1
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Smirnov AN, Solomonik VG. Composite ab initio vibrational spectroscopy and thermochemistry of low-valency lanthanide compounds: europium dihalides EuX 2 (X = F, Cl, Br, I). Phys Chem Chem Phys 2024; 26:24870-24880. [PMID: 39291639 DOI: 10.1039/d4cp02507e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
A unique diversity in chemical properties of lanthanide compounds making them very useful in various important applications stems not least from the existence of less common Ln oxidation states, in particular +2. However, the molecular properties of low-valency lanthanide compounds are not yet well studied even for the most stable divalent Ln-containing species, such as europium dihalides. In this paper, highly accurate molecular structures, vibrational spectra, and atomisation energies of the europium dihalides EuX2 (X = F, Cl, Br, I) are obtained at the complete basis set CCSD(T) level. All of the EuX2 species are calculated to be non-linear (C2v) exhibiting a regular increase in X-Eu-X bond angle on passing through the halogen series (F → Cl → Br → I), from 117° in EuF2 to 141° in EuI2, which is accompanied by a rapid decrease in the barriers to linearity, h = E(D∞h) - E(C2v), from 2180 cm-1 to 166 cm-1, respectively. The Eu-X bonds in EuX2 appear to be longer but energetically stronger than those in the respective monohalides EuX, whose properties are studied in this work at the same level of theory as EuX2. The performance of the Ln 4f-in-core pseudopotential (PP) approximation for EuX2 is assessed by comparing the Eu PP-based coupled-cluster (CC) calculations with all-electron CC benchmarks. Incorporating the Eu 4f electrons into the PP is shown to cause large errors: up to 10 deg. in X-Eu-X bond angles, 80% in barriers to linearity, and 0.05 Å in the Eu-X bond lengths, which proves the necessity of an explicit treatment of 4f electrons if high accuracy is the goal. The present results set a benchmark in the field of low-valency lanthanide chemistry, in particular for the calibration of DFT functionals.
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Affiliation(s)
- Alexander N Smirnov
- Department of Physics, Ivanovo State University of Chemistry and Technology, Ivanovo 153000, Russia.
| | - Victor G Solomonik
- Department of Physics, Ivanovo State University of Chemistry and Technology, Ivanovo 153000, Russia.
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2
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Schneider M, Rauhut G. Comparison of curvilinear coordinates within vibrational structure calculations based on automatically generated potential energy surfaces. J Chem Phys 2024; 161:094102. [PMID: 39225517 DOI: 10.1063/5.0225991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
For floppy molecules showing internal rotations and/or large amplitude motions, curvilinear internal coordinates are known to be superior to rectilinear normal coordinates within vibrational structure calculations. Due to the myriad definitions of internal coordinates, automated and efficient potential energy surface generators necessitate a high degree of flexibility, supporting the properties arising from these coordinates. Within this work, an approach to deal with these challenges is presented, including key elements, such as the selection of appropriate fit functions, the exploitation of symmetry, the positioning of grid points, or elongation limits for different coordinates. These elements are tested for five definitions of curvilinear coordinates, with three of them being generated in an automated manner. Calculations for semi-rigid molecules, namely H2O, H2CO, CH2F2, and H2CNH, demonstrate the general functionality of the implemented algorithms. Additional calculations for the HOPO molecule highlight the benefits of these curvilinear coordinates for systems with large amplitude motions. This new implementation allowed us to compare the performance of these different coordinate systems with respect to the convergence of the underlying expansion of the potential energy surface and subsequent vibrational configuration interaction calculations.
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Affiliation(s)
- Moritz Schneider
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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3
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Dinu D, Ončák M, Thorwirth S, Liedl KR, Brünken S, Schlemmer S, Jusko P. Zero-Point-Energy Driven Isotopic Exchange of the [H 3O] - anion Probed by Mid-Infrared Action Spectroscopy. J Am Chem Soc 2024; 146:21634-21641. [PMID: 39049192 PMCID: PMC11311240 DOI: 10.1021/jacs.4c05543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/18/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
We present the first observation of vibrational transitions in the [H3O]- anion, an intermediate in the anion-molecule reaction of water, H2O, and hydride, H-, using a laser-induced isotopic H/D exchange reaction action spectroscopy scheme applied to anions. The observed bands are assigned as the fundamental and first overtone of the H2O-H- vibrational stretching mode, based on anharmonic calculations within the vibrational perturbation theory and vibrational configuration interaction. Although the D2O·D- species has the lowest energy, our experiments confirm the D2O·H- isotope to be a sink of the H/D exchange reaction. Ab initio calculations corroborate that the formation of D2O·H- is favored, as the zero-point-energy difference is larger between D2 and H2 than between D2O·H- and D2O·D-.
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Affiliation(s)
- Dennis
F. Dinu
- Institute
of Materials Chemistry, TU Wien, Getreidemarkt 9/165, 1060 Vienna, Austria
- Department
of General, Inorganic and Theoretical Chemistry, Universität Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Milan Ončák
- Institut
für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Sven Thorwirth
- I.
Physikalisches Institut, Universität
zu Köln, Zülpicher Str. 77, 50937 Koln̈, Germany
| | - Klaus R. Liedl
- Department
of General, Inorganic and Theoretical Chemistry, Universität Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Sandra Brünken
- Radboud
University, FELIX Laboratory,
Institute for Molecules and Materials, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Stephan Schlemmer
- I.
Physikalisches Institut, Universität
zu Köln, Zülpicher Str. 77, 50937 Koln̈, Germany
| | - Pavol Jusko
- Max
Planck
Institute for Extraterrestrial Physics, Giessenbachstrasse 1, 85748 Garching, Germany
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4
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Sharma M, Banik S, Roy TK. Performance of Effective Harmonic Oscillator Approach for the Calculations of Vibrational Transition Energies of Large Molecules. J Phys Chem A 2024; 128:5762-5776. [PMID: 38979981 DOI: 10.1021/acs.jpca.4c01583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The accuracy and performance of the effective harmonic oscillator approximation for the description of anharmonic vibrational structure calculations are tested for large molecular systems and compared with experimental values along with vibrational self-consistent field and second-order perturbation theories. The effective harmonic oscillator approach is an effective single-particle approximation where the variational parameters are the centroids and widths of the multidimensional Gaussian product functions posited as the vibrational wave functions. A comprehensive calculation for 849 transitions that include the fundamentals, two and three quanta overtone transitions, and several combination bands of three polyaromatic hydrocarbons and one DNA nucleobase with a total of 231 normal modes are assessed. A comparison of EHO results with the experimental values is done for the polyaromatic hydrocarbons, and a close agreement is found between the two results. It also offers anharmonic eigenstates and eigenfunctions that are nearly identical with vibrational self-consistent field theory. An extensive analysis on the resultant wave functions of the excited states is performed. The overall root-mean-square deviation (RMSD) between these two methods for 849 transitions understudy is only about 8.3 cm-1, suggesting the effective harmonic oscillator as a viable alternative for the reliable calculations of transition energies of large molecular systems.
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Affiliation(s)
- Mokshi Sharma
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
| | - Subrata Banik
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
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5
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Flowers AM, Brown A, Klobukowski M. Anharmonic Vibrational Spectroscopy of Germanium-Containing Clusters, Ge xC 4-x and Ge xSi 4-x ( x = 0-4), for Interstellar Detection. J Phys Chem A 2024; 128:5351-5361. [PMID: 38942734 DOI: 10.1021/acs.jpca.4c02081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
An extensive, high-level theoretical study on tetra-atomic germanium carbide/silicide clusters is presented. Accurate harmonic and anharmonic vibrational frequencies and rotational constants are calculated at the CCSD(T)-F12a(b)/cc-pVT(Q)Z-F12 levels of theory. With growing capabilities to discern more of the chemical composition of the interstellar medium (ISM), an accurate database of reference material is required. The presence of carbon is ubiquitous in the ISM, and silicon is known to be present in interstellar dust grains; however, germanium-containing molecules remain elusive. To begin understanding the presence and role of germanium in the ISM, we present this study of the vibrational and rotational spectroscopic properties of various germanium-containing molecules to aid in their potential identification in the ISM with modern observational tools such as the James Webb Space Telescope. Structures studied herein include rhomboidal (r-), diamond (d-), and trapezoidal (t-) tetra-atomic molecules of the form GexC4-x and GexSi4-x, where x = 0-4. The most promising structure for detection is r-Ge2C2 via the ν4 mode with a frequency of 802.7 cm-1 (12.5 μm) and an intensity of 307.2 km mol-1. Other molecules that are potentially detectable, i.e., through vibrational modes or rotational transitions, include r-Ge3C, r-GeSi3, d-GeC3, r-GeC3, and t-Ge2C2.
