Article
Chemistry, Multidisciplinary
Markus Bursch, Jan-Michael Mewes, Andreas Hansen, Stefan Grimme
Summary: This work provides best-practice guidance on various methodological and technical aspects of DFT calculations, including how to choose computational protocols, functionals, basis sets, and achieve an optimal balance between accuracy, robustness, and efficiency through multi-level approaches.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biochemistry & Molecular Biology
Daniel T. Infield, Ali Rasouli, Grace D. Galles, Christophe Chipot, Emad Tajkhorshid, Christopher A. Ahern
Summary: Cation-pi interactions arise from the strong attraction between positively charged entities and the pi-electron cloud of aromatic groups, making them well-suited to the hydrophobic/hydrophilic environment of membrane proteins. As high-resolution structural data of membrane proteins become clearer, cation-pi interactions are increasingly recognized as essential contributors to membrane protein chemistry, function, and pharmacology. Prominent examples demonstrate the significant roles of cation-pi interactions in specialized biological chemistry.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Eduardo Schiavo, Kalishankar Bhattacharyya, Michael Mehring, Alexander A. Auer
Summary: The noncovalent interactions between heavy pnictogens and pi-arenes play a key role in crystal engineering and catalysis, with the strength of these bonds being influenced by dispersion and donor/acceptor interactions. Computational studies reveal that the interaction between heavy pnictogens and different compounds may impact the conformational equilibrium of cyclohexane.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Ander Camiruaga, Imanol Usabiaga, Camilla Calabrese, Iker Lamas, Francisco J. Basterretxea, Jose A. Fernandez
Summary: The article discusses why nature chose CGAT as the alphabet of life. Through analysis of intermolecular interactions and determination of dimer structures, it was found that adenine-theobromine and 4-aminopyrimidine-theobromine dimers have binding energies close to canonical nucleobases and can adopt Watson-Crick conformations. Nature may have had many options available for building the first informational polymers before ultimately selecting the now canonical CGAT.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Nathaniel L. Kitzmiller, Mark E. Wolf, Justin M. Turney, Henry F. Schaefer
Summary: This study presents a theoretical examination of HOXMIDLINE HORIZONTAL ELLIPSISSO2 complexes, showing that single-interaction hydrogen bonded complexes and halogen bonded complexes exhibit different sensitivities to heavier halogens. The findings provide insight into the interactions between HOX and SO2, guiding further research in related systems.
Article
Chemistry, Physical
Sergi Burguera, Antonio Bauza, Antonio Frontera
Summary: This study provides evidence that Hg(II)& sdot;& sdot;& sdot;d(8)[M] interactions should be more accurately described as spodium bonds.
Article
Chemistry, Multidisciplinary
Asja A. Kroeger, Amir Karton
Summary: Noncovalent interactions, including hydrogen bonding and pi-pi stacking interactions, play a crucial role in modern catalysis. In addition to providing additional stabilization, pi-pi interactions can enhance selectivity in catalytic processes. Computational studies have shown that pristine graphene can efficiently catalyze structural inversions of benzannulated cyclooctate-traene derivatives solely driven by pi-pi stacking interactions. Energy decomposition analysis reveals electrostatic and dispersion interactions as the main sources of stabilization, especially with increasing system size.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Physical
Tiddo Jonathan Mooibroek
Summary: This study interprets 36 charge neutral 'contact pairs' from the IsoStar database through DFT calculations of model molecules and bimolecular adducts, revealing that interactions are mainly dominated by electrostatic effects. Additionally, it is found that adducts with higher stability tend to exhibit greater directionality, which can be considered as a benchmark for the utility of interactions in crystal engineering.
Article
Chemistry, Inorganic & Nuclear
Sylwia Pawledzio, Maura Malinska, Florian Kleemiss, Simon Grabowsky, Krzysztof Wozniak
Summary: This study is the first to use a wave-function-based crystallographic method to characterize aurophilic interactions from X-ray diffraction data. It confirms the importance of relativistic corrections in addition to electron correlation and dispersion for the characterization of aurophilic interactions.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Organic
Chaowei Yin, Hanwei Lu, Hebo Ye, Zelin Feng, Hanxun Zou, Meilan Zhang, Lei You
Summary: This study presents double n -> nr* interactions between one common electron donor of the carbonyl oxygen and two individual acceptor aldehyde/imine units. The orientation and energetic dependence of orbital interactions were regulated by the size of cyclic urea scaffolds, the bulkiness of aldehydes/imines, and the flexibility of imine macrocycles, as revealed by experimental and computational evidence.
