Article
Chemistry, Physical
Anna K. Huff, Nathan Love, Kenneth R. Leopold
Summary: The rotational spectra of triflic acid hydrates show that the addition of water gradually induces ionization of the acid, with only three water molecules needed to fully ionize triflic acid in a cold molecular cluster. This low number of water molecules required for ionization likely reflects the superacidity of triflic acid and is consistent with both experimental and theoretical predictions.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Organic
Komal Mittal, Ashley V. Pham, Amanda G. Davis, Abigail D. Richardson, Clement De Hoe, Ryan T. Dean, Vi Baird, Ashley Ringer McDonald, Derik K. Frantz
Summary: At elevated temperatures, a strained, cyclic meta-quaterphenylene acetylene undergoes an intramolecular cyclization reaction to form benz[e]indeno[1,2,3-hi]acephenanthrylene. This reaction represents a Diels-Alder reaction at the 2-, 1-, 1 '-, and 2 '-positions of a biphenyl derivative, similar to the bay regions of perylene and other periacenes. Kinetics studies reveal that the reaction has a similar energy barrier to a concerted [4 + 2]-cycloaddition.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Vishal Kumar Jaiswal, Piotr Kabacinski, Barbara E. Nogueira de Faria, Marziogiuseppe Gentile, Ana Maria de Paula, Rocio Borrego-Varillas, Artur Nenov, Irene Conti, Giulio Cerullo, Marco Garavelli
Summary: By combining UV transient absorption spectroscopy with sub-30-fs temporal resolution and CASPT2/MM calculations, this study provides a complete description of the primary photoinduced processes in solvated tryptophan. The role of the solvent in the relaxation dynamics of tryptophan is clarified, and evidence of vibrational coherence is presented.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biology
Luka M. Breberina, Milan R. Nikolic, Srdan D. Stojanovic, Mario Zlatovic
Summary: This study analyzed the influences of cation-pi interactions in phycocyanin proteins and found that arginine formed more interactions than lysine, with Arg-Tyr and Arg-Phe being predominant interacting pairs. The energy contribution of these interactions was found to be in the lower range of strong hydrogen bonds, and the interacting residues may play a crucial role in stabilizing the phycocyanin proteins.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2022)
Article
Chemistry, Physical
Nathan Love, Anna K. Huff, Kenneth R. Leopold
Summary: The complex formed from trimethylamine and triflic acid is best described as a trimethylammonium triflate ion pair in the gas phase, with complete or near-complete proton transfer observed upon complexation. The unusual formation of an isolated ion pair in a 1:1 complex of a Bronsted acid and base is likely due to the strong acidity of triflic acid, and can be rationalized using simple energetic arguments based on proton affinities and Coulomb interaction energy.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Gastroenterology & Hepatology
Yuta Sugiyama, Yumiko Mori, Misaki Nara, Yusuke Kotani, Emiko Nagai, Hiroki Kawada, Mayu Kitamura, Rika Hirano, Hiromi Shimokawa, Akira Nakagawa, Hiromichi Minami, Aina Gotoh, Mikiyasu Sakanaka, Noriho Iida, Takashi Koyanagi, Takane Katayama, Shigefumi Okamoto, Shin Kurihara
Summary: Gut microbiota can produce aromatic amines, which are different from dietary sources. The production of these aromatic amines is related to the activity of aadc in gut bacteria and may have an impact on diseases such as osteoporosis and irritable bowel syndrome. Human AADC inhibitors can inhibit the production of aromatic amines in gut bacteria.
Article
Biochemistry & Molecular Biology
Andrey A. Buglak, Alexei I. Kononov
Summary: The interaction between tyrosine and silver nanoclusters plays a crucial role in the detection of tyrosine. Silver nanoclusters can be used for colorimetric, fluorescent, and Raman spectroscopy detection of tyrosine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Flor Maria Briceno-Vargas, Mariana Quesadas-Rojas, Gumersindo Miron-Lopez, David Caceres-Castillo, Ruben M. Carballo, Gonzalo J. Mena-Rejon, Ramiro F. Quijano-Quinones
Summary: This study investigates the n -> pi* interactions in amides and thioamides systems models through the analysis of electron density topology. The results suggest that dispersion forces play a significant role in the strength of these interactions.