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Affiliation(s)
- A Mackenzie Flowers
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Mariusz Klobukowski
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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6
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Schneider M, Rauhut G. VSCF/VCI theory based on the Podolsky Hamiltonian. J Chem Phys 2024; 160:214118. [PMID: 38832735 DOI: 10.1063/5.0213401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
While the vibrational spectra of semi-rigid molecules can be computed on approaches relying on the Watson Hamiltonian, floppy molecules or molecular clusters are better described by Hamiltonians, which are capable of dealing with any curvilinear coordinates. It is the kinetic energy operator (KEO) of these Hamiltonians, which render the correlated calculations relying on them rather costly. Novel implementation of vibrational self-consistent field theory and vibrational configuration interaction theory on the basis of the Podolsky Hamiltonian are reported, in which the inverse of the metric tensor, i.e., the G matrix, is represented by an n-mode expansion expressed in terms of polynomials. An analysis of the importance of the individual terms of the KEO with respect to the truncation orders of the n-mode expansion is provided. Benchmark calculations have been performed for the cis-HOPO and methanimine, H2CNH, molecules and are compared to experimental data and to calculations based on the Watson Hamiltonian and the internal coordinate path Hamiltonian.
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Affiliation(s)
- Moritz Schneider
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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7
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Spencer RJ, Zhanserkeev AA, Yang EL, Steele RP. The Near-Sightedness of Many-Body Interactions in Anharmonic Vibrational Couplings. J Am Chem Soc 2024; 146:15376-15392. [PMID: 38771156 DOI: 10.1021/jacs.4c03198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Couplings between vibrational motions are driven by electronic interactions, and these couplings carry special significance in vibrational energy transfer, multidimensional spectroscopy experiments, and simulations of vibrational spectra. In this investigation, the many-body contributions to these couplings are analyzed computationally in the context of clathrate-like alkali metal cation hydrates, including Cs+(H2O)20, Rb+(H2O)20, and K+(H2O)20, using both analytic and quantum-chemistry potential energy surfaces. Although the harmonic spectra and one-dimensional anharmonic spectra depend strongly on these many-body interactions, the mode-pair couplings were, perhaps surprisingly, found to be dominated by one-body effects, even in cases of couplings to low-frequency modes that involved the motion of multiple water molecules. The origin of this effect was traced mainly to geometric distortion within water monomers and cancellation of many-body effects in differential couplings, and the effect was also shown to be agnostic to the identity of the ion. These outcomes provide new understanding of vibrational couplings and suggest the possibility of improved computational methods for the simulation of infrared and Raman spectra.
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Affiliation(s)
- Ryan J Spencer
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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8
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Deng G, Reimann M, Müller C, Lu Y, Kaupp M, Riedel S. Spectroscopic Identification of Trifluorosilylphosphinidene and Isomeric Phosphasilene and Silicon Trifluorophosphine Complex. Inorg Chem 2024; 63:7286-7292. [PMID: 38592208 DOI: 10.1021/acs.inorgchem.4c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The perfluorinated silylphosphinidene, F3SiP, in the triplet ground state is generated by the reaction of laser-ablated silicon atoms with PF3 in solid neon and argon matrices. The reactions proceed with the initial formation of a silicon trifluorophosphine complex, F3PSi, in the triplet ground state, and a more stable inserted phosphasilene, FPSiF2, in the singlet ground state upon deposition. The trifluorosilylphosphinidene was formed through F-migration reactions of FPSiF2 and F3PSi following a two-state mechanism under irradiation with visible light (λ = 470 nm) and full arc light (λ > 220 nm), respectively. High-level quantum-chemical methods support the identification of F3PSi, FPSiF2, and F3SiP by matrix-isolation IR spectroscopy.
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Affiliation(s)
- Guohai Deng
- Institut für Chemie und Biochemie-Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34/36, Berlin 14195, Germany
| | - Marc Reimann
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Strasse des 17. Juni 135, Berlin 10623, Germany
| | - Carsten Müller
- Institut für Chemie und Biochemie-Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34/36, Berlin 14195, Germany
| | - Yan Lu
- Institut für Chemie und Biochemie-Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34/36, Berlin 14195, Germany
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Strasse des 17. Juni 135, Berlin 10623, Germany
| | - Sebastian Riedel
- Institut für Chemie und Biochemie-Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34/36, Berlin 14195, Germany
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9
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Bader F, Lauvergnat D, Christiansen O. Efficient vibrationally correlated calculations using n-mode expansion-based kinetic energy operators. Phys Chem Chem Phys 2024; 26:11469-11481. [PMID: 38546727 DOI: 10.1039/d4cp00423j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Due to its efficiency and flexibility, the n-mode expansion is a frequently used tool for representing molecular potential energy surfaces in quantum chemical simulations. In this work, we investigate the performance of n-mode expansion-based models of kinetic energy operators in general polyspherical coordinate systems. In particular, we assess the operators with respect to accuracy in vibrationally correlated calculations and their effect on potential energy surface construction with the adaptive density guided approach. Our results show that the n-mode expansion-based operator variants are reliable and systematically improvable approximations of the full kinetic energy operator. Moreover, we introduce a workflow to generate the n-mode expanded kinetic energy operators on-the-fly within the adaptive density guided approach. This scheme can be applied in studies of species and coordinate systems, for which an analytical form of the kinetic energy operator is not available.
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Affiliation(s)
- Frederik Bader
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark.
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France.
| | - Ove Christiansen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark.
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10
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Schröder B, Rauhut G. From the Automated Calculation of Potential Energy Surfaces to Accurate Infrared Spectra. J Phys Chem Lett 2024; 15:3159-3169. [PMID: 38478898 PMCID: PMC10961845 DOI: 10.1021/acs.jpclett.4c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Advances in the development of quantum chemical methods and progress in multicore architectures in computer science made the simulation of infrared spectra of isolated molecules competitive with respect to established experimental methods. Although it is mainly the multidimensional potential energy surface that controls the accuracy of these calculations, the subsequent vibrational structure calculations need to be carefully converged in order to yield accurate results. As both aspects need to be considered in a balanced way, we focus on approaches for molecules of up to 12-15 atoms with respect to both parts, which have been automated to some extent so that they can be employed in routine applications. Alternatives to machine learning will be discussed, which appear to be attractive, as long as local regions of the potential energy surface are sufficient. The automatization of these methods is still in its infancy, and the generalization to molecules with large amplitude motions or molecular clusters is far from trivial, but many systems relevant for astrophysical studies are already in reach.
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Affiliation(s)
- Benjamin Schröder
- Institute
of Physical Chemistry, University of Goettingen, Tammannstrasse 6, Göttingen 37077, Germany
| | - Guntram Rauhut
- Institute
for Theoretical Chemistry, University of
Stuttgart, Pfaffenwaldring 55, Stuttgart 70569, Germany
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11
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Høyer NM, Christiansen O. Quasi-direct Quantum Molecular Dynamics: The Time-Dependent Adaptive Density-Guided Approach for Potential Energy Surface Construction. J Chem Theory Comput 2024; 20:558-579. [PMID: 38183272 DOI: 10.1021/acs.jctc.3c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
We present a new quasi-direct quantum molecular dynamics computational method which offers a compromise between quantum dynamics using a precomputed potential energy surface (PES) and fully direct quantum dynamics. This method is termed the time-dependent adaptive density-guided approach (TD-ADGA) and is a method for constructing a PES on the fly during a dynamics simulation. This is achieved by acquisition of new single-point (SP) calculations and refitting of the PES, depending on the need of the dynamics. The TD-ADGA is a further development of the adaptive density-guided approach (ADGA) for PES construction where the placement of SPs is guided by the density of the nuclear wave function. In TD-ADGA, the ADGA framework has been integrated into the time propagation of the time-dependent nuclear wave function and we use the reduced one-mode density of this wave function to guide when and where new SPs are placed. The PES is thus extended or updated if the wave function moves into new areas or if a certain area becomes more important. Here, we derive equations for the reduced one-mode density for the time-dependent Hartree (TDH) method and for multiconfiguration time-dependent Hartree (MCTDH) methods, but the TD-ADGA can be used with any time-dependent wave function method as long as a density is available. The TD-ADGA method has been investigated on molecular systems containing single- and double-minimum potentials and on single-mode and multi-mode systems. We explore different approaches to handle the fact that the TD-ADGA involves a PES that changes during the computation and show how results can be obtained that are in very good agreement with results obtained by using an accurate reference PES. Dynamics with TD-ADGA is essentially a black box procedure, where only the initialization of the system and how to compute SPs must be provided. The TD-ADGA thus makes it easier to carry out quantum molecular dynamics and the quasi-direct framework opens up the possibility to compute quantum dynamics accurately for larger molecular systems.
