1
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Stienstra CMK, Hebert L, Thomas P, Haack A, Guo J, Hopkins WS. Graphormer-IR: Graph Transformers Predict Experimental IR Spectra Using Highly Specialized Attention. J Chem Inf Model 2024; 64:4613-4629. [PMID: 38845400 DOI: 10.1021/acs.jcim.4c00378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Infrared (IR) spectroscopy is an important analytical tool in various chemical and forensic domains and a great deal of effort has gone into developing in silico methods for predicting experimental spectra. A key challenge in this regard is generating highly accurate spectra quickly to enable real-time feedback between computation and experiment. Here, we employ Graphormer, a graph neural network (GNN) transformer, to predict IR spectra using only simplified molecular-input line-entry system (SMILES) strings. Our data set includes 53,528 high-quality spectra, measured in five different experimental media (i.e., phases), for molecules containing the elements H, C, N, O, F, Si, S, P, Cl, Br, and I. When using only atomic numbers for node encodings, Graphormer-IR achieved a mean test spectral information similarity (SISμ) value of 0.8449 ± 0.0012 (n = 5), which surpasses that the current state-of-the-art model Chemprop-IR (SISμ = 0.8409 ± 0.0014, n = 5) with only 36% of the encoded information. Augmenting node embeddings with additional node-level descriptors in learned embeddings generated through a multilayer perceptron improves scores to SISμ = 0.8523 ± 0.0006, a total improvement of 19.7σ (t = 19). These improved scores show how Graphormer-IR excels in capturing long-range interactions like hydrogen bonding, anharmonic peak positions in experimental spectra, and stretching frequencies of uncommon functional groups. Scaling our architecture to 210 attention heads demonstrates specialist-like behavior for distinct IR frequencies that improves model performance. Our model utilizes novel architectures, including a global node for phase encoding, learned node feature embeddings, and a one-dimensional (1D) smoothing convolutional neural network (CNN). Graphormer-IR's innovations underscore its value over traditional message-passing neural networks (MPNNs) due to its expressive embeddings and ability to capture long-range intramolecular relationships.
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Affiliation(s)
- Cailum M K Stienstra
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Liam Hebert
- Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Patrick Thomas
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Alexander Haack
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jason Guo
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories 999077, Hong Kong
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2
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Spiegel M. Unveiling the Antioxidative Potential of Galangin: Complete and Detailed Mechanistic Insights through Density Functional Theory Studies. J Org Chem 2024; 89:8676-8690. [PMID: 38861646 PMCID: PMC11197094 DOI: 10.1021/acs.joc.4c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
Abstract
A comprehensive quantum mechanical investigation delved into the antioxidative activity of galangin (Glg). Thermochemical and kinetic data were used to assess antiradical, chelating, and renewal potential under physiological conditions. A brief comparison with reference antioxidants and other flavonoids characterized Glg as a moderate antioxidative agent. The substance showed significantly lower performance in lipid compared to aqueous solvent─the reaction rates for scavenging •OOH in both media were established at 3.77 × 103 M-1 s-1 and 6.21 × 104 M-1 s-1, respectively, accounting for the molar fraction of both interacting molecules at the given pH. The impact of pH value on the kinetics was assessed. Although efficient at chelating Cu(II) ions, the formed complexes can still undergo the Fenton reaction. On the other hand, they persistently scavenge •OH in statu nascendi. The flavonoid effectively repairs oxidatively damaged biomolecules except model lipid acids. All Glg radicals are readily restored by physiologically prevailing O2•-. Given this, the polyphenol is expected to participate in antiradical and regenerating activities multiple times, amplifying its antioxidative potential.
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Affiliation(s)
- Maciej Spiegel
- Department of Organic Chemistry and
Pharmaceutical Technology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland
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3
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Di Grande S, Barone V. Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes. J Phys Chem A 2024; 128:4886-4900. [PMID: 38847454 DOI: 10.1021/acs.jpca.4c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The new versions of the Pisa composite scheme introduced in the present paper are based on the careful selection of different quantum chemical models for energies, geometries, and vibrational frequencies, with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.
