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Isotope Effects 2019
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Isotope Effects 2019

A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: closed (31 March 2020) | Viewed by 22578

Special Issue Editor

Prof. Dr. Poul Erik Hansen

E-Mail Website
Guest Editor
Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark
Interests: isotope effects in biological systems; intramolecular hydrogen bonding; tautomerism; natural products; theoretical calculations of spectroscopic properties
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The journal Molecules has asked me to be guest editor of a Special Issue on the topic of “Isotope Effects 2019”. This is a continuation of a previous, very successful volume. This volume will have approximately twenty contributions, which can either be review papers or cover new research. Subjects can typically be kinetic isotope effects, reaction mechanisms, isotope effects in H-bond research, isotope effects as a tool in structural studies, use of isotope effects in food research, theoretical calculations of isotope effects, or use of isotope effects in environmental studies, to mention some examples, but papers dealing with all types of isotope effects are invited.

Prof. Dr. Poul Erik Hansen
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Isotope effects on NMR parameters
  • Kinetic isotope effects
  • Theoretical calculations
  • Isotope effects in food research
  • Isotope effects in environmental science
  • Isotope effects as a tool in structural studies

Published Papers (7 papers)

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Research

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32 pages, 1762 KiB  
Article
The Structure of the “Vibration Hole” around an Isotopic Substitution—Implications for the Calculation of Nuclear Magnetic Resonance (NMR) Isotopic Shifts
by Jürgen Gräfenstein
Molecules 2020, 25(12), 2915; https://doi.org/10.3390/molecules25122915 - 24 Jun 2020
Cited by 3 | Viewed by 2747
Abstract
Calculations of nuclear magnetic resonance (NMR) isotopic shifts often rest on the unverified assumption that the “vibration hole”, that is, the change of the vibration motif upon an isotopic substitution, is strongly localized around the substitution site. Using our recently developed difference-dedicated (DD) [...] Read more.
Calculations of nuclear magnetic resonance (NMR) isotopic shifts often rest on the unverified assumption that the “vibration hole”, that is, the change of the vibration motif upon an isotopic substitution, is strongly localized around the substitution site. Using our recently developed difference-dedicated (DD) second-order vibrational perturbation theory (VPT2) method, we test this assumption for a variety of molecules. The vibration hole turns out to be well localized in many cases but not in the interesting case where the H/D substitution site is involved in an intra-molecular hydrogen bond. For a series of salicylaldehyde derivatives recently studied by Hansen and co-workers (Molecules 2019, 24, 4533), the vibrational hole was found to stretch over the whole hydrogen-bond moiety, including the bonds to the neighbouring C atoms, and to be sensitive to substituent effects. We discuss consequences of this finding for the accurate calculation of NMR isotopic shifts and point out directions for the further improvement of our DD-VPT2 method. Full article
(This article belongs to the Special Issue Isotope Effects 2019)
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17 pages, 3399 KiB  
Article
H/D Isotope Effects on 1H-NMR Chemical Shifts in Cyclic Heterodimers and Heterotrimers of Phosphinic and Phosphoric Acids
by Valeriia V. Mulloyarova, Daria O. Ustimchuk, Aleksander Filarowski and Peter M. Tolstoy
Molecules 2020, 25(8), 1907; https://doi.org/10.3390/molecules25081907 - 20 Apr 2020
Cited by 14 | Viewed by 3370
Abstract
Hydrogen-bonded heterocomplexes formed by POOH-containing acids (diphenylphosphoric 1, dimethylphosphoric 2, diphenylphosphinic 3, and dimethylphosphinic 4) are studied by the low-temperature (100 K) 1H-NMR and 31P-NMR using liquefied gases CDF3/CDF2Cl as a solvent. Formation [...] Read more.
Hydrogen-bonded heterocomplexes formed by POOH-containing acids (diphenylphosphoric 1, dimethylphosphoric 2, diphenylphosphinic 3, and dimethylphosphinic 4) are studied by the low-temperature (100 K) 1H-NMR and 31P-NMR using liquefied gases CDF3/CDF2Cl as a solvent. Formation of cyclic dimers and cyclic trimers consisting of molecules of two different acids is confirmed by the analysis of vicinal H/D isotope effects (changes in the bridging proton chemical shift, δH, after the deuteration of a neighboring H-bond). Acids 1 and 4 (or 1 and 3) form heterotrimers with very strong (short) H-bonds (δH ca. 17 ppm). While in the case of all heterotrimers the H-bonds are cyclically arranged head-to-tail, ···O=P–O–H···O=P–O–H···, and thus their cooperative coupling is expected, the signs of vicinal H/D isotope effects indicate an effective anticooperativity, presumably due to steric factors: when one of the H-bonds is elongated upon deuteration, the structure of the heterotrimer adjusts by shortening the neighboring hydrogen bonds. We also demonstrate the formation of cyclic tetramers: in the case of acids 1 and 4 the structure has alternating molecules of 1 and 4 in the cycle, while in case of acids 1 and 3 the cycle has two molecules of 1 followed by two molecules of 3. Full article
(This article belongs to the Special Issue Isotope Effects 2019)
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14 pages, 1694 KiB  
Article
Hydrogen Tunnelling as a Probe of the Involvement of Water Vibrational Dynamics in Aqueous Chemistry?
by Ana Karković Marković, Cvijeta Jakobušić Brala, Viktor Pilepić and Stanko Uršić
Molecules 2020, 25(1), 172; https://doi.org/10.3390/molecules25010172 - 31 Dec 2019
