. Chem Sci 2023; 14:8924-8935. [PMID: 37621436 PMCID: PMC10445465 DOI: 10.1039/d3sc02348f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The hydrogen bond enhanced halogen bond (HBeXB) has recently been used to effectively improve anion binding, organocatalysis, and protein structure/function. In this study, we present the first systematic investigation of substituent effects in the HBeXB. NMR analysis confirmed intramolecular HBing between the amine and the electron-rich belt of the XB donor (N-H⋯I). Gas-phase density functional theory studies showed that the influence of HBing on the halogen atom is more sensitive to substitution on the HB donor ring (R1). The NMR studies revealed that the intramolecular HBing had a significant impact on receptor performance, resulting in a 50-fold improvement. Additionally, linear free energy relationship (LFER) analysis was employed for the first time to study the substituent effect in the HBeXB. The results showed that substituents on the XB donor ring (R2) had a competing effect where electron donating groups strengthened the HB and weakened the XB. Therefore, selecting an appropriate substituent on the adjacent HB donor ring (R1) could be an alternative and effective way to enhance an electron-rich XB donor. X-ray crystallographic analysis demonstrated that intramolecular HBing plays an important role in the receptor adopting the bidentate conformation. Taken together, the findings imply that modifying distal substituents that affect neighboring noncovalent interactions can have a similar impact to conventional para substitution substituent effects.
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Affiliation(s)
- Jiyu Sun
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
| | - Daniel A Decato
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
| | | | - Eric A John
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
| | - Orion B Berryman
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive Missoula MT 59812 USA
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11
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Mallada B, Ondráček M, Lamanec M, Gallardo A, Jiménez-Martín A, de la Torre B, Hobza P, Jelínek P. Visualization of π-hole in molecules by means of Kelvin probe force microscopy. Nat Commun 2023; 14:4954. [PMID: 37587123 PMCID: PMC10432393 DOI: 10.1038/s41467-023-40593-3] [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: 03/31/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
Submolecular charge distribution significantly affects the physical-chemical properties of molecules and their mutual interaction. One example is the presence of a π-electron-deficient cavity in halogen-substituted polyaromatic hydrocarbon compounds, the so-called π-holes, the existence of which was predicted theoretically, but the direct experimental observation is still missing. Here we present the resolution of the π-hole on a single molecule using the Kelvin probe force microscopy, which supports the theoretical prediction of its existence. In addition, experimental measurements supported by theoretical calculations show the importance of π-holes in the process of adsorption of molecules on solid-state surfaces. This study expands our understanding of the π-hole systems and, at the same time, opens up possibilities for studying the influence of submolecular charge distribution on the chemical properties of molecules and their mutual interaction.
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Affiliation(s)
- B Mallada
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371, Olomouc, Czech Republic
- Department of Physical Chemistry, Palacký University Olomouc, Tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - M Ondráček
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - M Lamanec
- Department of Physical Chemistry, Palacký University Olomouc, Tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000, Prague, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic
| | - A Gallardo
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - A Jiménez-Martín
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371, Olomouc, Czech Republic
| | - B de la Torre
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371, Olomouc, Czech Republic.
| | - P Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Námĕstí 542/2, 16000, Prague, Czech Republic.
- IT4Innovations, VŠB - Technical University of Ostrava, 17. Listopadu 2172/15, 708 00, Ostrava-Poruba, Czech Republic.
| | - P Jelínek
- Institute of Physics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 78371, Olomouc, Czech Republic.
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12
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Hejna BG, Ganley JM, Shao H, Tian H, Ellefsen JD, Fastuca NJ, Houk KN, Miller SJ, Knowles RR. Catalytic Asymmetric Hydrogen Atom Transfer: Enantioselective Hydroamination of Alkenes. J Am Chem Soc 2023; 145:16118-16129. [PMID: 37432783 PMCID: PMC10544660 DOI: 10.1021/jacs.3c04591] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
We report a highly enantioselective radical-based hydroamination of enol esters with sulfonamides jointly catalyzed by an Ir photocatalyst, Brønsted base, and tetrapeptide thiol. This method is demonstrated for the formation of 23 protected β-amino-alcohol products, achieving selectivities up to 97:3 er. The stereochemistry of the product is set through selective hydrogen atom transfer from the chiral thiol catalyst to a prochiral C-centered radical. Structure-selectivity relationships derived from structural variation of both the peptide catalyst and olefin substrate provide key insights into the development of an optimal catalyst. Experimental and computational mechanistic studies indicate that hydrogen-bonding, π-π stacking, and London dispersion interactions are contributing factors for substrate recognition and enantioinduction. These findings further the development of radical-based asymmetric catalysis and contribute to the understanding of the noncovalent interactions relevant to such transformations.
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Affiliation(s)
- Benjamin G. Hejna
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jacob M. Ganley
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Huiling Shao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Haowen Tian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Jonathan D. Ellefsen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Nicholas J. Fastuca
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Robert R. Knowles
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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13
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Wang Z, Wang W, Li HB. Tuning of the Electrostatic Potentials on the Surface of the Sulfur Atom in Organic Molecules: Theoretical Design and Experimental Assessment. Molecules 2023; 28:molecules28093919. [PMID: 37175329 PMCID: PMC10180200 DOI: 10.3390/molecules28093919] [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: 03/29/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Noncovalent sulfur interactions are ubiquitous and play important roles in medicinal chemistry and organic optoelectronic materials. Quantum chemical calculations predicted that the electrostatic potentials on the surface of the sulfur atom in organic molecules could be tuned through the through-space effects of suitable substituents. This makes it possible to design different types of noncovalent sulfur interactions. The theoretical design was further confirmed by X-ray crystallographic experiments. The sulfur atom acts as the halogen atom acceptor to form the halogen bond in the cocrystal between 2,5-bis(2-pyridyl)-1,3,4-thiadiazole and 1,4-diiodotetrafluorobenzene, whereas it acts as the chalcogen atom donor to form the chalcogen bond in the cocrystal between 2,5-bis(3-pyridyl)-1,3,4-thiadiazole and 1,3,5-trifluoro-2,4,6-triiodobenzene.
