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Orabi EA, Faraldo-Gómez JD. New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. J Chem Theory Comput 2020; 16:5105-5126. [PMID: 32615034 DOI: 10.1021/acs.jctc.0c00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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Mazack MJM, Gao J. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization. J Chem Phys 2015; 140:204501. [PMID: 24880295 DOI: 10.1063/1.4875922] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.
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Affiliation(s)
- Michael J M Mazack
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431, USA
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431, USA
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McGrath MJ, Kuo IFW, Siepmann JI. Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional. Phys Chem Chem Phys 2011; 13:19943-50. [DOI: 10.1039/c1cp21890e] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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He Y, Müller HB, Quack M, Suhm MA. High Resolution FTIR and Diode Laser Supersonic Jet Spectroscopy of the N = 2 HF Stretching Polyad in (HF)2 and (HFDF): Hydrogen Bond Switching and Predissociation Dynamics. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zpch.2007.221.11-12.1581] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report Fourier transform infrared (FTIR) and high resolution diode laser spectra (∼ 1MHz instrumental bandwidth) obtained in cooled absorption cells as well as in a supersonic jet expansion for the N = 2 polyad region of the HF-stretching vibrations of (HF)2, HFDF and DFHF. Three vibrational transitions have been observed for (HF)2 and two for both monodeuterated isotopomers. For (HF)2 we have identified and analysed the observed transitions of the polyad member 22 of the type Δ K
a = 0 and Δ K
a = ± 1 up to rotational sublevel Δ K
a = 3. Band centers as well as rotational constants of all four K
a states have been determined. The tunneling splittings due to hydrogen bond switching for these four K
a states have been investigated, with the Δ K
a = 0 up to Δ K
a = 2 sublevels having tunneling symmetry Γ
vt = A
+ for the lower tunneling states, and switching periods ranging from 158ps for K
a = 0 to 1.35ns for K
a = 2. A tunneling level inversion is found at Δ K
a = 3, leading to a symmetry Γ
vt = B
+ for the lower tunneling state of this K
a-sublevel. The vibrational assignment of the measured spectra of (HF)2 was established by comparison with the monodeuterated isotopomers HFDF and DFHF. For HFDF we have identified and analysed five subbands between 7600cm-1 and 7730cm-1. We have determined the spectroscopic constants of the rotational levels Δ K
a = 0 and Δ K
a = 1 for the vibrationally excited state and of the levels of Δ K
a = 1 and Δ K
a = 2 of the ground state, the latter from combination differences. From the measurements in a supersonic jet expansion we determined the predissociation line width of the N = 22, K
a = 1 to be about 120MHz for the Γ
vt = A
+ tunneling state of (HF)2 and about 90MHz for Γ
vt = B
+. For the Δ K
a = 0 level of N = 22 we obtained predissociation line widths ranging around 100MHz, similar to those of the Δ K
a = 1 level. In the case of HFDF, the predissociation line width of Δ K
a = 1 is about 80MHz. Predissociation lifetimes for these levels with the unbonded HF stretching excited thus are in the range of about 1 to 2ns. The predissociation width in the N = 21 level is uncertain by about a factor three with lg(Δν/MHz) = (3 ± 0.5) and in N = 23 it is about 600MHz corresponding to rounded lifetimes of 0.1ns and 0.3ns when the bonded HF stretching is excited thereby demonstrating strongly mode selective predissociation rates in the N = 2 polyad. Under thermal equilibrium conditions we derived the pressure broadening coefficient for (HF)2 (γ = (6 ± 1) × 10-4cm-1/mbar in the wavenumber range between 7713cm-1 and 7721cm-1 for total gas pressures between 10 and 60mbar, all values as full widths half maximum). For absolute frequency calibrations we have remeasured the first overtone transitions of the monomer HF with much improved precision between P(5) (7515.80151cm-1) and R(7) (7966.22188cm-1).
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Fernandez-Alonso F, McLain SE, Taylor JW, Bermejo FJ, Bustinduy I, Ruiz-Martín MD, Turner JFC. Correlated atomic motions in liquid deuterium fluoride studied by coherent quasielastic neutron scattering. J Chem Phys 2007; 126:234509. [PMID: 17600427 DOI: 10.1063/1.2743021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The collective dynamics of liquid deuterium fluoride are studied by means of high-resolution quasielastic and inelastic neutron scattering over a range of four decades in energy transfer. The spectra show a low-energy coherent quasielastic component which arises from correlated stochastic motions as well as a broad inelastic feature originating from overdamped density oscillations. While these results are at variance with previous works which report on the presence of propagating collective modes, they are fully consistent with neutron diffraction, nuclear magnetic resonance, and infrared/Raman experiments on this prototypical hydrogen-bonded fluid.