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Affiliation(s)
- Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
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4
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Xu R, Jiang Z, Yang Q, Bloino J, Biczysko M. Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. J Comput Chem 2024. [PMID: 38682874 DOI: 10.1002/jcc.27377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.
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Affiliation(s)
- Ruiqin Xu
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | | | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czechia
| | - Julien Bloino
- Classe di Scienze, Scuola Normale Superiore, Pisa, Italy
| | - Malgorzata Biczysko
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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5
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Uribe L, Di Grande S, Crisci L, Lazzari F, Mendolicchio M, Barone V. Accurate Structures and Rotational Constants of Steroid Hormones at DFT Cost: Androsterone, Testosterone, Estrone, β-Estradiol, and Estriol. J Phys Chem A 2024; 128:2629-2642. [PMID: 38530336 DOI: 10.1021/acs.jpca.4c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
A comprehensive analysis of the structural, conformational, and spectroscopic properties in the gas phase has been performed for five prototypical steroid hormones, namely, androsterone, testosterone, estrone, β-estradiol, and estriol. The revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion and a suitable triple-ζ basis set provides accurate conformational energies and equilibrium molecular structures, with the latter being further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental ground state rotational constants are reached when adding to those equilibrium values vibrational corrections obtained at the cost of standard harmonic frequencies thanks to the use of a new computational tool. Together with the intrinsic interest of the studied hormones, the accuracy of the results obtained at DFT cost for molecules containing about 50 atoms paves the way toward the accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Lina Uribe
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Luigi Crisci
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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6
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Li H, Brémond E, Sancho-García JC, Pérez-Jiménez ÁJ, Scalmani G, Frisch MJ, Adamo C. Axial-equatorial equilibrium in substituted cyclohexanes: a DFT perspective on a small but complex problem. Phys Chem Chem Phys 2024; 26:8094-8105. [PMID: 38384253 DOI: 10.1039/d3cp06141h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
In Chemistry, complexity is not necessarily associated to large systems, as illustrated by the textbook example of axial-equatorial equilibrium in mono-substituted cyclohexanes. The difficulty in modelling such a simple isomerization is related to the need for reproducing the delicate balance between two forces, with opposite effects, namely the attractive London dispersion and the repulsive steric interactions. Such balance is a stimulating challenge for density-functional approximations and it is systematically explored here by considering 20 mono-substituted cyclohexanes. In comparison to highly accurate CCSD(T) reference calculations, their axial-equatorial equilibrium is studied with a large set of 48 exchange-correlation approximations, spanning from semilocal to hybrid to more recent double hybrid functionals. This dataset, called SAV20 (as Steric A-values for 20 molecules), allows to highlight the difficulties encountered by common and more original DFT approaches, including those corrected for dispersion with empirical potentials, the 6-31G*-ACP model, and our cost-effective PBE-QIDH/DH-SVPD protocol, in modeling these challenging interactions. Interestingly, the performance of the approaches considered in this contribution on the SAV20 dataset does not correlate with that obtained with other more standard datasets, such as S66, IDISP or NC15, thus indicating that SAV20 covers physicochemical features not already considered in previous noncovalent interaction benchmarks.
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Affiliation(s)
- Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.
| | - Eric Brémond
- Université Paris Cité, ITODYS, CNRS, F-75006 Paris, France
| | | | | | | | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France.