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Affiliation(s)
- Ziyu Wang
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, China
| | - Hai-Bei Li
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China
- Marine College, Shandong University, Weihai 264209, China
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14
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Yifrach Y, Rahimi R, Baraban JH, Bar I. Ionization energies and ionization-induced structural changes in 2-phenylethylamine and its monohydrate. J Chem Phys 2023; 158:114305. [PMID: 36948812 DOI: 10.1063/5.0138002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
We report the resonance-enhanced two-photon ionization combined with various detection approaches and quantum chemical calculations of biologically relevant neurotransmitter prototypes, the most stable conformer of 2-phenylethylamine (PEA), and its monohydrate, PEA-H2O, to reveal the possible interactions between the phenyl ring and amino group in the neutral and ionic species. Extracting the ionization energies (IEs) and appearance energy was achieved by measuring the photoionization and photodissociation efficiency curves of the PEA parent and photofragment ions, together with velocity and kinetic energy-broadened spatial map images of photoelectrons. We obtained coinciding upper bounds for the IEs for PEA and PEA-H2O of 8.63 ± 0.03 and 8.62 ± 0.04 eV, within the range predicted by quantum calculations. The computed electrostatic potential maps show charge separation, corresponding to a negative charge on phenyl and a positive charge on the ethylamino side chain in the neutral PEA and its monohydrate; in the cations, the charge distributions naturally become positive. The significant changes in geometries upon ionization include switching of the amino group orientation from pyramidal to nearly planar in the monomer but not in the monohydrate, lengthening of the N-H⋯π hydrogen bond (HB) in both species, Cα-Cβ bond in the side chain of the PEA+ monomer, and the intermolecular O-H⋯N HB in PEA-H2O cations, leading to distinct exit channels.
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Affiliation(s)
- Yair Yifrach
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Joshua H Baraban
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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15
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Sacristán-Martín A, Miguel D, Diez-Varga A, Barbero H, Álvarez CM. From Induced-Fit Assemblies to Ternary Inclusion Complexes with Fullerenes in Corannulene-Based Molecular Tweezers. J Org Chem 2022; 87:16691-16706. [DOI: 10.1021/acs.joc.2c02345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Adriana Sacristán-Martín
- GIR MIOMeT, IU CINQUIMA/Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Valladolid E47011, Spain
| | - Daniel Miguel
- GIR MIOMeT, IU CINQUIMA/Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Valladolid E47011, Spain
| | - Alberto Diez-Varga
- GIR MIOMeT, IU CINQUIMA/Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Valladolid E47011, Spain
| | - Héctor Barbero
- GIR MIOMeT, IU CINQUIMA/Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Valladolid E47011, Spain
| | - Celedonio M. Álvarez
- GIR MIOMeT, IU CINQUIMA/Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, Valladolid E47011, Spain
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16
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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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17
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Cons BD, Twigg DG, Kumar R, Chessari G. Electrostatic Complementarity in Structure-Based Drug Design. J Med Chem 2022; 65:7476-7488. [PMID: 35512344 DOI: 10.1021/acs.jmedchem.2c00164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optimization of electrostatic complementarity is an important strategy in structure-based drug discovery for improving the affinity of molecules against a specific protein target. In this Miniperspective we identify examples where deliberate optimization of protein-ligand electrostatic complementarity or intramolecular electrostatic interactions gave improvements in target affinity (up to 250-fold), physicochemical properties, in vitro properties, and off-target selectivity. We also look retrospectively at a series of factor Xa inhibitors that show an almost 8000-fold range in potency that can be correlated with the calculated electrostatic potential (ESP) surfaces. Recent developments using a graph-convolutional deep neural network to rapidly generate high quality ESP surfaces have the potential to make this useful tool more accessible for a wider audience within the field of medicinal chemistry.
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Affiliation(s)
- Benjamin D Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David G Twigg
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Rajendra Kumar
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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18
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Zhang X, Hu H, Huang X, Yin Y, Wang S, Jiao S, Liu Z, Zheng Y. Protective Mechanism of a Layer-by-Layer-Assembled Artificial Cell Wall on Probiotics. J Phys Chem B 2022; 126:1933-1940. [PMID: 35200022 DOI: 10.1021/acs.jpcb.1c09282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Constructing an artificial cell wall (AFCW) based on the layer-by-layer assembly of polymer films to protect probiotics in harsh conditions is highly desirable. Early findings showed that encapsulating yeast cells by an AFCW improved the cell viability by 50% in antibiotic solution. However, the detailed molecular interaction mechanism remains unclear by experiments. Herein, two ciprofloxacin (CPFX) permeation models, including models 1 and 2 that were, respectively, composed of just the yeast cell membrane and the AFCW coating cell membrane, were investigated by molecular dynamics simulations. The free energy profiles delineating the permeation process of CPFX reveal that the permeation of CPFX through the cell membrane of model 2 is more difficult than through that of model 1. The analysis results show that the AFCW leads to two sharp increases in free energy barriers, amounting to 8.9 and 6.2 kcal/mol, thereby reducing the penetrating rate of CPFX into the cell membrane. Moreover, decomposition of the potentials of mean force into free energy components suggested that the electrostatic interactions of CPFX with the AFCW predominantly contributed to the high free energy barriers. The current results provide a good understanding of the protective mechanism of the self-assembled cell walls against CPFX and help to design other AFCWs.