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Affiliation(s)
| | - Ove Christiansen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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12
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Oenen K, Dinu DF, Liedl KR. Determining internal coordinate sets for optimal representation of molecular vibration. J Chem Phys 2024; 160:014104. [PMID: 38180253 DOI: 10.1063/5.0180657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/10/2023] [Indexed: 01/06/2024] Open
Abstract
Arising from the harmonic approximation in solving the vibrational Schrödinger equation, normal modes dissect molecular vibrations into distinct degrees of freedom. Normal modes are widely used as they give rise to descriptive vibrational notations and are convenient for expanding anharmonic potential energy surfaces as an alternative to higher-order Taylor series representations. Usually, normal modes are expressed in Cartesian coordinates, which bears drawbacks that can be overcome by switching to internal coordinates. Considering vibrational notations, normal modes with delocalized characters are difficult to denote, but internal coordinates offer a route to clearer notations. Based on the Hessian, normal mode decomposition schemes for a given set of internal coordinates can describe a normal mode by its contributions from internal coordinates. However, choosing a set of internal coordinates is not straightforward. While the Hessian provides unique sets of normal modes, various internal coordinate sets are possible for a given system. In the present work, we employ a normal mode decomposition scheme to choose an optimal set. Therefore, we screen reasonable sets based on topology and symmetry considerations and rely on a metric that minimizes coupling between internal coordinates. Ultimately, the Nomodeco toolkit presented here generates internal coordinate sets to find an optimal set for representing molecular vibrations. The resulting contribution tables can be used to clarify vibrational notations. We test our scheme on small to mid-sized molecules, showing how the space of definable internal coordinate sets can significantly be reduced.
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Affiliation(s)
- Kemal Oenen
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Dennis F Dinu
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
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13
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Bader F, Lauvergnat D, Christiansen O. Vibrationally correlated calculations in polyspherical coordinates: Taylor expansion-based kinetic energy operators. J Chem Phys 2023; 159:214107. [PMID: 38047511 DOI: 10.1063/5.0171912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
The efficiency of quantum chemical simulations of nuclear motion can in many cases greatly benefit from the application of curvilinear coordinate systems. This is rooted in the fact that a set of smartly selected curvilinear coordinates may represent the motion naturally well, thus decreasing the couplings between motions in these coordinates. In this study, we assess the validity of different Taylor expansion-based approximations of kinetic energy operators in a (curvilinear) polyspherical parametrization. To this end, we investigate the accuracy as well as the numerical performance of the approximations in time-independent vibrational coupled cluster and full vibrational interaction calculations for several test cases ranging from tri- to penta-atomic molecules. We find that several of the proposed schemes reproduce the vibrational ground state and excitation energies to a decent accuracy, justifying their application in future investigations. Furthermore, due to the restricted mode coupling and their inherent sum-of-products form, the new approximations open up the possibility of treating large molecular systems with efficient vibrational coupled cluster schemes in general coordinates.
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Affiliation(s)
- F Bader
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - D Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - O Christiansen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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14
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De Vos J, Schröder B, Rauhut G. Comprehensive quantum chemical analysis of the (ro)vibrational spectrum of thiirane and its deuterated isotopologue. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:123083. [PMID: 37423098 DOI: 10.1016/j.saa.2023.123083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
The (ro)vibrational spectra of thiirane, c-C2H4S, and its fully deuterated isotopologue, c-C2D4S, have been studied by means of vibrational configuration interaction theory, VCI, its incremental variant, iVCI, and subsequent variational rovibrational calculations, RVCI, which rely on multidimensional potential energy surfaces of coupled-cluster quality including up to four-mode coupling terms. Accurate geometrical parameters, fundamental vibrational transitions and first overtones, rovibrational spectra and rotational spectroscopic constants have been determined from these calculations and were compared with experimental results whenever available. A number of tentative misassignments in the vibrational spectra could be resolved and most results for the deuterated thiirane are high-level predictions, which may guide experiments to come. Besides this, a new implementation of infrared intensities within the iVCI framework has been tested for the transitions of the title compounds and are compared with results obtained from standard VCI calculations.
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Affiliation(s)
- John De Vos
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany; Department of Chemistry, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium.
| | - Benjamin Schröder
- Institute for Physical Chemistry, University of Göttingen, Tammannstr. 6, 37077, Göttingen, Germany.
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany.
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15
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Yang EL, Talbot JJ, Spencer RJ, Steele RP. Pitfalls in the n-mode representation of vibrational potentials. J Chem Phys 2023; 159:204104. [PMID: 38010326 DOI: 10.1063/5.0176612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
Simulations of anharmonic vibrational motion rely on computationally expedient representations of the governing potential energy surface. The n-mode representation (n-MR)-effectively a many-body expansion in the space of molecular vibrations-is a general and efficient approach that is often used for this purpose in vibrational self-consistent field (VSCF) calculations and correlated analogues thereof. In the present analysis, a lack of convergence in many VSCF calculations is shown to originate from negative and unbound potentials at truncated orders of the n-MR expansion. For cases of strong anharmonic coupling between modes, the n-MR can both dip below the true global minimum of the potential surface and lead to effective single-mode potentials in VSCF that do not correspond to bound vibrational problems, even for bound total potentials. The present analysis serves mainly as a pathology report of this issue. Furthermore, this insight into the origin of VSCF non-convergence provides a simple, albeit ad hoc, route to correct the problem by "painting in" the full representation of groups of modes that exhibit these negative potentials at little additional computational cost. Somewhat surprisingly, this approach also reasonably approximates the results of the next-higher n-MR order and identifies groups of modes with particularly strong coupling. The method is shown to identify and correct problematic triples of modes-and restore SCF convergence-in two-mode representations of challenging test systems, including the water dimer and trimer, as well as protonated tropine.
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Affiliation(s)
- Emily L Yang
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Justin J Talbot
- Department of Chemistry, University of California-Berkeley, 420 Latimer Hall, Berkeley, California 94720, USA
| | - Ryan J Spencer
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Ryan P Steele
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
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16
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Broderick DR, Herbert JM. Scalable generalized screening for high-order terms in the many-body expansion: Algorithm, open-source implementation, and demonstration. J Chem Phys 2023; 159:174801. [PMID: 37921253 DOI: 10.1063/5.0174293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
The many-body expansion lies at the heart of numerous fragment-based methods that are intended to sidestep the nonlinear scaling of ab initio quantum chemistry, making electronic structure calculations feasible in large systems. In principle, inclusion of higher-order n-body terms ought to improve the accuracy in a controllable way, but unfavorable combinatorics often defeats this in practice and applications with n ≥ 4 are rare. Here, we outline an algorithm to overcome this combinatorial bottleneck, based on a bottom-up approach to energy-based screening. This is implemented within a new open-source software application ("Fragme∩t"), which is integrated with a lightweight semi-empirical method that is used to cull subsystems, attenuating the combinatorial growth of higher-order terms in the graph that is used to manage the calculations. This facilitates applications of unprecedented size, and we report four-body calculations in (H2O)64 clusters that afford relative energies within 0.1 kcal/mol/monomer of the supersystem result using less than 10% of the unique subsystems. We also report n-body calculations in (H2O)20 clusters up to n = 8, at which point the expansion terminates naturally due to screening. These are the largest n-body calculations reported to date using ab initio electronic structure theory, and they confirm that high-order n-body terms are mostly artifacts of basis-set superposition error.