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7
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Wilson CG, Plesniar J, Kuhn H, Armstrong J, Wood PA, Parsons S. The Advantages of Flexibility: The Role of Entropy in Crystal Structures Containing C-H···F Interactions. CRYSTAL GROWTH & DESIGN 2024; 24:2217-2225. [PMID: 38463616 PMCID: PMC10921377 DOI: 10.1021/acs.cgd.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 03/12/2024]
Abstract
Molecular crystal structures are often interpreted in terms of strong, structure directing, intermolecular interactions, especially those with distinct geometric signatures such as H-bonds or π-stacking interactions. Other interactions can be overlooked, perhaps because they are weak or lack a characteristic geometry. We show that although the cumulative effect of weak interactions is significant, their deformability also leads to occupation of low energy vibrational energy levels, which provides an additional stabilizing entropic contribution. The entropies of five fluorobenzene derivatives have been calculated by periodic DFT calculations to assess the entropic influence of C-H···F interactions in stabilizing their crystal structures. Calculations reproduce inelastic neutron scattering data and experimental entropies from heat capacity measurements. C-H···F contacts are shown to have force constants which are around half of those of more familiar interactions such as hydrogen bonds, halogen bonds, and C-H···π interactions. This feature, in combination with the relatively high mass of F, means that the lowest energy vibrations in crystalline fluorobenzenes are dominated by C-H···F contributions. C-H···F contacts occur much more frequently than would be expected from their enthalpic contributions alone, but at 150 K, the stabilizing contribution of entropy provides, at -10 to -15 kJ mol-1, a similar level of stabilization to the N-H···N hydrogen bond in ammonia and O-H···O hydrogen bond in water.
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Affiliation(s)
- Cameron
J. G. Wilson
- Centre
for Science at Extreme Conditions, School of Chemistry, The University of Edinburgh, King’s Buildings, West Mains
Road, Edinburgh EH9 3FJ, U.K.
| | - Jan Plesniar
- Centre
for Science at Extreme Conditions, School of Chemistry, The University of Edinburgh, King’s Buildings, West Mains
Road, Edinburgh EH9 3FJ, U.K.
| | - Heike Kuhn
- Centre
for Science at Extreme Conditions, School of Chemistry, The University of Edinburgh, King’s Buildings, West Mains
Road, Edinburgh EH9 3FJ, U.K.
| | - Jeff Armstrong
- ISIS
Facility, STFC, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Peter A. Wood
- The
Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K.
| | - Simon Parsons
- Centre
for Science at Extreme Conditions, School of Chemistry, The University of Edinburgh, King’s Buildings, West Mains
Road, Edinburgh EH9 3FJ, U.K.
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8
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Barone V. Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase. Phys Chem Chem Phys 2024; 26:5802-5821. [PMID: 38099409 DOI: 10.1039/d3cp05169b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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9
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Crisci L, Di Grande S, Cavallotti C, Barone V. Toward an Accurate Black-Box Tool for the Kinetics of Gas-Phase Reactions Involving Barrier-less Elementary Steps. J Chem Theory Comput 2023; 19:7626-7639. [PMID: 37880932 PMCID: PMC10653117 DOI: 10.1021/acs.jctc.3c00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
An enhanced computational protocol has been devised for the accurate characterization of gas-phase barrier-less reactions in the framework of the reaction-path (RP) and variable reaction coordinate variational transition-state theory. In particular, the synergistic combination of density functional theory and Monte Carlo sampling to optimize reactive fluxes led to a reliable yet effective computational workflow. A black-box strategy has been developed for selecting the most suited density functional with reference to a high-level one-dimensional reference potential. At the same time, different descriptions of hindered rotations are automatically selected, depending on the corresponding harmonic frequencies along the RP. The performance of the new tool is investigated by means of two prototypical reactions involving different degrees of static and dynamic correlation, namely, H2S + Cl and CH3 + CH3. The remarkable agreement of the computed kinetic parameters with the available experimental data confirms the accuracy and robustness of the proposed approach. Together with their intrinsic interest, these results also pave the way toward systematic investigations of gas-phase reactions involving barrier-less elementary steps by a reliable, user-friendly tool, which can be confidently used also by nonspecialists.