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Affiliation(s)
- Xia Zhang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Hanjiao Hu
- Guangxi Key Laboratory of Green Chemical Materials and Safety Technology, Beibu Gulf University, Qinzhou 535011, China
| | - Xin Huang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Yanzhen Yin
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.,Guangxi Key Laboratory of Green Chemical Materials and Safety Technology, Beibu Gulf University, Qinzhou 535011, China
| | - Shuangshuang Wang
- Guangxi Key Laboratory of Green Chemical Materials and Safety Technology, Beibu Gulf University, Qinzhou 535011, China
| | - Shufei Jiao
- Guangxi Key Laboratory of Green Chemical Materials and Safety Technology, Beibu Gulf University, Qinzhou 535011, China
| | - Zijie Liu
- Guangxi Key Laboratory of Green Chemical Materials and Safety Technology, Beibu Gulf University, Qinzhou 535011, China
| | - Yunying Zheng
- Guangxi Key Laboratory of Green Chemical Materials and Safety Technology, Beibu Gulf University, Qinzhou 535011, China
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19
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Fang X, Hu Y, Huang Z, Han L, Li B, Lu S, Cao Y. Exploring the formation mechanism of coamorphous andrographolide-oxymatrine based on molecular dynamics and spectroscopy. J Pharm Sci 2022; 111:2056-2071. [DOI: 10.1016/j.xphs.2022.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 12/18/2022]
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20
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Urner LM, Lee GY, Treacy JW, Turlik A, Khan SI, Houk KN, Jung ME. Intramolecular N-H⋅⋅⋅F Hydrogen Bonding Interaction in a Series of 4-Anilino-5-Fluoroquinazolines: Experimental and Theoretical Characterization of Electronic and Conformational Effects. Chemistry 2022; 28:e202103135. [PMID: 34767667 PMCID: PMC9482468 DOI: 10.1002/chem.202103135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Indexed: 01/12/2023]
Abstract
The 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline scaffold is presented as a novel model system for the characterization of the weak NH⋅⋅⋅F hydrogen bonding (HB) interaction. In this scaffold, the aniline NH proton is forced into close proximity with the nearby fluorine (dH,F ∼2.0 Å, ∠∼138°), and a through-space interaction is observed by NMR spectroscopy with couplings (1h JNH,F ) of 19±1 Hz. A combination of experimental (NMR spectroscopy and X-ray crystallography) and theoretical methods (DFT calculations) were used for the characterization of this weak interaction. In particular, the effects of conformational rigidity and steric compression on coupling were investigated. This scaffold was used for the direct comparison of fluoride with methoxy as HB acceptors, and the susceptibility of the NH⋅⋅⋅F interaction to changes in electron distribution and resonance was probed by preparing a series of molecules with different electron-donating or -withdrawing groups in the positions para to the NH and F. The results support the idea that fluorine can act as a weak HB acceptor, and the HB strength can be modulated through additive and linear electronic substituent effects.
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Affiliation(s)
- Lorenz M. Urner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Ga Young Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Aneta Turlik
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Saeed I. Khan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Michael E. Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
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21
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Haritha M, Suresh CH. Hydration patterns of rings in drugs and relationship to lipophilicity: A DFT study. J Comput Chem 2022; 43:477-490. [PMID: 34978337 DOI: 10.1002/jcc.26808] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/09/2021] [Accepted: 12/22/2021] [Indexed: 11/11/2022]
Abstract
Rings are one of the major scaffold components of drugs in medicinal chemistry, due to their unique electronic distribution, scaffold rigidity, and three-dimensionality while lipophilicity is considered as a vital parameter of rings that can influence the reactivity, metabolic stability, and toxicity. We have analyzed the electronic features, hydration patterns, solvation effect and lipophilicity data for 51 most widely used ring systems in drugs. Molecular electrostatic potential (MESP) topology analysis has been used to assess the electronic distribution in rings which provided an easy interpretation of the most suitable hydration patterns of the ring with H2 O molecule. Further, the global minimum of ring…H2 O complex has been utilized to predict lipophilicity (logP) with the incorporation of implicit solvation effect. Classification of ring systems based on their molecular weight into four categories, viz. small ring 'sr', medium ring 'mr', large ring 'lr' and extra large ring 'xlr' systems has led to the finding of strong correlations between logP and hydration energy with R = 0.942, 0.933, 0.968 and 0.933, respectively. The micro solvation model is found to be useful for locating the hydrophobic-hydrophilic border for each category of rings in terms of hydration energy whereas the implicit solvation model used for two solvents, n-octanol and water on the most stable hydrated structure led to a global correlation between logP and solvation energy ratio. This correlation predicts a limiting logP value -7.03 for the most hydrophilic ring system and also suggests a clear partitioning of the ring molecules into hydrophobic and hydrophilic classes. The MESP topology-guided approach to understand the electronic features and hydration patterns of rings in drugs lead to powerful predictions on their lipophilicity behavior.
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Affiliation(s)
- Mambatta Haritha
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Cherumuttathu H Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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22
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Lin B, Karki I, Pellechia PJ, Shimizu KD. Electrostatically-gated molecular rotors. Chem Commun (Camb) 2022; 58:5869-5872. [DOI: 10.1039/d2cc00512c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability to control molecular-scale motion using electrostatic interactions was demonstrated using an N-phenylsuccinimide molecular rotor with an electrostatic pyridyl-gate. Protonation of the pyridal-gate forms stabilizing electrostatic interactions in the...
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23
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Pagliari A, Meyer AR, Solner V, Rosa JML, Hoerner M, Gauze Bonacorso H, Zanatta N, Martins MAP. Effect of Hydrogen Bonds and π...π-interactions on the Crystallization of Phenyl-perfluorophenyl Amides: Understanding the Self-organization of a Cocrystal. CrystEngComm 2022. [DOI: 10.1039/d2ce00231k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of N-arylbenzamides containing amide group and phenyl−perfluorinated rings were used as the smallest molecules to investigate the direct influence of hydrogen bond and aromatic donor-acceptor complementarity in the...
