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

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.

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Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

The Journal of Chemical Physics ◽

10.1063/1.4941091 ◽

2016 ◽

Vol 144 (5) ◽

pp. 054111 ◽

Cited By ~ 34

Author(s):

V. Kapil ◽

J. VandeVondele ◽

M. Ceriotti

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Density Functional ◽

Low Cost ◽

Quantum Effects ◽

Imaginary Time ◽

Functional Theory ◽

Nuclear Quantum Effects ◽

Wavefunction Methods

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Molecular dynamics with constrained nuclear electronic orbital density functional theory: Accurate vibrational spectra from efficient incorporation of nuclear quantum effects

10.26434/chemrxiv-2021-w44b8 ◽

2021 ◽

Author(s):

Xi Xu ◽

Zehua Chen ◽

Yang Yang

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Vibrational Spectra ◽

Density Functional ◽

Molecular Simulations ◽

Quantum Effects ◽

Functional Theory ◽

Chemical And Biological Systems ◽

Nuclear Quantum Effects ◽

Orbital Density

Nuclear quantum effects play a crucial role in many chemical and biological systems involving hydrogen atoms yet are difficult to include in practical molecular simulations. In this Letter, we combine our recently developed methods of constrained nuclear-electronic orbital density functional theory (cNEO-DFT) and constrained minimized energy surface molecular dynamics (CMES-MD) to create a new method for accurately and efficiently describing nuclear quantum effects in molecular simulations. Using this new method, dubbed cNEO-MD, the vibrational spectra of a set of small molecules are calculated and compared with those from conventional ab initio molecular dynamics (AIMD) as well as from experiments. With the same formal scaling, cNEO-MD greatly outperforms AIMD in describing the vibrational modes with significant hydrogen motion characters, demonstrating the promise of cNEO-MD for simulating chemical and biological systems with significant nuclear quantum effects.

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Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

The Journal of Chemical Physics ◽

10.1063/1.4941093 ◽

2016 ◽

Vol 144 (5) ◽

pp. 054112 ◽

Cited By ~ 55

Author(s):

Ondrej Marsalek ◽

Thomas E. Markland

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Ab Initio ◽

Density Functional ◽

Quantum Effects ◽

Ab Initio Molecular Dynamics ◽

Functional Theory ◽

Ring Polymer ◽

Nuclear Quantum Effects

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Resonance-assisted stabilisation of hydrogen bonds probed by NMR spectroscopy and path integral molecular dynamics

Chemical Communications ◽

10.1039/c5cc05199a ◽

2015 ◽

Vol 51 (73) ◽

pp. 13986-13989 ◽

Cited By ~ 12

Author(s):

M. Dračínský ◽

L. Čechová ◽

P. Hodgkinson ◽

E. Procházková ◽

Z. Janeba

Keyword(s):

Molecular Dynamics ◽

Nmr Spectroscopy ◽

Hydrogen Bonds ◽

Path Integral ◽

Quantum Effects ◽

Intramolecular Hydrogen Bonds ◽

Intramolecular Hydrogen ◽

Nuclear Quantum Effects

Nuclear quantum effects are shown to be important for resonance stabilisation of intramolecular hydrogen bonds.

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Classical Ab Initio Molecular Dynamics Run at an Elevated Temperature is Not a Good Model for the Nuclear Quantum Effects in Water at Ambient Temperature

10.33774/chemrxiv-2021-c603x ◽

2021 ◽

Author(s):

Chenghan Li ◽

Francesco Paesani ◽

Gregory A. Voth

Keyword(s):

Molecular Dynamics ◽

Elevated Temperature ◽

Ambient Temperature ◽

Ab Initio ◽

Density Functional ◽

Quantum Effects ◽

Ab Initio Molecular Dynamics ◽

Higher Temperature ◽

Three Body ◽

Nuclear Quantum Effects

It is a common practice in ab initio molecular dynamics (AIMD) simulations of water to use an elevated temperature to overcome the over-structuring and slow diffusion predicted by most current density functional theory (DFT) models. The simulation results obtained in this distinct thermodynamic ensemble are then compared with experimental data at ambient temperature based on the rationale that a higher temperature effectively recovers nuclear quantum effects (NQEs) that are missing in the classical AIMD simulations. In this work, we systematically examine the foundation of this assumption for several DFT models as well as for the many-body MB-pol model. We find for the cases studied that a higher temperature does not correctly mimic NQEs at room temperature, which is especially manifest in significantly different three-body correlations as well as dynamics. In many of these cases, the effects of NQEs are exactly the opposite of the effects of carrying out the simulations at an elevated temperature.

