1
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Xu Y, Biczysko M. Toward the identification of cyano-astroCOMs via vibrational features: benzonitrile as a test case. Front Chem 2024; 12:1439194. [PMID: 39296366 PMCID: PMC11408737 DOI: 10.3389/fchem.2024.1439194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/12/2024] [Indexed: 09/21/2024] Open
Abstract
The James Webb Space Telescope (JWST) opened a new era for the identification of molecular systems in the interstellar medium (ISM) by vibrational features. One group of molecules of increasing interest is cyano-derivatives of aromatic organic molecules, which have already been identified in the ISM on the basis of the analysis of rotational signatures, and so, are plausible candidates for the detection by the JWST. Benzonitrile considered in this work represents a suitable example for the validation of a computational strategy, which can be further applied for different, larger, and not-yet observed molecules. For this purpose, anharmonic simulations of infrared (IR) spectra have been compared with recent FTIR experimental studies. The anharmonic computations using the generalized second-order vibrational perturbation theory (GVPT2) in conjunction with a hybrid force field combining the harmonic part of revDSD-PBEP86-D3/jun-cc-pVTZ with anharmonic corrections from B3LYP-D3/SNSD show very good agreement with those in the experiment, with a mean error of 11 c m - 1 for all fundamental transitions overall and only 2 c m - 1 for the C ≡ N stretching fundamental at 4.49 μ m . The inclusion of overtones up to three-quanta transitions also allowed the prediction of spectra in the near-infrared region, which shows distinct features due to C ≡ N overtones at the 2.26 μ m and 1.52 μ m . The remarkable accuracy of the GVPT2 results opens a pathway for the reliable prediction of spectra for a broader range of cyano-astroCOMs.
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Affiliation(s)
- Yanting Xu
- International Centre for Quantum and Molecular Structures, Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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2
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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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3
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Tyuterev V, Tashkun S, Rey M, Nikitin A. High-order contact transformations of molecular Hamiltonians: general approach, fast computational algorithm and convergence of ro-vibrational polyad models. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2096140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Vladimir Tyuterev
- Groupe de Spectrométrie Moléculaire et Atmosphérique, Université de Reims, Reims, France
- Laboratory of Molecular Quantum Mechanics and Radiative Transfer, Tomsk State University, Tomsk, Russia
| | - Sergey Tashkun
- Laboratory of Theoretical Spectroscopy, V.E. Zuev Institute of Atmospheric Optics, Siberian Branch, Russian Academy of Sciences, Tomsk, Russia
| | - Michael Rey
- Groupe de Spectrométrie Moléculaire et Atmosphérique, Université de Reims, Reims, France
| | - Andrei Nikitin
- Laboratory of Theoretical Spectroscopy, V.E. Zuev Institute of Atmospheric Optics, Siberian Branch, Russian Academy of Sciences, Tomsk, Russia
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4
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Abstract
We introduce DMRG[FEAST], a new method for optimizing excited-state many-body wave functions with the density matrix renormalization group (DMRG) algorithm. Our approach applies the FEAST algorithm, originally designed for large-scale diagonalization problems, to matrix product state wave functions. We show that DMRG[FEAST] enables the stable optimization of both low- and high-energy eigenstates, therefore overcoming the limitations of state-of-the-art excited-state DMRG algorithms. We demonstrate the reliability of DMRG[FEAST] by calculating anharmonic vibrational excitation energies of molecules with up to 30 fully coupled degrees of freedom.
