Complexes of Zn(2+)(H(2)O)(n), where n = 6-12, are examined using infrared photodissociation (IRPD) spectroscopy, blackbody infrared radiative dissociation (BIRD), and theory. Geometry optimizations and frequency calculations are performed at the B3LYP/6-311+G(d,p) level along with single point energy calculations for relative energetics at the B3LYP, B3P86, and MP2(full) levels with a 6-311+G(2d,2p) basis set. The IRPD spectrum of Zn(2+)(H(2)O)(8) is most consistent with the calculated spectrum of the five-coordinate MP2(full) ground-state (GS) species. Results from larger complexes also point toward a coordination number of five, although contributions from six-coordinate species cannot be ruled out. For n = 6 and 7, comparisons of the individual IRPD spectra with calculated spectra are less conclusive. However, in combination with the BIRD and laser photodissociation kinetics as well as a comparison to hydrated Cu(2+) and Ca(2+), the presence of five-coordinate species with some contribution from six-coordinate species seems likely. Additionally, the BIRD rate constants show that Zn(2+)(H(2)O)(6) and Zn(2+)(H(2)O)(7) complexes are less stable than Zn(2+)(H(2)O)(8). This trend is consistent with previous work that demonstrates the enthalpic favorability of the charge separation process forming singly charged hydrated metal hydroxide and protonated water complexes versus loss of a water molecule for complexes of n ≤ 7. Overall, these results are most consistent with the lowest-energy structures calculated at the MP2(full) level of theory and disagree with those calculated at B3LYP and B3P86 levels.
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http://dx.doi.org/10.1021/jp1078345 | DOI Listing |
Molecules
August 2024
Federal State Budgetary Scientific Institution, A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Science, 28 Vavilov St., 119991 Moscow, Russia.
The interaction between natural amino acids and hydrogen peroxide is of paramount importance due to the widespread use of hydrogen peroxide in biological and environmentally significant processes. Given that both amino acids and hydrogen peroxide occur in nature in two enantiomeric forms, it is crucial to investigate the formation of complexes between them, considering the role of molecular chirality. In this work, we report a theoretical study on the hydrogen peroxide enantiomers and their interactions with L- and S-serine and their clusters.
View Article and Find Full Text PDFJ Chem Inf Model
January 2024
Material and Analytical Sciences, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, United States.
Autoxidation of drugs and drug-like molecules is a major concern in the development of safe and effective therapeutics. Because active pharmaceutical ingredients (APIs) that contain sulfur atoms can form sulfoxides under oxidative stress, predicting oxidative susceptibilities within an organic molecule can have a major impact in accelerating the compound's stability assessment. For investigation of a sulfur atom's oxidative stability, density functional theory (DFT) methods were applied to accurately predict S-O estimated bond dissociation enthalpies (BDEs) of sulfoxides.
View Article and Find Full Text PDFJ Phys Chem A
April 2023
Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States.
The aromatic amino acids (AAA), phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), were cationized with ZnCl and CdCl, and the complexes were evaluated using infrared multiple photon dissociation (IRMPD) action spectroscopy. Specifically, the ZnCl(Phe), CdCl(Phe), ZnCl(Tyr), CdCl(Tyr), and ZnCl(Trp) species were examined because the CdCl(Trp) IRMPD spectrum is available in the literature. Several low-energy conformers for all complexes were found using quantum chemical calculations, and their simulated vibrational spectra were compared to the experimental IRMPD spectra to identify dominant isomers formed.
View Article and Find Full Text PDFPhys Chem Chem Phys
September 2022
Radboud University, FELIX Laboratory, Institute for Molecules and Materials, Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands.
The gas-phase structures of cationized glycine (Gly), including complexes with Li, Na, K, Rb, and Cs, are examined using infrared multiple-photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) for the Li, Na, and K complexes and at B3LYP/def2TZVP for the Rb and Cs complexes. Single-point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set for Li, Na, K and the def2TZVPP basis set for Rb and Cs.
View Article and Find Full Text PDFJ Am Soc Mass Spectrom
August 2022
Department of Chemistry, University of Utah, 315 South 1400 East Rm 2020, Salt Lake City, Utah 84112, United States.
Noncovalent interactions between alkali metals and amino acids are critical for many biological processes, especially for proper function of protein ion channels; however, many precise binding affinities between alkali metals and amino acids still need to be measured. This study addresses this need by using threshold collision-induced dissociation with a guided ion beam tandem mass spectrometer to measure binding affinities between potassium cations and the aliphatic amino acids: Gly, Ala, hAla, Val, Leu, and Ile. These measurements are supplemented by theoretical calculations and include commentary on effects of enthalpy, entropy, and structural preference.
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