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Structure-Property Relationship in Selected Naphtho- and Anthra-Quinone Derivatives on the Basis of Density Functional Theory and Car–Parrinello Molecular Dynamics

Symmetry ◽

10.3390/sym13040564 ◽

2021 ◽

Vol 13 (4) ◽

pp. 564

Author(s):

Beata Kizior ◽

Jarosław J. Panek ◽

Bartłomiej M. Szyja ◽

Aneta Jezierska

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Electronic Structure ◽

Hydrogen Bonds ◽

Proton Transfer ◽

Density Functional ◽

Molecular Assembly ◽

Structure Property ◽

Functional Theory ◽

Td Dft

Intra- and inter-molecular interactions were studied in 2,3-dichloro-5,8-dihydroxy-1,4-naphthoquinone and 1,4-dihydroxy-anthraquinone to shed more light on the molecular assembly phenomena. The electronic ground and excited states features of the compounds were investigated to find structure-property dependencies. The theoretical study was carried out on the basis of Density Functional Theory (DFT), its Time-Dependent (TD-DFT) extension, and using Car–Parrinello Molecular Dynamics (CPMD). In order to show how the environmental effects modulate the physico-chemical properties, the simulations were performed in vacuo, with the solvent reaction field (Polarizable Continuum Model (PCM) and water as a solvent) and crystalline phase. The intramolecular hydrogen bonds and the bridged proton dynamics were analyzed in detail. The aromatic rings and electronic structure changes were estimated using the Harmonic Oscillator Model of Aromaticity (HOMA) and Atoms in Molecules (AIM) theory. The Symmetry-Adapted Perturbation Theory (SAPT) was employed for interaction energy decomposition in the studied dimers and trimers. It was found that the presence of a polar solvent decreased the energy barrier for the bridged proton transfer. However, it did not significantly affect the aromaticity and electronic structure. The SAPT results showed that the mutual polarization of the monomers in the dimer was weak and that the dispersion was responsible for most of the intermolecular attraction. The intermolecular hydrogen bonds seem to be much weaker than the intramolecular bridges. The TD-DFT results confirmed that the electronic excitations do not play any significant role in the intramolecular proton transfer. The CPMD results indicated that the protons are very labile in the hydrogen bridges. Short proton transfer and proton-sharing events were observed, and a correlation between them in the twin bridges was noticed, especially for the first investigated compound.

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Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics simulations of hydrogen transfer reactions in enzymes

The Journal of Chemical Physics ◽

10.1063/1.1356441 ◽

2001 ◽

Vol 114 (15) ◽

pp. 6925-6936 ◽

Cited By ~ 81

Author(s):

Salomon R. Billeter ◽

Simon P. Webb ◽

Tzvetelin Iordanov ◽

Pratul K. Agarwal ◽

Sharon Hammes-Schiffer

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Hydrogen Transfer ◽

Hybrid Approach ◽

Quantum Effects ◽

Transfer Reactions ◽

Dynamics Simulations ◽

Nuclear Quantum Effects ◽

Hydrogen Transfer Reactions

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On-the-Fly Ring-Polymer Molecular Dynamics Calculations of the Dissociative Photodetachment Process of the Oxalate Anion

Molecules ◽

10.3390/molecules26237250 ◽

2021 ◽

Vol 26 (23) ◽

pp. 7250

Author(s):

Yukinobu Takahashi ◽

Yu Hashimoto ◽

Kohei Saito ◽

Toshiyuki Takayanagi

Keyword(s):

Molecular Dynamics ◽

Potential Energy ◽

Quantum Effects ◽

Experimental Spectrum ◽

Computational Time ◽

Oxalate Anion ◽

Dissociative Photodetachment ◽

Ring Polymer ◽

Ring Polymer Molecular Dynamics ◽

Nuclear Quantum Effects

The dissociative photodetachment dynamics of the oxalate anion, C2O4H− + hν → CO2 + HOCO + e−, were theoretically studied using the on-the-fly path-integral and ring-polymer molecular dynamics methods, which can account for nuclear quantum effects at the density-functional theory level in order to compare with the recent experimental study using photoelectron–photofragment coincidence spectroscopy. To reduce computational time, the force acting on each bead of ring-polymer was approximately calculated from the first and second derivatives of the potential energy at the centroid position of the nuclei beads. We find that the calculated photoelectron spectrum qualitatively reproduces the experimental spectrum and that nuclear quantum effects are playing a role in determining spectral widths. The calculated coincidence spectrum is found to reasonably reproduce the experimental spectrum, indicating that a relatively large energy is partitioned into the relative kinetic energy between the CO2 and HOCO fragments. This is because photodetachment of the parent anion leads to Franck–Condon transition to the repulsive region of the neutral potential energy surface. We also find that the dissociation dynamics are slightly different between the two isomers of the C2O4H− anion with closed- and open-form structures.

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