1
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Barclay AJ, McKellar ARW, Moazzen-Ahmadi N. Infrared spectra of partially deuterated water dimers in the fundamental O-D stretch region. J Chem Phys 2024; 161:024301. [PMID: 38973761 DOI: 10.1063/5.0218733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/21/2024] [Indexed: 07/09/2024] Open
Abstract
Spectra of mixed H/D water dimers are studied in the mid-infrared region of the O-D stretch fundamental (2630-2800 cm-1) using a pulsed supersonic slit jet and a tunable optical parametric oscillator infrared source. Over 30 bands, belonging to nine of the ten possible isotopologues (only H2O-HOD is missed), are observed and analyzed. The implications for excited state tunneling splittings, lifetime effects, and vibrational shifts are discussed. These are the first significant new experimental results on (gas phase) mixed water dimers in over 25 years, and they are valuable for testing water dimer theoretical calculations, a field which continues to be of lively current interest.
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Affiliation(s)
- A J Barclay
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
| | - A R W McKellar
- National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - N Moazzen-Ahmadi
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
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2
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Eraković M, Cvitaš MT. Tunneling splittings in the vibrationally excited states of water trimer. Phys Chem Chem Phys 2024; 26:12965-12981. [PMID: 38634688 DOI: 10.1039/d4cp00013g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Tunneling splitting (TS) patterns in vibrationally excited states of the water trimer are calculated, taking into account six tunneling pathways that describe the flips of free OH bonds and five bifurcation mechanisms that break and reform hydrogen bonds in the trimer ring. A tunneling matrix (TM) model is used to derive the energy shifts due to tunneling in terms of the six distinct TM elements in symbolic form. TM elements are calculated using the recently-developed modified WKB (Wentzel-Kramers-Brillouin) method in full dimensionality. Convergence was achieved for the lowest six excited vibrational modes. Bifurcation widths of the pseudorotational quartets are shown to be of comparable size to the ground-state widths, obtained using instanton theory, or increased for some particular modes of vibration. The largest increase is obtained for the excited out-of-phase flip of two adjacent water monomers with free OH bonds pointing in opposite directions relative to the ring plane. Bifurcation widths in (D2O)3 are found to be two orders of magnitude smaller than in (H2O)3. Geometrical arguments were used to explain the order of states in some TS multiplets in vibrationally excited water trimers.
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Affiliation(s)
- Mihael Eraković
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Marko T Cvitaš
- Department of Physics, University of Zagreb Faculty of Science, Zagreb, Croatia.
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3
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Barclay AJ, McKellar ARW, Moazzen-Ahmadi N. Spectra of the D2O dimer in the O-D fundamental stretch region: The acceptor symmetric stretch fundamental and new combination bands. J Chem Phys 2024; 160:114314. [PMID: 38501472 DOI: 10.1063/5.0200892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
The O-D stretch fundamental region of the deuterated water dimer, (D2O)2, is further studied using a pulsed supersonic slit jet and a tunable optical parametric oscillator infrared source. The previously unobserved acceptor symmetric O-D stretch fundamental vibration is detected, with Ka = 0 ← 0 and 1 ← 0 sub-bands at about 2669 and 2674 cm-1, respectively. The analysis indicates that the various water dimer tunneling splittings generally decrease in the excited vibrational state, similar to the three other previously observed O-D stretch fundamentals. Two new (D2O)2 combination bands are observed, giving information on intermolecular vibrations in the excited O-D stretch states. The likely vibrational assignments for these and a previously observed combination band are discussed.
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Affiliation(s)
- A J Barclay
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
| | - A R W McKellar
- National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - N Moazzen-Ahmadi
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
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4
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Lwin E, Fischer TL, Suhm MA. Microhydration of Tertiary Amines: Robust Resonances in Red-Shifted Water. J Phys Chem Lett 2023; 14:10194-10199. [PMID: 37930195 PMCID: PMC10658632 DOI: 10.1021/acs.jpclett.3c02517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/29/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Tertiary amines are strong hydrogen bond acceptors. When a water molecule donates one of the OH groups, its in-phase stretching vibration wavenumber is decreased to such an extent that it comes close to the water bending overtone. This gives rise to anharmonic phenomena such as classical Fermi resonance, resonance with multiple-quantum dark states, or combination transitions with low-frequency intermolecular modes. These effects, which contribute to the spectral breadth of room-temperature hydrogen-bonded amine complexes, are disentangled by Fourier transform infrared spectroscopy in pulsed supersonic slit jet expansions. Monohydrates of the amines quinuclidine, N-methylpyrrolidine, N-methylpiperidine, and dimethylcyclohexylamine exhibit systematic mode coupling signatures. These suggest relatively fast energy flow out of the excited OH stretching fundamental into intra- and intermolecular degrees of freedom of the hydrogen-bonded water molecule. Trimeric complexes are spectroscopically separated from the amine monohydrates.
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Affiliation(s)
- Eaindra Lwin
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Taija L. Fischer
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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5
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Vogt E, Simkó I, Császár AG, Kjaergaard HG. Quantum Chemical Investigation of the Cold Water Dimer Spectrum in the First OH-Stretching Overtone Region Provides a New Interpretation. J Phys Chem A 2023; 127:9409-9418. [PMID: 37930939 DOI: 10.1021/acs.jpca.3c03705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Intramolecular vibrational transition wavenumbers and intensities were calculated in the fundamental HOH-bending, fundamental OH-stretching, first OH-stretching-HOH-bending combination, and first OH-stretching overtone (ΔvOH = 2) regions of the water dimer's spectrum. Furthermore, the rotational-vibrational spectrum was calculated in the ΔvOH = 2 region at 10 K, corresponding to the temperature of the existing jet-expansion experiments. The calculated spectrum was obtained by combining results from a full-dimensional (12D) vibrational and a reduced-dimensional vibrational-rotational-tunneling model. The ΔvOH = 2 spectral region is rich in features due to contributions from multiple vibrational-rotational-tunneling sub-bands. Origins of the experimental vibrational bands depend on the assignment of the observed sub-bands. Based on our calculations, we assign the observed sub-bands, and our reassignment leads to new values for the vibrational band origins of the free donor and antisymmetric acceptor OH-stretching first overtones of ∼7227 and ∼7238 cm-1, respectively. The observed bands with origins at 7192.34 and ∼7366 cm-1 are assigned to the symmetric acceptor OH-stretching first overtone and the OH-stretching combination of the donor, respectively.
