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Journal articles on the topic 'Sigma-Hole interactions'

Author: Grafiati

Published: 8 June 2024

Last updated: 31 July 2025

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1

Lim, Jason Y. C., and Paul D. Beer. "Sigma-Hole Interactions in Anion Recognition." Chem 4, no. 4 (2018): 731–83. http://dx.doi.org/10.1016/j.chempr.2018.02.022.

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2

Pinheiro, Pedro de Sena Murteira, Daniel Alencar Rodrigues, Marina Amaral Alves та ін. "Theoretical and experimental characterization of 1,4-N⋯S σ-hole intramolecular interactions in bioactive N-acylhydrazone derivatives". New Journal of Chemistry 42, № 1 (2018): 497–505. http://dx.doi.org/10.1039/c7nj03543h.

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3

Aakeröy, Christer B., Saman Alavi, Lee Brammer, et al. "Computational approaches and sigma-hole interactions: general discussion." Faraday Discussions 203 (2017): 131–63. http://dx.doi.org/10.1039/c7fd90061a.

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4

Quiñonero, D. "Sigma-hole carbon-bonding interactions in carbon–carbon double bonds: an unnoticed contact." Physical Chemistry Chemical Physics 19, no. 23 (2017): 15530–40. http://dx.doi.org/10.1039/c7cp01780d.

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5

Julia, Bamberger, Ostler Florian, and García Mancheño Olga. "Frontiers in Halogen and Chalcogen‐Bond Donor Organocatalysis." ChemCatChem 11 (August 2, 2019): 5198–211. https://doi.org/10.1002/cctc.201901215.

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6

Hendinejad, Niloufar, and Qadir K. Timerghazin. "Biological control of S-nitrosothiol reactivity: potential role of sigma-hole interactions." Physical Chemistry Chemical Physics 22, no. 12 (2020): 6595–605. http://dx.doi.org/10.1039/c9cp06377c.

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S-Nitrosothiols, ubiquitous biological derivatives of nitric oxide, can engage in σ-hole/bonding with Lewis bases, which, in combination with hydrogen bonding with Lewis acids, could be the basis of enzymatic control of S-nitrosothiol reactions.

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7

Weinhold, Frank. "Anti-Electrostatic Pi-Hole Bonding: How Covalency Conquers Coulombics." Molecules 27, no. 2 (2022): 377. http://dx.doi.org/10.3390/molecules27020377.

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Intermolecular bonding attraction at π-bonded centers is often described as “electrostatically driven” and given quasi-classical rationalization in terms of a “pi hole” depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like charge, thereby yielding locally stable complexes that sharply violate classical electrostatic expectations. Standard DFT and MP2 computational methods are employed to investigate complexation of simple pi-bonded diatomic anions (BO−, CN−) with simple atomic anions (H−, F−) or

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8

Lee, Jiwon, Lucia Myongwon Lee, Zachary Arnott, Hilary Jenkins, James F. Britten, and Ignacio Vargas-Baca. "Sigma-hole interactions in the molecular and crystal structures of N-boryl benzo-2,1,3-selenadiazoles." New Journal of Chemistry 42, no. 13 (2018): 10555–62. http://dx.doi.org/10.1039/c8nj00553b.

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9

Jiao, Yinchun, and Frank Weinhold. "What Is the Nature of Supramolecular Bonding? Comprehensive NBO/NRT Picture of Halogen and Pnicogen Bonding in RPH2···IF/FI Complexes (R = CH3, OH, CF3, CN, NO2)." Molecules 24, no. 11 (2019): 2090. http://dx.doi.org/10.3390/molecules24112090.

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We employ a variety of natural bond orbital (NBO) and natural resonance theory (NRT) tools to comprehensively investigate the nature of halogen and pnicogen bonding interactions in RPH2···IF/FI binary complexes (R = CH3, OH, CF3, CN, and NO2) and the tuning effects of R-substituents. Though such interactions are commonly attributed to “sigma-hole”-type electrostatic effects, we show that they exhibit profound similarities and analogies to the resonance-type 3-center, 4-electron (3c/4e) donor-acceptor interactions of hydrogen bonding, where classical-type “electrostatics” are known to play only

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10

Zierkiewicz, Wiktor, Mariusz Michalczyk, and Steve Scheiner. "Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons." Molecules 26, no. 6 (2021): 1740. http://dx.doi.org/10.3390/molecules26061740.

