Article
Chemistry, Physical
Giorgia Ceselin, Zoi Salta, Julien Bloino, Nicola Tasinato, Vincenzo Barone
Summary: This study uses quantum chemical calculations to predict the structure and spectroscopic properties of glycolic acid, and provides a comparison with experimental data, enhancing the possibility of detecting this molecule.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Irene Vettori, Marina Macchiagodena, Marco Pagliai, Gavino Bassu, Emiliano Fratini, Piero Baglioni
Summary: This study investigates the structural and spectroscopic properties of HEMA and AA using computational and simulation methods. Two stable HEMA conformers are found to coexist, and their interactions with water are mainly through hydrogen bonding. IR spectra are used to differentiate the presence of conformers and obtain information on their ratio in the solution.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Steve-Jonathan Koyambo-Konzapa, Gilbert Yvon Mbesse Kongbonga, R. Premkumar, Berthelot Said Duvalier Ramlina Vamhindi, Mama Nsangou, A. Milton Franklin Benial
Summary: This paper provides a complete theoretical investigation of the HIPyA molecule, including conformational analysis, vibrational frequency simulation, and UV-visible spectra analysis. The molecule exhibits potential as an inhibitor against the amyloid b-protein enzyme associated with Alzheimer's disease, along with nonlinear optical activity. The results are supported by molecular docking and molecular dynamics analysis.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Vincenzo Barone
Summary: Accurate computations of structural, conformational, and spectroscopic properties were performed for two α, α-dialkylated α-amino acids using modern hybrid functionals and wave-function methods. The computed features closely matched the spectroscopic parameters obtained from microwave spectroscopic studies in the gas-phase for all the most stable conformers of the target amino acids. The accuracy of the results obtained with reasonable computer times opens up possibilities for accurate investigations of other flexible building blocks of life.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Goncagul Serdaroglu, Nesimi Uludag
Summary: The proposed new synthetic route offers an economical way to synthesize pharmaceutical important molecules, involving ring closure and cyclization reactions. Various compounds were synthesized and characterized using spectroscopic tools, and the chemical reactivity and optical properties of the final product were investigated through theoretical calculations.
Article
Chemistry, Multidisciplinary
Dibyajit Dash, Minati Baral, Bikram K. Kanungo
Summary: A new tripodal siderophore-mimic hexadentate chelator, TACH-1,2-HOPO, was designed and synthesized, and its solution thermodynamics and photophysical properties with lanthanide ions were experimentally and theoretically determined. The formation of lanthanide complexes and the bonding behavior between lanthanide ions and TACH-1,2-HOPO were investigated, showing weaker covalent Ln-L bonds with the trend Lu>Gd>La. Theoretical calculations by DFT supported the experimental results and provided insight into the protonation constants and spectral data.
Article
Polymer Science
Dhrubajyoti Majumdar, Burak Tuzun, Tapan Kumar Pal, Sourav Das, Kalipada Bankura
Summary: In this study, a novel Zn-Pb heterobinuclear coordination polymer was synthesized and characterized, and its structural properties were analyzed using various techniques. The study revealed important non-covalent interactions in the crystal structure of the complex, and identified possible binding mechanisms through molecular docking analysis. Furthermore, the significance of the complex was assessed by calculating its nonlinear optical properties.
JOURNAL OF INORGANIC AND ORGANOMETALLIC POLYMERS AND MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Emanuele Penocchio, Giulio Ragazzon
Summary: Molecular nonequilibrium systems have great potential for future nanotechnology, but their development is hindered by the lack of an informative representation. We extended the energy span model, an approach pertaining to catalytic networks, to provide an insightful visual representation of kinetic asymmetry in system dynamics. Our approach applies to both chemically and photochemically driven systems, ranging from unimolecular motors to simple self-assembly schemes. The obtained diagrams offer immediate access to information needed for guiding experiments and understanding the effects of design changes.
Article
Astronomy & Astrophysics
N. Marcelino, C. Puzzarini, M. Agundez, R. Fuentetaja, B. Tercero, P. de Vicente, J. Cernicharo
Summary: We report the discovery of HSO in several cold dark clouds, confirmed by observing rotational transitions. The HSO column densities were obtained and the abundances relative to H-2 were calculated. The widespread presence of HSO in cold dense cores suggests the need for further observations to understand its chemical production mechanisms.
