1
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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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2
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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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3
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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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4
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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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5
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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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6
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Brüggemann J, Wolter M, Jacob CR. Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI. J Chem Phys 2022; 157:244107. [PMID: 36586972 DOI: 10.1063/5.0135273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models which require an empirical parameterization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF)/vibrational configuration interaction (L-VCI) approach previously established for (linear) anharmonic theoretical vibrational spectroscopy [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365-3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parameterization of vibrational exciton models for predicting 2D IR spectra.
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Affiliation(s)
- Julia Brüggemann
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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7
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Ozaki Y, Beć KB, Morisawa Y, Yamamoto S, Tanabe I, Huck CW, Hofer TS. Advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Chem Soc Rev 2021; 50:10917-10954. [PMID: 34382961 DOI: 10.1039/d0cs01602k] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The purpose of this review is to demonstrate advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Molecular spectroscopy, particularly vibrational spectroscopy and electronic spectroscopy, has been used extensively for a wide range of areas of chemical sciences and materials science as well as nano- and biosciences because it provides valuable information about structure, functions, and reactions of molecules. In the meantime, quantum chemical approaches play crucial roles in the spectral analysis. They also yield important knowledge about molecular and electronic structures as well as electronic transitions. The combination of spectroscopic approaches and quantum chemical calculations is a powerful tool for science, in general. Thus, our article, which treats various spectroscopy and quantum chemical approaches, should have strong implications in the wider scientific community. This review covers a wide area of molecular spectroscopy from far-ultraviolet (FUV, 120-200 nm) to far-infrared (FIR, 400-10 cm-1)/terahertz and Raman spectroscopy. As quantum chemical approaches, we introduce several anharmonic approaches such as vibrational self-consistent field (VSCF) and the combination of periodic harmonic calculations with anharmonic corrections based on finite models, grid-based techniques like the Numerov approach, the Cartesian coordinate tensor transfer (CCT) method, Symmetry-Adapted Cluster Configuration-Interaction (SAC-CI), and the ZINDO (Semi-empirical calculations at Zerner's Intermediate Neglect of Differential Overlap). One can use anharmonic approaches and grid-based approaches for both infrared (IR) and near-infrared (NIR) spectroscopy, while CCT methods are employed for Raman, Raman optical activity (ROA), FIR/terahertz and low-frequency Raman spectroscopy. Therefore, this review overviews cross relations between molecular spectroscopy and quantum chemical approaches, and provides various kinds of close-reality advanced spectral simulation for condensed phases.
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Affiliation(s)
- Yukihiro Ozaki
- School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan. and Toyota Physical and Chemical Research Institute, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Yusuke Morisawa
- Department of Chemistry, School of Science and Engineering, Kindai University, Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ichiro Tanabe
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Thomas S Hofer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A6020 Innsbruck, Austria
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8
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Grabska J, Beć KB, Mayr S, Huck CW. Theoretical Simulation of Near-Infrared Spectrum of Piperine: Insight into Band Origins and the Features of Regression Models. APPLIED SPECTROSCOPY 2021; 75:1022-1032. [PMID: 34236925 PMCID: PMC8320572 DOI: 10.1177/00037028211027951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/05/2021] [Indexed: 06/13/2023]
Abstract
We investigated the near-infrared spectrum of piperine using quantum mechanical calculations. We evaluated two efficient approaches, DVPT2//PM6 and DVPT2//ONIOM [PM6:B3LYP/6-311++G(2df, 2pd)] that yielded a simulated spectrum with varying accuracy versus computing time factor. We performed vibrational assignments and unveiled complex nature of the near-infrared spectrum of piperine, resulting from a high level of band convolution. The most meaningful contribution to the near-infrared absorption of piperine results from binary combination bands. With the available detailed near-infrared assignment of piperine, we interpreted the properties of partial least square regression models constructed in our earlier study to describe the piperine content in black pepper samples. Two models were compared with spectral data sets obtained with a benchtop and a miniaturized spectrometer. The two spectrometers implement distinct technology which leads to a profound instrumental difference and discrepancy in the predictive performance when analyzing piperine content. We concluded that the sensitivity of the two instruments to certain types of piperine vibrations is different and that the benchtop spectrometer unveiled higher selectivity. Such difference in obtaining chemical information from a sample can be one of the reasons why the benchtop spectrometer performs better in analyzing the piperine content of black pepper. This evidenced direct correspondence between the features critical for applied near-infrared spectroscopic routine and the underlying vibrational properties of the analyzed constituent in a complex sample.
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Affiliation(s)
| | - Krzysztof B. Beć
- Krzysztof B. Beć, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria.