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24
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Andrade-Filho T, Silva T, Belo E, Raiol A, de Oliveira RV, Marinho PS, Bitencourt HR, Marinho AM, da Cunha AR, Gester R. Insights and modelling on the nonlinear optical response, reactivity, and structure of chalcones and dihydrochalcones. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Bravin C, Piękoś JA, Licini G, Hunter CA, Zonta C. Dissection of the Polar and Non‐Polar Contributions to Aromatic Stacking Interactions in Solution. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Carlo Bravin
- Dipartimento di Scienze Chimiche Università degli Studi di Padova via Marzolo 1 35131 Padova Italy
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Justyna A. Piękoś
- Dipartimento di Scienze Chimiche Università degli Studi di Padova via Marzolo 1 35131 Padova Italy
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Giulia Licini
- Dipartimento di Scienze Chimiche Università degli Studi di Padova via Marzolo 1 35131 Padova Italy
| | - Christopher A. Hunter
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Cristiano Zonta
- Dipartimento di Scienze Chimiche Università degli Studi di Padova via Marzolo 1 35131 Padova Italy
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26
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Bravin C, Piękoś JA, Licini G, Hunter CA, Zonta C. Dissection of the Polar and Non-Polar Contributions to Aromatic Stacking Interactions in Solution. Angew Chem Int Ed Engl 2021; 60:23871-23877. [PMID: 34472177 PMCID: PMC8596670 DOI: 10.1002/anie.202110809] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Indexed: 11/19/2022]
Abstract
Aromatic stacking interactions have been a matter of study and debate due to their crucial role in chemical and biological systems. The strong dependence on orientation and solvent together with the relatively small interaction energies have made evaluation and rationalization a challenge for experimental and theoretical chemists. We have used a supramolecular cage formed by two tris(pyridylmethyl)amines units to build chemical Double Mutant Cycles (DMC) for the experimental measurement of the free energies of π-stacking interactions. Extrapolating the substituent effects to remove the contribution due to electrostatic interactions reveals that there is a substantial contribution to the measured stacking interaction energies which is due to non-polar interactions (-3 to -6 kJ mol-1 ). The perfectly flat nature of the surface of an aromatic ring gives π-stacking an inherent advantage over non-polar interactions with alkyl groups and accounts for the wide-spread prevalence of stacking interactions in Nature.
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Affiliation(s)
- Carlo Bravin
- Dipartimento di Scienze ChimicheUniversità degli Studi di Padovavia Marzolo 135131PadovaItaly
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Justyna A. Piękoś
- Dipartimento di Scienze ChimicheUniversità degli Studi di Padovavia Marzolo 135131PadovaItaly
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Giulia Licini
- Dipartimento di Scienze ChimicheUniversità degli Studi di Padovavia Marzolo 135131PadovaItaly
| | - Christopher A. Hunter
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Cristiano Zonta
- Dipartimento di Scienze ChimicheUniversità degli Studi di Padovavia Marzolo 135131PadovaItaly
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27
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Herbert JM. Neat, Simple, and Wrong: Debunking Electrostatic Fallacies Regarding Noncovalent Interactions. J Phys Chem A 2021; 125:7125-7137. [PMID: 34388340 DOI: 10.1021/acs.jpca.1c05962] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multipole moments such as charge, dipole, and quadrupole are often invoked to rationalize intermolecular phenomena, but a low-order multipole expansion is rarely a valid description of electrostatics at the length scales that characterize nonbonded interactions. This is illustrated by examining several common misunderstandings rooted in erroneous electrostatic arguments. First, the notion that steric repulsion originates in Coulomb interactions is easily disproved by dissecting the interaction potential for Ar2. Second, the Hunter-Sanders model of π-π interactions, which is based on quadrupolar electrostatics, is shown to have no basis in accurate calculations. Third, curved "buckybowls" exhibit unusually large dipole moments, but these are ancillary to the forces that control their intermolecular interactions, as illustrated by two examples involving corannulene. Finally, the assumption that interactions between water and small anions are dictated by the dipole moment of H2O is shown to be false in the case of binary halide-water complexes. These examples present a compelling case that electrostatic explanations based on low-order multipole moments are very often counterfactual for nonbonded interactions at close range and should not be taken seriously in the absence of additional justification.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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28
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Abstract
It follows from the Schrödinger equation that the forces operating within molecules and molecular complexes are Coulombic, which necessarily entails both electrostatics and polarization. A common and important class of molecular complexes is due to π-holes. These are molecular regions of low electronic density that are perpendicular to planar portions of the molecular frameworks. π-Holes often have positive electrostatic potentials associated with them, which result in mutually polarizing attractive forces with negative sites such as lone pairs, π electrons or anions. In many molecules, π-holes correspond to a flattening of the electronic density surface but in benzene derivatives and in polyazines the π-holes are craters above and below the rings. The interaction energies of π-hole complexes can be expressed quite well in terms of regression relationships that account for both the electrostatics and the polarization. There is a marked gradation in the interaction energies, from quite weak (about -2 kcal mol-1) to relatively strong (about -40 kcal mol-1). Gradations are also evident in the ratios of the intermolecular separations to the sums of the respective van der Waals radii and in the gradual transition of the π-hole atoms from trigonal to quasi-tetrahedral configurations. These trends are consistent with the concept that chemical interactions form a continuum, from very weak to very strong.
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Affiliation(s)
- Peter Politzer
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA.
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29
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Ekramipooya A, Valadi FM, Farisabadi A, Gholami MR. Effect of the heteroatom presence in different positions of the model asphaltene structure on the self-aggregation: MD and DFT study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116109] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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The Neglected Nuclei. Molecules 2021; 26:molecules26102982. [PMID: 34069785 PMCID: PMC8157270 DOI: 10.3390/molecules26102982] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022] Open
Abstract
Since the nuclei in a molecule are treated as stationary, it is perhaps natural that interpretations of molecular properties and reactivity have focused primarily upon the electronic density distribution. The role of the nuclei has generally received little explicit consideration. Our objective has been to at least partially redress this imbalance in emphasis. We discuss a number of examples in which the nuclei play the determining role with respect to molecular properties and reactive behavior. It follows that conventional interpretations based solely upon electronic densities and donating or withdrawing tendencies should be made with caution.