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Affiliation(s)
- Dustin R Broderick
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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17
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Erba A, Desmarais JK, Casassa S, Civalleri B, Donà L, Bush IJ, Searle B, Maschio L, Edith-Daga L, Cossard A, Ribaldone C, Ascrizzi E, Marana NL, Flament JP, Kirtman B. CRYSTAL23: A Program for Computational Solid State Physics and Chemistry. J Chem Theory Comput 2023; 19:6891-6932. [PMID: 36502394 PMCID: PMC10601489 DOI: 10.1021/acs.jctc.2c00958] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Indexed: 12/14/2022]
Abstract
The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state physics for many years, since its first public version released back in 1988. This peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals (LCAO) approach and from the corresponding efficiency in the evaluation of the exact Fock exchange series. In particular, this has led to the implementation of a rich variety of hybrid density functional approximations since 1998. Nowadays, it is acknowledged by a broad community of solid state chemists and physicists that the inclusion of a fraction of Fock exchange in the exchange-correlation potential of the density functional theory is key to a better description of many properties of materials (electronic, magnetic, mechanical, spintronic, lattice-dynamical, etc.). Here, the main developments made to the program in the last five years (i.e., since the previous release, Crystal17) are presented and some of their most noteworthy applications reviewed.
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Affiliation(s)
- Alessandro Erba
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jacques K. Desmarais
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Silvia Casassa
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Bartolomeo Civalleri
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Lorenzo Donà
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Ian J. Bush
- STFC
Rutherford Appleton Laboratory, Chilton Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Barry Searle
- SFTC
Daresbury Laboratory, Daresbury, Cheshire WA4 4AD, United Kingdom
| | - Lorenzo Maschio
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Loredana Edith-Daga
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Alessandro Cossard
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Chiara Ribaldone
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Eleonora Ascrizzi
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Naiara L. Marana
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jean-Pierre Flament
- Université
de Lille, CNRS, UMR 8523 — PhLAM — Physique des Lasers, Atomes et Molécules, 59000 Lille, France
| | - Bernard Kirtman
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
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18
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Sharma D, Roy TK. Accuracy of Different Electronic Basis Set Families for Anharmonic Molecular Vibrations: A Comprehensive Benchmark Study. J Phys Chem A 2023; 127:7132-7147. [PMID: 37603414 DOI: 10.1021/acs.jpca.3c02874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
In this work, the accuracy and convergence of different electronic basis set families for the computation of anharmonic molecular vibrational spectroscopic calculations are benchmarked. A series of 39 different basis sets from different families following their hierarchy are assessed on VSCF and VSCF-PT2 algorithms with commonly used MP2 and DFT based B3LYP-D potentials for a set of molecular systems. Such an effort has been validated in a previous work ( J. Phys. Chem. A 2020, 124, 9203-9221) with split-valence basis sets for fundamentals and intensities. Here, fundamental transitions, vibrationally excited states, and intensities are compared with the experimental data to estimate the accuracy for a series of Jensen, Dunning, Calendar, Karlsruhe, and Sapporo basis set families. The convergence of basis sets are also compared with the large ANO basis set. Comprehensive statistical error analysis in terms of accuracy and precision was carried out to assess the performance of each basis set. It is observed that the improvement for the calculated harmonic and anharmonic values from the smaller basis sets to the medium (i.e., triple-ξ) is considerable. Beyond this, from medium to large basis sets, the convergence is slow and mostly posits nearly converged values. Basis sets with and without diffuse functions offer characteristically different accuracies and convergence patterns. Finally, recommendations are given on the choice of basis set chosen as black-box which can balance between accuracy and computational time, estimation of the errors, and their selections especially for large molecules.
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Affiliation(s)
- Dhiksha Sharma
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, J&K 181143 India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, J&K 181143 India
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19
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Zhanserkeev AA, Yang EL, Steele RP. Accelerating Anharmonic Spectroscopy Simulations via Local-Mode, Multilevel Methods. J Chem Theory Comput 2023; 19:5572-5585. [PMID: 37555634 DOI: 10.1021/acs.jctc.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Ab initio computer simulations of anharmonic vibrational spectra provide nuanced insight into the vibrational behavior of molecules and complexes. The computational bottleneck in such simulations, particularly for ab initio potentials, is often the generation of mode-coupling potentials. Focusing specifically on two-mode couplings in this analysis, the combination of a local-mode representation and multilevel methods is demonstrated to be particularly symbiotic. In this approach, a low-level quantum chemistry method is employed to predict the pairwise couplings that should be included at the target level of theory in vibrational self-consistent field (and similar) calculations. Pairs that are excluded by this approach are "recycled" at the low level of theory. Furthermore, because this low-level pre-screening will eventually become the computational bottleneck for sufficiently large chemical systems, distance-based truncation is applied to these low-level predictions without substantive loss of accuracy. This combination is demonstrated to yield sub-wavenumber fidelity with reference vibrational transitions when including only a small fraction of target-level couplings; the overhead of predicting these couplings, particularly when employing distance-based, local-mode cutoffs, is a trivial added cost. This combined approach is assessed on a series of test cases, including ethylene, hexatriene, and the alanine dipeptide. Vibrational self-consistent field (VSCF) spectra were obtained with an RI-MP2/cc-pVTZ potential for the dipeptide, at approximately a 5-fold reduction in computational cost. Considerable optimism for increased accelerations for larger systems and higher-order couplings is also justified, based on this investigation.
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Affiliation(s)
- Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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20
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Dahlmann F, Dinu DF, Jusko P, Lochmann C, Gstir T, Marimuthu AN, Liedl KR, Brünken S, Wester R. Vibrational Predissociation Spectra of C 2 N - and C 3 N - : Bending and Stretching Vibrations. Chemphyschem 2023; 24:e202300262. [PMID: 37199236 PMCID: PMC10962567 DOI: 10.1002/cphc.202300262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/19/2023]
Abstract
We present infrared predissociation spectra of C2 N- (H2 ) and C 3 N- (H2 ) in the 300-1850 cm-1 range. Measurements were performed using the FELion cryogenic ion trap end user station at the Free Electron Lasers for Infrared eXperiments (FELIX) laboratory. For C2 N- (H2 ), we detected the CCN bending and CC-N stretching vibrations. For the C3 N- (H2 ) system, we detected the CCN bending, the CC-CN stretching, and multiple overtones and/or combination bands. The assignment and interpretation of the presented experimental spectra is validated by calculations of anharmonic spectra within the vibrational configuration interaction (VCI) approach, based on potential energy surfaces calculated at explicitly correlated coupled cluster theory (CCSD(T)-F12/cc-pVTZ-F12). The H2 tag acts as an innocent spectator, not significantly affecting the C2,3 N- bending and stretching mode positions. The recorded infrared predissociation spectra can thus be used as a proxy for the vibrational spectra of the bare anions.