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Affiliation(s)
- Luigi Crisci
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126 Napoli, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Carlo Cavallotti
- Department
of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, I-20131 Milano, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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10
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Barone V, Uribe Grajales LM, Di Grande S, Lazzari F, Mendolicchio M. DFT Meets Wave-Function Methods for Accurate Structures and Rotational Constants of Histidine, Tryptophan, and Proline. J Phys Chem A 2023; 127:7534-7543. [PMID: 37665117 PMCID: PMC10510395 DOI: 10.1021/acs.jpca.3c04227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/12/2023] [Indexed: 09/05/2023]
Abstract
A new computational strategy has been applied to the conformational and spectroscopic properties in the gas phase of amino acids with very distinctive features, ranging from different tautomeric forms (histidine) to ring puckering (proline), and heteroaromatic structures with non-equivalent rings (tryptophan). The integration of modern double-hybrid functionals and wave-function composite methods has allowed us to obtain accurate results for a large panel of conformers with reasonable computer times. The remarkable agreement between computations and microwave experiments allows an unbiased interpretation of the latter in terms of stereoelectronic effects.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Lina Marcela Uribe Grajales
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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11
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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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12
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Barone V. Accurate structures and spectroscopic parameters of α,α-dialkylated α-amino acids in the gas-phase: a joint venture of DFT and wave-function composite methods. Phys Chem Chem Phys 2023; 25:22768-22774. [PMID: 37591810 DOI: 10.1039/d3cp02503a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Accurate computations of structural, conformational and spectroscopic properties in the gas phase have been performed for two α,α-dialkylated α-amino acids, namely aminoisobutyric acid and cyclopropylglycine. Thanks to the integration of modern double hybrid functionals and wave-function methods, several low-energy structures of the title molecules could be analyzed employing standard computer resources. The computed features of all the most stable conformers of the target amino acids closely match the corresponding spectroscopic parameters issued from microwave spectroscopic studies in the gas-phase. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the way for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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13
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Crane S, Garrow M, Lane PD, Robertson K, Waugh A, Woolley JM, Stavros VG, Paterson MJ, Greaves SJ, Townsend D. The Value of Different Experimental Observables: A Transient Absorption Study of the Ultraviolet Excitation Dynamics Operating in Nitrobenzene. J Phys Chem A 2023; 127:6425-6436. [PMID: 37494478 PMCID: PMC10424241 DOI: 10.1021/acs.jpca.3c02654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/16/2023] [Indexed: 07/28/2023]
Abstract
Excess energy redistribution dynamics operating in nitrobenzene under hexane and isopropanol solvation were investigated using ultrafast transient absorption spectroscopy (TAS) with a 267 nm pump and a 340-750 nm white light continuum probe. The use of a nonpolar hexane solvent provides a proxy to the gas-phase environment, and the findings are directly compared with a recent time-resolved photoelectron imaging (TRPEI) study on nitrobenzene using the same excitation wavelength [L. Saalbach et al., J. Phys. Chem. A 2021, 125, 7174-7184]. Of note is the observation of a 1/e lifetime of 3.5-6.7 ps in the TAS data that was absent in the TRPEI measurements. This is interpreted as a dynamical signature of the T2 state in nitrobenzene─analogous to observations in the related nitronaphthalene system, and additionally supported by previous quantum chemistry calculations. The discrepancy between the TAS and TRPEI measurements is discussed, with the overall findings providing an example of how different spectroscopic techniques can exhibit varying sensitivity to specific steps along the overall reaction coordinate connecting reactants to photoproducts.
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Affiliation(s)
- Stuart
W. Crane
- Institute
of Photonics & Quantum Sciences, Heriot-Watt
University, Edinburgh EH14 4AS, U.K.
| | - Malcolm Garrow
- Institute
of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
| | - Paul D. Lane
- Institute
of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
| | - Kate Robertson
- Institute
of Photonics & Quantum Sciences, Heriot-Watt
University, Edinburgh EH14 4AS, U.K.
| | - Alex Waugh
- Institute
of Photonics & Quantum Sciences, Heriot-Watt
University, Edinburgh EH14 4AS, U.K.
| | - Jack M. Woolley
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
| | - Vasilios G. Stavros
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Martin J. Paterson
- Institute
of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
| | - Stuart J. Greaves
- Institute
of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
| | - Dave Townsend
- Institute
of Photonics & Quantum Sciences, Heriot-Watt
University, Edinburgh EH14 4AS, U.K.