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Affiliation(s)
- Emil Vogt
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø DK-2100, Denmark
| | - Irén Simkó
- Laboratory of Molecular Structure and Dynamics, Institute of Chemistry ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest H-1117, Hungary
- HUN-REN-ELTE Complex Chemical Systems Research Group, P.O. Box 32, Budapest 112 H-1518, Hungary
| | - Attila G Császár
- Laboratory of Molecular Structure and Dynamics, Institute of Chemistry ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest H-1117, Hungary
- HUN-REN-ELTE Complex Chemical Systems Research Group, P.O. Box 32, Budapest 112 H-1518, Hungary
| | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø DK-2100, Denmark
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6
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Wang XG, Carrington T. Computing excited OH stretch states of water dimer in 12D using contracted intermolecular and intramolecular basis functions. J Chem Phys 2023; 158:084107. [PMID: 36859104 DOI: 10.1063/5.0139586] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Due to the ubiquity and importance of water, water dimer has been intensively studied. Computing the (ro-)vibrational spectrum of water dimer is challenging. The potential has eight wells separated by low barriers, which makes harmonic approximations of limited utility. A variational approach is imperative, but difficult because there are 12 coupled vibrational coordinates. In this paper, we use a product contracted basis whose functions are products of intramolecular and intermolecular functions computed using an iterative eigensolver. An intermediate matrix F facilitates calculating matrix elements. Using F, it is possible to do calculations on a general potential without storing the potential on the full quadrature grid. We find that surprisingly many intermolecular functions are required. This is due to the importance of coupling between inter- and intra-molecular coordinates. The full G16 symmetry of water dimer is exploited. We calculate, for the first time, monomer excited stretch states and compare P(1) transition frequencies with their experimental counterparts. We also compare with experimental vibrational shifts and tunneling splittings. Surprisingly, we find that the largest tunneling splitting, which does not involve the interchange of the two monomers, is smaller in the asymmetric stretch excited state than in the ground state. Differences between levels we compute and those obtained with a [6+6]D adiabatic approximation [Leforestier et al. J. Chem. Phys. 137 014305 (2012)] are ∼0.6 cm-1 for states without monomer excitation, ∼4 cm-1 for monomer excited bend states, and as large as ∼10 cm-1 for monomer excited stretch states.
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Affiliation(s)
- Xiao-Gang Wang
- Chemistry Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
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7
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Bowman JM, Qu C, Conte R, Nandi A, Houston PL, Yu Q. Δ-Machine Learned Potential Energy Surfaces and Force Fields. J Chem Theory Comput 2023; 19:1-17. [PMID: 36527383 DOI: 10.1021/acs.jctc.2c01034] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There has been great progress in developing machine-learned potential energy surfaces (PESs) for molecules and clusters with more than 10 atoms. Unfortunately, this number of atoms generally limits the level of electronic structure theory to less than the "gold standard" CCSD(T) level. Indeed, for the well-known MD17 dataset for molecules with 9-20 atoms, all of the energies and forces were obtained with DFT calculations (PBE). This Perspective is focused on a Δ-machine learning method that we recently proposed and applied to bring DFT-based PESs to close to CCSD(T) accuracy. This is demonstrated for hydronium, N-methylacetamide, acetyl acetone, and ethanol. For 15-atom tropolone, it appears that special approaches (e.g., molecular tailoring, local CCSD(T)) are needed to obtain the CCSD(T) energies. A new aspect of this approach is the extension of Δ-machine learning to force fields. The approach is based on many-body corrections to polarizable force field potentials. This is examined in detail using the TTM2.1 water potential. The corrections make use of our recent CCSD(T) datasets for 2-b, 3-b, and 4-b interactions for water. These datasets were used to develop a new fully ab initio potential for water, termed q-AQUA.
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Affiliation(s)
- Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Independent Researcher, Toronto, Canada 66777
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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8
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Eraković M, Cvitaš MT. Vibrational Tunneling Spectra of Molecules with Asymmetric Wells: A Combined Vibrational Configuration Interaction and Instanton Approach. J Chem Theory Comput 2022; 18:2785-2802. [PMID: 35439012 PMCID: PMC9097297 DOI: 10.1021/acs.jctc.2c00124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A combined approach
that uses the vibrational configuration interaction
(VCI) and semiclassical instanton theory was developed to study vibrational
tunneling spectra of molecules with multiple wells in full dimensionality.
The method can be applied to calculate low-lying vibrational states in the systems with an
arbitrary number of minima, which are not necessarily equal in energy
or shape. It was tested on a two-dimensional double-well model system
and on malonaldehyde, and the calculations reproduced the exact quantum
mechanical (QM) results with high accuracy. The method was subsequently
applied to calculate the vibrational spectrum of the asymmetrically
deuterated malonaldehyde with nondegenerate vibrational frequencies
in the two wells. The spectrum is obtained at a cost of single-well
VCI calculations used to calculate the local energies. The interactions
between states of different wells are computed semiclassically using
the instanton theory at a comparatively negligible computational cost.
The method is particularly suited to systems in which the wells are
separated by large potential barriers and tunneling splittings are
small, for example, in some water clusters, when the exact QM methods
come at a prohibitive computational cost.
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Affiliation(s)
- Mihael Eraković
- Department of Physical Chemistry, Rud̵er Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Marko T Cvitaš
- Department of Physics, Faculty of Science, University of Zagreb, Bijenička Cesta 32, 10000 Zagreb, Croatia
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9
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Vogt E, Simkó I, Császár AG, Kjaergaard HG. Reduced-dimensional vibrational models of the water dimer. J Chem Phys 2022; 156:164304. [PMID: 35490001 DOI: 10.1063/5.0090013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A model based on the finite-basis representation of a vibrational Hamiltonian expressed in internal coordinates is developed. The model relies on a many-mode, low-order expansion of both the kinetic energy operator and the potential energy surface (PES). Polyad truncations and energy ceilings are used to control the size of the vibrational basis to facilitate accurate computations of the OH stretch and HOH bend intramolecular transitions of the water dimer (H2 16O)2. Advantages and potential pitfalls of the applied approximations are highlighted. The importance of choices related to the treatment of the kinetic energy operator in reduced-dimensional calculations and the accuracy of different water dimer PESs are discussed. A range of different reduced-dimensional computations are performed to investigate the wavenumber shifts in the intramolecular transitions caused by the coupling between the intra- and intermolecular modes. With the use of symmetry, full 12-dimensional vibrational energy levels of the water dimer are calculated, predicting accurately the experimentally observed intramolecular fundamentals. It is found that one can also predict accurate intramolecular transition wavenumbers for the water dimer by combining a set of computationally inexpensive reduced-dimensional calculations, thereby guiding future effective-Hamiltonian treatments.