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Affiliation(s)
- Franziska Dahlmann
- Institut für Ionenphysik und Angewandte PhysikUniversität InnsbruckTechnikerstraße 256020InnsbruckAustria
| | - Dennis F. Dinu
- Department of GeneralInorganic and Theoretical ChemistryUniversität InnsbruckInnrain 80/826020InnsbruckAustria
| | - Pavol Jusko
- Max Planck Institute for Extraterrestrial PhysicsGießenbachstraße 185748GarchingGermany
| | - Christine Lochmann
- Institut für Ionenphysik und Angewandte PhysikUniversität InnsbruckTechnikerstraße 256020InnsbruckAustria
| | - Thomas Gstir
- Institut für Ionenphysik und Angewandte PhysikUniversität InnsbruckTechnikerstraße 256020InnsbruckAustria
| | - Aravindh N. Marimuthu
- Radboud UniversityInstitute for Molecules and MaterialsFELIX LaboratoryToernooiveld 76525EDNijmegen, theNetherlands
| | - Klaus R. Liedl
- Department of GeneralInorganic and Theoretical ChemistryUniversität InnsbruckInnrain 80/826020InnsbruckAustria
| | - Sandra Brünken
- Radboud UniversityInstitute for Molecules and MaterialsFELIX LaboratoryToernooiveld 76525EDNijmegen, theNetherlands
| | - Roland Wester
- Institut für Ionenphysik und Angewandte PhysikUniversität InnsbruckTechnikerstraße 256020InnsbruckAustria
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21
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Artiukhin DG, Godtliebsen IH, Schmitz G, Christiansen O. Gaussian process regression adaptive density-guided approach: Toward calculations of potential energy surfaces for larger molecules. J Chem Phys 2023; 159:024102. [PMID: 37428042 DOI: 10.1063/5.0152367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023] Open
Abstract
We present a new program implementation of the Gaussian process regression adaptive density-guided approach [Schmitz et al., J. Chem. Phys. 153, 064105 (2020)] for automatic and cost-efficient potential energy surface construction in the MidasCpp program. A number of technical and methodological improvements made allowed us to extend this approach toward calculations of larger molecular systems than those previously accessible and maintain the very high accuracy of constructed potential energy surfaces. On the methodological side, improvements were made by using a Δ-learning approach, predicting the difference against a fully harmonic potential, and employing a computationally more efficient hyperparameter optimization procedure. We demonstrate the performance of this method on a test set of molecules of growing size and show that up to 80% of single point calculations could be avoided, introducing a root mean square deviation in fundamental excitations of about 3 cm-1. A much higher accuracy with errors below 1 cm-1 could be achieved with tighter convergence thresholds still reducing the number of single point computations by up to 68%. We further support our findings with a detailed analysis of wall times measured while employing different electronic structure methods. Our results demonstrate that GPR-ADGA is an effective tool, which could be applied for cost-efficient calculations of potential energy surfaces suitable for highly accurate vibrational spectra simulations.
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Affiliation(s)
- Denis G Artiukhin
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Ian H Godtliebsen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
| | - Gunnar Schmitz
- Lehrstuhl für Theoretische Chemie II, Ruhr-Universität Bochum, Universitätstraße 150, 44801 Bochum, Germany
| | - Ove Christiansen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
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22
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Tan JA, Barbarona RF, Kuo JL. Approaching the "Zundel" Limit: Tuning the Vibrational Coupling in N 2H +Ng, Ng = {He, Ne, Ar, Kr, Xe, and Rn}. J Phys Chem A 2023. [PMID: 37418837 DOI: 10.1021/acs.jpca.3c01956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
The diazenylium ion (N2H+) is a ubiquitous ion in dense molecular clouds. This ion is often used as a dense gas tracer in outer space. Most of the previous works on diazenylium ion have focused on the shared-proton stretch band, νH+. In this work, we have performed reduced-dimensional calculations to investigate the vibrational structure of N2H+Ng, Ng = {He, Ne, Ar, Kr, Xe, and Rn}. We demonstrate a few interesting things about this system. First, the vibrational coupling in N2H+ can be tuned to switch on interesting anharmonic effects such as Fermi resonance or combination bands by tagging it with different noble gases. Second, a comparison of the vibrational spectrum from N2H+He to N2H+Rn shows that the νH+ can be swept from an "Eigen-like" to a "Zundel-like" limiting case. Anharmonic calculations were performed using a multilevel approach, which utilized the MP2 and CCSD(T) levels of theories. Binding energies for the elimination of Ng in N2H+Ng are also reported.
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Affiliation(s)
- Jake A Tan
- Institute of Atomic and Molecular Science, Academia Sinica, Taipei 10617, Taiwan
| | - Rona F Barbarona
- Institute of Atomic and Molecular Science, Academia Sinica, Taipei 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Physics, National Central University, Taoyuan 32001, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Science, Academia Sinica, Taipei 10617, Taiwan
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
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23
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Schiltz C, Rappoport D, Mandelshtam VA. Implementation of the self-consistent phonons method with ab initio potentials (AI-SCP). J Chem Phys 2023; 158:2890485. [PMID: 37184023 DOI: 10.1063/5.0146682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/24/2023] [Indexed: 05/16/2023] Open
Abstract
The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate its various dynamic and static properties. In this paper, we combine SCP with ab initio (AI) potential energy evaluation in which case the numerical bottleneck of AI-SCP is the evaluation of Gaussian averages of the AI potential energy and its derivatives. These averages are computed efficiently by the quasi-Monte Carlo method utilizing low-discrepancy sequences leading to a fast convergence with respect to the number, S, of the AI energy evaluations. Moreover, a further substantial (an-order-of-magnitude) improvement in efficiency is achieved once a numerically cheap approximation of the AI potential is available. This is based on using a perturbation theory-like (the two-grid) approach in which it is the average of the difference between the AI and the approximate potential that is computed. The corresponding codes and scripts are provided.
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Affiliation(s)
- Colin Schiltz
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | - Dmitrij Rappoport
- Department of Chemistry, University of California, Irvine, California 92697, USA
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24
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Trabelsi T, Francisco JS. Spectroscopic characterization of [H, Cl, S, O] molecular system: Potential candidate for detection in Venus atmosphere. J Chem Phys 2023; 158:2887767. [PMID: 37129141 DOI: 10.1063/5.0146450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023] Open
Abstract
Accurate spectroscopic parameters have been obtained for the identification of the [H, Cl, S, O] molecular system in the Venus atmosphere using computational methods. These calculations employed both standard and explicitly correlated coupled cluster techniques. All isomers possess C1 symmetry, with HOSCl being the most stable isomer. Only HOSCl and trigonal-HSOCl isomers are thermodynamically stable relative to the first dissociation limit HCl + SO. Fundamental modes of the lowest three isomers exhibit many anharmonic resonances, resulting in complex spectra. All isomers are found to be stable in the visible region as the calculation of vertical energy transition indicates. No electronic states were found to strongly absorb in the near UV-vis region.
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Affiliation(s)
- Tarek Trabelsi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, USA
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, USA
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25
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Schneider M, Born D, Kästner J, Rauhut G. Positioning of grid points for spanning potential energy surfaces-How much effort is really needed? J Chem Phys 2023; 158:144118. [PMID: 37061506 DOI: 10.1063/5.0146020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
The positions of grid points for representing a multidimensional potential energy surface (PES) have a non-negligible impact on its accuracy and the associated computational effort for its generation. Six different positioning schemes were studied for PESs represented by n-mode expansions as needed for the accurate calculation of anharmonic vibrational frequencies by means of vibrational configuration interaction theory. A static approach, which has successfully been used in many applications, and five adaptive schemes based on Gaussian process regression have been investigated with respect to the number of necessary grid points and the accuracy of the fundamental modes for a small set of test molecules. A comparison with a related, more sophisticated, and consistent approach by Christiansen et al. is provided. The impact of the positions of the ab initio grid points is discussed for multilevel PESs, for which the computational effort of the individual electronic structure calculations decreases for increasing orders of the n-mode expansion. As a result of that, the ultimate goal is not the maximal reduction of grid points but rather the computational cost, which is not directly related.
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Affiliation(s)
- Moritz Schneider
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Daniel Born
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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26
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Fayaz A, Banik S, Kanchan Roy T. The importance of electron correlations on vibrational anharmonicities and potential energy surfaces. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2023.114059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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27
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Tschöpe M, Rauhut G. Convergence of series expansions in rovibrational configuration interaction (RVCI) calculations. J Chem Phys 2022; 157:234105. [PMID: 36550038 DOI: 10.1063/5.0129828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Rotational and rovibrational spectra are a key in astrophysical studies, atmospheric science, pollution monitoring, and other fields of active research. The ab initio calculation of such spectra is fairly sensitive with respect to a multitude of parameters and all of them must be carefully monitored in order to yield reliable results. Besides the most obvious ones, i.e., the quality of the multidimensional potential energy surface and the vibrational wavefunctions, it is the representation of the μ-tensor within the Watson Hamiltonian, which has a significant impact on the desired line lists or simulated spectra. Within this work, we studied the dependence of high-resolution rovibrational spectra with respect to the truncation order of the μ-tensor within the rotational contribution and the Coriolis coupling operator of the Watson operator. Moreover, the dependence of the infrared intensities of the rovibrational transitions on an n-mode expansion of the dipole moment surface has been investigated as well. Benchmark calculations are provided for thioformaldehyde, which has already served as a test molecule in other studies and whose rovibrational spectrum was found to be fairly sensitive. All calculations rely on rovibrational configuration interaction theory and the discussed high-order terms of the μ-tensor are a newly implemented feature, whose theoretical basics are briefly discussed.