- Institute
of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
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14
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Barone V. DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase. J Chem Theory Comput 2023; 19:4970-4981. [PMID: 37479680 PMCID: PMC10413851 DOI: 10.1021/acs.jctc.3c00465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Indexed: 07/23/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase has been further improved and validated with a special reference to tautomeric equilibria. The main improvements concern the use of the cc-pVTZ-F12 basis set in both DFT and CCSD(T)-F12 computations, the inclusion of core-valence correlation in geometry optimizations by double hybrid functionals, and the use of the cc-pVQZ-F12 basis set for complete basis set extrapolation at the MP2-F12 level. The resulting model chemistry is applied to the challenging problem of cytosine tautomers in the gas phase. The results are in remarkable agreement with experiment concerning both rotational and vibrational spectroscopic parameters and permit their unbiased interpretation in terms of structural and thermochemical features. Together with the intrinsic interest of the studied molecule, the accuracy of the results obtained at reasonable cost without any empirical parameter suggests that the proposed composite method can be profitably employed for accurate investigations of other molecular bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore
di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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15
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Liang J, Feng X, Liu X, Head-Gordon M. Analytical harmonic vibrational frequencies with VV10-containing density functionals: Theory, efficient implementation, and benchmark assessments. J Chem Phys 2023; 158:204109. [PMID: 37218699 PMCID: PMC10208678 DOI: 10.1063/5.0152838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
VV10 is a powerful nonlocal density functional for long-range correlation that is used to include dispersion effects in many modern density functionals, such as the meta-generalized gradient approximation (mGGA), B97M-V, the hybrid GGA, ωB97X-V, and the hybrid mGGA, ωB97M-V. While energies and analytical gradients for VV10 are already widely available, this study reports the first derivation and efficient implementation of the analytical second derivatives of the VV10 energy. The additional compute cost of the VV10 contributions to analytical frequencies is shown to be small in all but the smallest basis sets for recommended grid sizes. This study also reports the assessment of VV10-containing functionals for predicting harmonic frequencies using the analytical second derivative code. The contribution of VV10 to simulating harmonic frequencies is shown to be small for small molecules but important for systems where weak interactions are important, such as water clusters. In the latter cases, B97M-V, ωB97M-V, and ωB97X-V perform very well. The convergence of frequencies with respect to the grid size and atomic orbital basis set size is studied, and recommendations are reported. Finally, scaling factors to allow comparison of scaled harmonic frequencies with experimental fundamental frequencies and to predict zero-point vibrational energy are presented for some recently developed functionals (including r2SCAN, B97M-V, ωB97X-V, M06-SX, and ωB97M-V).