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Affiliation(s)
- F Fernandez-Alonso
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom.
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Fernandez-Alonso F, Bermejo FJ, McLain SE, Turner JFC, Molaison JJ, Herwig KW. Observation of fractional Stokes-Einstein behavior in the simplest hydrogen-bonded liquid. PHYSICAL REVIEW LETTERS 2007; 98:077801. [PMID: 17359062 DOI: 10.1103/physrevlett.98.077801] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Indexed: 05/14/2023]
Abstract
Quasielastic neutron scattering has been used to investigate the single-particle dynamics of hydrogen fluoride across its entire liquid range at ambient pressure. For T>230 K, translational diffusion obeys the celebrated Stokes-Einstein relation, in agreement with nuclear magnetic resonance studies. At lower temperatures, we find significant deviations from the above behavior in the form of a power law with exponent xi=-0.71+/-0.05. More striking than the above is a complete breakdown of the Debye-Stokes-Einstein relation for rotational diffusion. Our findings provide the first experimental verification of fractional Stokes-Einstein behavior in a hydrogen-bonded liquid, in agreement with recent computer simulations [S. R. Becker, Phys. Rev. Lett. 97, 055901 (2006)10.1103/PhysRevLett.97.055901].
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Affiliation(s)
- F Fernandez-Alonso
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, United Kingdom.
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Goldman N, Fried LE. First principles simulation of a superionic phase of hydrogen fluoride (HF) at high pressures and temperatures. J Chem Phys 2006; 125:44501. [PMID: 16942150 DOI: 10.1063/1.2220036] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have conducted ab initio molecular dynamics simulations of hydrogen fluoride (HF) at pressures of 5-66 GPa along the 900 K isotherm. We predict a superionic phase at 33 GPa, where the fluorine atoms are fixed in a bcc lattice while the hydrogen atoms diffuse rapidly with a diffusion constant between 2 x 10(-5) and 5 x 10(-5)cm(2)s. We find that a transformation from asymmetric to symmetric hydrogen bonding occurs in HF at 66 GPa and 900 K. With superionic HF we have discovered a model system where symmetric hydrogen bonding occurs at experimentally achievable conditions. Given previous results on superionic H(2)O [Goldman et al., Phys. Rev. Lett. 94, 217801 (2005)] and NH(3) [Cavazzoni et al., Science 283, 44 (1999)], we conclude that high P, T superionic phases of electronegative element hydrides could be common.
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Affiliation(s)
- Nir Goldman
- Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, California 94550, USA.
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Chen L, Groß T, Lüdemann HD. T,p-Dependence of Self-Diffusion in the Lower N-methylsubstituted Amides. ACTA ACUST UNITED AC 2000. [DOI: 10.1524/zpch.2000.214.2.239] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Self-diffusion coefficients
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Buchhauser J, Groß T, Karger N, Lüdemann HD. Self-diffusion in CD4 and ND3: With notes on the dynamic isotope effect in liquids. J Chem Phys 1999. [DOI: 10.1063/1.477898] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Groß T, Buchhauser J, Lüdemann HD. Self-diffusion in fluid carbon dioxide at high pressures. J Chem Phys 1998. [DOI: 10.1063/1.477055] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Karger N, Lüdemann HD. Density dependence of self-diffusion in liquid hydrogen fluoride. J Chem Phys 1998. [DOI: 10.1063/1.476925] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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FTIR spectroscopy of hydrogen fluoride clusters in synchronously pulsed supersonic jets. Isotopic isolation, substitution and 3-d condensation. Chem Phys Lett 1997. [DOI: 10.1016/s0009-2614(97)00203-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Röthlisberger U, Parrinello M. Ab initio molecular dynamics simulation of liquid hydrogen fluoride. J Chem Phys 1997. [DOI: 10.1063/1.473988] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Karger N, Wappmann S, Shaker-Gaafar N, Lüdemann HD. The p, T - dependence of self diffusion in liquid 1-, 2- and 3-pentanol. J Mol Liq 1995. [DOI: 10.1016/0167-7322(95)00810-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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