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Affiliation(s)
- Martin Tschöpe
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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28
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Vibrational Spectrum of ‘3-iodo-2-propynenitrile (IC3N)’ from accurate CCSD(T)-F12b/MP2-F12 potential energy surface. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02923-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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29
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Tan JA, Kuo JL. Spectral Signatures of Protonated Noble Gas Clusters of Ne, Ar, Kr, and Xe: From Monomers to Trimers. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103198. [PMID: 35630674 PMCID: PMC9143425 DOI: 10.3390/molecules27103198] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/08/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022]
Abstract
The structures and spectral features of protonated noble gas clusters are examined using a first principles approach. Protonated noble gas monomers (NgH+) and dimers (NgH+Ng) have a linear structure, while the protonated noble gas trimers (Ng3H+) can have a T-shaped or linear structure. Successive binding energies for these complexes are calculated at the CCSD(T)/CBS level of theory. Anharmonic simulations for the dimers and trimers unveil interesting spectral features. The symmetric NgH+Ng are charactized by a set of progression bands, which involves one quantum of the asymmetric Ng-H+ stretch with multiple quanta of the symmetric Ng-H+ stretch. Such a spectral signature is very robust and is predicted to be observed in both T-shaped and linear isomers of Ng3H+. Meanwhile, for selected asymmetric NgH+Ng’, a Fermi resonance interaction involving the first overtone of the proton bend with the proton stretch is predicted to occur in ArH+Kr and XeH+Kr.
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30
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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
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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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31
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Schröder B, Rauhut G. Comparison of body definitions for incremental vibrational configuration interaction theory (iVCI). J Chem Phys 2022; 156:174103. [DOI: 10.1063/5.0085082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Within incremental vibrational configuration interaction theory (iVCI), the vibrational state energy is determined by means of a many-body expansion, i.e., it is a sum of terms of increasing order, which allow for an embarrassingly parallel evaluation. The convergence of this expansion depends strongly on the definition of the underlying bodies, which essentially decompose the correlation space into fragments. The different definitions considered here comprise mode-based bodies, excitation level-based bodies, and energy-based bodies. An analysis of the convergence behavior revealed that accounting for resonances within these definitions is mandatory and leads to a substantial improvement of the convergence, that is, the expansions can be truncated at lower orders. Benchmark calculations and systematic comparisons of the different body definitions for a small set of molecules, i.e., ketene, ethene, and diborane, have been conducted to study the overall performance of these iVCI implementations with respect to accuracy and central processing unit time.
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Affiliation(s)
- Benjamin Schröder
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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32
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Erfort S, Tschoepe M, Rauhut G. Efficient and Automated Quantum Chemical Calculation of Rovibrational Nonresonant Raman Spectra. J Chem Phys 2022; 156:124102. [DOI: 10.1063/5.0087359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
An outline of a newly developed program for the simulation of rovibrational nonresonant Raman spectra is presented. This program is an extension of our recently developed code for rovibrational infrared spectra [J. Chem Phys. 152 (2020) 244104] and relies on vibrational wavefunctions from variational configuration interaction theory to allow for an almost fully automated calculation of such spectra in pure ab initio fashion. Due to efficient contraction schemes this program requires modest computational resources and it can be controlled by only a few lines of input. As the required polarizability surfaces are also computed in an automated fashion, this implementation enables the routine application to small molecules. For demonstrating its capabilities, benchmark calculations for water H216O are compared to reference data and spectra for the beryllium dihydride dimer, Be2H4 (D2h), are predicted. The inversion symmetry of the D2h systems lead to complementary infrared and Raman spectra, which are needed both for a comprehensive investigation of this system.
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Affiliation(s)
- Sebastian Erfort
- Institute for Theoretical Chemistry, University of Stuttgart Faculty of Chemistry, Germany
| | | | - Guntram Rauhut
- Institut fuer Theoretische Chemie, University of Stuttgart Faculty of Chemistry, Germany
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33
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Roy TK. Performance of Vibrational Self-Consistent Field Theory for Accurate Potential Energy Surfaces: Fundamentals, Excited States, and Intensities. J Phys Chem A 2022; 126:608-622. [PMID: 35050620 DOI: 10.1021/acs.jpca.1c09989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The performance of vibrational structure calculations beyond harmonic approximation in the framework of the vibrational self-consistent field method with second-order perturbation corrections (VSCF-PT2) is investigated in conjunction with very accurate potential energy surfaces (PESs) given by various coupled-cluster electronic structure theories. The quality of anharmonic calculations depends on the accuracy of the underlying multidimensional PES obtained from its functional form, which is given by the level of electronic structure theory. Two such highest levels of typical coupled-cluster electronic structure methods, CCSD and the ″gold standard″ CCSD(T), along with their variants such as CCD, CR-CCL (completely renormalized CR-CC(2,3) approach), and CCSD(TQ) are tested for the construction of accurate anharmonic potentials without any fitting or ad hoc scaling and using cc-pVTZ basis sets. The accuracy of VSCF-PT2 theory in comparison to experimental values is tested for a series of 16 molecules with 135 fundamental bands, 64 overtones, and combination bands and also for 39 intensities. It is found that CCD and CCSD bind the potential tighter than CCSD(T) and the computed VSCF-PT2 transitions are more blue-shifted showing higher deviation from the experiment. In general, VSCF-PT2 results computed at the CCSD(T) potential offer a good cost/accuracy ratio, with the mean absolute deviation and the mean absolute percentage error with the experiment being ∼16 cm-1 and 1.38, respectively, for fundamentals. Additionally, while the CR-CCL and CCSD(TQ) methods offer similar levels of accuracies as compared to CCSD(T), the former offers a better accuracy/cost ratio than the latter and is a suitable alternative to CCSD(T).
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Samba, Jammu and Kashmir 181143, India
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34
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Mathea T, Rauhut G. Advances in vibrational configuration interaction theory - part 1: Efficient calculation of vibrational angular momentum terms. J Comput Chem 2021; 42:2321-2333. [PMID: 34651703 DOI: 10.1002/jcc.26762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 02/02/2023]
Abstract
Finite basis vibrational configuration interaction theory (VCI) is a highly accurate method for the variational calculation of state energies and related properties, but suffers from fast growing computational costs in dependence of the size of the correlation space. In this series of papers, concepts and techniques will be presented, which diminish the computational demands and thus broaden the applicability of this method to larger molecules or more complex situations. This first part focuses on a highly efficient implementation of the vibrational angular momentum (VAM) terms as occurring in the Watson Hamiltonian and the prediagonalization of initial subspaces within an iterative configuration selective VCI implementation. Working equations and benchmark calculations are provided, the latter demonstrating the increased performance of the new algorithm.
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Affiliation(s)
- Tina Mathea
- Institute for Theoretical Chemistry, University of Stuttgart, Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Stuttgart, Germany
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35
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Barlow KR, Goodlett SM, Arradondo SN, Tschumper GS. Fundamental vibrational frequencies of isolated 2-phosphaethynolate and 2-phosphaethynthiolate anions: OCP – and SCP –. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1967495] [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)
- Kayleigh R. Barlow
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA
| | - Stephen M. Goodlett
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA
| | | | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA
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36
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Maiti KS. Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein. Molecules 2021; 26:molecules26226893. [PMID: 34833985 PMCID: PMC8618531 DOI: 10.3390/molecules26226893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.