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Affiliation(s)
- Alberto Baiardi
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Anna Klára Kelemen
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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5
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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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6
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Krasnoshchekov SV, Laptev VB, Klimin SA, Gainullin IK, Makarov AA. Overtone spectroscopy of v(C=O) stretching vibration of hexafluoroacetone: Experimental and ab initio determination of peak positions, absolute intensities, and band shapes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 238:118396. [PMID: 32408225 DOI: 10.1016/j.saa.2020.118396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/08/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Infrared overtone spectra of the ν(C = O) stretching vibration (ν1) of gaseous hexafluoroacetone ((CF3)2C = O, HFA) were recorded in the spectral range of 7450-3300 cm-1 with a resolution of 0.1 cm-1. Experimental absolute IR intensities and vibrational band centers of the overtones 2ν1, 3ν1, 4ν1 of HFA were measured and compared with their ab initio counterparts, calculated by the second-order canonical vibrational perturbation theory (CVPT2). A hybrid potential energy surface (PES) was evaluated using the quantum-mechanical models MP2/cc-pVQZ for harmonic and MP2/cc-pVTZ for anharmonic parts. Cubic surfaces of dipole moment components were determined using the MP2/cc-pVTZ model. The predicted IR intensities for the first and second overtones reproduced the experimental values with a discrepancy of 6% and 9%, respectively. A weak Fermi resonance between the first overtone 2ν1 and combination tone ν1 + ν2 + ν8 was predicted. The appropriate model was employed for simulating the bands studied using: (i) the asymmetric-top vibration-rotational structure of the ν1 mode, (ii) the inhomogeneous band structure due to contributions of the vibrational states populated at the room temperature, and (iii) the homogeneous broadening of each vibration-rotation transition due to the intramolecular vibrational redistribution (IVR). The rotational and vibrational anharmonic constants were taken from the ab initio calculations, whereas the IVR data were obtained from the experimental data of Chekalin et al. (JPCA 2014, 118:955) with a time resolution of ≈100 fs. A good level of agreement of the predicted shapes of bands studied with experiment is achieved.
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Affiliation(s)
- Sergey V Krasnoshchekov
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow 119991, Russian Federation.
| | - Vladimir B Laptev
- Institute of Spectroscopy, Russian Academy of Sciences, Fizicheskaya 5, Troitsk, Moscow 108840, Russian Federation
| | - Sergey A Klimin
- Institute of Spectroscopy, Russian Academy of Sciences, Fizicheskaya 5, Troitsk, Moscow 108840, Russian Federation
| | - Ivan K Gainullin
- Department of Physics, Lomonosov Moscow State University, Leninskiye Gory 1-2, 119991 Moscow, Russian Federation
| | - Alexander A Makarov
- Institute of Spectroscopy, Russian Academy of Sciences, Fizicheskaya 5, Troitsk, Moscow 108840, Russian Federation; Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region 141700, Russian Federation; National Research University, Higher School of Economics, Myasnitskaya 20, Moscow 101000, Russian Federation
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7
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Lu M, Zheng Z, Zhu G, Wang Y, Yang Y. Elucidating the Coupling Mechanisms of Rapid Intramolecular Vibrational Energy Redistribution in Nitromethane: Ab Initio Molecular Dynamics Simulation. J Phys Chem A 2020; 124:8184-8191. [DOI: 10.1021/acs.jpca.0c04995] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meilin Lu
- School of Physics, Harbin Institute of Technology, Harbin 150001, China
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, China
| | - Zhaoyang Zheng
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, China
| | - Gangbei Zhu
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, China
| | - Yuxiao Wang
- School of Physics, Harbin Institute of Technology, Harbin 150001, China
| | - Yanqiang Yang
- School of Physics, Harbin Institute of Technology, Harbin 150001, China
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, China
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8
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Pandey A, Poirier B. Plumbing Potentials for Molecules with Up To Tens of Atoms: How to Find Saddle Points and Fix Leaky Holes. J Phys Chem Lett 2020; 11:6468-6474. [PMID: 32687368 DOI: 10.1021/acs.jpclett.0c01435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Potential energy surfaces (PESs) play an indispensable role in molecular dynamics but are notoriously difficult to flesh out properly in large-dimensional spaces. In particular, the undetected presence of PES holes, i.e., unphysical saddle points beyond which the potential energy drops arbitrarily, can have devastating effects on both classical and quantum dynamics calculations. In this study, the Crystal algorithm is developed as a tool for efficiently and accurately finding PES holes, as well as legitimate saddle points, even in very large-dimensional configuration spaces. The approach is applied to three large-dimensional PESs for molecular systems of current interest: uracil, naphthalene, and formic acid dimer. Low-lying PES holes are discovered and located for the first two systems-including naphthalene, for which no holes were previously suspected, to the best of our knowledge. Likewise, the double-well, double-proton-transfer isomerization saddle point for formic acid dimer is also located.
