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, Applied
Soumalya Roy, Pooja Shukla, Raman Kumar, Subash Chandra Sahoo, Tapan K. Pal, Amit Rajput, Julia Klak, Masahiko Hada, Kuduva R. Vignesh, Sourav Das
Summary: A series of dimetallic Zn-II-Ln(III) compounds were successfully prepared, and the single crystal XRD analysis revealed the connection between metallic ions through the phenolic oxygen atom of ligands. Magnetic studies showed the existence of antiferromagnetic interaction between Zn-II and Ln(III) metal centers.
APPLIED ORGANOMETALLIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Sourav Dey, Gopalan Rajaraman, Helene Bolvin
Summary: The SMM compound [{Mn(TPA)I}{UO2(Mesaldien)}{Mn(TPA)I}]I has been fully characterized and its spin Hamiltonian parameters extracted using ab initio CAS and DFT methods. The study reveals that the signs of magnetic coupling and g-factors are interconnected, with the central magnetic unit [(UO2)-O-V]+ described by a Kramers Doublet with negative g-factors. Furthermore, the study suggests that the spin polarization on the U(V) center favors ferromagnetic coupling and that the J(Z)/J(perpendicular to) ratio, related to the barrier height, can be estimated from the corresponding g(S)-values.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Mohammed-Amine Bouammali, Nicolas Suaud, Cyril Martins, Remi Maurice, Nathalie Guihery
Summary: This paper showcases how on-site first-order spin-orbit coupling can generate giant Dzyaloshinskii-Moriya interactions in binuclear transition metal complexes, providing insight into controlling and increasing the magnitude of this interaction.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Raissa Lohanna Gomes Quintino Correa, Matheus Morato Ferreira de Moraes, Kleber Thiago de Oliveira, Yuri Alexandre Aoto, Mauricio Domingues Coutinho-Neto, Paula Homem-de-Mello
Summary: This research validates the accuracy and applicability of different density functional theory (DFT) methods in describing the UV spectra of curcumin and its metal complexes. The results show that DFT methods accurately describe the absorption spectra of curcumin due to its intra-ligand excitations. However, for MLCT transitions in metal complexes, no DFT method achieved acceptable accuracy.
JOURNAL OF MOLECULAR MODELING
(2023)
Article
Chemistry, Physical
Zohreh Amanollahi, Lukas Lampe, Moritz Bensberg, Johannes Neugebauer, Milica Feldt
Summary: In this study, the accuracy of the LMOMO scheme and WF-in-DFT embedding for predicting reaction energies and barriers of transition metal reactions was investigated. The accuracy was analyzed by applying manual and direct orbital selection methods. Benchmark tests on 30 closed shell reactions involving 16 different transition metals were conducted. Guidelines for orbital selection and settings for accurate results within an error of 2 kcal mol(-1) compared to local coupled cluster were proposed. LMOMO was found to provide more reliable relative energies for small embedded regions than WF-in-DFT embedding.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
Tomasz Maciazek
Summary: The reduced density matrix functional theory is a powerful tool for studying properties of ground states of strongly interacting quantum many body systems, especially Bose-Einstein condensation and systems of strongly correlated electrons. It has been shown that the density functional in these systems exhibits a repulsive gradient, known as the Bose-Einstein condensation force, which is universal for different types of pair-interaction and non-homogeneous gases. The theory has also been extended to fermionic systems, showing the existence of a similar repulsive gradient in the fermionic RDMFT.
NEW JOURNAL OF PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Loic Groslambert, Yann Cornaton, Matej Ditte, Emmanuel Aubert, Patrick Pale, Alexandre Tkatchenko, Jean-Pierre Djukic, Victor Mamane
Summary: Telluronium salts [Ar2MeTe]X were synthesized and their Lewis acidic properties in solution were investigated using physical and theoretical methods. The study revealed the electrophilicity of the Te centers and the ability of telluroniums to form Lewis pairs. The affinity of telluroniums for OPPh3 was determined by state-of-the-art computational methods, showing the importance of Coulombic and dispersion interactions in solution.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Inorganic & Nuclear
Terezia Laluhova, Jan Titis, Cyril Rajnak, Jan Moncol', Roman Boca
Summary: Two hexacoordinate Ni(II) complexes formed by methylpyridine ligands and pseudohalido coligands have been successfully synthesized and characterized. X-ray structure analysis reveals that the coordination polyhedron exhibits a compressed tetragonal bipyramid geometry. Magnetometric measurements confirm that the axial zero-field splitting parameter D has small negative values. This finding is supported by the Generalized Crystal-Field Theory and analyzed through ab initio CASSCF + NEVPT2 calculations. The magnetic parameters have been compared with complexes of similar architecture.
