Born-Oppenheimer molecular dynamics (BOMD) simulations were performed to investigate the structure and dynamics of the first hydration shells of five trivalent lanthanide ions (Ln) at room temperature. These ions are relevant in various environments, including the bulk aqueous solution. Despite numerous studies, accurately classifying the molecular geometry of the first hydration sphere remains a challenge. To addres this, a cluster microsolvation approach was employed to study the interaction of Ln ions (La, Nd, Gd, Er, and Lu) with up to 27 explicit water molecules. Electronic structure calculations were performed with the composite rSCAN-3c method. The results demonstrate that this method offers an optimal balance between precision and computational efficiency. Specifically, it accurately predicts average Ln-O distances (MAE = 0.02 Å) of the first hydration sphere and preferred coordination numbers (CN) for the different lanthanide cations as compared to reported data in bulk. Highly dynamic first hydration shells for the examined Ln ions were found, with noticeable and rapid rearrangements in their coordination geometries, some of which can be recognized as the tricapped trigonal prism (TTP) and the capped square antiprism (CSAP) for CN = 9, and as the square antiprism (SAP), the bicapped trigonal prism (BTP), and the trigonal dodecahedron (DDH) for CN = 8. However, ca. 70% of the nonacoordinated configurations did not meet the criteria of TTP or CSAP structures. For CN = 8, the percentage of configurations that could not be assigned to SAP, BTP, or DDH was lower, around 30%. The theoretical EXAFS spectra obtained from the BOMD simulations are in good agreement with the experimental data and confirm that model microsolvated environments accurately represent the near-solvation structure of these trivalent rare-earth ions. Moreover, this demonstrates that the faster dynamics of the first hydration shell can be studied separately from the dynamics of water exchange in the bulk aqueous solution.
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http://dx.doi.org/10.1021/acsomega.4c04947 | DOI Listing |
ACS Omega
December 2024
Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México.
J Phys Chem A
January 2025
Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.
We revisit the naked transition metal cation (Ti) and methanol reaction and go beyond the standard Landau-Zener (LZ) picture when modeling the intersystem crossing (ISC) rate between the lowest doublet and quartet states. We use both (i) unconstrained Born-Oppenheimer molecular dynamics (BOMD) calculations with an approximate two-state method to estimate population transfer between spin diabats and (ii) constrained dynamics to explore energetically accessible portions of the - 1 crossing seam, where is the total number of internal degrees of freedom. Whereas previous LZ calculations (that necessarily relied on the Condon approximation to be valid) fell short and predicted much slower crossing probabilities than shown in experiment, we show that ISC can occur rapidly because the spin-orbit coupling (SOC) between the doublet and quartet surfaces can vary by 2 orders of magnitude (depending on where in the seam the crossing occurs during dynamics) and the crossing region is revisited multiple times during a dynamics run of a few hundred femtoseconds.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Physics, Stockholm University, AlbaNova University Center, SE-10691 Stockholm, Sweden.
Vibrational polaritons are formed by strong coupling of molecular vibrations and photon modes in an optical cavity. Experiments have demonstrated that vibrational strong coupling can change molecular properties and even affect chemical reactivity. However, the interactions in a molecular ensemble are complex, and the exact mechanisms that lead to modifications are not fully understood yet.
View Article and Find Full Text PDFProtein Sci
January 2025
Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.
Cyclooxygenase-2 (COX-2) plays a crucial role in inflammation and has been implicated in cancer development. Understanding the behavior of COX-2 in different cellular contexts is essential for developing targeted therapeutic strategies. In this study, we investigate the fluorescence spectrum of a fluorogenic probe, NANQ-IMC6, when bound to the active site of human COX-2 in both its monomeric and homodimeric forms.
View Article and Find Full Text PDFJ Am Soc Mass Spectrom
January 2025
Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States.
We report a study of internal covalent cross-linking with photolytically generated diarylnitrile imines of N-terminal arginine, lysine, and histidine residues in peptide conjugates. Conjugates in which a 4-(2-phenyltetrazol-5-yl)benzoyl group was attached to C-terminal lysine, that we call RAAA--K, KAAA--K, and HAAA--K, were ionized by electrospray and subjected to UV photodissociation (UVPD) at 213 nm. UVPD triggered loss of N and proceeded by covalent cross-linking to nitrile imine intermediates that involved the side chains of N-terminal arginine, lysine, and histidine, as well as the peptide amide groups.
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