Article
Chemistry, Physical
Kristaps Ermanis, David C. Gibson, Georgi R. Genov, Robert J. Phipps
Summary: This study explores the interactions and potential origin of selectivity between ions, ligands, and substrates in the enantioselective borylation reaction through computational analysis of a complex system. By gradually building up a detailed understanding of the pairwise components of the system, substantial differences in noncovalent interactions occurring at the stereodetermining transition state for two substrate classes are revealed. Experimental support suggests that prochiral substrates lacking hydrogen bond donor functionality can also achieve high levels of enantioselectivity, potentially through direct interactions with the chiral cation.
Article
Chemistry, Physical
Cameron Mackie, Alexander Zech, Martin Head-Gordon
Summary: This study examines the effects of cooperative or nonadditive interactions on the pairwise noncovalent interaction between two molecules in a cluster or condensed phase. General expressions for an effective two-body interaction are provided, which are correct to increasing orders in the many-body expansion. The research demonstrates that electrical polarization has the largest impact on cooperative effects on the central hydrogen bond.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Sibali Debnath, Krishnan Raghavachari
Summary: This study investigates the noncovalent forces involved in the self-assembly of tricarb macrocycles and reveals the major contributing interactions through computational analysis. The results obtained shed light on the stability and construction of 3D structures in tricarb and related compounds.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Yang Jiao, Haochuan Mao, Yunyan Qiu, Guangcheng Wu, Hongliang Chen, Long Zhang, Han Han, Xuesong Li, Xingang Zhao, Chun Tang, Xiao-Yang Chen, Yuanning Feng, Charlotte L. Stern, J. Fraser Stoddart, Michael R. Wasielewski
Summary: Molecular recognition based on noncovalent bonding is important in directing supramolecular phenomena. Weakly associated recognition motifs are challenging to identify and investigate. This study synthesized a [2]catenane compound to enhance weak interactions and reduce system complexity. By using this compound as a model, three possible binding modes between CBPQT and BIPY were discovered and characterized. These findings have potential applications in self-assembled materials and supramolecular catalysis.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Organic
Ga Young Lee, Elizabeth Hu, Arnold L. Rheingold, K. N. Houk, Ellen M. Sletten
Summary: A systematic study of arene-perfluoroarene interactions in solution reveals that factors such as fluorination, extension of pi systems, and enhancement of solvent polarity significantly influence the stability of stacking energy. Experimental results in aqueous solution show that electrostatic and dispersion interactions, as well as the hydrophobic effect, play key roles in the impressive binding energy observed.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Physical
Fabio Gabas, Riccardo Conte, Michele Ceotto
Summary: This paper demonstrates the possibility of performing spectroscopy simulations of solvated biological species considering quantum effects and explicit solvation. They achieve this by combining a recently developed divide-and-conquer approach for semiclassical initial value representation molecular dynamics with a polarizable AMOEBABIO18 force field. The method is applied to the study of solvation of the thymidine nucleoside in two polar solvents. The study shows that this approach is computationally affordable and insightful for understanding solvated biological systems.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Xinghua Yu, Ying-Chuan Zhang, Xing Yang, Ziyang Huang, Tianfu Zhang, Liusi Yang, Wenjing Meng, Xiaotong Liu, Ping Gong, Alessandra Forni, Zheng Zheng, Bilu Liu, Pengfei Zhang, Lintao Cai, Ben Zhong Tang
Summary: A bonsai-inspired oxygen self-sufficient photodynamic cancer therapeutic system was developed using AIEgen/vermiculite nanohybrid, which effectively improved the efficiency of radiation therapy in the hypoxic tumor microenvironment and induced ferroptosis for enhanced therapeutic effect.
Article
Chemistry, Applied
Matteo Formenti, Delia Blasi, Elena Cariati, Lucia Carlucci, Alessandra Forni, Clelia Giannini, Matteo Guidotti, Stefano Econdi, Daniele Malpicci, Daniele Marinotto, Elena Lucenti
Summary: In this study, two derivatives were used as sensor species for the quantitative detection of explosives. The fluorescence of (CHO)2TTPyr at 565 nm showed a sensitive response towards picric acid, making it a potential alternative to TTPyr for analytes absorbing in the blue region.