Article
Chemistry, Multidisciplinary
Amjad Ali Pasha, Musawer Iqbal, Hukam Khan, Mohammad Sohail, Nasir Rahman, Rajwali Khan, Abid Ali Khan, Omar H. Alsalmi, Dilsora Abduvalieva, Atef El Jery, Mouataz Adrdery
Summary: In this study, the physical behavior of SrMO3 (M = Hf and Pt) compounds was investigated using the WIEN2k software. The structural stability of SrHfO3 and SrPtO3 was verified, and their elastic stability was also checked. The results showed that these compounds have anisotropic, ductility, scratch-resistive, and plastic strain-resistant characteristics. Optical property research was conducted, and it was found that these compounds have low energy absorption and reflectivity, making them suitable for use in high-frequency UV devices.
Article
Chemistry, Physical
Ilya S. Sosulin, Mariia A. Lukianova, Anastasia D. Volosatova, Vladimir D. Drabkin, Svetlana V. Kameneva
Summary: Hydrogen bonding between saturated alkanes and HX is a unique type of interaction. Experimental and ab initio studies on the HCN...C2H6 complex show that only one structure is stabilized under experimental conditions, in good agreement with previous rotational spectroscopy studies.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Organic
Jinxia Li, Dingyi Tang, Yu Zhang, Weichi Chen, Xiaoxi Su, Peiyuan Yu, Shuanglin Qu
Summary: Here, we investigate the mechanism and selectivity of the intramolecular cyclization of alkynones catalyzed by Ni catalysts using DFT computations. The Ni(0) catalyst system forms 5-exocyclic products, while the Ni(II) catalyst system generates 6-endocyclic or 5-exocyclic products due to different reaction pathways. The regioselectivity is determined by the alkyne insertion and the enantioselectivity is determined by the carbonyl insertion.
ORGANIC CHEMISTRY FRONTIERS
(2023)
Article
Chemistry, Organic
Thibaut Duhail, Tommaso Bortolato, Javier Mateos, Elsa Anselmi, Benson Jelier, Antonio Togni, Emmanuel Magnier, Guillaume Dagousset, Luca Dell'Amico
Summary: A light-driven method for the alpha-trifluoromethoxylation of ketones has been developed, showing good generality and efficiency under batch and flow conditions. The method demonstrates the potential in accessing a variety of elusive trifluoromethoxylated bioactive ingredients.
Article
Chemistry, Physical
Fabio Pichierri
Summary: This study investigates the molecular complex between the auride ion and borane using ab initio calculations and the quantum theory of atoms in molecules (QTAIM). The results show that about 1/3 of the negative charge of Au- is transferred to borane, establishing a mainly covalent shared interaction. The replacement of BH3 by BF3 weakens the interaction strength. Similar trends are observed in isoelectronic complexes with mercury, which are stabilized by weaker interactions. The interaction of AuBH3- with alkali metal ions (Li+ to Cs+) results in neutral complexes stabilized by electrostatic effects.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Sergi Burguera, Antonio Frontera, Antonio Bauza
Summary: In this study, the effects of substituents on silicon tetrel bonding (TtB) complexes were investigated using theoretical calculations. The electronic nature of substituents in both donor and acceptor moieties was found to influence the interaction energy. Different tetrafluorophenyl silane derivatives with various electron donating and electron withdrawing groups were used, along with hydrogen cyanide derivatives as electron donor molecules. The results showed good regression plots between interaction energies and Hammett's sigma parameter.