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Affiliation(s)
- Ankit Pandey
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Bill Poirier
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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9
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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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10
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Beć KB, Grabska J, Ozaki Y, Czarnecki MA, Huck CW. Simulated NIR spectra as sensitive markers of the structure and interactions in nucleobases. Sci Rep 2019; 9:17398. [PMID: 31758033 PMCID: PMC6874539 DOI: 10.1038/s41598-019-53827-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
Near-infrared (near-IR; NIR) spectroscopy is continuously advancing in biophysical and biochemical fields of investigation. For instance, recent progresses in NIR hyperspectral imaging of biological systems may be noted. However, interpretation of NIR bands for biological samples is difficult and creates a considerable barrier in exploring the full potential of NIR spectroscopy in bioscience. For this reason, we carried out a systematic study of NIR spectra of adenine, cytosine, guanine, and thymine in polycrystalline state. Interpretation of NIR spectra of these nucleobases was supported by anharmonic vibrational analysis using Deperturbed Vibrational Second-Order Perturbation Theory (DVPT2). A number of molecular models of nucleobases was applied to study the effect of the inter-molecular interactions on the NIR spectra. The accuracy of simulated NIR spectra appears to depend on the intra-layer interactions; in contrast, the inter-layer interactions are less influential. The best results were achieved by combining the simulated spectra of monomers and dimers. It is of particular note that in-plane deformation bands are far more populated than out-of-plane ones and the importance of ring modes is relatively small. This trend is in contrast to that observed in mid-IR region. As shown, the local, short-range chemical neighborhood of nucleobase molecules influence their NIR spectra more considerably. This suggests that NIR spectra are more sensitive probe of the nucleobase pairing than mid-IR ones. The obtained results allow, for the first time, to construct a frequency correlation table for NIR spectra of purines and pyrimidines.
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Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria.
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Mirosław A Czarnecki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Christan W Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
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11
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Gabas F, Di Liberto G, Ceotto M. Vibrational investigation of nucleobases by means of divide and conquer semiclassical dynamics. J Chem Phys 2019; 150:224107. [PMID: 31202241 DOI: 10.1063/1.5100503] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report a computational study of the vibrational features of four different nucleobases employing the divide-and-conquer semiclassical initial value representation molecular dynamics method. Calculations are performed on uracil, cytosine, thymine, and adenine. Results show that the overall accuracy with respect to experiments is within 20 wavenumbers, regardless of the dimensionality of the nucleobase. Vibrational estimates are accurate even in the complex case of cytosine, where two relevant conformers are taken into account. These results are promising in the perspective of future studies on more complex systems, such as nucleotides or nucleobase pairs.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Giovanni Di Liberto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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12
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DFT modelling of the infrared spectra for the isolated and the micro-hydrated forms of uracil. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2431-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Raman spectra of aqueous uracil stacked dimer: First principle molecular dynamics simulation. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Lee S, Johnson SN, Ellington TL, Mirsaleh-Kohan N, Tschumper GS. Energetics and Vibrational Signatures of Nucleobase Argyrophilic Interactions. ACS OMEGA 2018; 3:12936-12943. [PMID: 31458017 PMCID: PMC6645001 DOI: 10.1021/acsomega.8b01895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/27/2018] [Indexed: 06/10/2023]
Abstract
This study investigates the interactions of both purine (adenine and guanine) and pyrimidine (cytosine, thymine, and uracil) nucleobases with a pair of silver atoms (Ag2). Full geometry optimizations were performed on several structures of each nucleobase/Ag2 complex and the corresponding isolated monomers using the M06-2X density functional with a correlation consistent triple-ζ basis set augmented with diffuse functions on all atoms and a relativistic pseudopotential on Ag (aug-cc-pVTZ for H, C, N, and O and aug-cc-pVTZ-PP for Ag; denoted aVTZ). Harmonic vibrational frequency computations indicate that each optimized structure corresponds to a minimum on the M06-2X/aVTZ potential energy surface. Relative electronic energies for interactions between Ag2 and each nucleobase were compared to elucidate energetic differences between isomers. Further analysis of the changes in vibrational frequencies, infrared intensities, and Raman scattering activities reveals how different Ag2 binding sites might be differentiated spectroscopically. These results provide molecular-level insight into the interactions between nucleobases and silver, which may lead to better understanding and interpretation of surface-enhanced Raman spectroscopy experiments on nucleobases and related systems.