Article
Chemistry, Inorganic & Nuclear
Giovanni Ricci, Giuseppe Leone, Giorgia Zanchin, Anna Sommazzi, Francesco Masi, Alessandra Forni
Summary: New cobalt dichloride complexes with pyridyl-phosphine bidentate ligands were synthesized and characterized. Their molecular structure was determined by single crystal X-ray diffraction method. The complexes were used in the polymerization of 1,3-butadiene with methylaluminoxane (MAO), resulting in predominantly cis-1,4 polymers or mixed cis-1,4/1,2 structures depending on the ligand and MAO/Co molar ratio. A plausible interpretation for this behavior is provided.
INORGANICA CHIMICA ACTA
(2023)
Article
Biochemistry & Molecular Biology
Daniele Malpicci, Alessandra Forni, Elena Cariati, Riku Inoguchi, Daniele Marinotto, Daniele Maver, Federico Turco, Elena Lucenti
Summary: The development of organic room-temperature phosphorescent materials has significant advantages over their organometallic counterparts, making it an active field of research. Two cyclic triimidazole derivatives, TT-HThio and TT-(HThio)(3), have been synthesized and characterized. These compounds exhibit enhanced quantum yields in their crystalline form, as compared to the solution state, showing crystallization-enhanced emissive behavior. Importantly, while single fluorescence is observed in solution, crystalline powders exhibit dual organic room-temperature phosphorescence, with their molecular and aggregate origins revealed through X-ray diffraction analysis and DFT/TDDFT calculations. The relationship between the photophysical properties of TT-HThio and its crystallinity degree has been confirmed, demonstrating mechanochromic behavior and confirming crystallization-enhanced emissive features.
Article
Biochemistry & Molecular Biology
Andrea Citarella, Davide Moi, Martina Pedrini, Helena Perez-Pena, Stefano Pieraccini, Claudio Stagno, Nicola Micale, Tanja Schirmeister, Giulia Sibille, Giorgio Gribaudo, Alessandra Silvani, Daniele Passarella, Clelia Giannini
Summary: SARS-CoV-2 M-pro is a significant enzyme in the replication and infectivity of SARS-CoV-2. We synthesized and evaluated MPD112, a novel inhibitor of SARS-CoV-2 M-pro, which displayed inhibition activity at a low micromolar level in vitro. The compound showed selectivity for M-pro and demonstrated good tolerability and biological activity in human cells.
Article
Crystallography
Daniele Malpicci, Delia Blasi, Daniele Marinotto, Alessandra Forni, Elena Cariati, Elena Lucenti, Lucia Carlucci
Summary: The coordination ability of TT-Py, a pyridine derivative of cyclic triimidazole, towards Cu(I) was investigated. TT-Py is a nitrogen-rich ligand with three imidazole nitrogen atoms and a pyridine moiety, which can coordinate with metal ions. The reaction of TT-Py with CuI at room temperature resulted in the formation of a one-dimensional coordination network [Cu2I2(TT-Py)](n) (1). The unique structure of 1 is composed of two common motifs for Cu(I) halides coordination polymers, namely the double-stranded stair and the zig-zag chain. 1 exhibits a broad long-lived emission in the solid state, which has been associated with low-energy transitions of MLCT or XMLCT character based on DFT and TDDFT calculations.
Review
Biochemistry & Molecular Biology
Helena Perez-Pena, Anne-Catherine Abel, Maxim Shevelev, Andrea E. E. Prota, Stefano Pieraccini, Dragos Horvath
Summary: Microtubules are essential in cellular processes and have potential as targets for cancer and neurodegeneration research. However, current tubulin binders have limitations, making the discovery of safer and more efficient agents necessary. Computer-aided design techniques and accessible tubulin-ligand structures can aid in the selection and design of new tubulin-targeting agents.