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Affiliation(s)
- Kiran Sankar Maiti
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; ; Tel.: +49-89-289-54056
- Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Coulombwall 1, 85748 Garching, Germany
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37
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Tan JA, Teh S, Kuo JL. Structural and vibrational characterization of HCO + and Rg-HCO +, Rg = {He, Ne, Ar, Kr, and Xe}. J Chem Phys 2021; 155:174306. [PMID: 34742194 DOI: 10.1063/5.0069726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structures of the formyl ion (HCO+) and its rare gas tagged counterparts (Rg-HCO+, Rg = He, Ne, Ar, Kr, and Xe) were studied at the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)]/aug-cc-pVTZ level of theory and basis set. A linear structure for these tagged complexes was predicted. The Rg binding energies for Rg-HCO+ are also examined at the CCSD(T) level. It was found that the binding interaction increases from He-HCO+ to Xe-HCO+. A multilevel potential energy surface built at the CCSD(T) and second-order Møller-Plesset perturbation levels of theory were used to study these species' vibrational spectra. By changing the Rg in the first-solvation shell for HCO+, the Fermi resonance interaction between the first H+ bend overtone and the asymmetric and symmetric H-C-O stretches can be modulated. This Fermi resonance modulation is demonstrated by examining a series of rare gas solvated HCO+.
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Affiliation(s)
- Jake A Tan
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Da-an District, Taipei City 10617, Taiwan
| | - Soon Teh
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Da-an District, Taipei City 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Da-an District, Taipei City 10617, Taiwan
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38
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Qian W, Lu B, Tan G, Rauhut G, Grützmacher H, Zeng X. Vibrational spectrum and photochemistry of phosphaketene HPCO. Phys Chem Chem Phys 2021; 23:19237-19243. [PMID: 34524290 DOI: 10.1039/d1cp02860j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational spectra of the simplest phosphaketene HPCO and its isotopologue DPCO in solid Ar-matrices at 12.0 K have been analyzed with the aid of the computations at the CCSD(T)-F12a/cc-pVTZ-F12 level using configuration-selective vibrational configuration interaction (VCI). In addition to the four IR fundamentals, four overtone and ten combination bands have been unambiguously identified. Furthermore, the photochemistry of HPCO in the matrix has been investigated for the first time. Upon UV-light irradiation (365 or 266 nm), CO-elimination occurs by forming the parent phosphinidene HP that can be trapped by ˙NO to yield the elusive phosphinimine-N-oxyl radical HPNO˙. In contrast, an excimer laser (193 nm) irradiation of HPCO causes additional decomposition to H˙ and ˙PCO with concomitant formation of the long-sought phosphaethyne HOCP.
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Affiliation(s)
- Weiyu Qian
- Department of Chemistry, Fudan University, 200433 Shanghai, China.
| | - Bo Lu
- Department of Chemistry, Fudan University, 200433 Shanghai, China.
| | - Gengwen Tan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 215123 Suzhou, China.
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, Stuttgart 70569, Germany
| | | | - Xiaoqing Zeng
- Department of Chemistry, Fudan University, 200433 Shanghai, China.
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39
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Yagi K, Sugita Y. Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin. J Chem Theory Comput 2021; 17:5007-5020. [PMID: 34296615 PMCID: PMC10986902 DOI: 10.1021/acs.jctc.1c00060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An efficient anharmonic vibrational method is developed exploiting the locality of molecular vibration. Vibrational coordinates localized to a group of atoms are employed to divide the potential energy surface (PES) of a system into intra- and inter-group contributions. Then, the vibrational Schrödinger equation is solved based on a PES, in which the inter-group coupling is truncated at the harmonic level while accounting for the intra-group anharmonicity. The method is applied to a pentagonal hydrogen bond network (HBN) composed of internal water molecules and charged residues in a membrane protein, bacteriorhodopsin. The PES is calculated by the quantum mechanics/molecular mechanics (QM/MM) calculation at the level of B3LYP-D3/aug-cc-pVDZ. The infrared (IR) spectrum is computed using a set of coordinates localized to each water molecule and amino acid residue by second-order vibrational quasi-degenerate perturbation theory (VQDPT2). Benchmark calculations show that the proposed method yields the N-D/O-D stretching frequencies with an error of 7 cm-1 at the cost reduced by more than five times. In contrast, the harmonic approximation results in a severe error of 150 cm-1. Furthermore, the size of QM regions is carefully assessed to find that the QM regions should include not only the pentagonal HBN itself but also its HB partners. VQDPT2 calculations starting from transient structures obtained by molecular dynamics simulations have shown that the structural sampling has a significant impact on the calculated IR spectrum. The incorporation of anharmonicity, sufficiently large QM regions, and structural samplings are of essential importance to reproduce the experimental IR spectrum. The computational spectrum paves the way for decoding the IR signal of strong HBNs and helps elucidate their functional roles in biomolecules.
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Affiliation(s)
- Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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40
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Ji T, Zhu B, Zhao J, Yu W, Wang X. Infrared Spectra and Theoretical Calculations of BSe 2 and BSe 2-: The Pseudo-Jahn-Teller Effect. J Phys Chem A 2021; 125:3606-3613. [PMID: 33891822 DOI: 10.1021/acs.jpca.1c01345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Matrix isolation infrared spectroscopy has been employed to study the reaction of laser-ablated boron atoms with hydrogen selenide in a 5 K solid argon matrix. On the basis of the isotopic shifts as well as the theoretical frequency calculations, triatomic molecule BSe2 and its anion BSe2- were identified. Both BSe2 and BSe2- were predicted to have D∞h symmetric structures with nearly identical structure parameters and bond strengths by quantum chemical calculations. Whereas the observed antisymmetric B-Se stretching frequency of BSe2 is much lower than that of BSe2-, the anomalously low antisymmetric B-Se stretching frequency of BSe2 is attributed to a pseudo-Jahn-Teller effect due to the mixing of the X2Πg ground state with the A2Πu excited state. In addition, H2BSe, HBSe, and HSeBSe molecules were produced in the reaction.
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Affiliation(s)
- Ting Ji
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Bixue Zhu
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Jie Zhao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China.,School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
| | - Wenjie Yu
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xuefeng Wang
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
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41
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Tan JA, Kuo JL. Fermi resonance switching in KrH +Rg and XeH +Rg (Rg = Ne, Ar, Kr, and Xe). J Chem Phys 2021; 154:134302. [PMID: 33832263 DOI: 10.1063/5.0044703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Matrix isolation experiments have been successfully employed to extensively study the infrared spectrum of several proton-bound rare gas complexes. Most of these studies have focused on the spectral signature for the H+ stretch (ν3) and its combination bands with the intermolecular stretch coordinate (ν1). However, little attention has been paid to the Fermi resonance interaction between the H+ stretch (ν3) and H+ bend overtone (2ν2) in the asymmetric proton-bound rare gas dimers, RgH+Rg'. In this work, we have investigated this interaction on KrH+Rg and XeH+Rg with Rg = (Ne, Ar, Kr, and Xe). A multilevel potential energy surface (PES) was used to simulate the vibrational structure of these complexes. This PES is a dual-level comprising of second-order Møller-Plesset perturbation theory and coupled-cluster singles doubles with perturbative triples [CCSD(T)] levels of ab initio theories. We found that when both the combination bands (nν1 + ν3) and bend overtone 2ν2 compete to borrow intensity from the ν3 band, the latter wins over the former, which then results in the suppression of the nν1 + ν3 bands. The current simulations offer new assignments for the ArH+Xe and KrH+Xe spectra. Complete basis set (CBS) binding energies for these complexes were also calculated at the CCSD(T)/CBS level.
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Affiliation(s)
- Jake A Tan
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Da-an District, Taipei City 10617, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Da-an District, Taipei City 10617, Taiwan
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42
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Schröder B, Rauhut G. Incremental vibrational configuration interaction theory, iVCI: Implementation and benchmark calculations. J Chem Phys 2021; 154:124114. [DOI: 10.1063/5.0045305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Benjamin Schröder
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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43
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Bader F, Tremblay JC, Paulus B. A pair potential modeling study of F3− in neon matrices. Phys Chem Chem Phys 2021; 23:886-899. [DOI: 10.1039/d0cp05031h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
First-principles investigations of the trifluoride anion in a neon environment reveal a small blue-shift of the fundamental vibrational excitations.