Article
Chemistry, Physical
Sole Atahan-Evrenk
Summary: By studying the dimer interactions of molecular sets composed of porphyrin derivatives, it was found that metal complexation increases binding energy, while the introduction of keto and hydroxy groups can further stabilize dimers.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Xabier Telleria-Allika, Jesus M. Ugalde, Eduard Matito, Eloy Ramos-Cordoba, Mauricio Rodriguez-Mayorga, Xabier Lopez
Summary: In this study, the singlet and triplet spin state energies for three-dimensional Hooke atoms, specifically with an even number of electrons, were investigated using Full-CI and CASSCF wavefunctions and various basis sets. The screening effect of electron-electron interaction was also examined using a Yukawa-type potential. The results reveal that the ground state is a singlet for two and eight electron Hooke atoms, while it is a triplet for 4, 6, and 10-electron systems. This study provides insights into the energy components and effects of confinement and electron-electron interaction.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Tianjiao Xue, You-Song Ding, Daniel Reta, Qi-Wei Chen, Xiaofei Zhu, Zhiping Zheng
Summary: In this study, three new single-molecule magnets (SMMs) were reported for potential applications in information storage and quantum processing. These SMMs demonstrated similar magnetic properties but distinct quantum tunnelling of magnetization (QTM) relaxation times, suggesting the influence of nonmagnetic components and crystal environment on the behavior of SMMs.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Chemistry, Physical
Xabier Telleria-Allika, Jose M. Mercero, Jesus M. Ugalde, Xabier Lopez, Jon M. Matxain
Summary: In this work, we computed and implemented one-body integrals for Gaussian confinement potentials and established an equivalence between Gaussian and Hooke atoms. We observed that both systems are equivalent for a series of even number of electrons at large confinement depths. Unlike harmonic potentials, Gaussian confinement potentials are dissociative and crucial for modeling phenomena like ionization.
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
(2023)
Article
Chemistry, Physical
Juan Felipe Huan Lew-Yee, Jorge M. del Campo, Mario Piris
Summary: The relative stability of the singlet, triplet, and quintet spin states of iron(II) porphyrin (FeP) is a challenge for electronic structure methods. Different methods lead to conflicting predictions, with some suggesting a quintet ground state and others suggesting a triplet ground state. The Global Natural Orbital Functional (GNOF), along with the Piris Natural Orbital Functionals (PNOFs), provides a balanced treatment of static and dynamic correlations and allows for a more accurate understanding of the stability order of FeP states.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Organic
Leire Villaescusa, Iker Hernandez, Laura Azcune, Ainhoa Rudi, Jose M. Mercero, Aitor Landa, Mikel Oiarbide, Claudio Palomo
Summary: The catalytic addition of hydantoin surrogates to rigidified vinylidene bis(sulfone) reagents was achieved, overcoming the unreactivity of commonly used beta-substituted vinylic sulfones. The resulting adducts were transformed into enantioenriched 5,5-disubstituted hydantoins through hydrolysis and reductive desulfonylation processes, offering new structures for potential bioassays. Density functional theory studies provided insights into the observed reactivity and stereoselectivity trends.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Physics, Multidisciplinary
Antonio Reifs, Irene Ruiz Ortiz, Amaia Ochandorena Saa, Jorg Schonfelder, David De Sancho, Victor Munoz, Raul Perez-Jimenez
Summary: Ultrafast folding proteins have low energetic barriers and fast kinetics, making them suitable for study by both experiments and simulations. However, single molecule force spectroscopy experiments on these proteins are challenging due to the lack of mechanical fingerprints. In this study, the unfolding of an ultrafast protein is investigated using atomic force microscopy experiments.
COMMUNICATIONS PHYSICS
(2023)
Article
Chemistry, Physical
Patricia Poths, Borna Zandkarimi, Anastassia N. Alexandrova, Elisa Jimenez-Izal
Summary: This study explores the effect of Ge content on PtGe cluster alloys for ethane dehydrogenation. It is found that the addition of Ge improves the stability and selectivity of the catalyst, with the optimal Ge to Pt ratio being 1:4. The concentration of Ge plays an important role in the stability and selectivity of Pt clusters.