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Affiliation(s)
- Emil Vogt
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Irén Simkó
- Laboratory of Molecular Structure and Dynamics, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Attila G Császár
- Laboratory of Molecular Structure and Dynamics, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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10
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Vogt E, Kjaergaard HG. Vibrational Spectroscopy of the Water Dimer at Jet-Cooled and Atmospheric Temperatures. Annu Rev Phys Chem 2022; 73:209-231. [PMID: 35044791 DOI: 10.1146/annurev-physchem-082720-104659] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The vibrational spectroscopy of the water dimer provides an understanding of basic hydrogen bonding in water clusters, and with about one water dimer for every 1,000 water molecules, it plays a critical role in atmospheric science. Here, we review how the experimental and theoretical progress of the past decades has improved our understanding of water dimer vibrational spectroscopy under both cold and warm conditions. We focus on the intramolecular OH-stretching transitions of the donor unit, because these are the ones mostly affected by dimer formation and because their assignment has proven a challenge. We review cold experimental results from early matrix isolation to recent mass-selected jet expansion techniques and, in parallel, the improvements in the theoretical anharmonic models. We discuss and illustrate changes in the vibrational spectra of complexes upon increasing temperature, and the difficulties in recording and calculating these spectra. In the atmosphere, water dimer spectra at ambient temperature are crucial. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Emil Vogt
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark;
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11
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Jankowski P, Grabowska E, Szalewicz K. On the role of coupled-clusters' full triple and perturbative quadruple excitations on rovibrational spectra of van der Waals complexes. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1955989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Piotr Jankowski
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Ewelina Grabowska
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, DE, USA
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12
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DiRisio RJ, Lu F, McCoy AB. GPU-Accelerated Neural Network Potential Energy Surfaces for Diffusion Monte Carlo. J Phys Chem A 2021; 125:5849-5859. [PMID: 34165989 DOI: 10.1021/acs.jpca.1c03709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Diffusion Monte Carlo (DMC) provides a powerful method for understanding the vibrational landscape of molecules that are not well-described by conventional methods. The most computationally demanding step of these calculations is the evaluation of the potential energy. In this work, a general approach is developed in which a neural network potential energy surface is trained by using data generated from a small-scale DMC calculation. Once trained, the neural network can be evaluated by using highly parallelizable calls to a graphics processing unit (GPU). The power of this approach is demonstrated for DMC simulations on H2O, CH5+, and (H2O)2. The need to include permutation symmetry in the neural network potentials is explored and incorporated into the molecular descriptors of CH5+ and (H2O)2. It is shown that the zero-point energies and wave functions obtained by using the neural network potentials are nearly identical to the results obtained when using the potential energy surfaces that were used to train the neural networks at a substantial savings in the computational requirements of the simulations.
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Affiliation(s)
- Ryan J DiRisio
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Fenris Lu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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13
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Curnow OJ, Crittenden DL. Are "Bright-State" Models Appropriate for Analyzing Fermi-Coupled Bands in Molecular Vibrational Spectra? J Phys Chem A 2021; 125:1355-1358. [PMID: 33544603 DOI: 10.1021/acs.jpca.0c10404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bright-state models are often applied to "deperturb" Fermi-coupled bands in molecular vibrational spectra, in cases where a harmonically forbidden transition "borrows" intensity from an energetically nearby allowed transition. However, forbidden transitions can also acquire intensity through anharmonic couplings on the potential energy surface ("mechanical anharmonicity") or dipole moment surface ("electrical anharmonicity") that are not accounted for within the bright-state model. In this work, we compare deperturbation shifts obtained by analysis of experimental data with those predicted using the bright-state model, for a series of discrete encapsulated chloride hydrate isotopomers. Predicted band center shifts and Fermi coupling matrix elements obtained using the bright-state model are larger than those estimated from experimental data.
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Affiliation(s)
- Owen J Curnow
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Deborah L Crittenden
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand
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14
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Li G, Wang C, Zheng HJ, Wang TT, Xie H, Yang XM, Jiang L. Infrared spectroscopy of neutral clusters based on a vacuum ultraviolet free electron laser. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2101018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Gang Li
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chong Wang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui-jun Zheng
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian-tong Wang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Xie
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xue-ming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ling Jiang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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15
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Grein F. Dimers and trimers of HF, H 2O, NH 3 and CH 4 with N 2. Ab initio studies on structures and vibrational frequencies. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1878303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Friedrich Grein
- Department of Chemistry, University of New Brunswick, Fredericton, Canada
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16
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Eraković M, Cvitaš MT. Tunneling splittings of vibrationally excited states using general instanton paths. J Chem Phys 2020; 153:134106. [PMID: 33032414 DOI: 10.1063/5.0024210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A multidimensional semiclassical method for calculating tunneling splittings in vibrationally excited states of molecules using Cartesian coordinates is developed. It is an extension of the theory by Mil'nikov and Nakamura [J. Chem. Phys. 122, 124311 (2005)] to asymmetric paths that are necessary for calculating tunneling splitting patterns in multi-well systems, such as water clusters. Additionally, new terms are introduced in the description of the semiclassical wavefunction that drastically improves the splitting estimates for certain systems. The method is based on the instanton theory and builds the semiclassical wavefunction of the vibrationally excited states from the ground-state instanton wavefunction along the minimum action path and its harmonic neighborhood. The splittings of excited states are thus obtained at a negligible added numerical effort. The cost is concentrated, as for the ground-state splittings, in the instanton path optimization and the hessian evaluation along the path. The method can thus be applied without modification to many mid-sized molecules in full dimensionality and in combination with on-the-fly evaluation of electronic potentials. The tests were performed on several model potentials and on the water dimer.
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Affiliation(s)
- Mihael Eraković
- Department of Physical Chemistry, Ruder Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Marko T Cvitaš
- Department of Physical Chemistry, Ruder Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
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17
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Martins JBL, Quintino RP, Politi JRDS, Sethio D, Gargano R, Kraka E. Computational analysis of vibrational frequencies and rovibrational spectroscopic constants of hydrogen sulfide dimer using MP2 and CCSD(T). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 239:118540. [PMID: 32502813 DOI: 10.1016/j.saa.2020.118540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
Previous studies have shown that the weakly bonded H2S dimer demands high level quantum chemical calculations to reproduce experimental values. We investigated the hydrogen bonding of H2S dimer using MP2 and CCSD(T) levels of theory in combination with aug-cc-pV(D,T,Q)Z basis sets. More precisely, the binding energies, potential energy curves, rovibrational spectroscopic constants, decomposition lifetime, and normal vibrational frequencies were calculated. In addition, we introduced the local mode analysis of Konkoli-Cremer to quantify the hydrogen bonding in the H2S dimer as well as providing for the first time the comprehensive decomposition of normal vibrational modes into local modes contributions, and a decomposition lifetime based on rate constant. The local mode force constant of the H2S dimer hydrogen bond is smaller than that of the water dimer, in accordance with the weaker hydrogen bonding in the H2S dimer.