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9
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Schmitz G, Klinting EL, Christiansen O. A Gaussian process regression adaptive density guided approach for potential energy surface construction. J Chem Phys 2020; 153:064105. [DOI: 10.1063/5.0015344] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Gunnar Schmitz
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
| | | | - Ove Christiansen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
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10
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The Structure of the "Vibration Hole" around an Isotopic Substitution-Implications for the Calculation of Nuclear Magnetic Resonance (NMR) Isotopic Shifts. Molecules 2020; 25:molecules25122915. [PMID: 32599937 PMCID: PMC7355873 DOI: 10.3390/molecules25122915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 11/17/2022] Open
Abstract
Calculations of nuclear magnetic resonance (NMR) isotopic shifts often rest on the unverified assumption that the “vibration hole”, that is, the change of the vibration motif upon an isotopic substitution, is strongly localized around the substitution site. Using our recently developed difference-dedicated (DD) second-order vibrational perturbation theory (VPT2) method, we test this assumption for a variety of molecules. The vibration hole turns out to be well localized in many cases but not in the interesting case where the H/D substitution site is involved in an intra-molecular hydrogen bond. For a series of salicylaldehyde derivatives recently studied by Hansen and co-workers (Molecules2019, 24, 4533), the vibrational hole was found to stretch over the whole hydrogen-bond moiety, including the bonds to the neighbouring C atoms, and to be sensitive to substituent effects. We discuss consequences of this finding for the accurate calculation of NMR isotopic shifts and point out directions for the further improvement of our DD-VPT2 method.
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11
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Artiukhin DG, Klinting EL, König C, Christiansen O. Adaptive density-guided approach to double incremental potential energy surface construction. J Chem Phys 2020; 152:194105. [PMID: 33687258 DOI: 10.1063/5.0004686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We present a combination of the recently developed double incremental expansion of potential energy surfaces with the well-established adaptive density-guided approach to grid construction. This unique methodology is based on the use of an incremental expansion for potential energy surfaces, known as n-mode expansion; an incremental many-body representation of the electronic energy; and an efficient vibrational density-guided approach to automated determination of grid dimensions and granularity. The reliability of the method is validated calculating potential energy surfaces and obtaining fundamental excitation energies for three moderate-size chain-like molecular systems. The use of our methodology leads to considerable computational savings for potential energy surface construction compared to standard approaches while maintaining a high level of accuracy in the resulting potential energy surfaces. Additional investigations indicate that our method can be applied to covalently bound and strongly interacting molecular systems, even though these cases are known to be very unfavorable for fragmentation schemes. We therefore conclude that the presented methodology is a robust and flexible approach to potential energy surface construction, which introduces considerable computational savings without compromising the accuracy of vibrational spectra calculations.
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Affiliation(s)
- Denis G Artiukhin
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
| | | | - Carolin König
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Max-Eyth-Straße 1, D-24118 Kiel, Germany
| | - Ove Christiansen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
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12
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Green JA, Improta R. Vibrations of the guanine-cytosine pair in chloroform: an anharmonic computational study. Phys Chem Chem Phys 2020; 22:5509-5522. [PMID: 32104818 DOI: 10.1039/c9cp06373k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We compute at the anharmonic level the vibrational spectra of the Watson-Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500-1700 cm-1) and in the N-H stretching region (2800-3600 cm-1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N-H amido streching mode of G falls at ∼2900 cm-1, while the N-H amino of G and C falls at ∼3100 cm-1 when hydrogen-bonded, or ∼3500 cm-1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm-1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute-solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.
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Affiliation(s)
- James A Green
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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13
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Klinting EL, Christiansen O, König C. Toward Accurate Theoretical Vibrational Spectra: A Case Study for Maleimide. J Phys Chem A 2020; 124:2616-2627. [DOI: 10.1021/acs.jpca.9b11915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Ove Christiansen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Carolin König
- Institute of Physical Chemistry, Kiel University, Max-Eyth-Straße 1, D-24118 Kiel, Germany
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14
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Gräfenstein J. Efficient calculation of NMR isotopic shifts: Difference-dedicated vibrational perturbation theory. J Chem Phys 2019; 151:244120. [PMID: 31893883 DOI: 10.1063/1.5134538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We present difference-dedicated second-order vibrational perturbation theory (VPT2) as an efficient method for the computation of nuclear magnetic resonance (NMR) isotopic shifts, which reflect the geometry dependence of the NMR property in combination with different vibration patterns of two isotopologues. Conventional calculations of isotopic shifts, e.g., by standard VPT2, require scanning the geometry dependence over the whole molecule, which becomes expensive rapidly as the molecule size increases. In DD-VPT2, this scan can be restricted to a small region around the substitution site. At the heart of DD-VPT2 is a set of localized vibration modes common to the two isotopologues and designed such that the difference between the vibration patterns is caught by a small subset of them (usually fewer than 10). We tested the DD-VPT2 method for a series of molecules with increasing size and found that this method provides results with the same quality as VPT2 and in good agreement with the experiment, with computational savings up to 95% and less numerical instabilities. The method is easy to automatize and straightforward to generalize to other molecular properties.