Article
Chemistry, Physical
Ben Shpiro, Marcel David Fabian, Eran Rabani, Roi Baer
Summary: In this paper, we develop a formalism for calculating forces on the nuclei within a nonorthogonal atom-centered basis set representation and apply it to a peptide solvated in water. We use an embedded-fragment approach to reduce statistical errors and find that the systematic bias is sufficiently small when using 120 stochastic orbitals.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Juan J. J. Aucar, Alejandro F. F. Maldonado, Juan I. I. Melo
Summary: In this work, relativistic corrections to the electric field gradient (EFG) are presented, including spin-dependent corrections for the first time. The results show that these new corrections significantly improve the performance of the existing method and are in close agreement with calculations at the four-component Dirac-Hartree-Fock (4c-DHF) level. The accuracy of the EFG values obtained with this new method allows for the analysis of the electronic origin of relativistic effects using well-known nonrelativistic operators.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Tao Zhang, Kangbao Zhong, Zhi-Keng Lin, Linbin Niu, Zi-Qi Li, Ruopeng Bai, Keary M. Engle, Yu Lan
Summary: In this study, computational evidence is presented to support the role of Zn coordination in accelerating reductive elimination from Ni(II) centers in Ni-catalyzed cross-couplings. The Zn-assisted pathway was found to have lower energy compared with direct reductive elimination from a Sigma-coordinated Ni(II) intermediate. Theoretical calculations reveal a significant Z-type Ni-Zn interaction that enhances reductive elimination.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Paul Schmid, Felipe Fantuzzi, Jonas Klopf, Niklas B. Schroeder, Rian D. Dewhurst, Holger Braunschweig, Volker Engel, Bernd Engels
Summary: This issue features the research work of Bernd Engels, Holger Braunschweig, Volker Engel and their coworkers at University of Wurzburg on bridged boron compounds, highlighting the fascinating relationships between their composition, geometrical structures, and electronic structures.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Materials Science, Multidisciplinary
Lucas Rodrigues da Silva, Felipe Orlando Morais, Joao Paulo A. de Mendonca, Breno R. L. Galvao, Juarez L. F. Da Silva
Summary: In this study, density functional theory calculations were used to investigate the structural, energetic, and electronic properties of A55-nBn nanoalloys. The results showed that CuAl, CuAg, CuZn, and AlAg systems are the most energetically favorable, with Al42Cu13 and Al42Ag13 compositions having stable structures. Structural properties were found to be the most important descriptors correlated with the energy stability of the nanoalloys, while certain properties showed a linear dependence on composition.
COMPUTATIONAL MATERIALS SCIENCE
(2022)
Article
Materials Science, Multidisciplinary
A. C. Martinez-Olguin, R. Ponce-Perez, Leonardo Morales De la Garza, Maria G. Moreno-Armenta, Gregorio H. Cocoletzi
Summary: The study investigates the structural, electronic, and magnetic properties of cobalt adsorption and incorporation on the AlN surface, showing different magnetic behaviors depending on coverage and configuration.
JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS
(2022)
Article
Chemistry, Medicinal
Natalia Diaz, Dimas Suarez
Summary: This research investigates the conformational properties of unguisin A and its difluorinated stereoisomers using NMR experiments and enhanced MD techniques. The study reveals that fluorination significantly alters the secondary structure of the macrocycle, except for one diastereomer, suggesting that fluorination can select conformations accessible to the unsubstituted peptide. Computational characterization of macrocyclic peptides may thus aid in the rational design of stereoselective fluorinated peptides with fine-tuned conformation and activity.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Analytical
F. J. Pereira, R. Lopez, A. Rodriguez-Cordero, L. C. Robles, D. Suarez, A. J. Aller
Summary: The researchers introduced the Gumbel distribution as a new tool for modeling the chromatographic peak shape and developed mathematical models to evaluate the effects of experimental variables and quantum parameters on chromatographic indices. Finally, they proposed a mechanistic behavior for the chromatographic separation process based on the structure-retention relationship of selected drugs and molecular quantum parameters.