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Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work

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11

Thomas, Sajesh P., Amol G. Dikundwar, Sounak Sarkar, et al. "The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals." Molecules 27, no. 12 (2022): 3690. http://dx.doi.org/10.3390/molecules27123690.

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The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on hal

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12

Arjmand, Farukh, Salman khursheed, Thierry Roisnel, and Hifzur R. Siddique. "Copper (II)-based halogen-substituted chromone antitumor drug entities: Studying biomolecular interactions with ct-DNA mediated by sigma hole formation and cytotoxicity activity." Bioorganic Chemistry 104 (November 2020): 104327. http://dx.doi.org/10.1016/j.bioorg.2020.104327.

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13

Potapskyi, Eduard, Karolina Kustrzyńska, Dawid Łażewski, Paulina Skupin-Mrugalska, Roman Lesyk, and Marcin Wierzchowski. "Introducing bromine in the molecular structure as a good strategy to the drug design." Journal of Medical Science 93, no. 3 (2024): e1128. https://doi.org/10.20883/medical.e1128.

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Nowadays, the search for new pharmaceuticals results in the development of thousands of new substances. One of the effective drug design strategies is to modify a previously obtained and studied substance. A very popular modification is the introduction of halogens into the structure of drugs, most often these are fluorine or chlorine atoms. However, the introduction of bromine into the structure of a potential drug also has a number of advantages. A good example would be natural substances extracted from marine organisms, which have been studied and proven to be effective in various diseases,

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14

Michalczyk, Zierkiewicz, Wysokiński, and Scheiner. "Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment." Molecules 24, no. 18 (2019): 3329. http://dx.doi.org/10.3390/molecules24183329.

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Various types of σ-hole bond complexes were formed with FX, HFY, H2FZ, and H3FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A–F bond, which lies opposite the base and is responsible for the σ-hole on the A atom (A refers to the bridging atom), elongates and its stretching frequency undergo

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15

Radha, Anu, Sandeep Kumar, Deepika Sharma, et al. "Indirect influence of alkyl substituent on sigma-hole interactions: The case study of antimony(III) diphenyldithiophosphates with covalent Sb-S and non-covalent Sb⋯S pnictogen bonds." Polyhedron 173 (November 2019): 114126. http://dx.doi.org/10.1016/j.poly.2019.114126.

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16

Elakkat, Vijayanath, Chu-Chun Chang, Jun-Yu Chen, et al. "Correction: The first two examples of halogen bonding with a sigma hole-donating fluorine in the Csp3–F⋯Osp3 interaction from polyfluorinated trans-dihalo-palladium(ii) di-substituted pyridine complexes." Chemical Communications 55, no. 99 (2019): 15004. http://dx.doi.org/10.1039/c9cc90530h.

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Correction for ‘The first two examples of halogen bonding with a sigma hole-donating fluorine in the C<sub>sp</sub><sup>3</sup>–F⋯O<sub>sp</sub><sup>3</sup> interaction from polyfluorinated trans-dihalo-palladium(ii) di-substituted pyridine complexes’ by Vijayanath Elakkat et al., Chem. Commun., 2019, DOI: 10.1039/c9cc06731k.

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17

St-Gallay, Stephen A., Neil Bennett, Susan E. Critchlow, et al. "A High-Throughput Screening Triage Workflow to Authenticate a Novel Series of PFKFB3 Inhibitors." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 1 (2017): 11–22. http://dx.doi.org/10.1177/2472555217732289.

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A high-throughput screen (HTS) of human 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) resulted in several series of compounds with the potential for further optimization. Informatics was used to identify active chemotypes with lead-like profiles and remove compounds that commonly occurred as actives in other HTS screens. The activities were confirmed with IC50 measurements from two orthogonal assay technologies, and further analysis of the Hill slopes and comparison of the ratio of IC50 values at 10 times the enzyme concentration were used to identify artifact compounds. Sever

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18

Elakkat, Vijayanath, Chu-Chun Chang, Jun-Yu Chen, et al. "The first two examples of halogen bonding with a sigma hole-donating fluorine in the Csp3–F⋯Osp3 interaction from polyfluorinated trans-dihalo-palladium(ii) di-substituted pyridine complexes." Chemical Communications 55, no. 95 (2019): 14259–62. http://dx.doi.org/10.1039/c9cc06731k.

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Molecular packing diagram of trans-[PdCl<sub>2</sub>(3-HCF<sub>2</sub>CF<sub>2</sub>CH<sub>2</sub>OCH<sub>2</sub>py)<sub>2</sub>] (left) showing a C8–F2⋯O1 halogen bond; (right) its stacking piles showing a herringbone pattern.

