Article
Chemistry, Physical
Jeremy P. Coe, Andres Moreno Carrascosa, Mats Simmermacher, Adam Kirrander, Martin J. Paterson
Summary: We propose an efficient approach to calculate two-electron reduced density matrices (2-RDMs) using selected configuration interaction wavefunctions, demonstrated with Monte Carlo configuration interaction (MCCI) as a specific example. The computation of 2-RDMs is accelerated by incorporating ideas from fast implementations of full configuration interaction (FCI) and recent advances in implementing the Slater-Condon rules using hardware bitwise operations. This method allows for a comparison between MCCI and truncated CI 2-RDMs with FCI values for various molecules, including stretched bonds and excited states. The accuracy in energies, wavefunctions, and 2-RDMs exhibits similar behavior. We find that MCCI can achieve sufficient accuracy of 2-RDMs using significantly fewer configurations than truncated CI, especially for systems with strong multireference character.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Kaihua Zhang, Marco Caricato
Summary: Metal-doped amorphous silicates are promising materials for heterogeneous catalysis due to their easy preparation and tunable properties. However, the characterization of their amorphous surface is challenging, and improvements are mostly based on trial and error. This study focuses on the Nb-catalyzed epoxidation of ethylene as a test reaction to understand the factors affecting effective reaction rates. The researchers found that multiple transition state structures can exist at each site, which significantly affect the reaction barrier, and sampling of different sites is necessary.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Kaihua Zhang, Marco Caricato
Summary: Metal-doped amorphous silicates are promising materials for heterogeneous catalysis due to their easy fabrication and tunable properties. However, their amorphous surface makes characterization challenging, and improvements rely on a trial and error approach. In this study, we use the Nb-catalyzed epoxidation of ethylene as a test reaction to analyze various aspects of simulation modeling for effective reaction rate predictions. We find that each site can have multiple transition state structures with varying reaction barriers, and that sampling of multiple sites is necessary. Machine learning is employed to identify key descriptors of the active site that correlate with energy barriers.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Henrik H. Kristoffersen
Summary: An explicit charging approach is introduced in atomic level electrochemistry modeling to account for constant potential. This method allows for calculating electrochemical reaction barriers and reproducing results from the computation hydrogen electrode (CHE) approach under constant potential conditions. The approach is used to obtain activation and adsorption free energies for proton adsorption from a static water bilayer to the Cu(111) surface.
Article
Materials Science, Multidisciplinary
Raill Mendoza Baez, A. Marco Morales, Adan Luna Flores, Ricardo Agustin Serrano
Summary: In this study, the synthesis of zinc oxide nanoparticles (ZnONPs) was investigated using a multiscale modeling approach based on a three-stage reaction mechanism via the hydrothermal method. The reactivity of chemical compounds in the reaction mechanism was evaluated using Density Functional Theory (DFT) with the B3LYP/6-311+G method. Computational simulations and numerical solutions were employed to replicate the three-dimensional morphologies of ZnONPs, such as rods, spheres, octahedra, and others, reported experimentally.
MATERIALS TODAY COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Stevan Armakovic, Milena Aleksic, Stamatios Giannoukos, Boris Brkic
Summary: In this study, computational investigation was conducted to study the interactions between VOCs and functionalized graphene nanosheets. The results suggest that functionalized graphene surfaces have potential for efficient trapping of specific compounds.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2023)
Article
Chemistry, Physical
Henrik H. Kristoffersen, Karen Chan
Summary: The authors utilized density functional theory, molecular dynamics, and metadynamics to investigate the *CO-*CO coupling reaction in explicit electrolyte. They found that under different charging conditions, the reaction mechanism and product formation are influenced, with implications for electrochemical processes.
JOURNAL OF CATALYSIS
(2021)
Article
Chemistry, Physical
Andras B. Nacsa, Viktor Tajti, Gabor Czako
Summary: A full-dimensional analytical ab initio potential energy surface (PES) has been developed for the Cl- + CH3I reaction using the Robosurfer program system. The energy points were computed using a composite method and have been fitted by the permutationally invariant polynomial approach. Quasi-classical trajectory simulations on the new PES reveal two product channels, S(N)2 and iodine abstraction, with different reaction mechanisms. The results show agreement with experiments and previous simulations, indicating the importance of further research.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Moritz Schneider, Daniel Born, Johannes Kaestner, Guntram Rauhut
Summary: The positions of grid points have a significant impact on the accuracy and computational effort of a multidimensional potential energy surface (PES) represented by n-mode expansions. Six different positioning schemes were studied, including a static approach and five adaptive schemes based on Gaussian process regression. Comparison with a more sophisticated approach by Christiansen et al. was made. The impact of grid point positions on multilevel PESs was discussed with respect to computational effort.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Kevin-P. Gradwohl, Peter Benedek, Maxim Popov, Aleksandar Matkovic, Jurgen Spitaler, Maksym Yarema, Vanessa Wood, Christian Teichert
Summary: LiFePO4 (LFP) microparticles with faceted crystal habits were fabricated using hydrothermal synthesis, with different surfactants controlling the crystal habits. Analysis based on atomic force microscopy data revealed crystallographic models with the lowest matching Miller indices, highlighting the importance of the previously neglected (2 1 0) facet. First-principles investigations using density functional theory showed the surface energy of the (2 1 0) facet and its contribution to the surface area of LFP crystals.