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31
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Jian J, Hammink R, McKenzie CJ, Bickelhaupt FM, Poater J, Mecinović J. Do Sulfonamides Interact with Aromatic Rings? Chemistry 2021; 27:5721-5729. [PMID: 33377554 DOI: 10.1002/chem.202004732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Indexed: 11/07/2022]
Abstract
Aromatic rings form energetically favorable interactions with many polar groups in chemical and biological systems. Recent molecular studies have shown that sulfonamides can chelate metal ions and form hydrogen bonds, however, it is presently not established whether the polar sulfonamide functionality also interacts with aromatic rings. Here, synthetic, spectroscopic, structural, and quantum chemical analyses on 2,6-diarylbenzenesulfonamides are reported, in which two flanking aromatic rings are positioned close to the central sulfonamide moiety. Fine-tuning the aromatic character by substituents on the flanking rings leads to linear trends in acidity and proton affinity of sulfonamides. This physical-organic chemistry study demonstrates that aromatic rings have a capacity to stabilize sulfonamides via through-space NH-π interactions. These results have implications in rational drug design targeting electron-rich aromatic rings in proteins.
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Affiliation(s)
- Jie Jian
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej, 55, 5230, Odense, Denmark
| | - Roel Hammink
- Division of Immunotherapy, Oncode Institute, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 26, 6525 GA, Nijmegen, The Netherlands
| | - Christine J McKenzie
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej, 55, 5230, Odense, Denmark
| | - F Matthias Bickelhaupt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.,Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Jordi Poater
- ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain.,Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej, 55, 5230, Odense, Denmark
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Mondal T, Shaik S, Kenttämaa H, Stuyver T. Modulating the radical reactivity of phenyl radicals with the help of distonic charges: it is all about electrostatic catalysis. Chem Sci 2021; 12:4800-4809. [PMID: 34163733 PMCID: PMC8179573 DOI: 10.1039/d0sc07111k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/16/2021] [Indexed: 11/21/2022] Open
Abstract
This manuscript reports the modulation of H-abstraction reactivity of phenyl radicals by (positive and negative) distonic ions. Specifically, we focus on the origins of this modulating effect: can the charged functional groups truly be described as "extreme forms of electron-withdrawing/donating substituents" - implying a through-bond mechanism - as argued in the literature, or is the modulation mainly caused by through-space effects? Our analysis indicates that the effect of the remote charges can be mimicked almost perfectly with the help of a purely electrostatic treatment, i.e. replacing the charged functional groups by a simple uniform electric field is sufficient to recover the quantitative reactivity trends. Hence, through-space effects dominate, whereas through-bond effects play a minor role at best. We elucidate our results through a careful Valence Bond (VB) analysis and demonstrate that such a qualitative analysis not only reveals through-space dominance, but also demonstrates a remarkable reversal in the reactivity trends of a given polarity upon a rational modification of the reaction partner. As such, our findings demonstrate that VB theory can lead to productive predictions about the behaviour of distonic radical ions.
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Affiliation(s)
- Totan Mondal
- Institute of Chemistry, The Hebrew University Jerusalem 91904 Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University Jerusalem 91904 Israel
| | - Hilkka Kenttämaa
- Department of Chemistry, Purdue University West Lafayette Indiana 47907-1393 USA
| | - Thijs Stuyver
- Institute of Chemistry, The Hebrew University Jerusalem 91904 Israel
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Politzer P, Murray JS. Oxatriazoles: Potential Frameworks for Energetic Compounds? PROPELLANTS EXPLOSIVES PYROTECHNICS 2021. [DOI: 10.1002/prep.202000243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Peter Politzer
- Department of Chemistry University of New Orleans New Orleans LA 71048 USA
| | - Jane S. Murray
- Department of Chemistry University of New Orleans New Orleans LA 71048 USA
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Peluso P, Dessì A, Dallocchio R, Sechi B, Gatti C, Chankvetadze B, Mamane V, Weiss R, Pale P, Aubert E, Cossu S. Enantioseparation of 5,5'-Dibromo-2,2'-Dichloro-3-Selanyl-4,4'-Bipyridines on Polysaccharide-Based Chiral Stationary Phases: Exploring Chalcogen Bonds in Liquid-Phase Chromatography. Molecules 2021; 26:molecules26010221. [PMID: 33406753 PMCID: PMC7794968 DOI: 10.3390/molecules26010221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/26/2020] [Accepted: 12/29/2020] [Indexed: 12/25/2022] Open
Abstract
The chalcogen bond (ChB) is a noncovalent interaction based on electrophilic features of regions of electron charge density depletion (σ-holes) located on bound atoms of group VI. The σ-holes of sulfur and heavy chalcogen atoms (Se, Te) (donors) can interact through their positive electrostatic potential (V) with nucleophilic partners such as lone pairs, π-clouds, and anions (acceptors). In the last few years, promising applications of ChBs in catalysis, crystal engineering, molecular biology, and supramolecular chemistry have been reported. Recently, we explored the high-performance liquid chromatography (HPLC) enantioseparation of fluorinated 3-arylthio-4,4′-bipyridines containing sulfur atoms as ChB donors. Following this study, herein we describe the comparative enantioseparation of three 5,5′-dibromo-2,2′-dichloro-3-selanyl-4,4′-bipyridines on polysaccharide-based chiral stationary phases (CSPs) aiming to understand function and potentialities of selenium σ-holes in the enantiodiscrimination process. The impact of the chalcogen substituent on enantioseparation was explored by using sulfur and non-chalcogen derivatives as reference substances for comparison. Our investigation also focused on the function of the perfluorinated aromatic ring as a π-hole donor recognition site. Thermodynamic quantities associated with the enantioseparation were derived from van’t Hoff plots and local electron charge density of specific molecular regions of the interacting partners were inspected in terms of calculated V. On this basis, by correlating theoretical data and experimental results, the participation of ChBs and π-hole bonds in the enantiodiscrimination process was reasonably confirmed.
