Article
Chemistry, Multidisciplinary
Davide Mitoli, Jefferson Maul, Alessandro Erba
Summary: In the framework of density functional theory (DFT) simulations of molecules and materials, an efficient approach to calculate cubic and quartic interatomic force constants in the basis of normal modes was implemented in the CRYSTAL program. By applying group theory, the associated computational cost can be further reduced by exploiting point symmetry. The proposed group theoretical approach, implemented in the CRYSTAL program, shows significant speedup in high-symmetry molecular and periodic systems.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Chemistry, Multidisciplinary
Davide Mitoli, Jefferson Maul, Alessandro Erba
Summary: In the framework of density functional theory, a group theoretical approach was implemented to reduce computational cost and improve efficiency. The approach was assessed on six test case systems, showing significant speedup in high-symmetry molecular and periodic systems.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Chemistry, Multidisciplinary
Dillan Stengel, J. Bennett Addison, David Onofrei, Nha Uyen Huynh, George Youssef, Gregory P. Holland
Summary: This study revealed the unique water-induced cross-linking mechanism in orb-weaving spider aciniform silk, increasing the beta-sheet content and stiffness of the silk. Mechanical shear further enhances beta-sheet cross-linking, resulting in 4-6 nm beta-sheet domains. The observation of converting a flexible alpha-helix-rich fiber to a rigid beta-sheet mat through water treatment may open new possibilities in bioinspired materials design.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Materials Science, Multidisciplinary
Boris Apter, Nadezda Lapshina, Igor Lapsker, Amir Handelman, Antonella Accardo, Carlo Diaferia, Giancarlo Morelli, Gil Rosenman
Summary: This study investigates a fold-sensitive fluorescence phenomenon observed in biological and bioinspired amyloid samples, demonstrating different properties compared to classical fluorescence. This phenomenon exhibits a wideband spectrum with high quantum yield and tunable wavelength, paving the way for advanced fluorescence optical nanomaterials and new methods of bioimaging and diagnostics.
ADVANCED OPTICAL MATERIALS
(2021)
Article
Materials Science, Ceramics
Lixia Pang, Xiaolong Wang, Di Zhou, Zhen Fang, Xingyu Tian, Weiguo Liu, Zeming Qi, Song Xia, Moustafa Adel Darwish
Summary: In this study, (Na0.5xLa1-0.5x)(Nb1-xMox)O4 ceramics were synthesized using the solid-state reaction method, and samples with temperature stability and good dielectric performance were obtained.
JOURNAL OF THE EUROPEAN CERAMIC SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Kei Fujise, Eiji Tsurumaki, Kan Wakamatsu, Shinji Toyota
Summary: New long expanded helicenes consisting of four or five fused anthracene units were synthesized through PtCl2-catalyzed cycloisomerization. These compounds exhibit helical structures with significant stacking of anthracene moieties. The UV-vis and fluorescence spectra showed red shifts in absorption and emission bands as the number of fused anthracene units increased. Photophysical and cyclic voltammetric data were discussed based on pi-conjugation and interlayer pi...pi interactions in molecular structures. The mechanism of helical inversion was also reported.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Editorial Material
Chemistry, Multidisciplinary
Kei Fujise, Eiji Tsurumaki, Kan Wakamatsu, Shinji Toyota
Summary: Polycyclic aromatic compounds, synthesized by PtCl2-catalyzed cycloisomerization, have helical structures with significant stacking between the terminal anthracene moieties. As the number of fused anthracene units increases, the absorption and emission bands are red-shifted. The long-lived emission bands of the long analogues are explained by the excimer-like stabilization of the excited state.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Physical
Fortunatus Jacob
Summary: This study investigates the properties of cluster ions SrI3-, Sr2I3+, Sr3I5+, Sr4I7+, and Sr5I9+ detected in vapor over strontium diiodide at high temperatures. The researchers used DFT, MP2, and MP4 methods to analyze equilibrium geometrical properties, vibrational spectra, and thermodynamic properties. Different geometrical structures were considered, and it was observed that SrI3-, Sr2I3+, Sr3I5+, and Sr5I9+ had a D3h point group, while Sr4I7+ had a C-2v configuration. No isomers were identified among the considered alternative structures for all ions. The results for the enthalpies of dissociation reactions and formation of the ions are presented in kJ mol(-1) for each ion.
Article
Chemistry, Multidisciplinary
Zewdu Bezu Gemechu, Boobalan Maria Susai, Abi M. Taddesse, Endale Teju Bedada, R. Ramamoorthy
Summary: A new heterocyclic ligand was synthesized using a two-step cyclocondensation reaction with 2-aminophenol and 2-chloroacetyl chloride, followed by the formation of Zn2+ and Cd2+ complexes. The metal complexes showed better antimicrobial activities compared to the free ligand, indicating potential for further research in understanding their electronic structure behavior.