Article
Chemistry, Inorganic & Nuclear
Mario Prejano, Marirosa Toscano, Tiziana Marino
Summary: LanM is a natural protein that can reversibly bind ions of rare earth elements and some actinides. This study systematically investigated the affinity of LanM for lanthanides and actinides, and provided a detailed structural and electronic description. The experimental results are in agreement with available data, and the possible reasons for the affinity of LanM for these metal ions are discussed.
INORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Federica De Castro, Giada Ciardullo, Francesco Paolo Fanizzi, Mario Prejano, Michele Benedetti, Tiziana Marino
Summary: In this work, the mechanism of action of cisplatin anticancer drug was elucidated through comprehensive molecular modeling analysis. The study revealed the interactions between Thermus aquaticus (Taq) DNA polymerase and different N7-platinated deoxyguanosine triphosphates, providing valuable insights into the binding site interactions and contribution to a better understanding of experimental results.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Juan Felipe Huan Lew-Yee, Mario Piris, Jorge M. del Campo
Summary: This study evaluated the performance of the recently proposed global natural orbital functional (GNOF) in addressing the charge delocalization error. GNOF achieves a good balance between static and dynamic electronic correlations, resulting in accurate total energies and preserved spin for systems with a highly multi-configurational character. Various analyses were conducted to assess the functional, including the charge distribution in super-systems of two fragments, stability of ionization potentials with increasing system size, and potential energy curves of a neutral and charged diatomic system. Results showed that GNOF effectively eliminates or improves the charge delocalization error in many studied systems, surpassing the previous results obtained with PNOF7.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Mario Prejano, Marta Erminia Alberto, Bruna Clara De Simone, Tiziana Marino, Marirosa Toscano, Nino Russo
Summary: The effect of sulfur and selenium replacement in the DMNP molecule on its photophysical properties has been investigated using density functional theory (DFT). Computed structural parameters, excitation energies, singlet-triplet energy gaps (?ES-T), and spin-orbit coupling constants (SOC) suggest an enhanced probability of intersystem crossing (ISC) in the thio- and seleno-derivatives, leading to increased singlet oxygen quantum yields. Additionally, electron transfer mechanisms indicating dual Type I/Type II activity were found for all compounds.
Article
Physics, Multidisciplinary
C. Medina, A. o Laegdsmand, L. Ben Ltaief, Z. Hoque, A. H. Roos, L. Jurkovicova, O. Hort, O. Finke, M. Albrecht, J. Nejdl, F. Stienkemeier, J. Andreasson, E. Klimesova, M. Krikunova, A. Heidenreich, M. Mudrich
Summary: We investigate the dynamics of avalanche ionization in pure helium nanodroplets activated by a weak extreme-ultraviolet (XUV) pulse and driven by an intense near-infrared (NIR) pulse. Short-term activation is caused by the injection of seed electrons into the droplets by XUV photoemission, while long-term activation is due to electrons remaining loosely bound to photoions, forming stable snowball structures in the droplets. These findings demonstrate that XUV irradiation can induce long-lasting changes in the optical properties of nanoparticles, potentially enabling control of avalanche-ionization phenomena in nanostructures and condensed-phase systems.
NEW JOURNAL OF PHYSICS
(2023)
Article
Chemistry, Physical
Slawomir J. Grabowski
Summary: Omega B97XD/aug-cc-pVDZ and Omega B97XD/aug-cc-pVTZ calculations were performed on complexes of imidazol-2-ylidene linked by halogen bonds. The properties of interactions in the complexes were analyzed using DFT calculations, QTAIM and NBO methods, as well as energy decomposition analysis. Most of the complexes were linked by medium and strong halogen bonds, often exhibiting characteristics of covalent bonds. Searches through the Cambridge Structural Database also found analogous structures to the theoretically analyzed complexes, which are discussed in this study.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