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Affiliation(s)
- Paola Peluso
- Institute of Biomolecular Chemistry ICB, CNR, Secondary Branch of Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy; (A.D.); (R.D.); (B.S.)
- Correspondence: (P.P.); (V.M.); Tel.: +39-079-2841218 (P.P.); +33-3-68851612 (V.M.)
| | - Alessandro Dessì
- Institute of Biomolecular Chemistry ICB, CNR, Secondary Branch of Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy; (A.D.); (R.D.); (B.S.)
| | - Roberto Dallocchio
- Institute of Biomolecular Chemistry ICB, CNR, Secondary Branch of Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy; (A.D.); (R.D.); (B.S.)
| | - Barbara Sechi
- Institute of Biomolecular Chemistry ICB, CNR, Secondary Branch of Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy; (A.D.); (R.D.); (B.S.)
| | - Carlo Gatti
- CNR-SCITEC, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, sezione di via Golgi, via C. Golgi 19, 20133 Milano, Italy;
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, 0179 Tbilisi, Georgia;
| | - Victor Mamane
- Strasbourg Institute of Chemistry, UMR CNRS 7177, Team LASYROC, 1 rue Blaise Pascal, University of Strasbourg, 67008 Strasbourg CEDEX, France; (R.W.); (P.P.)
- Correspondence: (P.P.); (V.M.); Tel.: +39-079-2841218 (P.P.); +33-3-68851612 (V.M.)
| | - Robin Weiss
- Strasbourg Institute of Chemistry, UMR CNRS 7177, Team LASYROC, 1 rue Blaise Pascal, University of Strasbourg, 67008 Strasbourg CEDEX, France; (R.W.); (P.P.)
| | - Patrick Pale
- Strasbourg Institute of Chemistry, UMR CNRS 7177, Team LASYROC, 1 rue Blaise Pascal, University of Strasbourg, 67008 Strasbourg CEDEX, France; (R.W.); (P.P.)
| | - Emmanuel Aubert
- Crystallography, Magnetic Resonance and Modelling (CRM2), UMR CNRS 7036, University of Lorraine, Bd des Aiguillettes, 54506 Vandoeuvre-les-Nancy, France;
| | - Sergio Cossu
- Department of Molecular Sciences and Nanosystems DSMN, Venice Ca’ Foscari University, Via Torino 155, 30172 Mestre Venezia, Italy;
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Abstract
The nature of π-π interactions has long been debated. The term "π-stacking" is considered by some to be a misnomer, in part because overlapping π-electron densities are thought to incur steric repulsion, and the physical origins of the widely-encountered "slip-stacked" motif have variously been attributed to either sterics or electrostatics, in competition with dispersion. Here, we use quantum-mechanical energy decomposition analysis to investigate π-π interactions in supramolecular complexes of polycyclic aromatic hydrocarbons, ranging in size up to realistic models of graphene, and for comparison we perform the same analysis on stacked complexes of polycyclic saturated hydrocarbons, which are cyclohexane-based analogues of graphane. Our results help to explain the short-range structure of liquid hydrocarbons that is inferred from neutron scattering, trends in melting-point data, the interlayer separation of graphene sheets, and finally band gaps and observation of molecular plasmons in graphene nanoribbons. Analysis of intermolecular forces demonstrates that aromatic π-π interactions constitute a unique and fundamentally quantum-mechanical form of non-bonded interaction. Not only do stacked π-π architectures enhance dispersion, but quadrupolar electrostatic interactions that may be repulsive at long range are rendered attractive at the intermolecular distances that characterize π-stacking, as a result of charge penetration effects. The planar geometries of aromatic sp2 carbon networks lead to attractive interactions that are "served up on a molecular pizza peel", and adoption of slip-stacked geometries minimizes steric (rather than electrostatic) repulsion. The slip-stacked motif therefore emerges not as a defect induced by electrostatic repulsion but rather as a natural outcome of a conformational landscape that is dominated by van der Waals interactions (dispersion plus Pauli repulsion), and is therefore fundamentally quantum-mechanical in its origins. This reinterpretation of the forces responsible for π-stacking has important implications for the manner in which non-bonded interactions are modeled using classical force fields, and for rationalizing the prevalence of the slip-stacked π-π motif in protein crystal structures.
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Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
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36
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Xiang L, Zhang J, Wang W, Gong L, Zhang L, Yan B, Zeng H. Nanomechanics of π-cation-π interaction with implications for bio-inspired wet adhesion. Acta Biomater 2020; 117:294-301. [PMID: 33007483 DOI: 10.1016/j.actbio.2020.09.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022]
Abstract
Cation-π interactions play a vital role in modulating various biological processes, e.g., potassium-selective channel, protein folding and adhesion of marine organism. Previous studies mainly focus on binary cation-π interaction, whereas due to the complexity of biological systems and surrounding environments, a single cation is often in close proximity with more than one π-conjugated unit, which could exhibit essentially different binding behavior. Herein, the first experimental evidence of ternary π-cation-π interaction is reported through direct nanomechanical force measurement in a model π-conjugated poly(catechol) (PC) system coexisting with K+. Ternary π-cation-π interactions can bridge π-conjugated moieties, resulting in robust adhesion and promoting PC assembly and deposition. Particularly, these ternary complexes are discovered to transit to binary binding pairs by increasing K+ concentration, undermining adhesion and assembly due to lack of bridging. The π-cation-π binding strength follows the trend of NMe4+ > K+ > Na+ > Li+. Employing the π-cation-π interaction, a deposition strategy to fabricate π-conjugated moiety based adhesive coatings on different substrates is realized. Our findings provide useful insights in engineering wet adhesives and coatings with reversible adhesion properties, and more broadly, with implications on rationalizing biological assembly.
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Affiliation(s)
- Li Xiang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Jiawen Zhang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Wenda Wang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Lu Gong
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Ling Zhang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Bin Yan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada; College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, China
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada.