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Affiliation(s)
- Jiashu Liang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
| | | | - Xiao Liu
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
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16
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Chawananon S, Asselin P, Claus JA, Goubet M, Roucou A, Georges R, Sobczuk J, Bracquart C, Pirali O, Cuisset A. Rovibrational Spectroscopy of Trans and Cis Conformers of 2-Furfural from High-Resolution Fourier Transform and QCL Infrared Measurements. Molecules 2023; 28:molecules28104165. [PMID: 37241905 DOI: 10.3390/molecules28104165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
The ortho-isomer 2-furfural (2-FF), which is a primary atmospheric pollutant produced from biomass combustion, is also involved in oxidation processes leading to the formation of secondary organic aerosols. Its contribution to radiative forcing remains poorly understood. Thus, monitoring 2-FF directly in the atmosphere or in atmospheric simulation chambers to characterize its reactivity is merited. The present study reports an extensive jet-cooled rovibrational study of trans and cis conformers of 2-FF in the mid-IR region using two complementary setups: a continuous supersonic jet coupled to a high-resolution Fourier transform spectrometer on the IR beamline of the SOLEIL synchrotron (JET-AILES), and a pulsed jet coupled to a mid-IR tunable quantum cascade laser spectrometer (SPIRALES). Firstly, jet-cooled spectra recorded at rotational temperatures ranging between 20 and 50 K were exploited to derive reliable excited-state molecular parameters of trans- and cis-2-FF vibrational bands in the fingerprint region. The parameters were obtained from global fits of 11,376 and 3355 lines distributed over eight and three vibrational states (including the ground state), respectively, with a root mean square of 12 MHz. In a second step, the middle resolution spectrum of 2-FF recorded at 298.15 K and available in the HITRAN database was reconstructed by extrapolating the data derived from our low-temperature high-resolution analyses to determine the cross sections of each vibrational band of both 2-FF conformers in the 700-1800 cm-1 region. Finally, we clearly demonstrated that the contribution of hot bands observed in the room temperature 2-FF spectrum, estimated between 40 and 63% of the fundamental band, must be imperatively introduced in our simulation to correctly reproduce the HITRAN vibrational cross sections of 2-FF with a deviation smaller than 10%.
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Affiliation(s)
- Sathapana Chawananon
- Sorbonne Université, MONARIS, CNRS, UMR8233, 4 Pl Jussieu, F-75005 Paris, France
| | - Pierre Asselin
- Sorbonne Université, MONARIS, CNRS, UMR8233, 4 Pl Jussieu, F-75005 Paris, France
| | - Jordan A Claus
- Université de Lille, CNRS, UMR8523-PhLAM-Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Manuel Goubet
- Université de Lille, CNRS, UMR8523-PhLAM-Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Anthony Roucou
- Université du Littoral Côte d'Opale, UR4493, LPCA, Laboratoire de Physico-Chimie de l'Atmosphère, F-59140 Dunkerque, France
| | - Robert Georges
- Université de Rennes, CNRS, IPR (Institut de Physique de Rennes)-UMR 6251, F-35000 Rennes, France
| | - Joanna Sobczuk
- Smoluchowski Institute of Physics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Colwyn Bracquart
- Université de Lille, CNRS, UMR8523-PhLAM-Physique des Lasers Atomes et Molécules, F-59000 Lille, France
- Université du Littoral Côte d'Opale, UR4493, LPCA, Laboratoire de Physico-Chimie de l'Atmosphère, F-59140 Dunkerque, France
| | - Olivier Pirali
- Université de Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, F-91405 Orsay, France
| | - Arnaud Cuisset
- Université du Littoral Côte d'Opale, UR4493, LPCA, Laboratoire de Physico-Chimie de l'Atmosphère, F-59140 Dunkerque, France
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17
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Barone V, Fusè M. Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods. J Phys Chem A 2023; 127:3648-3657. [PMID: 37052318 PMCID: PMC10150396 DOI: 10.1021/acs.jpca.3c01174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A general strategy for the accurate computation of conformational and spectroscopic properties of flexible molecules in the gas phase is applied to two representative proteinogenic amino acids with aromatic side chains, namely, phenylalanine and tyrosine. The main features of all the most stable conformers predicted by this computational strategy closely match those of the species detected in microwave and infrared experiments. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the route for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Fusè
- DMMT-sede Europa, Università di Brescia, Viale Europa 11, 25121 Brescia, Italy
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18
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Designing of thiazolidinones against chicken pox, monkey pox, and hepatitis viruses: A computational approach. Comput Biol Chem 2023; 103:107827. [PMID: 36805155 PMCID: PMC9922439 DOI: 10.1016/j.compbiolchem.2023.107827] [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: 12/17/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/14/2023]
Abstract
Computational designing of four different series (D-G) of thiazolidinone was done starting from different amines which was further condensed with various aldehydes. These underwent in silico molecular investigations for density functional theory (DFT), molecular docking, and absorption, distribution metabolism, excretion, and toxicity (ADMET) studies. The different electrochemical parameters of the compounds are predicted using quantum mechanical modeling approach with Gaussian. The docking software was used to dock the compounds against choosing PDB file for chickenpox, human immunodeficiency, hepatitis, and monkeypox virus as 1OSN, 1VZV, 6VLK, 1RTD, 3I7H, 3TYV, 4JU3, and 4QWO, respectively. The molecular interactions were visualized with discovery studio and maximum binding affinity was observed with D8 compounds against 4QWO (-13.383 kcal/mol) while for compound D5 against 1VZV which was -12.713 kcal/mol. Swiss ADME web tool was used to assess the drug-likeness of the designed compounds under consideration, and it is concluded that these molecules had a drug-like structure with almost zero violations.
