Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: Proton transfer in triosephosphate isomerase

2006 ◽  
Vol 124 (12) ◽  
pp. 124516 ◽  
Author(s):  
Mingliang Wang ◽  
Zhenyu Lu ◽  
Weitao Yang
Keyword(s):  
Proton Transfer ◽  
Triosephosphate Isomerase ◽  
Reaction Path ◽  
Quantum Effects ◽  
Nuclear Quantum Effects

scholarly journals Proton transfer in guanine–cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations

2018 ◽  
Vol 212 ◽  
pp. 331-344 ◽  
Author(s):  
Radek Pohl ◽  
Ondřej Socha ◽  
Petr Slavíček ◽  
Michal Šála ◽  
Paul Hodgkinson ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Proton Transfer ◽  
Base Pair ◽  
Quantum Effects ◽  
Isotope Shifts ◽  
Unique Possibility ◽  
Nuclear Quantum Effects ◽  
Hydrogen Bonded

NMR isotope shifts provide a unique possibility to study the nuclear quantum effects of hydrogen-bonded nucleobases.

scholarly journals Significance of nuclear quantum effects in hydrogen bonded molecular chains

2021 ◽  
Author(s):  
Ales Cahlik ◽  
Jack Hellerstedt ◽  
Jesus Mendieta-Moreno ◽  
Martin Švec ◽  
Vijai Santhini ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Mechanical Stability ◽  
Dominant Role ◽  
Zero Point ◽  
Quantum Effects ◽  
Molecular Networks ◽  
Hydrogen Bonded Systems ◽  
Low Dimensional ◽  
Nuclear Quantum Effects ◽  
Hydrogen Bonded

Abstract In hydrogen bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemical processes. Presently, direct observation of the influence of nuclear quantum effects on the strength of hydrogen bonds with resulting structural and electronic implications remains elusive, leaving opportunities for deeper understanding to harness their fascinating properties. We studied hydrogen-bonded one-dimensional quinonediimine molecular networks which may adopt two isomeric electronic configurations via proton transfer. Herein, we demonstrate that concerted proton transfer promotes a delocalization of π-electrons along the molecular chain, which enhances the cohesive energy between molecular units, increasing the mechanical stability of the chain and giving rise to new electronic in-gap states localized at the ends. These findings demonstrate the identification of a new class of isomeric hydrogen bonded molecular systems where nuclear quantum effects play a dominant role in establishing their chemical and physical properties. We anticipate that this work will open new research directions towards the control of mechanical and electronic properties of low-dimensional molecular materials via concerted proton tunneling.

scholarly journals Collective proton transfer in ordinary ice: local environments, temperature dependence and deuteration effects

2017 ◽  
Vol 19 (4) ◽  
pp. 2623-2635 ◽  
Author(s):  
Christof Drechsel-Grau ◽  
Dominik Marx
Keyword(s):  
Low Temperature ◽  
Proton Transfer ◽  
Temperature Dependence ◽  
Quantum Effects ◽  
Local Environments ◽  
Nuclear Quantum Effects

Ordinary ice at low temperature: what about collective nuclear quantum effects in its chiral six rings?

scholarly journals Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5642
Author(s):  
Karol Kułacz ◽  
Michał Pocheć ◽  
Aneta Jezierska ◽  
Jarosław J. Panek
Keyword(s):  
Perturbation Theory ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Gas Phase ◽  
Quantum Effects ◽  
Broad Absorption ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen ◽  
Nuclear Quantum Effects

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller–Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers’ stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm−1–1700 cm−1 and 2300 cm−1–3400 cm−1 in the gas phase and 600 cm−1–1800 cm−1 and 2200 cm−1–3400 cm−1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm−1–1700 cm−1 and 2300 cm−1–3300 cm−1 for the gas phase and one broad absorption region in the solid state between 700 cm−1 and 3100 cm−1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.

scholarly journals Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

2021 ◽  
Vol 22 (10) ◽  
pp. 5220
Author(s):  
Jarosław J. Panek ◽  
Joanna Zasada ◽  
Bartłomiej M. Szyja ◽  
Beata Kizior ◽  
Aneta Jezierska
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Quantum Effects ◽  
Potential Of Mean Force ◽  
Probability Density Distribution ◽  
Donor And Acceptor ◽  
Nuclear Quantum Effects ◽  
Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

scholarly journals Dynamical strengthening of covalent and non-covalent molecular interactions by nuclear quantum effects at finite temperature

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Huziel E. Sauceda ◽  
Valentin Vassilev-Galindo ◽  
Stefan Chmiela ◽  
Klaus-Robert Müller ◽  
Alexandre Tkatchenko
Keyword(s):  
Finite Temperature ◽  
Electrostatic Interactions ◽  
Zero Point ◽  
Quantum Effects ◽  
Van Der Waals Interactions ◽  
Interatomic Distances ◽  
Point Energy ◽  
Molecular Bond ◽  
Energy Surfaces ◽  
Nuclear Quantum Effects

AbstractNuclear quantum effects (NQE) tend to generate delocalized molecular dynamics due to the inclusion of the zero point energy and its coupling with the anharmonicities in interatomic interactions. Here, we present evidence that NQE often enhance electronic interactions and, in turn, can result in dynamical molecular stabilization at finite temperature. The underlying physical mechanism promoted by NQE depends on the particular interaction under consideration. First, the effective reduction of interatomic distances between functional groups within a molecule can enhance the n → π* interaction by increasing the overlap between molecular orbitals or by strengthening electrostatic interactions between neighboring charge densities. Second, NQE can localize methyl rotors by temporarily changing molecular bond orders and leading to the emergence of localized transient rotor states. Third, for noncovalent van der Waals interactions the strengthening comes from the increase of the polarizability given the expanded average interatomic distances induced by NQE. The implications of these boosted interactions include counterintuitive hydroxyl–hydroxyl bonding, hindered methyl rotor dynamics, and molecular stiffening which generates smoother free-energy surfaces. Our findings yield new insights into the versatile role of nuclear quantum fluctuations in molecules and materials.

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