MICROCHEMICAL JOURNAL
(2021)
Article
Chemistry, Applied
Ismael Marcet, Jaime Delgado, Natalia Diaz, Manuel Rendueles, Mario Diaz
Summary: This study hydrolyzed lipoproteins using trypsin and evaluated the bioactivity of resulting peptides through in silico analysis. The transmission of valuable peptides through PES and SC membranes at different pHs was also assessed. The most promising antihypertensive peptide, K.VQWGIIPSWIK.K, was found in the permeates.
Article
Chemistry, Medicinal
Roberto Lopez, Natalia Diaz, Evelio Francisco, Angel Martin-Pendas, Dimas Suarez
Summary: The interacting quantum atoms (IQA) method allows for the decomposition of the quantum mechanical (QM) energy of a molecular system using the quantum theory of atoms in molecules framework. This method, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, can be extended to hybrid QM/MM methodologies. The IQA QM/MM approach has been demonstrated to successfully characterize metal-water interactions and QM/MM boundary artifacts, as well as describe covalent and noncovalent bonding interactions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Dimas Suarez, Natalia Diaz
Summary: Amphiphilic cyclodextrins can spontaneously form supramolecular assemblies with potential applications in drug release. Molecular dynamics simulations were used to characterize the structure, dynamics, binding properties, and aggregation capabilities of several amphiphilic derivatives of beta-cyclodextrin. The length of alkyl side chains in these derivatives plays a crucial role in determining their complexing abilities and aggregation tendencies.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Analytical
F. J. Pereira, R. Lopez, D. Suarez, A. J. Aller
Summary: This study compares the experimental Raman spectra of inorganic arsenic oxoacids in different aqueous solutions with the dry precipitates obtained from these solutions. The ability of quantum chemical methods to model the Raman spectra of the arsenic oxoacids in solution is also explored. It was found that hydrogen bridges and the coexistence of arsenic oxoacids contribute to strong overlapping in the Raman spectra of As-(III) aqueous samples compared to As-(V) samples. Furthermore, some Raman shifts of the dry arsenic precipitates correlate well with the corresponding Raman spectra of the same arsenic species in aqueous solutions, allowing for practical use of Raman spectroscopy in indirect screening of arsenic speciation in condensed phases.
MICROCHEMICAL JOURNAL
(2022)
Article
Chemistry, Analytical
R. Lopez, F. J. Pereira, D. Suarez, A. J. Aller
Summary: This study provides a comparative evaluation of the Raman spectra of four organoarsenicals in aqueous solutions under different pH conditions. It also examines the proficiency of computational chemistry in obtaining theoretical Raman spectra for these compounds. The results show that Raman spectrometry and computational chemistry can effectively identify the species and spectral features of organoarsenicals under different pH conditions.
MICROCHEMICAL JOURNAL
(2022)
Article
Chemistry, Physical
Natalia Diaz, Dimas Suarez
Summary: This study demonstrates the accuracy of estimating the entropy of flexible molecules using a partitioning approach based on rigid-rotor-harmonic-oscillator (RRHO) entropy and Gibbs-Shannon entropy. By employing discretization and expansion techniques that capture the correlation effects among torsional motions, the entropy of single molecules of varying sizes can be accurately computed. Extensive sampling, such as classical molecular dynamics simulations, is crucial for reliable entropy estimation.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Angel Martin Pendas, Evelio Francisco, Dimas Suarez, Aurora Costales, Natalia Diaz, Julen Munarriz, Tomas Rocha-Rinza, Jose Manuel Guevara-Vela
Summary: In this study, recent advances in the concept of atoms-in-molecules are reviewed from a real space perspective. The general formalism of atomic weight factors, which unifies fuzzy and non-fuzzy decompositions, is introduced. The use of reduced density matrices and their cumulants for partitioning quantum mechanical observables into atomic or group contributions is discussed. The importance of this study is 9 out of 10.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Natalia Diaz, Dimas Suarez
Summary: While computational simulations support a neutral state for the catalytic dyad of the SARS-CoV-2 main protease, a recently-reported neutron structure shows a zwitterionic form. Molecular Dynamics study reveals that the enzyme charge configuration from the neutron structure is not compatible with a catalytically-competent binding mode for peptide substrates.
CHEMICAL COMMUNICATIONS
(2021)