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Affiliation(s)
- João B L Martins
- Institute of Chemistry, University of Brasília, Brasília, DF 70910-900, Brazil.
| | - Rabeshe P Quintino
- Institute of Chemistry, University of Brasília, Brasília, DF 70910-900, Brazil
| | - José R Dos S Politi
- Institute of Chemistry, University of Brasília, Brasília, DF 70910-900, Brazil
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, United States
| | - Ricardo Gargano
- Institute of Physics, University of Brasília, Brasília, DF 70910-900, Brazil
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, United States
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18
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Wang L, Zhang XL, Zhai Y, Nooijen M, Li H. Explicitly correlated ab initio potential energy surface and predicted rovibrational spectra for H 2O-N 2 and D 2O-N 2 complexes. J Chem Phys 2020; 153:054303. [PMID: 32770926 DOI: 10.1063/5.0009098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
An ab initio intermolecular potential energy surface (PES) for the van der Waals complex of H2O-N2 that explicitly incorporates the intramolecular Q2 bending normal mode of the H2O monomer is presented. The electronic structure computations have been carried out at the explicitly correlated coupled cluster theory [CCSD(T)-F12] with an augmented correlation-consistent triple zeta basis set and an additional bond function. Analytic five-dimensional intermolecular PESs for ν2(H2O) = 0 and 1 are obtained by fitting to the multi-dimensional Morse/long-range potential function form. These fits to 40 890 points have the root-mean-square (rms) discrepancy of 0.88 cm-1 for interaction energies less than 2000.0 cm-1. The resulting vibrationally averaged PESs provide good representations of the experimental microwave and infrared data: for microwave transitions of H2O-N2, the rms discrepancy is only 0.0003 cm-1, and for infrared transitions of the A1 symmetry of the H2O(ν2 = 1 ← 0)-N2, the rms discrepancy is 0.001 cm-1. The calculated infrared band origin shifts associated with the ν2 bending vibration of water are 2.210 cm-1 and 1.323 cm-1 for H2O-N2 and D2O-N2, respectively, in good agreement with the experimental values of 2.254 cm-1 and 1.266 cm-1. The benchmark tests and comparisons of the predicted spectral properties are carried out between CCSD(T)-F12a and CCSD(T)-F12b approaches.
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Affiliation(s)
- Lu Wang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, China
| | - Xiao-Long Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, China
| | - Yu Zhai
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, China
| | - Marcel Nooijen
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Hui Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, China
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19
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Schwan R, Qu C, Mani D, Pal N, Schwaab G, Bowman JM, Tschumper GS, Havenith M. Observation of the Low‐Frequency Spectrum of the Water Trimer as a Sensitive Test of the Water‐Trimer Potential and the Dipole‐Moment Surface. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Raffael Schwan
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Chen Qu
- Department of Chemistry Biochemistry University of Maryland College Park MD 20742 USA
| | - Devendra Mani
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Nitish Pal
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Gerhard Schwaab
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Joel M. Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry University of Mississippi University MS 38677 USA
| | - Martina Havenith
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
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20
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Schwan R, Qu C, Mani D, Pal N, Schwaab G, Bowman JM, Tschumper GS, Havenith M. Observation of the Low-Frequency Spectrum of the Water Trimer as a Sensitive Test of the Water-Trimer Potential and the Dipole-Moment Surface. Angew Chem Int Ed Engl 2020; 59:11399-11407. [PMID: 32307809 PMCID: PMC7383990 DOI: 10.1002/anie.202003851] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Indexed: 12/03/2022]
Abstract
Intermolecular interactions in bulk water are dominated by pairwise and non‐pairwise cooperative interactions. While accurate descriptions of the pairwise interactions are available and can be tested by precise low‐frequency spectra of the water dimer up to 550 cm−1, the same does not hold for the three‐body interactions. Here, we report the first comprehensive spectrum of the water trimer in the frequency region from 70 to 620 cm−1 using helium‐nanodroplet isolation and free‐electron lasers. By comparison to accompanying high‐level quantum calculations, the experimentally observed intermolecular bands can be assigned. The transition frequencies of the degenerate translation, the degenerate in‐plane and the non‐degenerate out‐of‐plane libration, as well as additional bands of the out‐of‐plane librational mode are reported for the first time. These provide a benchmark for state‐of‐the‐art water potentials and dipole‐moment surfaces, especially with respect to three‐body interactions.
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Affiliation(s)
- Raffael Schwan
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Chen Qu
- Department of Chemistry Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Devendra Mani
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Nitish Pal
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Gerhard Schwaab
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Joel M Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, 38677, USA
| | - Martina Havenith
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
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21
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Aliyari E, Konermann L. Formation of Gaseous Proteins via the Ion Evaporation Model (IEM) in Electrospray Mass Spectrometry. Anal Chem 2020; 92:10807-10814. [DOI: 10.1021/acs.analchem.0c02290] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Elnaz Aliyari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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22
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Burd TAH, Clary DC. Analytic Route to Tunneling Splittings Using Semiclassical Perturbation Theory. J Chem Theory Comput 2020; 16:3486-3493. [DOI: 10.1021/acs.jctc.0c00207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy A. H. Burd
- Physical and Theoretical Chemical Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David C. Clary
- Physical and Theoretical Chemical Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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23
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Metz MP, Szalewicz K. Automatic Generation of Flexible-Monomer Intermolecular Potential Energy Surfaces. J Chem Theory Comput 2020; 16:2317-2339. [PMID: 32240593 DOI: 10.1021/acs.jctc.9b01241] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A method is developed for automatic generation of nonreactive intermolecular two-body potential energy surfaces (PESs) including intramonomer degrees of freedom. This method, called flex-autoPES, is an extension of the autoPES method developed earlier, which assumes rigid monomers. In both cases, the whole PES development proceeds without any human intervention. The functional form used is a sum of products of site-site functions (both atomic and off-atomic sites can be used). The leading terms with sites involving different monomers are of physically motivated form. The long-range part of a PES is computed from monomer properties without using any dimer information. The close-range part is fitted to dimer interaction energies computed using electronic structure methods. Virtually any method can be used in such calculations, but the use of symmetry-adapted perturbation theory provides a seamless connection to the long-range part of the PES. The performance of the flex-autoPES code was tested by developing a full-dimensional PES for the water dimer and PESs including only some soft intramonomer degrees of freedom for the ethylene glycol dimer and for the ethylene glycol-water dimer. In the case of the water dimer, the root-mean-square error (RMSE) of the PES from the data points with negative total energies is 0.03 kcal/mol, and we expect this PES to be more accurate than any previously published PES of this type. For the ethylene glycol dimer and the ethylene glycol-water dimers, the analogous RMSEs are 0.25 and 0.1 kcal/mol, respectively.
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Affiliation(s)
- Michael P Metz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
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24
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Eraković M, Vaillant CL, Cvitaš MT. Instanton theory of ground-state tunneling splittings with general paths. J Chem Phys 2020; 152:084111. [PMID: 32113369 DOI: 10.1063/1.5145278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We derive a multidimensional instanton theory for calculating ground-state tunneling splittings in Cartesian coordinates for general paths. It is an extension of the method by Mil'nikov and Nakamura [J. Chem. Phys. 115, 6881 (2001)] to include asymmetric paths that are necessary for calculating tunneling splitting patterns in multi-well systems, such as water clusters. The approach avoids multiple expensive matrix diagonalizations to converge the fluctuation prefactor in the ring-polymer instanton (RPI) method, and instead replaces them by an integration of a Riccati differential equation. When combined with the string method for locating instantons, we avoid the need to converge the calculation with respect to the imaginary time period of the semiclassical orbit, thereby reducing the number of convergence parameters of the optimized object to just one: the number of equally spaced system replicas used to represent the instanton path. The entirety of the numerical effort is thus concentrated in optimizing the shape of the path and evaluating hessians along the path, which is a dramatic improvement over RPI. In addition to the standard instanton approximations, we neglect the coupling of vibrational modes to external rotations. The method is tested on the model potential of malonaldehyde and on the water dimer and trimer, giving close agreement with RPI at a much-reduced cost.