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19
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Zapata Trujillo JC, McKemmish LK. Model Chemistry Recommendations for Scaled Harmonic Frequency Calculations: A Benchmark Study. J Phys Chem A 2023; 127:1715-1735. [PMID: 36753303 DOI: 10.1021/acs.jpca.2c06908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Despite the widespread popularity of scaled harmonic frequency calculations to predict experimental fundamental frequencies in chemistry, sparse benchmarking is available to guide users on the appropriate level of theory and basis set choices (model chemistry) or deep understanding of expected errors. An updated assessment of the best approach for scaling to minimize errors is also overdue. Here, we assess the performance of over 600 popular, contemporary, and robust model chemistries in the calculation of scaled harmonic frequencies, evaluating different scaling factor types and their implications in the scaled harmonic frequencies and model chemistry performance. We can summarize our results into three main findings: (1) Using model-chemistry-specific scaling factors optimized for three different frequency regions (low (<1,000 cm-1), mid (1,000-2,000 cm-1), and high (>2,000 cm-1)) results in substantial improvements in the agreement between the scaled harmonic and experimental frequencies compared to other choices. (2) Larger basis sets and more robust levels of theory generally lead to superior performance; however, the particular model chemistry choice matters and poor choices lead to significantly reduced accuracies. (3) Outliers are expected in routine calculations regardless of the model chemistry choice. Our benchmarking results here do not consider the intensity of vibrational transitions; however, we draw upon previous benchmarking results for dipole moments that highlight the importance of diffuse functions (i.e., augmented basis sets) in high-quality intensity predictions. In terms of specific recommendations, overall, the highest accuracy model chemistries are double-hybrid density functional approximations with a non-Pople augmented triple-ζ basis set, which can produce median frequency errors down to 7.6 cm-1 (DSD-PBEP86/def2-TZVPD), which is very close to the error in the harmonic approximation, i.e., the anharmonicity error. Double-ζ basis sets should not be used with double-hybrid functionals as there is no improvement compared to hybrid functional results (unlike for double-hybrid triple-ζ model chemistries). Note that 6-311G* and 6-311+G* basis sets perform like a double-ζ basis set for vibrational frequencies. After scaling, all studied hybrid functionals with non-Pople triple-ζ basis sets will produce median errors of less than 15 cm-1, with the best result of 9.9 cm-1 with B97-1/def2-TZVPD. Appropriate matching of double-ζ basis sets with hybrid functionals can produce high-quality results, but the precise choice of functional and basis set is more important. The B97-1, TPSS0-D3(BJ), or ωB97X-D hybrid density functionals with 6-31G*, pc-1, or pcseg-1 are recommended for fast routine calculations, all delivering median errors of 11-12 cm-1. Note that dispersion corrections are not easily available for B97-1; given its strong performance here, we recommend these be added to major programs in coming updates.