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Affiliation(s)
- Frederik Bader
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- D-14195, Berlin
- Germany
| | | | - Beate Paulus
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- D-14195, Berlin
- Germany
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44
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Dinu DF, Podewitz M, Grothe H, Loerting T, Liedl KR. On the synergy of matrix-isolation infrared spectroscopy and vibrational configuration interaction computations. Theor Chem Acc 2020; 139:174. [PMID: 33192169 PMCID: PMC7652801 DOI: 10.1007/s00214-020-02682-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 10/05/2020] [Indexed: 11/08/2022]
Abstract
The key feature of matrix-isolation infrared (MI-IR) spectroscopy is the isolation of single guest molecules in a host system at cryogenic conditions. The matrix mostly hinders rotation of the guest molecule, providing access to pure vibrational features. Vibrational self-consistent field (VSCF) and configuration interaction computations (VCI) on ab initio multimode potential energy surfaces (PES) give rise to anharmonic vibrational spectra. In a single-sourced combination of these experimental and computational approaches, we have established an iterative spectroscopic characterization procedure. The present article reviews the scope of this procedure by highlighting the strengths and limitations based on the examples of water, carbon dioxide, methane, methanol, and fluoroethane. An assessment of setups for the construction of the multimode PES on the example of methanol demonstrates that CCSD(T)-F12 level of theory is preferable to compute (a) accurate vibrational frequencies and (b) equilibrium or vibrationally averaged structural parameters. Our procedure has allowed us to uniquely assign unknown or disputed bands and enabled us to clarify problematic spectral regions that are crowded with combination bands and overtones. Besides spectroscopic assignment, the excellent agreement between theory and experiment paves the way to tackle questions of rather fundamental nature as to whether or not matrix effects are systematic, and it shows the limits of conventional notations used by spectroscopists.
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Affiliation(s)
- Dennis F Dinu
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria.,Institute of Material Chemistry, TU Vienna, Vienna, Austria.,Institute of Physical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Hinrich Grothe
- Institute of Material Chemistry, TU Vienna, Vienna, Austria
| | - Thomas Loerting
- Institute of Physical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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45
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Roy TK, Gerber RB. Dual Basis Approach for Ab Initio Anharmonic Calculations of Vibrational Spectroscopy: Application to Microsolvated Biomolecules. J Chem Theory Comput 2020; 16:7005-7016. [PMID: 32991804 DOI: 10.1021/acs.jctc.0c00725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A dual electronic basis set approach is introduced for more efficient but accurate calculations of the anharmonic vibrational spectra in the framework of the vibrational self-consistent field (VSCF) theory. In this approach, an accurate basis set is used to compute the vibrational spectra at the harmonic level. The results are used to scale the potential surface from a more modest but much more efficient basis set. The scaling is such that at the harmonic level the new, scaled potential agrees with one of the accurate basis sets. The approach is tested in the application of the microsolvated, protected amino acid Ac-Phe-OMe, using the scaled anharmonic hybrid potential in the VSCF and VSCF-PT2 algorithms. The hybrid potential method yields results that are in good accord with the experiment and very close to those obtained in calculations with the high-level, very costly potential from the large basis set. At the same time, the hybrid potential calculations are considerably less expensive. The results of the hybrid calculations are much more accurate than those computed from the potential surface corresponding to the modest basis set. The results are very encouraging for using the hybrid potential method for inexpensive yet sufficiently accurate anharmonic calculations for the spectra of large biomolecules.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Dist: Samba Jammu-181143, India
| | - R Benny Gerber
- Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel.,Department of Chemistry, University of California, Irvine, California 92697, United States
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46
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Mitra H, Roy TK. Comprehensive Benchmark Results for the Accuracy of Basis Sets for Anharmonic Molecular Vibrations. J Phys Chem A 2020; 124:9203-9221. [DOI: 10.1021/acs.jpca.0c06634] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hrishit Mitra
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
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47
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Manzhos S, Carrington T. Neural Network Potential Energy Surfaces for Small Molecules and Reactions. Chem Rev 2020; 121:10187-10217. [PMID: 33021368 DOI: 10.1021/acs.chemrev.0c00665] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We review progress in neural network (NN)-based methods for the construction of interatomic potentials from discrete samples (such as ab initio energies) for applications in classical and quantum dynamics including reaction dynamics and computational spectroscopy. The main focus is on methods for building molecular potential energy surfaces (PES) in internal coordinates that explicitly include all many-body contributions, even though some of the methods we review limit the degree of coupling, due either to a desire to limit computational cost or to limited data. Explicit and direct treatment of all many-body contributions is only practical for sufficiently small molecules, which are therefore our primary focus. This includes small molecules on surfaces. We consider direct, single NN PES fitting as well as more complex methods that impose structure (such as a multibody representation) on the PES function, either through the architecture of one NN or by using multiple NNs. We show how NNs are effective in building representations with low-dimensional functions including dimensionality reduction. We consider NN-based approaches to build PESs in the sums-of-product form important for quantum dynamics, ways to treat symmetry, and issues related to sampling data distributions and the relation between PES errors and errors in observables. We highlight combinations of NNs with other ideas such as permutationally invariant polynomials or sums of environment-dependent atomic contributions, which have recently emerged as powerful tools for building highly accurate PESs for relatively large molecular and reactive systems.
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Affiliation(s)
- Sergei Manzhos
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650, Boulevard Lionel-Boulet, Varennes, Québec City, Québec J3X 1S2, Canada
| | - Tucker Carrington
- Chemistry Department, Queen's University, Kingston Ontario K7L 3N6, Canada
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Zhao J, Ji T, Xiao X, Wang X, Beckers H, Riedel S. Charge-Inverted Hydrogen-Bridged Bond in HCa(μ-H) 3E (E = Si, Ge, and Sn): Matrix Isolation Infrared Spectroscopic and Theoretical Studies. Inorg Chem 2020; 59:14355-14366. [PMID: 32975409 DOI: 10.1021/acs.inorgchem.0c02132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Matrix isolation infrared spectroscopy combined with quantum-chemical calculations were employed to study the reactions of calcium atoms with silane, germane, and stannane in a 4 K argon matrix. The ion pairs [HCa]+ and [EH3]- (E = Si, Ge, and Sn) in both the classical structure HCaEH3 and the bridged structure HCa(μ-H)3E were identified based on the H/D isotopic substitution experiments and quantum-chemical calculations. The results show that the reaction between ground-state Ca and EH4 proceeds inefficiently, and only after the photolytic activation of Ca atoms to the Ca(1P:4s4p) state does insertion occur to give HCaEH3, which rearranges to HCa(μ-H)3E upon photolysis. Topological analysis of the electronic structure suggests that the nonclassical structure HCa(μ-H)3E is formed by the electrostatic interaction with charge-inverted hydrogen bridge bond, while HCaEH3 is dominated by (HCa)+(EH3)- ion pair interactions.
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Affiliation(s)
- Jie Zhao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China.,School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ting Ji
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Xin Xiao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Xuefeng Wang
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
| | - Helmut Beckers
- Institut fur Chemie und Biochemie-Anorganische Chemie, Freie Universitat Berlin, Fabeckstrase 34/36, Berlin D-14195, Germany
| | - Sebastian Riedel
- Institut fur Chemie und Biochemie-Anorganische Chemie, Freie Universitat Berlin, Fabeckstrase 34/36, Berlin D-14195, Germany
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Dargelos A, Pouchan C. CCSD(T)-F12 calculations of the IR spectrum of cyanoacetylene HC3N beyond the harmonic approximation. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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50
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Boussaidi MA, Ren O, Voytsekhovsky D, Manzhos S. Random Sampling High Dimensional Model Representation Gaussian Process Regression (RS-HDMR-GPR) for Multivariate Function Representation: Application to Molecular Potential Energy Surfaces. J Phys Chem A 2020; 124:7598-7607. [DOI: 10.1021/acs.jpca.0c05935] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mohamed Ali Boussaidi
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 boulevard Lionel-Boulet, Varennes QC J3X 1S2, Canada
- Ecole Nationale d’Ingénieurs de Tunis, Rue Béchir Salem Belkhiria Campus universitaire, BP 37, 1002, Le Bélvédère, Tunis, Tunisia
| | - Owen Ren
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 boulevard Lionel-Boulet, Varennes QC J3X 1S2, Canada
- Purefacts Inc., 48 Yonge Street, Suite 400, Toronto, ON M5E 1G6, Canada
| | | | - Sergei Manzhos
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 boulevard Lionel-Boulet, Varennes QC J3X 1S2, Canada
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