Cited by 3 | Viewed by 2259
Abstract
Our study of tunnelling in proton-coupled electron transfer (PCET) oxidation of ascorbate with hexacyanoferrate(III) follows the insights obtained from ultrafast 2D IR spectroscopy and theoretical studies of the vibrational water dynamics that led to the proposal of the involvement of collective intermolecular excitonic [...] Read more.
Our study of tunnelling in proton-coupled electron transfer (PCET) oxidation of ascorbate with hexacyanoferrate(III) follows the insights obtained from ultrafast 2D IR spectroscopy and theoretical studies of the vibrational water dynamics that led to the proposal of the involvement of collective intermolecular excitonic vibrational water dynamics in aqueous chemistry. To test the proposal, the hydrogen tunnelling modulation observed in the PCET reaction studied in the presence of low concentrations of various partial hydrophobic solutes in the water reaction system has been analyzed in terms of the proposed involvement of the collective intermolecular vibrational water dynamics in activation process in the case. The strongly linear correlation between common tunnelling signatures, isotopic values of Arrhenius prefactor ratios ln AH/AD and isotopic differences in activation enthalpies ΔΔH‡ (H,D) observed in the process in fairly diluted water solutions containing various partial hydrophobic solutes (such as dioxane, acetonitrile, ethanol, and quaternary ammonium ions) points to the common physical origin of the phenomenon in all the cases. It is suggested that the phenomenon can be rooted in an interplay of delocalized collective intermolecular vibrational dynamics of water correlated with vibrations of the coupled transition configuration, where the donor-acceptor oscillations, the motions being to some degree along the reaction coordinate, lead to modulation of hydrogen tunnelling in the reaction. Full article
(This article belongs to the Special Issue Isotope Effects 2019)
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15 pages, 2646 KiB  
Article
Intramolecular Hydrogen Bonds in Normal and Sterically Compressed o-Hydroxy Aromatic Aldehydes. Isotope Effects on Chemical Shifts and Hydrogen Bond Strength
by Poul Erik Hansen, Fadhil S. Kamounah, Bahjat A. Saeed, Mark J. MacLachlan and Jens Spanget-Larsen
Molecules 2019, 24(24), 4533; https://doi.org/10.3390/molecules24244533 - 11 Dec 2019
Cited by 14 | Viewed by 3478
Abstract
A number of o-hydroxy aromatic aldehydes have been synthesized to illustrate the effect of steric compression and O···O distances on the intramolecular hydrogen bond and the hydrogen bond energies. Hydrogen bond energies have been calculated using the ‘hb and out’ method using [...] Read more.
A number of o-hydroxy aromatic aldehydes have been synthesized to illustrate the effect of steric compression and O···O distances on the intramolecular hydrogen bond and the hydrogen bond energies. Hydrogen bond energies have been calculated using the ‘hb and out’ method using either the MP2 method or the B3LYP functional with the basis set 6-311++G(d,p). However, several compounds cannot be treated this way. Hydrogen bond energies are also determined using electron densities at bond critical points and these results are in good agreement with the results of the ‘hb and out’ model. Two-bond deuterium isotope effects on 13C chemical shifts are suggested as an experimental way to obtain information on hydrogen bond energies as they easily can be measured. Isotope effects on aldehyde proton chemical shifts have also been measured. The former show very good correlation with the hydrogen bond energies and the latter are related to short O···O distances. Short O···O distances can be obtained as the result of short C=C bond lengths, conjugative effects, and steric compression of the aldehyde group. Short O···O distances are in general related to high hydrogen bond energies in these intramolecularly hydrogen-bonded systems of resonance assisted hydrogen bond (RAHB) type. Full article
(This article belongs to the Special Issue Isotope Effects 2019)
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7 pages, 590 KiB  
Article
Path Integral Calculation of the Hydrogen/Deuterium Kinetic Isotope Effect in Monoamine Oxidase A-Catalyzed Decomposition of Benzylamine
by Mateusz Z. Brela, Alja Prah, Marek Boczar, Jernej Stare and Janez Mavri
Molecules 2019, 24(23), 4359; https://doi.org/10.3390/molecules24234359 - 28 Nov 2019
Cited by 9 | Viewed by 2507
Abstract
Monoamine oxidase A (MAO A) is a well-known enzyme responsible for the oxidative deamination of several important monoaminergic neurotransmitters. The rate-limiting step of amine decomposition is hydride anion transfer from the substrate α–CH2 group to the N5 atom of the flavin cofactor moiety. [...] Read more.
Monoamine oxidase A (MAO A) is a well-known enzyme responsible for the oxidative deamination of several important monoaminergic neurotransmitters. The rate-limiting step of amine decomposition is hydride anion transfer from the substrate α–CH2 group to the N5 atom of the flavin cofactor moiety. In this work, we focus on MAO A-catalyzed benzylamine decomposition in order to elucidate nuclear quantum effects through the calculation of the hydrogen/deuterium (H/D) kinetic isotope effect. The rate-limiting step of the reaction was simulated using a multiscale approach at the empirical valence bond (EVB) level. We applied path integral quantization using the quantum classical path method (QCP) for the substrate benzylamine as well as the MAO cofactor flavin adenine dinucleotide. The calculated H/D kinetic isotope effect of 6.5 ± 1.4 is in reasonable agreement with the available experimental values. Full article
(This article belongs to the Special Issue Isotope Effects 2019)
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Review