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Affiliation(s)
- Suhwan
Paul Lee
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Sarah N. Johnson
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Thomas L. Ellington
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Nasrin Mirsaleh-Kohan
- Department
of Chemistry and Biochemistry, Texas Woman’s
University, Denton, Texas 76204, United States
| | - Gregory S. Tschumper
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
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15
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Thomas PS, Carrington T, Agarwal J, Schaefer HF. Using an iterative eigensolver and intertwined rank reduction to compute vibrational spectra of molecules with more than a dozen atoms: Uracil and naphthalene. J Chem Phys 2018; 149:064108. [DOI: 10.1063/1.5039147] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Phillip S. Thomas
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Jay Agarwal
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-0525, USA
| | - Henry F. Schaefer
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-0525, USA
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16
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Milovanović B, Kojić M, Petković M, Etinski M. New Insight into Uracil Stacking in Water from ab Initio Molecular Dynamics. J Chem Theory Comput 2018; 14:2621-2632. [DOI: 10.1021/acs.jctc.8b00139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Marko Kojić
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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17
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Krasnoshchekov SV, Schutski RS, Craig NC, Sibaev M, Crittenden DL. Comparing the accuracy of perturbative and variational calculations for predicting fundamental vibrational frequencies of dihalomethanes. J Chem Phys 2018; 148:084102. [DOI: 10.1063/1.5020295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sergey V. Krasnoshchekov
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow 119991, Russian Federation
| | | | - Norman C. Craig
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, USA
| | - Marat Sibaev
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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18
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Tikhonov DS, Sharapa DI, Schwabedissen J, Rybkin VV. Application of classical simulations for the computation of vibrational properties of free molecules. Phys Chem Chem Phys 2018; 18:28325-28338. [PMID: 27722605 DOI: 10.1039/c6cp05849c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS2, benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I2-1,2-closo-C2B10H10. The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results.
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Affiliation(s)
- Denis S Tikhonov
- Universität Bielefeld, Lehrstuhl für Anorganische Chemie und Strukturchemie, Universitätsstrasse 25, 33615, Bielefeld, Germany. and M. V. Lomonosov Moscow State University, Department of Physical Chemistry, GSP-1, 1-3 Leninskiye Gory, 119991 Moscow, Russia
| | - Dmitry I Sharapa
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Jan Schwabedissen
- Universität Bielefeld, Lehrstuhl für Anorganische Chemie und Strukturchemie, Universitätsstrasse 25, 33615, Bielefeld, Germany.
| | - Vladimir V Rybkin
- ETH Zurich, Department of Materials, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich, Switzerland.