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Affiliation(s)
- Mihael Eraković
- Department of Physical Chemistry, Rudđđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Christophe L Vaillant
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marko T Cvitaš
- Department of Physical Chemistry, Rudđđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
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25
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Zhang B, Yu Y, Zhang Z, Zhang YY, Jiang S, Li Q, Yang S, Hu HS, Zhang W, Dai D, Wu G, Li J, Zhang DH, Yang X, Jiang L. Infrared Spectroscopy of Neutral Water Dimer Based on a Tunable Vacuum Ultraviolet Free Electron Laser. J Phys Chem Lett 2020; 11:851-855. [PMID: 31944117 DOI: 10.1021/acs.jpclett.9b03683] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Infrared (IR) spectroscopy provides detailed structural and dynamical information on clusters at the fingerprint level. Herein, we demonstrate the capability of a tunable vacuum ultraviolet free electron laser (VUV-FEL) for selective detection of a wide variety of neutral water clusters and for recording the size-dependent IR spectra. The present technique does not require the presence of an ultraviolet chromophore or a dipole moment and is generally applicable for IR spectroscopy of neutral clusters free from confinement. To show the features of our technique, we report here the IR spectra of neutral water dimer in the OH stretch region, providing benchmarks for theoretical study of the accurate description of hydrogen bonding structures involved in liquid water and ice. Quantum mechanical calculations on a 12-dimensional ab initio potential energy surface are utilized to simulate the anharmonic vibrational spectra of water dimer. These results help to resolve the controversy of the exact vibrational assignment of each band feature of the water dimer.
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Affiliation(s)
- Bingbing Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Yong Yu
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
- University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Zhaojun Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Yang-Yang Zhang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Shukang Jiang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
- University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Qinming Li
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
- University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Shuo Yang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
- University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Han-Shi Hu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Weiqing Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Dongxu Dai
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Guorong Wu
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Jun Li
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry , Tsinghua University , Beijing 100084 , China
- Department of Chemistry, School of Science , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Dong H Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
| | - Xueming Yang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
- Department of Chemistry, School of Science , Southern University of Science and Technology , Shenzhen 518055 , China
| | - Ling Jiang
- State Key Laboratory of Molecular Reaction Dynamics, Collaborative Innovation Center of Chemistry for Energy and Materials , Dalian Institute of Chemical Physics , Chinese Academy of Sciences, 457 Zhongshan Road , Dalian 116023 , China
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26
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Affiliation(s)
- Jongbaik Ree
- Department of Chemistry EducationChonnam National University Gwangju 61186 South Korea
| | - Yoo Hang Kim
- Department of ChemistryInha University Incheon 22212 South Korea
| | - Hyung Kyu Shin
- Department of ChemistryUniversity of Nevada Reno 89557 USA
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27
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Boccia AC, Lukeš V, Eckstein-Andicsová A, Kozma E. Solvent- and concentration-induced self-assembly of an amphiphilic perylene dye. NEW J CHEM 2020. [DOI: 10.1039/c9nj05674b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PDA-CA self-assembly behavior depends on temperature, concentration, and solvent.
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Affiliation(s)
| | - Vladimir Lukeš
- Department of Chemical Physics
- Slovak University of Technology in Bratislava
- Bratislava
- Slovakia
| | | | - Erika Kozma
- Istituto di Scienze e Tecnologie Chimiche-SCITEC “G. Natta”
- CNR-National Research Council
- Milano
- Italy
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28
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Schwan R, Qu C, Mani D, Pal N, van der Meer L, Redlich B, Leforestier C, Bowman JM, Schwaab G, Havenith M. Observation of the Low‐Frequency Spectrum of the Water Dimer as a Sensitive Test of the Water Dimer Potential and Dipole Moment Surfaces. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Raffael Schwan
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Chen Qu
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry Emory University Atlanta Georgia 30322 USA
| | - Devendra Mani
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Nitish Pal
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Lex van der Meer
- Radboud University Institute for Molecules and Materials, FELIX Laboratory 6525 ED Nijmegen The Netherlands
| | - Britta Redlich
- Radboud University Institute for Molecules and Materials, FELIX Laboratory 6525 ED Nijmegen The Netherlands
| | - Claude Leforestier
- Institut Charles Gerhardt, UMR 5253 CNRS-UM-ENSCM Université de Montpellier Place Eugène Bataillon 34090 Montpellier France
| | - Joel M. Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry Emory University Atlanta Georgia 30322 USA
| | - Gerhard Schwaab
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
| | - Martina Havenith
- Physical Chemistry II Department of Chemistry and Biochemistry Ruhr-Universität Bochum Bochum Germany
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29
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Schwan R, Qu C, Mani D, Pal N, van der Meer L, Redlich B, Leforestier C, Bowman JM, Schwaab G, Havenith M. Observation of the Low-Frequency Spectrum of the Water Dimer as a Sensitive Test of the Water Dimer Potential and Dipole Moment Surfaces. Angew Chem Int Ed Engl 2019; 58:13119-13126. [PMID: 31350942 PMCID: PMC7687217 DOI: 10.1002/anie.201906048] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/23/2019] [Indexed: 11/12/2022]
Abstract
Using the helium nanodroplet isolation setup at the ultrabright free-electron laser source FELIX in Nijmegen (BoHeNDI@FELIX), the intermolecular modes of water dimer in the frequency region from 70 to 550 cm-1 were recorded. Observed bands were assigned to donor torsion, acceptor wag, acceptor twist, intermolecular stretch, donor torsion overtone, and in-plane and out-of-plane librational modes. This experimental data set provides a sensitive test for state-of-the-art water potentials and dipole moment surfaces. Theoretical calculations of the IR spectrum are presented using high-level quantum and approximate quasiclassical molecular dynamics approaches. These calculations use the full-dimensional ab initio WHHB potential and dipole moment surfaces. Based on the experimental data, a considerable increase of the acceptor switch and a bifurcation tunneling splitting in the librational mode is deduced, which is a consequence of the effective decrease in the tunneling barrier.