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37
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Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4'-Bipyridine Derivatives. Molecules 2020; 25:molecules25194409. [PMID: 32992941 PMCID: PMC7582854 DOI: 10.3390/molecules25194409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/08/2023] Open
Abstract
Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader-Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4'-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C-Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way.
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38
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Krone MW, Travis CR, Lee GY, Eckvahl HJ, Houk KN, Waters ML. More Than π-π-π Stacking: Contribution of Amide-π and CH-π Interactions to Crotonyllysine Binding by the AF9 YEATS Domain. J Am Chem Soc 2020; 142:17048-17056. [PMID: 32926780 DOI: 10.1021/jacs.0c06568] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lysine crotonylation (Kcr) is a histone post-translational modification that is implicated in numerous epigenetic pathways and diseases. Recognition of Kcr by YEATS domains has been proposed to occur through intermolecular amide-π and alkene-π interactions, but little is known about the driving force of these key interactions. Herein, we probed the recognition of lysine crotonylation and acetylation by the AF9 YEATS domain through incorporation of noncanonical Phe analogs with distinct electrostatics at two positions. We found that amide-π interactions between AF9 and acyllysines are electrostatically tunable, with electron-rich rings providing more favorable interactions. This differs from trends in amide-heteroarene interactions and provides insightful information for therapeutic design. Additionally, we report for the first time that CH-π interactions at Phe28 directly contribute to AF9's recognition of acyllysines, illuminating differences among YEATS domains, as this residue is not highly conserved but has been shown to impart selectivity for specific post-translational modification.
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Affiliation(s)
- Mackenzie W Krone
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Christopher R Travis
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ga Young Lee
- Department of Chemistry and Biochemistry, University of California at Los Angeles, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - Hannah J Eckvahl
- Department of Chemistry and Biochemistry, University of California at Los Angeles, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California at Los Angeles, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - Marcey L Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Burns RJ, Mati IK, Muchowska KB, Adam C, Cockroft SL. Quantifying Through-Space Substituent Effects. Angew Chem Int Ed Engl 2020; 59:16717-16724. [PMID: 32542910 PMCID: PMC7540488 DOI: 10.1002/anie.202006943] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Indexed: 01/12/2023]
Abstract
The description of substituents as electron donating or withdrawing leads to a perceived dominance of through-bond influences. The situation is compounded by the challenge of separating through-bond and through-space contributions. Here, we probe the experimental significance of through-space substituent effects in molecular interactions and reaction kinetics. Conformational equilibrium constants were transposed onto the Hammett substituent constant scale revealing dominant through-space substituent effects that cannot be described in classic terms. For example, NO2 groups positioned over a biaryl bond exhibited similar influences as resonant electron donors. Meanwhile, the electro-enhancing influence of OMe/OH groups could be switched off or inverted by conformational twisting. 267 conformational equilibrium constants measured across eleven solvents were found to be better predictors of reaction kinetics than calculated electrostatic potentials, suggesting utility in other contexts and for benchmarking theoretical solvation models.
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Affiliation(s)
- Rebecca J. Burns
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Ioulia K. Mati
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Kamila B. Muchowska
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Catherine Adam
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
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40
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Jabłoński M, Krygowski TM. Changes in Electron Structure of the Triple Bond in Substituted Acetylene and Diacetylene Derivatives. Chemphyschem 2020; 21:1847-1857. [PMID: 32511830 DOI: 10.1002/cphc.202000378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Indexed: 11/06/2022]
Abstract
The substituent effect is usually considered by means of various Hammett-like substituent constants and is most often related to aromatic systems. Unlike this, we present results of our research on the influence of 27 substituents spanning a wide range of electronic properties, from strongly electron-withdrawing to strongly electron-donating, on the electron structure of X-substituted acetylenes and diacetylenes - thus the systems which until now have practically not been subject of any deeper studies. It is shown that the interaction through triple bond(s) is associated with a significant advantage of resonance effects and that the substituent effect transmitted by the C≡C-C≡C unit is about half of that transmitted by the C≡C unit alone. Substituent X mainly affects the closest carbon atom by means of proximity effect, hence changes of charge on this atom do not follow any substituent constants. The effect on further carbon atoms is much smaller. The presence of the C≡C-C≡C unit withdraws more charge from X than a triple bond alone, and hinders communication between X and the terminal H atom. Comparison of substituent effects to those present in X-substituted benzene derivatives shows that the electronic properties of the terminal hydrogen atom in acetylenes and diacetylenes are most similar to the electronic properties of ortho and para hydrogen atoms in X-substituted benzene derivatives.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100, Toruń, Poland
| | - Tadeusz M Krygowski
- Department of Chemistry, Warsaw University, Pasteura 1, 02-093, Warsaw, Poland
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41
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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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42
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Burns RJ, Mati IK, Muchowska KB, Adam C, Cockroft SL. Quantifying Through‐Space Substituent Effects. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rebecca J. Burns
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Ioulia K. Mati
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Kamila B. Muchowska
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Catherine Adam
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of EdinburghJoseph Black Building David Brewster Road Edinburgh EH9 3FJ UK
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Henle JJ, Zahrt AF, Rose BT, Darrow WT, Wang Y, Denmark SE. Development of a Computer-Guided Workflow for Catalyst Optimization. Descriptor Validation, Subset Selection, and Training Set Analysis. J Am Chem Soc 2020; 142:11578-11592. [PMID: 32568531 DOI: 10.1021/jacs.0c04715] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Modern, enantioselective catalyst development is driven largely by empiricism. Although this approach has fostered the introduction of most of the existing synthetic methods, it is inherently limited by the skill, creativity, and chemical intuition of the practitioner. Herein, we present a complementary approach to catalyst optimization in which statistical methods are used at each stage to streamline development. To construct the optimization informatics workflow, a number of critical components had to be subjected to rigorous validation. First, the critically important molecular descriptors were validated in two case studies to establish the importance of conformation-dependent molecular representations. Next, with a large data set available, it was possible to investigate the amount of data necessary to make predictive models with different modeling methods. Given the commercial availability of many catalyst structures, it was possible to compare models generated with algorithmically selected training sets and commercially available training sets. Finally, the augmentation of limited data sets is demonstrated in a method informed by unsupervised learning to restore the accuracy of the generated models.
