Role of symmetry in the tunneling of the proton in double-minimum potentials

Vega, J. R. De La

doi:10.1021/ar00078a004

Cited by 81 publications

(11 citation statements)

References 12 publications

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“…The C

symmetry structure is thermodynamically preferable, which could be related to cooperativity of the intramolecular non-covalent forces. The OH groups position in Naphthazarin is according to our expectations and in agreement with previous findings reported in the literature [ 34 , 40 , 52 ]. Next, we have studied the thermodynamics of the reaction path of single (asynchronous) proton transfer based on DFT and MP2 methods.…”

Section: Resultssupporting

confidence: 93%

Non-Covalent Forces in Naphthazarin—Cooperativity or Competition in the Light of Theoretical Approaches

Jezierska

Błaziak

Klahm

et al. 2021

IJMS

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Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

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“…The C

Section: Resultssupporting

confidence: 93%

Non-Covalent Forces in Naphthazarin—Cooperativity or Competition in the Light of Theoretical Approaches

Jezierska

Błaziak

Klahm

et al. 2021

IJMS

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“…The main feature of malonaldehyde, making it particularly attractive for theoretical chemists, is the effective double-well-like potentiale nergy surfacee xperiencedb yt he proton between the oxygen atoms.F igure 1a schematically depicts the doublewell assuming just as ingle variable, termed q,w hich describes the proton transfer qualitatively;t his variablec an be an intrinsic reaction coordinateo ra ny other suitably designed variable. [70] Although just asingle variable is enough for aqualitative discussion, it is known from the studies conducted in the mideighties that more than as ingle variable is required to construct an accurate quantitative model of the multi-dimensional energy surface. [71,72] Usually within the BO paradigm the two local minima, with C s symmetry,o nt his effective energy curve are assumedt ob et he representatives of the two stable conformers (hereafter denoted structure 1).…”

Section: Resultsmentioning

confidence: 99%

Muon‐Substituted Malonaldehyde: Transforming a Transition State into a Stable Structure by Isotope Substitution

Goli

Shahbazian

2016

Chemistry A European J

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Isotopes ubstitutionsa re usually conceived to play am arginal role on the structure and bondingp attern of molecules. However,arecent study [Angew.C hem. Int. Ed. 2014, 53,1 3706-13709; Angew.C hem. 2014, 126,1 3925-13929]f urther demonstrates that upon replacing ap roton with ap ositively charged muon, as the lightest radioisotope of hydrogen, radical changes in the nature of the structure and bonding of certains peciesm ay take place. The present report is ap rimary attemptt oi ntroduce another example of structural transformation on the basis of the malonaldehyde system.A ccordingly,u pon replacing the protonb etween the two oxygen atoms of malonaldehydew ith the positively charged muon as erious structuralt ransformationi so bserved. By using the ab initio nuclear-electronic orbitaln onBorn-Oppenheimer procedure, the nuclear configuration of the muon-substituted speciesi sd erived. The resulting nuclear configuration is much more similart ot he transition state of the proton transferi nm alonaldehyde rather than to the stable configuration of malonaldehyde. The comparison of the "atoms in molecules" (AIM) structureoft he muon-substituted malonaldehyde and the AIM structureo ft he stable and the transition-state configurations of malonaldehyde also unequivocally demonstrates substantial similarities of the muon-substituted malonaldehydet ot he transition state.

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“…This equivalence and the short 2.5-Å O•••O distance observed for the Y16-Y57 hydrogen bond in the 1.25-Å resolution D40N-phenol (pK a = 10) X-ray structure (8) are physical features that can favor formation of a single-well hydrogen bond in which negative charge and the bridging proton would be equally shared and delocalized between the interacting groups (39,40). Alternatively, interactions with the anisotropic distribution of charges and dipoles within the surrounding heterogeneous protein matrix might result in a double-well potential energy surface for this hydrogen bond despite closely matched proton affinities (41)(42)(43), with negative charge discretely localized on either Y16 or Y57.…”

Section: Measuring the Electrostatic Field Changes From Proton Transfersmentioning

confidence: 99%

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

Sigala¹,

Fafarman²,

Schwans³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated sitespecific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol-Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations.computational modeling | enzyme catalysis | protein electrostatics | protein semisynthesis | active site environment H ydrogen bond networks are ubiquitous structural features within proteins, and they play key roles linking secondary and tertiary structural elements and spanning protein-protein interfaces. Such networks are especially common within enzyme active sites, where they position protein and substrate groups for catalysis, stabilize charge rearrangements during chemical transformations, and mediate proton transfers (1). Despite the prevalence and critical structural and functional roles of hydrogen bond networks, incisive dissection of their physical properties within the idiosyncratic interior of folded proteins remains difficult.Hydrogen-bonded protons are not observed in the vast majority of protein X-ray structures due to the low X-ray scattering power of hydrogen atoms (2). Thus, the presence of hydrogen bond networks is typically inferred from the proximity and orientation of hydrogen bond donor and acceptor groups within refined protein structural models. The inherent inability of most X-ray diffraction studies to monitor proton positions imposes additional challenges for dissecting the physical features that influence the equilibrium protonation states of specific residues along a hydrogen-bonded proton transfer network. Furthermore, it remains extremely challenging t...

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Role of symmetry in the tunneling of the proton in double-minimum potentials

Cited by 81 publications

References 12 publications

Non-Covalent Forces in Naphthazarin—Cooperativity or Competition in the Light of Theoretical Approaches

Non-Covalent Forces in Naphthazarin—Cooperativity or Competition in the Light of Theoretical Approaches

Muon‐Substituted Malonaldehyde: Transforming a Transition State into a Stable Structure by Isotope Substitution

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

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