JOURNAL OF CHEMISTRY
(2021)
Article
Biochemical Research Methods
Vahidreza Darugar, Mohammad Vakili, Sayyed Faramarz Tayyari, Fadhil S. Kamounah
Summary: The study calculated the harmonic vibrational frequencies of cis-enol forms of beta-diketones with different substitutions using DFT and obtained potential energy distribution (PED) with VEDA software. Results show similar outcomes for most bands, but the largest discrepancies were observed in the 1700-1000 cm-1 region due to coupling with OH and CHα in-plane bending vibrations.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Chemistry, Physical
Nichole O'Neill, Thamires A. Lima, Fabio Furlan Ferreira, Lavenia Thursch, Nicolas Alvarez, Reinhard Schweitzer-Stenner
Summary: In an aqueous solution, the zwitterionic L-tripeptide glycylphenylalanylglycine self-assembles into very long crystalline fibrils, resulting in an exceptionally strong gel phase. The analysis of its structure reveals an unusual helical conformation stabilized by numerous intermolecular interactions. This study provides powerful tools for determining the secondary structure and fibril axis.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Michele Larocca, Giuseppe Floresta, Agostino Cilibrizzi
Summary: The folding process is driven by main mechanical forces generated from specific chemical interactions among residues of an amino acid chain. A new parameter, folding factor, has been reported for calculating dihedral angle values in (poly)peptides. Accurate rules for defining degrees of freedom and folding factors have not been reported so far.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Anna-Maria Tsirigoni, Melis Goktas, Zeynep Atris, Angelo Valleriani, Ana Vila Verde, Kerstin G. Blank
Summary: Coiled coils are crucial for biogenic materials and their mechanical response. A transition from alpha-helices to beta-sheets occurs in CC-based materials under force, which depends on the pulling speed and CC length. This transition is observed in simulations and experiments, highlighting the importance of both factors.
MACROMOLECULAR BIOSCIENCE
(2023)
Article
Spectroscopy
Bhagwat Kharat, Mahadevappa Naganathappa, Vasant Jagrut, Ajay Chaudhari
Summary: This study investigates the spectroscopic characterization and second hyperpolarizability of odd spin states of acetonitrile in gas phase and water solvent. The results show that the second hyperpolarizability values for odd spin states are more positive than the first hyperpolarizability, and spin has an effect on spectroscopic parameters except for energy.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Physical
Lukasz Boda, Marek Boczar, Marek J. Wojcik, Takahito Nakajima
Summary: Theoretical study on proton tunneling in the hydrogen-bonded imidazole-imidazolium complex ion was conducted, using ab initio calculations and model construction to analyze proton dynamics and vibration properties in the hydrogen bond, explaining the experimentally observed splitting and broadening of the high-frequency N-H stretching infrared absorption band.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Biochemical Research Methods
Celine Douat, Megane Bornerie, Stephanie Antunes, Gilles Guichard, Antoine Kichler
BIOCONJUGATE CHEMISTRY
(2019)
Article
Chemistry, Physical
Christopher Aisenbrey, Celine Douat, Antoine Kichler, Gilles Guichard, Burkhard Bechinger
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Chemistry, Multidisciplinary
Sung Hyun Yoo, Gavin W. Collie, Laura Mauran, Gilles Guichard
Article
Chemistry, Multidisciplinary
Leonie Cussol, Laura Mauran-Ambrosino, Jeremie Buratto, Anna Y. Belorusova, Maxime Neuville, Judit Osz, Sebastien Fribourg, Juliette Fremaux, Christel Dolain, Sebastien R. Goudreau, Natacha Rochel, Gilles Guichard
Summary: Efficient optimization of peptide leads into drug candidates often requires further transformation to enhance properties such as bioavailability. Foldamers, specifically oligourea foldamers, have been introduced to reduce the peptide character of protein-protein interaction inhibitors. The study reports X-ray structures of peptide-oligourea hybrids bound to ubiquitin ligase MDM2 and vitamin D receptor, demonstrating their high affinity binding to protein targets.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Johanne Mbianda, May Bakail, Christophe Andre, Gwenaelle Moal, Marie E. Perrin, Guillaume Pinna, Raphael Guerois, Francois Becher, Pierre Legrand, Seydou Traore, Celine Douat, Gilles Guichard, Francoise Ochsenbein
Summary: The study demonstrates that the structural plasticity of foldamer backbone is crucial for optimal interaction with protein surface. By designing a foldamer/peptide hybrid inhibitor using oligoureas as α-helix mimics, effective inhibition of the key regulator of chromatin dynamics, histone chaperone ASF1, was achieved. Additionally, the ASF1 ligands with nonpeptide oligourea segments showed significantly improved resistance to proteolysis in human plasma compared to alpha-helical peptides.