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Affiliation(s)
- Jeremy J Henle
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Andrew F Zahrt
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Brennan T Rose
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - William T Darrow
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Yang Wang
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott E Denmark
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
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44
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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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45
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Carter-Fenk K, Herbert JM. Electrostatics does not dictate the slip-stacked arrangement of aromatic π-π interactions. Chem Sci 2020; 11:6758-6765. [PMID: 34094127 PMCID: PMC8159364 DOI: 10.1039/d0sc02667k] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Benzene dimer has long been an archetype for π-stacking. According to the Hunter–Sanders model, quadrupolar electrostatics favors an edge-to-face CH⋯π geometry but competes with London dispersion that favors cofacial π-stacking, with a compromise “slip-stacked” structure emerging as the minimum-energy geometry. This model is based on classical electrostatics, however, and neglects charge penetration. A fully quantum-mechanical analysis, presented here, demonstrates that electrostatics actually exerts very little influence on the conformational landscape of (C6H6)2. Electrostatics also cannot explain the slip-stacked arrangement of C6H6⋯C6F6, where the sign of the quadrupolar interaction is reversed. Instead, the slip-stacked geometry emerges in both systems due to competition between dispersion and Pauli repulsion, with electrostatics as an ambivalent spectator. This revised interpretation helps to rationalize the persistence of offset π-stacking in larger polycyclic aromatic hydrocarbons and across the highly varied electrostatic environments that characterize π–π interactions in proteins. According to the Hunter–Sanders model, geometries in π–π systems arise from competition between quadrupolar electrostatics (favoring an edge-to-face geometry) and London dispersion (favoring stacking), but this model misrepresents the molecular physics.![]()
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Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry & Biochemistry, The Ohio State University Columbus OH USA
| | - John M Herbert
- Department of Chemistry & Biochemistry, The Ohio State University Columbus OH USA
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46
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Cabaleiro-Lago EM, Rodríguez-Otero J, Vázquez SA. The relative position of π-π interacting rings notably changes the nature of the substituent effect. Phys Chem Chem Phys 2020; 22:12068-12081. [PMID: 32441295 DOI: 10.1039/d0cp01253j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The substituent effect in monosubstituted benzene dimers mostly follows changes on electrostatics mainly controlled by the direct interaction of the substituent and the other phenyl ring, whereas the contribution from the interacting rings is smaller. As the substituent is located further away the two contributions become of similar magnitude, so the global result is a combination of both effects. These trends are confirmed in larger systems containing a contact between phenyl rings; at closer distances the interaction of the substituent and the other ring clearly dominates over changes associated with the substituted ring, but as the substituent is located further away its contribution decreases and the contribution from the ring becomes more relevant. Care should be taken in larger systems because the observed energy change can also be affected by interactions with other regions of the molecule not directly involved in the π-π interaction.
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Affiliation(s)
- Enrique M Cabaleiro-Lago
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo, Av. Alfonso X El Sabio, s/n 27002 Lugo, Galicia, Spain.
| | - Jesús Rodríguez-Otero
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain.
| | - Saulo A Vázquez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain.
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47
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Ernst BG, Lao KU, Sullivan AG, DiStasio Jr. RA. Attracting Opposites: Promiscuous Ion−π Binding in the Nucleobases. J Phys Chem A 2020; 124:4128-4140. [DOI: 10.1021/acs.jpca.0c02766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brian G. Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Andrew G. Sullivan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Robert A. DiStasio Jr.
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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48
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Pikoli S, Hosten E, Abrahams A. The effect of ligand design on the structural and photophysical properties of Nd(III) complexes with Schiff bases of the [(phenylimino)methyl]phenol-type. J COORD CHEM 2020. [DOI: 10.1080/00958972.2020.1750604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Sibongile Pikoli
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, South Africa
| | - Eric Hosten
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, South Africa
| | - Abubak’r Abrahams
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, South Africa
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Yadav S, Sharma AK, Kumar P. Nanoscale Self-Assembly for Therapeutic Delivery. Front Bioeng Biotechnol 2020; 8:127. [PMID: 32158749 PMCID: PMC7051917 DOI: 10.3389/fbioe.2020.00127] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/10/2020] [Indexed: 12/23/2022] Open
Abstract
Self-assembly is the process of association of individual units of a material into highly arranged/ordered structures/patterns. It imparts unique properties to both inorganic and organic structures, so generated, via non-covalent interactions. Currently, self-assembled nanomaterials are finding a wide variety of applications in the area of nanotechnology, imaging techniques, biosensors, biomedical sciences, etc., due to its simplicity, spontaneity, scalability, versatility, and inexpensiveness. Self-assembly of amphiphiles into nanostructures (micelles, vesicles, and hydrogels) happens due to various physical interactions. Recent advancements in the area of drug delivery have opened up newer avenues to develop novel drug delivery systems (DDSs) and self-assembled nanostructures have shown their tremendous potential to be used as facile and efficient materials for this purpose. The main objective of the projected review is to provide readers a concise and straightforward knowledge of basic concepts of supramolecular self-assembly process and how these highly functionalized and efficient nanomaterials can be useful in biomedical applications. Approaches for the self-assembly have been discussed for the fabrication of nanostructures. Advantages and limitations of these systems along with the parameters that are to be taken into consideration while designing a therapeutic delivery vehicle have also been outlined. In this review, various macro- and small-molecule-based systems have been elaborated. Besides, a section on DNA nanostructures as intelligent materials for future applications is also included.
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Affiliation(s)
| | | | - Pradeep Kumar
- Nucleic Acids Research Laboratory, CSIR Institute of Genomics and Integrative Biology, Delhi, India
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50
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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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