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19

Becerra González, J., J. A. Acosta-Pulido, and R. Clavero. "Optical spectral characterization of the TeV extreme blazar 2WHSP J073326.7+515354." Monthly Notices of the Royal Astronomical Society 494, no. 4 (2020): 6036–42. http://dx.doi.org/10.1093/mnras/staa1144.

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ABSTRACT The emission from the relativistic jets in blazars usually outshines their host galaxies, challenging the determination of their distances and the characterization of the stellar population. The situation becomes more favourable in the case of the extreme blazars (EHBLs), for which the bulk of the emission of the relativistic jets is emitted at higher energies, unveiling the optical emission from the host galaxy. The distance determination is fundamental for the study of the intrinsic characteristics of the blazars, especially to estimate the intrinsic gamma-ray spectra distorted due

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20

Andriollo, Paolo, George Procopiou, Daniella M. di Mascio, et al. "Abstract 1750: Design and development of a novel highly sequence-selective guanine mono-alkylating DNA-interactive ADC payload suitable for solid tumor treatments." Cancer Research 82, no. 12_Supplement (2022): 1750. http://dx.doi.org/10.1158/1538-7445.am2022-1750.

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Abstract Antibody-Drug Conjugates (ADCs) are a fast-growing class of targeted cancer therapeutic agents with over ten approved and greater than 100 in various stages of clinical development. The pyridinobenzodiazepines (PDDs) are a new class of DNA-interactive sequence-selective Guanine mono-alkylating ADC payloads which contain a sequence recognition component with sufficient span to guide them to specific DNA sequences (e.g., transcription factor binding sites). A high potency PDD, FGX15-147, has been developed that contains a bi-aryl moiety capable of forming an intramolecular ‘sigma-hole’

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21

Docker, Andrew, and Matthew J. Langton. "Transmembrane anion transport mediated by sigma-hole interactions." Trends in Chemistry, June 2023. http://dx.doi.org/10.1016/j.trechm.2023.06.001.

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22

Singh, Anurag, Aaron Torres-Huerta, Franck Meyer, and Hennie Valkenier. "Anion transporters based on halogen, chalcogen, and pnictogen bonds: towards biological applications." Chemical Science, 2024. http://dx.doi.org/10.1039/d4sc04644g.

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Synthetic anion receptors based on sigma-hole interactions are increasingly used to transport anions across membranes. This article discusses the progress in the field and prospects for biological applications.

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23

Hein, Robert, and Paul D. Beer. "Halogen Bonding and Chalcogen Bonding Mediated Sensing." Chemical Science, 2022. http://dx.doi.org/10.1039/d2sc01800d.

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Sigma-hole interactions, in particular halogen bonding (XB) and chalcogen bonding (ChB), have become indispensible tools in supramolecular chemistry, with wide-ranging applications in crystal engineering, catalysis and materials chemistry as well...

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24

Pantig, Reggie C., and Ali Övgün. "Imprints of a gravitational wave through the weak field deflection of photons." Chinese Physics C, May 21, 2024. http://dx.doi.org/10.1088/1674-1137/ad4e25.

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Abstract This paper investigates the novel phenomenon of gravitational lensing experienced by gravitational waves traveling past a Schwarzschild black hole perturbed by a specific, first-order, polar gravitational wave. We utilize the Gauss-Bonnet theorem, uncovering a topological contribution to the deflection of light rays passing near the black hole. We demonstrate that the deflection angle can be determined by analyzing a region entirely outside the light ray's path, leading to a calculation based solely on the parameters of the perturbing wave (Legendre polynomial order, $l$, and frequenc

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25

Ibrahim, Mahmoud A. A., Rehab R. A. Saeed, Mohammed N. I. Shehata, et al. "Sigma-Hole and Lone-Pair-Hole Site-Based Interactions of Seesaw Tetravalent Chalcogen-Bearing Molecules with Lewis Bases." ACS Omega, August 30, 2023. http://dx.doi.org/10.1021/acsomega.3c03981.

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26

Siddiqui, Rafia, Raphael F. Ligorio, Hatem M. Titi, Sushil Kumar Pandey, Anna Krawczuk, and Ranjan Patra. "Polarization and Dipole Moment Effects on Sigma‐Hole Potential in Tin(IV)‐Porphyrins." Chemistry – A European Journal, July 22, 2025. https://doi.org/10.1002/chem.202502099.