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Affiliation(s)
- Raffael Schwan
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Chen Qu
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry, Emory University, Atlanta, Georgia, 30322, USA
| | - Devendra Mani
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Nitish Pal
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Lex van der Meer
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, 6525 ED, Nijmegen, The Netherlands
| | - Britta Redlich
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, 6525 ED, Nijmegen, The Netherlands
| | - Claude Leforestier
- Institut Charles Gerhardt, UMR 5253 CNRS-UM-ENSCM, Université de Montpellier, Place Eugène Bataillon, 34090, Montpellier, France
| | - Joel M Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry, Emory University, Atlanta, Georgia, 30322, USA
| | - Gerhard Schwaab
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Martina Havenith
- Physical Chemistry II, Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
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30
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Zhang XL, Ma YT, Zhai Y, Li H. Full quantum calculation of the rovibrational states and intensities for a symmetric top-linear molecule dimer: Hamiltonian, basis set, and matrix elements. J Chem Phys 2019; 151:074301. [PMID: 31438702 DOI: 10.1063/1.5115496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rovibrational energy levels and intensities of the CH3F-H2 dimer have been obtained using our recent global intermolecular potential energy surface [X.-L. Zhang et al., J. Chem. Phys. 148, 124302 (2018)]. The Hamiltonian, basis set, and matrix elements are derived and given for a symmetric top-linear molecule complex. This approach to the generation of energy levels and wavefunctions can readily be utilized for studying the rovibrational spectra of other van der Waals complexes composed of a symmetric top molecule and a linear molecule, and may readily be extended to other complexes of nonlinear molecules and linear molecules. To confirm our method, the rovibrational levels of the H2O-H2 dimer have been computed and shown to be in good agreement with experiment and with previous theoretical results. The rovibrational Schrödinger equation has been solved using a Lanczos algorithm together with an uncoupled product basis set. As expected, dimers containing ortho-H2 are more strongly bound than dimers containing para-H2. Energies and wavefunctions of the discrete rovibrational levels of CH3F-paraH2 complexes obtained from the direct vibrationally averaged 5-dimensional potentials are in good agreement with the results of the reduced 3-dimensional adiabatic-hindered-rotor (AHR) approximation. Accurate calculations of the transition line strengths for the orthoCH3F-paraH2 complex are also carried out, and are consistent with results obtained using the AHR approximation. The microwave spectrum associated with the orthoCH3F-orthoH2 dimer has been predicted for the first time.
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Affiliation(s)
- Xiao-Long Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, China
| | - Yong-Tao Ma
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, China
| | - Yu Zhai
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, China
| | - Hui Li
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, China
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31
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Felker PM, Bačić Z. Weakly bound molecular dimers: Intramolecular vibrational fundamentals, overtones, and tunneling splittings from full-dimensional quantum calculations using compact contracted bases of intramolecular and low-energy rigid-monomer intermolecular eigenstates. J Chem Phys 2019; 151:024305. [DOI: 10.1063/1.5111131] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Peter M. Felker
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
| | - Zlatko Bačić
- Department of Chemistry, New York University, New York, New York 10003, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai, 200062, China
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32
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Avila G, Mátyus E. Toward breaking the curse of dimensionality in (ro)vibrational computations of molecular systems with multiple large-amplitude motions. J Chem Phys 2019; 150:174107. [PMID: 31067897 DOI: 10.1063/1.5090846] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Methodological progress is reported in the challenging direction of a black-box-type variational solution of the (ro)vibrational Schrödinger equation applicable to floppy, polyatomic systems with multiple large-amplitude motions. This progress is achieved through the combination of (i) the numerical kinetic-energy operator (KEO) approach of Mátyus et al. [J. Chem. Phys. 130, 134112 (2009)] and (ii) the Smolyak nonproduct grid method of Avila and Carrington, Jr. [J. Chem. Phys. 131, 174103 (2009)]. The numerical representation of the KEO makes it possible to choose internal coordinates and a body-fixed frame best suited for the molecular system. The Smolyak scheme reduces the size of the direct-product grid representation by orders of magnitude, while retaining some of the useful features of it. As a result, multidimensional (ro)vibrational states are computed with system-adapted coordinates, a compact basis- and grid-representation, and an iterative eigensolver. Details of the methodological developments and the first numerical applications are presented for the CH4·Ar complex treated in full (12D) vibrational dimensionality.
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Affiliation(s)
- Gustavo Avila
- Institute of Chemistry, ELTE, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest 1117, Hungary
| | - Edit Mátyus
- Institute of Chemistry, ELTE, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest 1117, Hungary
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33
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Barclay AJ, McKellar ARW, Moazzen-Ahmadi N. Spectra of the D 2O dimer in the O-D fundamental stretch region: Vibrational dependence of tunneling splittings and lifetimes. J Chem Phys 2019; 150:164307. [PMID: 31042915 DOI: 10.1063/1.5092503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The fundamental O-D stretch region (2600-2800 cm-1) of the fully deuterated water dimer (D2O)2 is studied using a pulsed supersonic slit jet source and a tunable optical parametric oscillator source. Relatively high spectral resolution (0.002 cm-1) enables all six dimer tunneling components to be observed, in most cases, for the acceptor asymmetric O-D stretch, the donor free O-D stretch, and the donor bound O-D stretch vibrations. The dominant acceptor switching tunneling splittings are observed to decrease moderately in the excited O-D stretch states, to roughly 75% of their ground state values, whereas the smaller donor-acceptor interchange splittings show more dramatic and irregular decreases. Excited state predissociation lifetimes, as determined from the observed line broadening, show large variations (0.2 ≤ τ ≤ 5 ns) depending on the vibrational state, K-value, and tunneling symmetry. Another very weak band is tentatively assigned to a combination mode involving an intramolecular O-D stretch plus an intermolecular twist overtone. Asymmetric O-D stretch bands of the mixed isotopologue dimers D2O-DOH and D2O-HOD are also observed and analyzed.
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Affiliation(s)
- A J Barclay
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
| | - A R W McKellar
- National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - N Moazzen-Ahmadi
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
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34
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Pitsevich G, Malevich A, Kozlovskaya E, Sablinskas V, Balevicius V. Anharmonicity of the bonded O H group vibrations in water dimer. DFT study including dispersion interaction. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Wang XG, Carrington T. Computing vibration-rotation-tunnelling levels of HOD dimer. Phys Chem Chem Phys 2019; 21:3527-3536. [PMID: 30123894 DOI: 10.1039/c8cp04451a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using an accurate 6D water dimer potential energy surface, we compute vibration-rotation-tunnelling levels of HOD dimer, by assuming that the two monomers are rigid. HOD dimer has two isomers, a D-bonded isomer and an H-bonded isomer, and the wavefunctions of both isomers have amplitude in four wells. HOD dimer is important because, unlike the case of H2O dimer or D2O dimer, it is possible to measure the largest tunnelling splitting. Results for HOD dimer, therefore facilitate the testing of H2O dimer potentials. In J. Chem. Phys., 1995, 102, 1114, experimental results were interpreted in terms of 1D models. Experimental splittings of both isomers, obtained by fitting an energy level equation to spectra, are in good agreement with those we compute.
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Affiliation(s)
- Xiao-Gang Wang
- Chemistry Department, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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36
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Barclay AJ, van der Avoird A, McKellar ARW, Moazzen-Ahmadi N. The water–carbon monoxide dimer: new infrared spectra, ab initio rovibrational energy level calculations, and an interesting in-termolecular mode. Phys Chem Chem Phys 2019; 21:14911-14922. [DOI: 10.1039/c9cp02815c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bound state rovibrational energy level calculations using a high-level intermolecular potential surface are reported for H2O–CO and D2O–CO.