Article
Multidisciplinary Sciences
Masaya Nakajima, Tetsuhiro Nemoto
Summary: Machine learning enables predictions from new input data by creating models based on big data. It has the potential to reduce the time required for computing BDE values. Tasks previously done by humans can now be achieved in various fields through machine learning algorithms.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Physical
C. F. O. Correia, J. M. C. Marques, M. Bartolomei, F. Pirani, E. Macoas, J. M. G. Martinho
Summary: This study evaluates the influence of carboxyl and amine substituting groups on the aggregation of coronene, finding an increase in the number of local minima and enhanced attractive component interaction in clusters with substituted monomers.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Applied
Mostafa Mohamed Elsaady, Ahmed Osman Youssef, Mohamed Said Attia, Mohamed Sabry A. Abdel-Mottaleb
Summary: The study successfully used TbAcI as a novel sensor to detect shallow concentration of epinephrine in serum samples, explaining the quenching mechanism through simulating molecular structure and kinetic energy changes.
APPLIED ORGANOMETALLIC CHEMISTRY
(2021)
Article
Chemistry, Physical
Veronica Idebohn, Alistair J. Sterling, Mans Wallner, Emelie Olsson, Richard J. Squibb, Ugne Miniotaite, Emma Forsmalm, Malin Forsmalm, Stefano Stranges, John M. Dyke, Fernanda Duarte, John H. D. Eland, Raimund Feifel
Summary: The study of double and triple ionization of allene supports a previously proposed roaming mechanism in H-3(+) formation during double ionization, with double ionization energy at 27.9 eV and triple ionization energy close to 50 eV in agreement with theoretical predictions. The doubly charged parent ion is stable up to about 2 eV above the threshold, after which dissociations occur through charge separation and double charge retention.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Lixue Cheng, Jiace Sun, J. Emiliano Deustua, Vignesh C. Bhethanabotla, Thomas F. Miller
Summary: In this paper, a novel machine learning strategy, KA-GPR, is introduced for learning the total correlation energies of closed- and open-shell systems in molecular-orbital-based machine learning. The KA-GPR method has shown high accuracy in various chemical systems through training.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Eva Zunzunegui-Bru, Elisabeth Gruber, Teresa Lazaro, Massimiliano Bartolomei, Marta I. Hernandez, Jose Campos-Martinez, Tomas Gonzalez-Lezana, Stefan Bergmeister, Fabio Zappa, Paul Scheier, Ricardo Perez de Tudela, Javier Hernandez-Rojas, Jose Breton
Summary: In this study, we have observed the largest ordered structure of helium atoms surrounding a monatomic impurity using a newly developed technique. The investigation of HeNCa2+ clusters formed in helium nanodroplets shows magic numbers at N = 12, 32, 44, and 74, indicating the presence of well-ordered shells surrounding the calcium dication. These shells exhibit Mozartkugellike structures and consist of different shapes such as an icosahedron, dodecahedron, and icosidodecahedron.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Cahit Orek, Massimiliano Bartolomei, Cecilia Coletti, Niyazi Bulut
Summary: Gold(I) metal complexes have potential applications as therapeutic agents, and graphene and its derivatives show promise as drug nanocarriers. In this study, the adsorption of a gold(I) N-heterocyclic monocarbene on graphene was computationally investigated. The study found that the drug adsorption on graphene was very favorable, mainly driven by dispersion and electrostatic attraction.
Article
Biochemistry & Molecular Biology
Pedro M. C. Matias, Joana F. M. Sousa, Eva F. Bernardino, Joao P. Vareda, Luisa Duraes, Paulo E. Abreu, Jorge M. C. Marques, Dina Murtinho, Artur J. M. Valente
Summary: Toxic heavy metals, commonly found in dangerous concentrations in wastewater, can be effectively removed by chitosan and its derivatives. Among the synthesized reduced chitosan derivatives (RCDs), RCD3 exhibited the highest adsorption efficiency for Cu(II) under optimal conditions. Molecular dynamics simulations revealed that RCDs had stronger interactions with Cu(II) compared to chitosan, resulting in improved adsorption.