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Affiliation(s)
- Jürgen Gräfenstein
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Göteborg, Sweden
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15
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Sibert EL. Modeling vibrational anharmonicity in infrared spectra of high frequency vibrations of polyatomic molecules. J Chem Phys 2019; 150:090901. [DOI: 10.1063/1.5079626] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edwin L. Sibert
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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16
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Panek PT, Hoeske AA, Jacob CR. On the choice of coordinates in anharmonic theoretical vibrational spectroscopy: Harmonic vs. anharmonic coupling in vibrational configuration interaction. J Chem Phys 2019; 150:054107. [PMID: 30736699 DOI: 10.1063/1.5083186] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
By a suitable choice of coordinates, the computational effort required for calculations of anharmonic vibrational spectra can be reduced significantly. By using suitable localized-mode coordinates obtained from an orthogonal transformation of the conventionally used normal-mode coordinates, anharmonic couplings between modes can be significantly reduced. However, such a transformation introduces harmonic couplings between the localized modes. To elucidate the role of these harmonic couplings, we consider the vibrational self-consistent field (VSCF)/vibrational configuration interaction (VCI) calculations for both few-mode model systems and for ethene as a molecular test case. We show that large harmonic couplings can result in significant errors in localized-mode L-VSCF/L-VCI calculations and study the convergence with respect to the size of the VCI excitation space. To further elucidate the errors introduced by harmonic couplings, we discuss the connection between L-VSCF/L-VCI and vibrational exciton models. With the help of our results, we propose an algorithm for the localization of normal modes in suitable subsets that are chosen to strictly limit the errors introduced by the harmonic couplings while still leading to maximally localized modes.
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Affiliation(s)
- Paweł T Panek
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Adrian A Hoeske
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
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17
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Yagi K, Yamada K, Kobayashi C, Sugita Y. Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations. J Chem Theory Comput 2019; 15:1924-1938. [PMID: 30730746 PMCID: PMC8864611 DOI: 10.1021/acs.jctc.8b01193] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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Quantum
mechanics/molecular mechanics (QM/MM) calculations are
applied for anharmonic vibrational analyses of biomolecules and solvated
molecules. The QM/MM method is implemented into a molecular dynamics
(MD) program, GENESIS, by interfacing with external electronic structure
programs. Following the geometry optimization and the harmonic normal-mode
analysis based on a partial Hessian, the anharmonic potential energy
surface (PES) is generated from QM/MM energies and gradients calculated
at grid points. The PES is used for vibrational self-consistent field
(VSCF) and post-VSCF calculations to compute the vibrational spectrum.
The method is first applied to a phosphate ion in solution. With both
the ion and neighboring water molecules taken as a QM region, IR spectra
of representative hydration structures are calculated by the second-order
vibrational quasi-degenerate perturbation theory (VQDPT2) at the level
of B3LYP/cc-pVTZ and TIP3P force field. A weight-average of IR spectra
over the structures reproduces the experimental spectrum with a mean
absolute deviation of 16 cm–1. Then, the method
is applied to an enzyme, P450 nitric oxide reductase (P450nor), with
the NO molecule bound to a ferric (FeIII) heme. Starting
from snapshot structures obtained from MD simulations of P450nor in
solution, QM/MM calculations have been carried out at the level of
B3LYP-D3/def2-SVP(D). The spin state of FeIII(NO) is likely
a closed-shell singlet state based on a ratio of N–O and Fe–NO
stretching frequencies (νN–O and νFe–NO) calculated for closed- and open-shell singlet
states. The calculated νN–O and νFe–NO overestimate the experimental ones by 120 and
75 cm–1, respectively. The electronic structure
and solvation of FeIII(NO) affect the structure around
the heme of P450nor leading to an increase in νN–O and νFe–NO.
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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
| | - Kenta Yamada
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, 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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18
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Qu C, Bowman JM. Quantum approaches to vibrational dynamics and spectroscopy: is ease of interpretation sacrificed as rigor increases? Phys Chem Chem Phys 2019; 21:3397-3413. [DOI: 10.1039/c8cp04990d] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The subject of this Perspective is quantum approaches, beyond the harmonic approximation, to vibrational dynamics and IR spectroscopy.
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Affiliation(s)
- Chen Qu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University
- Atlanta
- USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University
- Atlanta
- USA
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