ASTRONOMY & ASTROPHYSICS
(2023)
Article
Chemistry, Physical
Mattia Melosso, Ningjing Jiang, Juergen Gauss, Cristina Puzzarini
Summary: Despite their simplicity, the spectroscopic investigation of light hydrides like hydrogen sulfide is challenging due to hyperfine interactions and anomalous centrifugal-distortion effects. Accurate knowledge of the rotational spectrum, especially for isotopic species with deuterium, is important for understanding astronomical objects and interstellar chemistry. This study combines quantum-chemical calculations and sub-Doppler measurements to investigate the hyperfine structure of the rotational spectrum of mono-deuterated hydrogen sulfide, extending the centrifugal analysis and modeling the spectrum accurately across different wavelengths.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Vincenzo Barone, Jacopo Lupi, Zoi Salta, Nicola Tasinato
Summary: A recently developed strategy for the computation of reliable barrier heights in gas-phase reactions has been extended to the use of explicitly correlated methods. The new model, referred to as junChS-F12, shows improved performance compared to traditional models and well-known model chemistries, without the need for empirical parameters and at affordable computational cost. Benchmark tests demonstrate that the combination of revDSD-PBEP86-D3(BJ) structures and force fields with junChS-F12 electronic energies provides accurate reaction rates in the framework of the ab initio transition-state theory.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Vincenzo Barone, Giorgia Ceselin, Federico Lazzari, Nicola Tasinato
Summary: The SE100 database has been extended to include species containing Br and I atoms, providing accurate equilibrium geometries of medium size molecules obtained by the semiexperimental approach. An improved Nano-LEGO tool has been developed, which offers geometrical parameters on par with state-of-the-art composite wave function methods.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Vincenzo Barone, Marco Fuse
Summary: A general strategy is utilized to accurately calculate the conformational and spectroscopic properties of phenylalanine and tyrosine, two proteinogenic amino acids with aromatic side chains, in the gas phase. The predicted stable conformers closely match those detected in microwave and infrared experiments. This accurate computation method opens up possibilities for investigating other flexible components of life.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Vincenzo Barone
Summary: A fully unsupervised computational protocol is proposed to obtain reliable structural properties for molecular bricks of life in the gas phase at a moderate cost. The results of the new composite scheme approach spectroscopic accuracy without any empirical parameter, providing optimized geometries and equilibrium rotational constants. The accuracy of the new tool is comparable to state-of-the-art composite wave function methods for small semirigid molecules.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Lorna Binks, Stefan Borsley, Todd R. Gingrich, David A. Leigh, Emanuele Penocchio, Benjamin M. W. Roberts
Summary: The study found that kinetic asymmetry determines the directionality of the information ratchets, while power strokes influence the performance and energy storage form. These findings have important implications for understanding biological ratchets and designing artificial molecular machines.
Review
Chemistry, Multidisciplinary
Thitiporn Sangchai, Shaymaa Al Shehimy, Emanuele Penocchio, Giulio Ragazzon
Summary: Non-equilibrium chemical systems play a crucial role in various contemporary domains, such as supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now at the forefront of developing artificial systems that can harvest energy from non-equilibrium states. In this tutorial Review, we present an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on mechanism types rather than application domains or energy sources, we provide a unifying perspective on seemingly disparate phenomena, aiming to facilitate progress in this fascinating field.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Luigi Crisci, Silvia Di Grande, Carlo Cavallotti, Vincenzo Barone
Summary: An enhanced computational protocol has been developed for accurately characterizing gas-phase barrier-less reactions using density functional theory and Monte Carlo sampling. The tool shows good performance in two prototypical reactions and can be used for systematic investigations of barrier-less elementary steps in gas-phase reactions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
S. Di Grande, M. Kallay, V. Barone
Summary: The junChS-F12 composite method has been improved with the latest implementation of CCSD(F12*)(T+) ansatz and validated for thermochemistry of molecules containing atoms of the first three rows of the periodic table. Benchmark tests showed that this model, combined with cost-effective revDSD-PBEP86-D3(BJ) reference geometries, strikes an optimal balance between accuracy and computational cost. In addition, the model proves effective and reliable in pilot applications to noncovalent intermolecular interactions, conformational landscapes, and tautomeric equilibria.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Vincenzo Barone, Lina Marcela Uribe Grajales, Silvia Di Grande, Federico Lazzari, Marco Mendolicchio
Summary: A new computational strategy has been applied to study the conformational and spectroscopic properties of amino acids in the gas phase, including tautomeric forms, ring puckering, and heteroaromatic structures. Accurate results for a large number of conformers have been obtained using modern double-hybrid functionals and wave-function composite methods. The agreement between computations and microwave experiments allows for an unbiased interpretation of the latter in terms of stereoelectronic effects.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Vincenzo Barone, Silvia Di Grande, Federico Lazzari, Marco Mendolicchio
Summary: A general strategy for computing the properties of biomolecule building blocks in the gas phase has been proposed and validated for tautomeric equilibria. The strategy includes core-valence correlation and wave-function composite methods with basis sets for accurate computation. The results show agreement with experimental structures and spectroscopic signatures, making it possible for non-specialists to investigate other molecular bricks of life.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Cristina Puzzarini, Silvia Alessandrini, Luca Bizzocchi, Mattia Melosso
Summary: Interstellar molecules, including radicals, ions, and unsaturated carbon chains, are highly reactive and unstable under terrestrial conditions. Detecting them in space relies on observing their rotational fingerprints. However, producing and preserving these molecules during rotational spectroscopy measurements present challenges in the laboratory.
FARADAY DISCUSSIONS
(2023)
Article
Chemistry, Multidisciplinary
Cristina Puzzarini, Hexu Ye, Silvia Alessandrini
Summary: A recent study has discovered the gas-phase formation of t-HC(O)SH, which has been detected in the interstellar medium, and identified the trans form of HC(S)OH as a potential candidate for astronomical observations. From an energetic point of view, the CH2SO family of isomers has been examined, revealing that the cis and trans forms of HC(O)SH and HC(S)OH are the most stable species. Structural and spectroscopic characterization using a composite scheme has allowed for the prediction of rotational constants with 0.1% accuracy and fundamental vibrational frequencies with approximately 1% mean absolute error.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)