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De La Pierre M, Pouchan C. Ab initio periodic modelling of the vibrational spectra of molecular crystals: the case of uracil. Theor Chem Acc 2018. [DOI: 10.1007/s00214-017-2191-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Krasnoshchekov SV, Craig NC, Koroleva LA, Stepanov NF. Anharmonic vibrational analysis of s-trans and s-cis conformers of acryloyl fluoride using numerical-analytic Van Vleck operator perturbation theory. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 189:66-79. [PMID: 28800431 DOI: 10.1016/j.saa.2017.07.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/22/2017] [Accepted: 07/30/2017] [Indexed: 06/07/2023]
Abstract
A new gas-phase infrared (IR) spectrum of acryloyl fluoride (ACRF, CH2CHCFO) with a resolution of 0.1cm-1 in the range 4000-450cm-1 was measured. Theoretical ab initio molecular structures, full quartic potential energy surfaces (PES), and cubic surfaces of dipole moments and polarizability tensor components (electro-optical properties, EOP) of the s-trans and s-cis conformers of the ACRF were calculated by the second-order Møller-Plesset electronic perturbation theory with a correlation consistent Dunning triple-ζ basis set. The numerical-analytic implementation of the second-order operator canonical Van Vleck perturbation theory was employed for predicting anharmonic IR and Raman scattering (RS) spectra of ACRF. To improve the anharmonic predictions, harmonic frequencies were replaced by their counterparts evaluated with the higher-level CCSD(T)/cc-pVTZ model, to form a "hybrid" PES. The original operator representation of the Hamiltonian is analytically reduced to a quasi-diagonal form, integrated in the harmonic oscillator basis and diagonalized to account for strong resonance couplings. Double canonical transformations of EOP expansions enabled prediction of integral intensities of both fundamental and multi-quanta transitions in IR/RS spectra. Enhanced band shape analysis reinforced the assignments. A thorough interpretation of the new IR experimental spectra and existing matrix-isolation literature data for the mixture of two conformers of ACRF was accomplished, and a number of assignments clarified.
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Affiliation(s)
- Sergey V Krasnoshchekov
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, 119991 Moscow, Russian Federation.
| | - Norman C Craig
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, USA
| | - Lidiya A Koroleva
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, 119991 Moscow, Russian Federation
| | - Nikolay F Stepanov
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, 119991 Moscow, Russian Federation
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Spectroscopic Characterization of Key Aromatic and Heterocyclic Molecules: A Route toward the Origin of Life. ACTA ACUST UNITED AC 2017; 154. [DOI: 10.3847/1538-3881/aa7d54] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Effects of hydrogen bonding with H2O on the resonance Raman spectra of uracil and thymine. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Bloino J, Biczysko M, Barone V. Anharmonic Effects on Vibrational Spectra Intensities: Infrared, Raman, Vibrational Circular Dichroism, and Raman Optical Activity. J Phys Chem A 2015; 119:11862-74. [PMID: 26580121 PMCID: PMC5612400 DOI: 10.1021/acs.jpca.5b10067] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aim of this paper is 2-fold. First, we want to report the extension of our virtual multifrequency spectrometer (VMS) to anharmonic intensities for Raman optical activity (ROA) with the full inclusion of first- and second-order resonances for both frequencies and intensities in the framework of the generalized second-order vibrational perturbation theory (GVPT2) for all kinds of vibrational spectroscopies. Then, from a more general point of view, we want to present and validate the performance of VMS for the parallel analysis of different vibrational spectra for medium-sized molecules (IR, Raman, VCD, ROA) including both mechanical and electric/magnetic anharmonicity. For the well-known methyloxirane benchmark, careful selection of density functional, basis set, and resonance thresholds permitted us to reach qualitative and quantitative agreement between experimental and computed band positions and shapes. Next, the whole series of halogenated azetidinones is analyzed, showing that it is now possible to interpret different spectra in terms of mass, electronegativity, polarizability, and hindrance variation between closely related substituents, chiral spectroscopies being particular effective in this connection.
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Affiliation(s)
- Julien Bloino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei
Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G.
Moruzzi 1, I-56124 Pisa, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei
Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G.
Moruzzi 1, I-56124 Pisa, Italy
- International Center of Quantum and Molecular Structures,
College of Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444
China
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa,
Italy
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Krasnoshchekov SV, Craig NC, Boopalachandran P, Laane J, Stepanov NF. Anharmonic Vibrational Analysis of the Infrared and Raman Gas-Phase Spectra of s-trans- and s-gauche-1,3-Butadiene. J Phys Chem A 2015; 119:10706-23. [DOI: 10.1021/acs.jpca.5b07650] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Norman C. Craig
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | | | - Jaan Laane
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Nikolay F. Stepanov
- Lomonosov Moscow State University, Leninskiye Gory, 119991, Moscow, Russian Federation
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