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18 pages, 2351 KiB  
Review
Inverse Solvent Isotope Effects in Enzyme-Catalyzed Reactions
by Patrick L. Fernandez and Andrew S. Murkin
Molecules 2020, 25(8), 1933; https://doi.org/10.3390/molecules25081933 - 21 Apr 2020
Cited by 21 | Viewed by 3954
Abstract
Solvent isotope effects have long been used as a mechanistic tool for determining enzyme mechanisms. Most commonly, macroscopic rate constants such as kcat and kcat/Km are found to decrease when the reaction is performed in D2O [...] Read more.
Solvent isotope effects have long been used as a mechanistic tool for determining enzyme mechanisms. Most commonly, macroscopic rate constants such as kcat and kcat/Km are found to decrease when the reaction is performed in D2O for a variety of reasons including the transfer of protons. Under certain circumstances, these constants are found to increase, in what is termed an inverse solvent kinetic isotope effect (SKIE), which can be a diagnostic mechanistic feature. Generally, these phenomena can be attributed to an inverse solvent equilibrium isotope effect on a rapid equilibrium preceding the rate-limiting step(s). This review surveys inverse SKIEs in enzyme-catalyzed reactions by assessing their underlying origins in common mechanistic themes. Case studies for each category are presented, and the mechanistic implications are put into context. It is hoped that readers may find the illustrative examples valuable in planning and interpreting solvent isotope effect experiments. Full article
(This article belongs to the Special Issue Isotope Effects 2019)
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16 pages, 2725 KiB  
Review
Kinetic Isotope Effects and Hydrogen Tunnelling in PCET Oxidations of Ascorbate: New Insights into Aqueous Chemistry?
by Ana Karković Marković, Cvijeta Jakobušić Brala, Viktor Pilepić and Stanko Uršić
Molecules 2020, 25(6), 1443; https://doi.org/10.3390/molecules25061443 - 23 Mar 2020
Cited by 6 | Viewed by 3756
Abstract
Recent experimental studies of kinetic isotope effects (KIE-s) and hydrogen tunnelling comprising three proton-coupled electron transfer (PCET) oxidations of ascorbate monoanion, (a) in aqueous reaction solutions, (b) in the mixed water-organic cosolvent systems, (c) in aqueous solutions of various salts and (d) in [...] Read more.
Recent experimental studies of kinetic isotope effects (KIE-s) and hydrogen tunnelling comprising three proton-coupled electron transfer (PCET) oxidations of ascorbate monoanion, (a) in aqueous reaction solutions, (b) in the mixed water-organic cosolvent systems, (c) in aqueous solutions of various salts and (d) in fairly diluted aqueous solutions of the various partial hydrophobes are reviewed. A number of new insights into the wealth of the kinetic isotope phenomena in the PCET reactions have been obtained. The modulation of KIE-s and hydrogen tunnelling observed when partially hydrophobic solutes are added into water reaction solution, in the case of fairly diluted solutions is revealed as the strong linear correlation of the isotopic ratios of the Arrhenius prefactors Ah/Ad and the isotopic differences in activation energies ΔEa (D,H). The observation has been proposed to be a signature of the involvement of the collective intermolecular excitonic vibrational dynamics of water in activation processes and aqueous chemistry. Full article
(This article belongs to the Special Issue Isotope Effects 2019)
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