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AbstractThis study investigates how electron‐withdrawing substitution, molecular polarization, and dipole moment influence the σ‐hole potential in six‐coordinate metalloporphyrins. To evaluate halogen bonding tendencies, we synthesized a series of five Sn(IV)‐5,10,15,20‐meso‐tetrakis(4‐iodophenyl)porphyrin complexes with various fluorinated phenolate axial ligands. Single‐crystal X‐ray diffraction analysis revealed distinct halogen‐bonded supramolecular motifs, which vary depending on the degree of fluorination at the axial ligands. Our findings highlight the critical role of ligand‐induced po

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27

Pakhira, Anindya, Shruti Hariyani, George Agbeworvi, et al. "Interplay between Stereochemically Active Lone Pair Repulsions, Sigma Hole Interactions, and Delocalized Redox Processes in Topochemical Fluoride‐Ion Insertion." Angewandte Chemie, June 17, 2025. https://doi.org/10.1002/ange.202507650.

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Topochemical insertion/extraction of cations has emerged as a generalizable strategy for modulating the crystal structure and electronic structure of periodic solids. In contrast, strategies for topochemical anion insertion are poorly explored and fundamental design principles for designing insertion hosts to accommodate anions remain scarce. Here, we observe reversible room‐temperature fluoride‐ion insertion within tunnels of Sn2TiO4 defined by the stereochemical expression of Sn 5s2 lone pairs. X‐ray scattering studies of fluoride‐ion‐insertion‐induced modulation of crystal structure and X‐r

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28

Pakhira, Anindya, Shruti Hariyani, George Agbeworvi, et al. "Interplay between Stereochemically Active Lone Pair Repulsions, Sigma Hole Interactions, and Delocalized Redox Processes in Topochemical Fluoride‐Ion Insertion." Angewandte Chemie International Edition, June 17, 2025. https://doi.org/10.1002/anie.202507650.

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Topochemical insertion/extraction of cations has emerged as a generalizable strategy for modulating the crystal structure and electronic structure of periodic solids. In contrast, strategies for topochemical anion insertion are poorly explored and fundamental design principles for designing insertion hosts to accommodate anions remain scarce. Here, we observe reversible room‐temperature fluoride‐ion insertion within tunnels of Sn2TiO4 defined by the stereochemical expression of Sn 5s2 lone pairs. X‐ray scattering studies of fluoride‐ion‐insertion‐induced modulation of crystal structure and X‐r

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29

Schwartz, Mathieu, Valentin Boichot, Mariam Muradova, et al. "Structure–activity analysis suggests an olfactory function for the unique antennal delta glutathione transferase of Apis mellifera." FEBS Letters, November 7, 2023. http://dx.doi.org/10.1002/1873-3468.14770.

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Glutathione transferases (GST) are detoxification enzymes that conjugate glutathione to a wide array of molecules. In the honey bee Apis mellifera, AmGSTD1 is the sole member of the delta class of GSTs, with expression in antennae. Here, we structurally and biochemically characterized AmGSTD1 to elucidate its function. We showed that AmGSTD1 can efficiently catalyse the glutathione conjugation of classical GST substrates. Additionally, AmGSTD1 exhibits binding properties with a range of odorant compounds. AmGSTD1 has a peculiar interface with a structural motif we propose to call ‘sulfur sandw

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30

Nandi, Goutam, Rohith Phaneendra Bandaru, Ranjan Patra, Ananda Kumar Jami, and Bharat Kumar Tripuramallu. "Impact of Electron-Withdrawing Effect on Sigma Hole Via Bromine-Based Interactions in Zn-5,10,15,20-tetra(4-bromo-2,6-difluoro Phenyl) Porphyrin." Crystal Growth & Design, July 10, 2023. http://dx.doi.org/10.1021/acs.cgd.3c00543.

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31

Tay, Hui Min, Toby Johnson, Andrew Docker, Matthew Langton, and Paul D. Beer. "Exploiting the Catenane Mechanical Bond Effect for Selective Halide Anion Transmembrane Transport." Angewandte Chemie International Edition, September 29, 2023. http://dx.doi.org/10.1002/anie.202312745.