Article
Chemistry, Multidisciplinary
Daniele Malpicci, Alessandra Forni, Chiara Botta, Clelia Giannini, Elena Lucenti, Daniele Marinotto, Daniele Maver, Lucia Carlucci, Elena Cariati
Summary: TT-Ph-Cz is a responsive luminescent material with high conformational freedom and multi-stimuli responsive behavior. Its solvated form exhibits a higher quantum yield and strong phosphorescence contribution, which is preserved in DMSO/water solutions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Lorenzo Marchi, Stefano Carlino, Carlo Castellano, Francesco Demartin, Alessandra Forni, Anna M. Ferretti, Alessandro Ponti, Alessandro Pasini, Luca Rigamonti
Summary: The tetranuclear iron(III) compounds [Fe-4(mu(3)-O)(2)(mu-L-Z)(4)] (1-3) were obtained by reacting FeCl3 with shortened salen-type Schiff bases. The one-carbon bridge between the two iminic nitrogen atoms and the substituent Z on the central phenyl ring played crucial roles in the formation of oligonuclear species and Fe-4 bis-oxido clusters, respectively. The compounds exhibited a flat almost-symmetric butterfly-like conformation of the {Fe-4(mu(3)-O)(2)} core, surrounded by the four Schiff base ligands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Silvia Bruni, Margherita Longoni, Camilla Minzoni, Martina Basili, Ilaria Zocca, Stefano Pieraccini, Maurizio Sironi
Summary: Microanalysis techniques based on resonance Raman and reflection visible spectroscopy were used to characterize the pigments responsible for blue or violet coloration in flowers such as Lobelia erinus, Campanula portenschlagiana, Cineraria, Viola tricolor, Anemone coronaria, Agapanthus, Platycodon, Salvia farinacea, Plumbago capensis, Ceratostigma plumbaginoides, Commelina communis, and Salvia patens. The spectroscopic methods were applied both in vivo on the flower petals and in vitro on extracts obtained through solid-phase extraction. Different patterns in the Raman spectra were correlated with substitution schemes of anthocyanins' benzopyrilium nucleus and copigmentation forms responsible for blue color stabilization. The results were confirmed through comparison with analysis by liquid chromatography-electrospray ionization-mass spectrometry.
Article
Chemistry, Applied
Daniele Malpicci, Alessandra Forni, Chiara Botta, Clelia Giannini, Elena Lucenti, Daniele Marinotto, Daniele Maver, Lucia Carlucci, Elena Cariati
Summary: Two derivatives of cyclic triimidazole functionalized with carbazole, connected through different bonds, exhibit different emissive behavior due to molecular conformation and aggregation. TT-(N)-Cz shows structure-dependent dual fluorescence and dual phosphorescence, with the aggregation-induced fluorescence highly sensitive to grinding. TT-(C)-Cz displays a single red-shifted fluorescence with long-lived components of molecular and supramolecular origin in the crystal.
Article
Electrochemistry
Daniele Malpicci, Silvia Rosa Araneo, Serena Arnaboldi, Elena Cariati, Alessandra Forni, Sara Grecchi, Elena Lucenti, Daniele Marinotto, Daniele Maver, Patrizia Romana Mussini
Summary: Cyclic triimidazole TT and its derivatives have versatile properties ranging from photoluminescence to supramolecular chemistry and biological activity. Electrochemical techniques can rationalize the structure-property relationships of TTs and provide a valuable tool to transfer molecular properties to molecular materials. The modulation of the electronic/redox properties of TT derivatives as a function of terminal nature and multiplicity was highlighted through thorough voltammetry investigation integrated with absorption and emission spectroscopy and supported by theoretical calculations. Additionally, the successful electrooligomerization of TT derivatives into highly active films shows promise in developing molecular materials with both TT functional properties and high electroactivity.
ELECTROCHIMICA ACTA
(2023)
Article
Chemistry, Physical
Francesca Limosani, Francesca Tessore, Alessandra Forni, Angelo Lembo, Gabriele Di Carlo, Cecilia Albanese, Stefano Bellucci, Pietro Tagliatesta
Summary: In this study, the second order nonlinear optical (NLO) response of new hybrids with two-dimensional graphene nanoplates (GNP) as the acceptor unit was investigated. The experimental data and calculations indicate that the extended π-conjugation of the carbonaceous acceptor moiety enhances the contribution of the cubic electronic term γ(-2ω; ω,ω,0).
Article
Chemistry, Organic
Andrea Citarella, Davide Moi, Martina Pedrini, Helena Perez-Pena, Stefano Pieraccini, Alessandro Dimasi, Claudio Stagno, Nicola Micale, Tanja Schirmeister, Giulia Sibille, Giorgio Gribaudo, Alessandra Silvani, Clelia Giannini, Daniele Passarella
Summary: COVID-19 is one of the most devastating global pandemics in history caused by a new human coronavirus (SARS-CoV-2) that spreads among humans and animals. Efforts have been made to develop therapeutic agents to treat COVID-19, and the cysteine protease SARS-CoV-2 M-pro is considered a promising target. In this study, cinnamic ester was used to inhibit M-pro and showed potential antiviral activity against human coronaviruses.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