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Affiliation(s)
- A. J. Barclay
- Department of Physics and Astronomy
- University of Calgary
- Calgary
- Canada
| | - A. van der Avoird
- Theoretical Chemistry
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
| | | | - N. Moazzen-Ahmadi
- Department of Physics and Astronomy
- University of Calgary
- Calgary
- Canada
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37
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Metz MP, Szalewicz K, Sarka J, Tóbiás R, Császár AG, Mátyus E. Molecular dimers of methane clathrates: ab initio potential energy surfaces and variational vibrational states. Phys Chem Chem Phys 2019; 21:13504-13525. [DOI: 10.1039/c9cp00993k] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Motivated by the energetic and environmental relevance of methane clathrates, highly accurate ab initio potential energy surfaces (PESs) have been developed for the three possible dimers of the methane and water molecules: (H2O)2, CH4·H2O, and (CH4)2.
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Affiliation(s)
- Michael P. Metz
- Department of Physics and Astronomy
- University of Delaware
- Newark
- USA
| | | | - János Sarka
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
| | - Roland Tóbiás
- Institute of Chemistry
- ELTE Eötvös Loránd University
- Budapest
- Hungary
- MTA-ELTE Complex Chemical Systems Research Group
| | - Attila G. Császár
- Institute of Chemistry
- ELTE Eötvös Loránd University
- Budapest
- Hungary
- MTA-ELTE Complex Chemical Systems Research Group
| | - Edit Mátyus
- Institute of Chemistry
- ELTE Eötvös Loránd University
- Budapest
- Hungary
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38
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Garberoglio G, Jankowski P, Szalewicz K, Harvey AH. Fully quantum calculation of the second and third virial coefficients of water and its isotopologues from ab initio potentials. Faraday Discuss 2018; 212:467-497. [PMID: 30302450 PMCID: PMC6561489 DOI: 10.1039/c8fd00092a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Path-Integral Monte Carlo methods were applied to calculate the second, B(T), and the third, C(T), virial coefficients for water. A fully quantum approach and state-of-the-art flexible-monomer pair and three-body potentials were used. Flexible-monomer potentials allow calculations for any isotopologue; we performed calculations for both H2O and D2O. For B(T) of H2O, the quantum effect contributes 25% of the value at 300 K and is not entirely negligible even at 1000 K, in accordance with recent literature findings. The effect of monomer flexibility, while not as large as some claims in the literature, is significant compared to the experimental uncertainty. It is of opposite sign to the quantum effect, smaller in magnitude than the latter below 500 K, and varies from 2% at 300 K to 10% at 700 K. When monomer flexibility is accounted for, results from the CCpol-8sf pair potential are in excellent agreement with the available experimental data and provide reliable B(T) values at temperatures outside the range of experimental data. The flexible-monomer MB-pol pair potential yields B(T) values that are slightly too high compared to experiment. For C(T), our calculations confirm earlier findings that the use of three-body potential is necessary for meaningful predictions. However, due to various uncertainties of the potentials used, especially the three-body ones, we were not able to establish benchmark values of C(T), although our results are in qualitative agreement with available experimental data. The quantum effect, never before included for water, reduces the magnitude of the classical value for H2O by a factor of 2.5 at 300 K and is not entirely negligible even at 1000 K.
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Affiliation(s)
- Giovanni Garberoglio
- European Centre for Theoretical Studies in Nuclear Physics and Related Areas (FBK-ECT*), strada delle Tabarelle 286, I-38123 Trento, Italy. and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN), via Sommarive 18, I-38213 Trento, Italy
| | - Piotr Jankowski
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, PL-87-100 Torun, Poland.
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA.
| | - Allan H Harvey
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, Colorado 80305-3337, USA.
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39
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Lindsey RK, Fried LE, Goldman N. Application of the ChIMES Force Field to Nonreactive Molecular Systems: Water at Ambient Conditions. J Chem Theory Comput 2018; 15:436-447. [DOI: 10.1021/acs.jctc.8b00831] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rebecca K. Lindsey
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Department of Chemical Engineering, University of California, Davis, California 95616, United States
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40
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41
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Wang XG, Carrington T. Using monomer vibrational wavefunctions to compute numerically exact (12D) rovibrational levels of water dimer. J Chem Phys 2018; 148:074108. [DOI: 10.1063/1.5020426] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xiao-Gang Wang
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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42
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Zhao Z, Chen J, Zhang Z, Zhang DH, Wang XG, Carrington T, Gatti F. Computing energy levels of CH4, CHD3, CH3D, and CH3F with a direct product basis and coordinates based on the methyl subsystem. J Chem Phys 2018; 148:074113. [DOI: 10.1063/1.5019323] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhiqiang Zhao
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jun Chen
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Siming South Road 422, 361005 Xiamen, China
| | - Zhaojun Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Dong H. Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiao-Gang Wang
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Fabien Gatti
- ISMO, Institut des Sciences Moléculaires d’Orsay - UMR 8214 CNRS/Université Paris-Sud, F-91405 Orsay, France
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43
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Affiliation(s)
- Xinzijian Liu
- Beijing National Laboratory For Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jian Liu
- Beijing National Laboratory For Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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44
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Zhang X, Bowen K. Designer Metallic Acceptor-Containing Halogen Bonds: General Strategies. Chemistry 2017; 23:5439-5442. [PMID: 28295738 DOI: 10.1002/chem.201701067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Indexed: 11/11/2022]
Abstract
Being electrostatic interactions in nature, hydrogen bonding (HB) and halogen bonding (XB) are considered to be two parallel worlds. In principle, all the applications that HB have could also be applied to XB. However, there has been no report on an anionic, metallic XB acceptor, but metal anions have been observed to be good HB acceptors. This missing mosaic piece of XB theory is because common metal anions are reactive for XB donors. In view of this, two strategies are proposed for designing metallic acceptor-containing XB using ab initio calculations. The first one is to utilize a metal cluster anion with a high electron detachment energy, such as the superatom, Al13- as the XB acceptor. The second strategy is to design a ligand-passivated/protected metal core that can maintain the negative charge; several exotic clusters, such as PtH5- , PtZnH5- , and PtMgH5- , are used as examples. Based on these two strategies, it is anticipated that more metallic acceptor-containing XBs will be discovered.