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The first examples of [2]catenanes capable of selective anion transport across a lipid bilayer are reported. The neutral halogen bonding (XB) [2]catenanes were prepared via a chloride template‐directed strategy in an unprecedented demonstration of using XB∙∙∙anion interactions to direct catenane assembly from all‐neutral components. Anion binding experiments in aqueous‐organic solvent media revealed strong halide over oxoanion selectivity, and a marked enhancement in the chloride and bromide affinities of the catenanes relative to their constituent macrocycles. The catenanes displayed an anti‐

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32

Tay, Hui Min, Toby Johnson, Andrew Docker, Matthew Langton, and Paul D. Beer. "Exploiting the Catenane Mechanical Bond Effect for Selective Halide Anion Transmembrane Transport." Angewandte Chemie, September 29, 2023. http://dx.doi.org/10.1002/ange.202312745.

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The first examples of [2]catenanes capable of selective anion transport across a lipid bilayer are reported. The neutral halogen bonding (XB) [2]catenanes were prepared via a chloride template‐directed strategy in an unprecedented demonstration of using XB∙∙∙anion interactions to direct catenane assembly from all‐neutral components. Anion binding experiments in aqueous‐organic solvent media revealed strong halide over oxoanion selectivity, and a marked enhancement in the chloride and bromide affinities of the catenanes relative to their constituent macrocycles. The catenanes displayed an anti‐

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33

O'Brien, James, Nika Melnyk, Rico Shing Lee, Michael James, and Cristina Trujillo. "Computational Design of Bidentate HypervalentIodine Catalysts in Halogen Bond‐MediatedOrganocatalysis." ChemPhysChem, July 8, 2024. http://dx.doi.org/10.1002/cphc.202400515.

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In recent years, halogen bond‐based organocatalysis has garnered significant attention as an alternative to hydrogen‐based catalysis, capturing considerable interest within the scientific community. This transition has witnessed the evolution of catalytic scaffolds from monodentate to bidentate architectures, and from monovalent to hypervalent species. In this DFT‐based study, we explored a bidentate hypervalent iodine(III)‐based system that has already undergone experimental validation. Additionally, we explore various functionalisations (‐CF$_3$, ‐CH$_3$, ‐tBu, ‐OH, ‐OMe, ‐NO$_2$, ‐CN) and s

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34

Balthazar, Bruno, Amit Giveon, David Kutasov, and Emil J. Martinec. "Asymptotically free AdS3/CFT2." Journal of High Energy Physics 2022, no. 1 (2022). http://dx.doi.org/10.1007/jhep01(2022)008.

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Abstract We propose a new AdS3/CFT2 duality, in which the bulk string theory has a target spacetime AdS3 times a squashed three-sphere $$ {\mathbbm{S}}_{\flat}^3 $$ S ♭ 3 , and the dual CFT2 is a symmetric product of sigma models on ℝϕ×$$ {\mathbbm{S}}_{\flat}^3 $$ S ♭ 3 , deformed by a ϕ-dependent ℤ2 twist operator. The duality maps the asymptotic region of AdS3 to the region ϕ → ∞, where the twist interaction in the CFT2 turns off. The AdS3 backgrounds in question have RAdS< ℓs, and so lie on the string side of the string/black hole correspondence transition. As a consequence, the high en

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35

Ameku, W.A., V.N. Ataide, E.T. Costab, et al. "A pencil-lead immunosensor for the rapid electrochemical measurement of anti-Diphtheria Toxin antibodies." October 30, 2021. https://doi.org/10.5281/zenodo.5628477.

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<strong>Abstract: </strong>Diphtheria is a vaccine-preventable disease, yet immunization can wane over time to non-protective levels. We have developed a low-cost, miniaturized electroanalytical biosensor to quantify anti-diphtheria toxin (DTx) immunoglobulin G (IgG) antibody to minimize the risk for localized outbreaks. Two epitopes specific to DTx and recognized by antibodies generated post-vaccination were selected to create a bi-epitope peptide, biEP, by synthesizing the epitopes in tandem. The biEP peptide was conjugated to the surface of a pencil-lead electrode (PLE) integrated into a po

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36

sprotocols. "Simultaneous and long-term measurement of gene expression and neuronal activity from a brain slice." December 31, 2014. https://doi.org/10.5281/zenodo.13660.

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Authors: Daisuke Ono, Ken-ichi Honma & Sato Honma ### Abstract Photonic bioimaging is a powerful tool for measurement of biological functions in living cells. It enables us to identify when, how, and where a phenomenon of interest takes place such as gene expression and interaction of molecules. To understand the sequential events happening in the brain, it is of special importance to assess more than one parameter simultaneously. In this protocol, we describe detailed methods of simultaneous and long-term measurement of gene expression and neuronal activity from a cultured brain slice. We

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