Article
Chemistry, Organic
Yaidel Toledo-Gonzalez, Jean-Marc Sotiropoulos, Diane Becart, Gilles Guichard, Philippe Carbonniere
Summary: Peptides and foldamers have shown high reactivity and selectivity as chiral catalysts for transformations. Using density functional theory, this study analyzed the interaction between substrates and catalysts, and found that electrostatic interactions play a major role in molecular recognition and catalytic properties.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Polymer Science
Mohamed Samir Zaky, Anne-Laure Wirotius, Olivier Coulembier, Gilles Guichard, Daniel Taton
Summary: Stereochemical control is a key strategy in polymer chemistry for achieving semicrystalline engineering plastics. However, the study of stereoselective ring-opening polymerization using chiral organocatalysts is relatively under-explored. This research demonstrates that a commercially available chiral thiourea or its urea homologue, when used in conjunction with an appropriately selected N-heterocyclic carbene, can trigger the stereoselective ring-opening polymerization of lactide at room temperature in toluene, achieving high stereoselectivity and catalytic activity.
Article
Chemistry, Multidisciplinary
Nagendar Pendem, Yella-Reddy Nelli, Leonie Cussol, Claude Didierjean, Brice Kauffmann, Christel Dolain, Gilles Guichard
Summary: Oligomers with a helix-turn-helix super-secondary structure were prepared by covalently bridging aliphatic oligourea foldamer helices with either rigid aromatic or flexible aliphatic spacers. The relative orientation of the helices in these dimers was studied using high-resolution X-ray diffraction analysis. Racemic crystallography was employed in some cases to facilitate crystallization and structure determination. All structures were solved using direct methods. Well-defined parallel helical hairpin motifs were observed in all cases when 4,4'-methylene diphenyl diisocyanate was used as a dimerizing agent, regardless of the primary sequence and chain length.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Polymer Science
Mohamed Samir Zaky, Gilles Guichard, Daniel Taton
Summary: This study investigates the stereoselective ring-opening polymerization (ROP) of racemic lactide (rac-LA) using a series of chiral amino(thio)ureas and phosphazene organic bases. The chiral binary organocatalytic pairs showed fast and highly selective ROP of rac-LA, resulting in semicrystalline and metal-free stereoblock-like materials based on polylactide (PLA). The reaction rates and stereocontrol were found to be influenced by the components of the pairs and the phosphazene bases used.
Article
Chemistry, Multidisciplinary
Aline Delamare, Guillaume Naulet, Brice Kauffmann, Gilles Guichard, Guillaume Compain
Summary: The hexafluoroisobutyl group is a commonly found hydrophobic group in drugs, and its introduction can provide new advantages to compounds. However, the lack of a general and practical synthetic methodology has hindered the exploration of this modification. In this study, the first general method for introducing the hexafluoroisobutyl group into various compounds was reported. This method overcomes the usual fluoride beta-elimination observed with other CF3-vinyl groups, and it has been successfully applied to the multigram-scale synthesis of enantiopure (S)-5,5,5,5',5',5'-hexafluoroleucine.
Article
Chemistry, Multidisciplinary
Gavin W. Collie, Caterina M. Lombardo, Sung Hyun Yoo, Karolina Pulka-Ziach, Valerie Gabelica, Cameron D. Mackereth, Frederic Rosu, Gilles Guichard
Summary: In this study, an oligourea foldamer is shown to self-assemble into helix bundles of different stoichiometries in aqueous conditions. The crystal structures of several of these stoichiometries provide high-resolution snapshots of the structural polymorphism of this foldamer and reveal a novel self-assembly process.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Mohamed Samir Zaky, Anne-Laure Wirotius, Olivier Coulembier, Gilles Guichard, Daniel Taton
Summary: The stereoselective ring-opening polymerization of racemic lactide was achieved using Takemoto's catalyst and a phosphazene base, resulting in highly isotactic, semi-crystalline, and metal-free polylactide.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Megane Bornerie, Anais Brion, Gilles Guichard, Antoine Kichler, Celine Douat
Summary: Tailored helical CPFs with specific end-groups (pyridylthio- or n-octyl-ureas) have been reported as effective molecular systems in combination with helper lipids to intracellularly deliver biologically-relevant siRNA.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Christophe Andre, Florian Veillard, Philippe Wolff, Anne-Marie Lobstein, Guillaume Compain, Clement Monsarrat, Jean-Marc Reichhart, Camille Nous, Dominique Y. Burnouf, Gilles Guichard, Jerome E. Wagner
RSC CHEMICAL BIOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Juliette Fremaux, Claire Venin, Laura Mauran, Robert Zimmer, Florian Koensgen, Didier Rognan, Stavroula Bitsi, Maria A. Lucey, Ben Jones, Alejandra Tomas, Gilles Guichard, Sebastien R. Goudreau