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Affiliation(s)
- Xinxing Zhang
- Departments of Chemistry and Material Sciences, Johns Hopkins University, Baltimore, Maryland, MD, 21218, USA
| | - Kit Bowen
- Departments of Chemistry and Material Sciences, Johns Hopkins University, Baltimore, Maryland, MD, 21218, USA
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45
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Wang XG, Carrington T. Using monomer vibrational wavefunctions as contracted basis functions to compute rovibrational levels of an H2O-atom complex in full dimensionality. J Chem Phys 2017; 146:104105. [DOI: 10.1063/1.4977179] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Xiao-Gang Wang
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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46
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Che X, Du XX, Cai X, Zhang J, Xie WJ, Long Z, Ye ZY, Zhang H, Yang L, Su XD, Gao YQ. Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex. J Phys Chem B 2017; 121:2073-2082. [PMID: 28178416 DOI: 10.1021/acs.jpcb.6b12472] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Subtle changes in protein sequences are able to alter ligand-protein interactions. Unraveling the mechanism of such phenomena is important for understanding ligand-protein interactions, including the DMXAA-STING interaction. DMXAA specifically binds to mouse STING instead of human STING. However, the S162A mutation and a newly discovered E260I mutation endow human STINGAQ with DMXAA sensitivity. Through molecular dynamics simulations, we revealed how these single mutations alter the DMXAA-STING interaction. Compared to mutated systems, structural correlations in the interaction of STINGAQ with DMXAA are stronger, and the correlations are cross-protomers in the dimeric protein. Analyses on correlation coefficients lead to the identification of two key interactions that mediate the strong cross-protomer correlation in the DMXAA-STINGAQ interaction network: DMXAA-267T-162S* and 238R-260E*. These two interactions are partially and totally interrupted by the S162A and E260I mutations, respectively. Moreover, a smaller number of water molecules are displaced upon DMXAA binding to STINGAQ than that on binding to its mutants, leading to a larger entropic penalty for the former. Considering the sensitivity of STINGAQ and two of its mutants to DMXAA, a strong structural correlation appears to discourage DMXAA-STING binding. Such an observation suggests that DMXAA derivatives, which are deprived of hydrogen-bond interaction with both 162S* and 267T, are potential agonists of human STING.
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Affiliation(s)
- Xing Che
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Xiao-Xia Du
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Xiaoxia Cai
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Jun Zhang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Wen Jun Xie
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Zhuoran Long
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Zhao-Yang Ye
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Heng Zhang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Lijiang Yang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Xiao-Dong Su
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center and ‡State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center, School of Life Sciences, Peking University , Beijing 100871, China
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47
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Garberoglio G, Jankowski P, Szalewicz K, Harvey AH. All-dimensional H 2-CO potential: Validation with fully quantum second virial coefficients. J Chem Phys 2017; 146:054304. [PMID: 28178790 DOI: 10.1063/1.4974993] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We use a new high-accuracy all-dimensional potential to compute the cross second virial coefficient B12(T) between molecular hydrogen and carbon monoxide. The path-integral method is used to fully account for quantum effects. Values are calculated from 10 K to 2000 K and the uncertainty of the potential is propagated into uncertainties of B12. Our calculated B12(T) are in excellent agreement with most of the limited experimental data available, but cover a much wider range of temperatures and have lower uncertainties. Similar to recently reported findings from scattering calculations, we find that the reduced-dimensionality potential obtained by averaging over the rovibrational motion of the monomers gives results that are a good approximation to those obtained when flexibility is fully taken into account. Also, the four-dimensional approximation with monomers taken at their vibrationally averaged bond lengths works well. This finding is important, since full-dimensional potentials are difficult to develop even for triatomic monomers and are not currently possible to obtain for larger molecules. Likewise, most types of accurate quantum mechanical calculations, e.g., spectral or scattering, are severely limited in the number of dimensions that can be handled.
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Affiliation(s)
- Giovanni Garberoglio
- European Centre for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK), via Sommarive 18, I-38123 Trento, Italy
| | - Piotr Jankowski
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, PL-87-100 Torun, Poland
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
| | - Allan H Harvey
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305-3337, USA
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48
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Cisneros G, Wikfeldt KT, Ojamäe L, Lu J, Xu Y, Torabifard H, Bartók AP, Csányi G, Molinero V, Paesani F. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. Chem Rev 2016; 116:7501-28. [PMID: 27186804 PMCID: PMC5450669 DOI: 10.1021/acs.chemrev.5b00644] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 12/17/2022]
Abstract
Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.
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Affiliation(s)
| | - Kjartan Thor Wikfeldt
- Science
Institute, University of Iceland, VR-III, 107, Reykjavik, Iceland
- Department
of Physics, Albanova, Stockholm University, S-106 91 Stockholm, Sweden
| | - Lars Ojamäe
- Department
of Chemistry, Linköping University, SE-581 83 Linköping, Sweden
| | - Jibao Lu
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Yao Xu
- Lehrstuhl
Physikalische Chemie II, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Hedieh Torabifard
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Albert P. Bartók
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Gábor Csányi
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Valeria Molinero
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Francesco Paesani
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
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49
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Loboda O, Ingrosso F, Ruiz-López MF, Reis H, Millot C. Dipole and quadrupole polarizabilities of the water molecule as a function of geometry. J Comput Chem 2016; 37:2125-32. [DOI: 10.1002/jcc.24431] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 05/24/2016] [Accepted: 05/27/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Oleksandr Loboda
- SRSMC UMR 7565, Faculté des Sciences et Technologies, Boulevard des Aiguillettes, BP 70239; Université de Lorraine, CNRS; Vandoeuvre-lès-Nancy F-54506 France
| | - Francesca Ingrosso
- SRSMC UMR 7565, Faculté des Sciences et Technologies, Boulevard des Aiguillettes, BP 70239; Université de Lorraine, CNRS; Vandoeuvre-lès-Nancy F-54506 France
| | - Manuel F. Ruiz-López
- SRSMC UMR 7565, Faculté des Sciences et Technologies, Boulevard des Aiguillettes, BP 70239; Université de Lorraine, CNRS; Vandoeuvre-lès-Nancy F-54506 France
| | - Heribert Reis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation; 48 Vas. Constantinou Avenue Athens 11635 Greece
| | - Claude Millot
- SRSMC UMR 7565, Faculté des Sciences et Technologies, Boulevard des Aiguillettes, BP 70239; Université de Lorraine, CNRS; Vandoeuvre-lès-Nancy F-54506 France
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50
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On the importance of full-dimensionality in low-energy molecular scattering calculations. Sci Rep 2016; 6:28449. [PMID: 27333870 PMCID: PMC4917847 DOI: 10.1038/srep28449] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/02/2016] [Indexed: 11/29/2022] Open
Abstract
Scattering of H2 on CO is of great importance in astrophysics and also is a benchmark system for comparing theory to experiment. We present here a new 6-dimensional potential energy surface for the ground electronic state of H2-CO with an estimated uncertainty of about 0.6 cm−1 in the global minimum region, several times smaller than achieved earlier. This potential has been used in nearly exact 6-dimensional quantum scattering calculations to compute state-to-state cross-sections measured in low-energy crossed-beam experiments. Excellent agreement between theory and experiment has been achieved in all cases. We also show that the fully 6-dimensional approach is not needed with the current accuracy of experimental data since an equally good agreement with experiment was obtained using only a 4-dimensional treatment, which validates the rigid-rotor approach widely used in scattering calculations. This finding, which disagrees with some literature statements, is important since for larger systems full-dimensional scattering calculations are currently not possible.
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