Article
Chemistry, Physical
Esther Garcia-Arroyo, Jose Campos-Martinez, Massimiliano Bartolomei, Marta I. Hernandez, Fernando Pirani, Nadine Halberstadt
Summary: In this study, an adiabatic separation of the rotational motion of H2 molecules is applied to build effective pseudoatom-ion potentials for (H2)nNa+/Cl- clusters. The accuracy of this adiabatic model is confirmed by comparing with simulations that explicitly describe molecular rotations. Additionally, differences in cluster stabilities and coordination shells are found depending on the spin isomer, particularly for anionic clusters.
Article
Optics
Qizhen Hong, Loriano Storchi, Massimiliano Bartolomei, Fernando Pirani, Quanhua Sun, Cecilia Coletti
Summary: Rate coefficients for vibrational energy transfer between molecular nitrogen and hydrogen were calculated using a mixed quantum-classical method. These data are crucial for simulating discharges in N-2/H-2 plasma and atmospheric/interstellar medium chemistry. The obtained rates differed significantly from those predicted by first-order perturbation theories. Additionally, different Machine Learning models based on Gaussian Process or Neural Network techniques were analyzed to generate complete datasets of inelastic scattering rate coefficients.
EUROPEAN PHYSICAL JOURNAL D
(2023)
Article
Biochemistry & Molecular Biology
Luca Schio, Michele Alagia, Robert Richter, Vitali Zhaunerchyk, Stefano Stranges, Fernando Pirani, Franco Vecchiocattivi, Marco Parriani, Stefano Falcinelli
Summary: The behavior of nitrosyl chloride (ClNO) exposed to ionizing radiation was studied by directly probing valence-shell electrons in temporal coincidence with ions originating from the fragmentation process of transient ClNO2+. A molecular dication, ClNO2+, was produced through double photoionization with synchrotron radiation. The experiment was conducted at the Elettra Synchrotron Facility of Basovizza (Trieste, Italy) with a linearly polarized light beam parallel to the ClNO molecular beam axis. The double ionization threshold energy of ClNO and six dissociation channels producing various ion pairs have been measured.
Article
Chemistry, Physical
J. R. C. Santos, P. E. Abreu, J. M. C. Marques
Summary: This work investigates the aggregation patterns of curcumin and piperine in different solvents through molecular dynamics simulations. In water, curcumin forms stable dimers while piperine forms less stable dimers. Both curcumin and piperine are soluble in ethanol, resulting in less dimer formation. A mixture of ethanol and water reduces the probability of dimer formation for both compounds. The simulations also reveal the presence of complex structures such as stacks and cages within larger clusters.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
J. R. C. Santos, P. E. Abreu, J. M. C. Marques
Summary: This study investigates the aggregation patterns of curcumin and piperine in different solvents using molecular dynamics simulations. The results show that curcumin forms stable dimers in water, while piperine forms less stable dimers. In ethanol, neither curcumin nor piperine forms dimers. A mixture of ethanol and water reduces the formation of dimers. Larger clusters with stack or cage structures are observed. Each molecule in the cluster exhibits mobility without dissociation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Review
Chemistry, Physical
Stefano Falcinelli, David Cappelletti, Franco Vecchiocattivi, Fernando Pirani
Summary: The present review focuses on the role of the precursor state in controlling the dynamical evolution of elementary processes. The structures and stability of the precursor state are difficult to characterize quantitatively. The formulation of intermolecular forces and the application of phenomenological methods have provided important insights into understanding the precursor state and its evolution. This information is particularly valuable for chemi-ionization reactions and has the potential to benefit other elementary processes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Qizhen Hong, Loriano Storchi, Quanhua Sun, Massimiliano Bartolomei, Fernando Pirani, Cecilia Coletti
Summary: In this study, complete data sets of vibration-to-vibration and vibration-to-translation rate coefficients for N-2-N-2 collisions, as well as transport properties, were calculated in the temperature range 100-9000 K. The improved mixed quantum-classical dynamics approach allowed for more realistic and flexible representations, and the role of intra- and intermolecular potentials on the rates and properties was analyzed. The obtained values are reliable and valuable for communities studying nonlocal thermal equilibrium conditions.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Maria Rutigliano, Fernando Pirani
Summary: The adsorption of nitrogen molecules on a (100) tungsten surface has been studied using a new potential energy surface. Molecular dynamics simulations with a semiclassical collisional method were performed, which included the interaction with surface phonons. The results showed good agreement with experimental data and improved upon previous calculations using Density Functional Theory and long-range van der Waals corrections. Additionally, the dependence of trapping probability on surface temperature for a given collision energy was investigated.
Article
Chemistry, Physical
A. Kurnosov, M. Cacciatore, F. Pirani
Summary: In this study, vibration-to-vibration (VV') exchanges between excited CO and unexcited O2 were investigated using the semiclassical coupled state method. The VV' rate constants were calculated based on a recently proposed accurate surface for the N2-O2 system. The results showed good agreement with experimental determinations.
CHEMICAL PHYSICS LETTERS
(2023)