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Affiliation(s)
| | - Laura K McKemmish
- School of Chemistry, University of New South Wales, 2052 Sydney, NSW, Australia
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20
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Barone V, Fusè M, Lazzari F, Mancini G. Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy. J Chem Theory Comput 2023; 19:1243-1260. [PMID: 36731119 PMCID: PMC9979611 DOI: 10.1021/acs.jctc.2c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy,
| | - Marco Fusè
- DMMT-sede
Europa, Universitá di Brescia, viale Europa 11, 25121 Brescia, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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21
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Krupa J, Wierzejewska M, Lundell J. Experimental FTIR-MI and Theoretical Studies of Isocyanic Acid Aggregates. Molecules 2023; 28:molecules28031430. [PMID: 36771094 PMCID: PMC9921473 DOI: 10.3390/molecules28031430] [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: 01/06/2023] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Homoaggregates of isocyanic acid (HNCO) were studied using FTIR spectroscopy combined with a low-temperature matrix isolation technique and quantum chemical calculations. Computationally, the structures of the HNCO dimers and trimers were optimized at the MP2, B3LYPD3 and B2PLYPD3 levels of theory employing the 6-311++G(3df,3pd) basis set. Topological analysis of the electron density (AIM) was used to identify the type of non-covalent interactions in the studied aggregates. Five stable minima were located on the potential energy surface for (HNCO)2, and nine were located on the potential energy surface for (HNCO)3. The most stable dimer (D1) involves a weak, almost linear N-H⋯N hydrogen bond. Other structures are bound by a N-H⋯O hydrogen bond or by O⋯C or N⋯N van der Waals interactions. Similar types of interactions as in (HNCO)2 were found in the case of HNCO trimers. Among nine stable (HNCO)3 structures, five represent cyclic forms. The most stable T1 trimer structure is characterized by a six-membered ring formed by three N-H⋯N hydrogen bonds and representing high symmetry (C3h). The analysis of the HNCO/Ar spectra after deposition indicates that the N-H⋯O hydrogen-bonded dimers are especially prevalent. Upon annealing, HNCO trimers were observed as well. Identification of the experimentally observed species relied on previous experimental data on HNCO complexes as well as computed data on HNCO homoaggregates' vibrational spectra.
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Affiliation(s)
- Justyna Krupa
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
- Correspondence: (J.K.); (J.L.); Tel.: +358-40-744-5270 (J.L.)
| | - Maria Wierzejewska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Jan Lundell
- Department of Chemistry, University of Jyväskylä, FI-40014 Jyväskylä, Finland
- Correspondence: (J.K.); (J.L.); Tel.: +358-40-744-5270 (J.L.)
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22
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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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23
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Barone V, Di Grande S, Puzzarini C. Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020913. [PMID: 36677970 PMCID: PMC9863398 DOI: 10.3390/molecules28020913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/01/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Correspondence: (V.B.); (C.P.)
| | - Silvia Di Grande
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Cristina Puzzarini
- Rotational and Computational Spectroscopy Lab, Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
- Correspondence: (V.B.); (C.P.)
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24
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Recio P, Alessandrini S, Vanuzzo G, Pannacci G, Baggioli A, Marchione D, Caracciolo A, Murray VJ, Casavecchia P, Balucani N, Cavallotti C, Puzzarini C, Barone V. Intersystem crossing in the entrance channel of the reaction of O( 3P) with pyridine. Nat Chem 2022; 14:1405-1412. [PMID: 36175514 DOI: 10.1038/s41557-022-01047-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/25/2022] [Indexed: 01/04/2023]
Abstract
Two quantum effects can enable reactions to take place at energies below the barrier separating reactants from products: tunnelling and intersystem crossing between coupled potential energy surfaces. Here we show that intersystem crossing in the region between the pre-reactive complex and the reaction barrier can control the rate of bimolecular reactions for weakly coupled potential energy surfaces, even in the absence of heavy atoms. For O(3P) plus pyridine, a reaction relevant to combustion, astrochemistry and biochemistry, crossed-beam experiments indicate that the dominant products are pyrrole and CO, obtained through a spin-forbidden ring-contraction mechanism. The experimental findings are interpreted-by high-level quantum-chemical calculations and statistical non-adiabatic computations of branching fractions-in terms of an efficient intersystem crossing occurring before the high entrance barrier for O-atom addition to the N-atom lone pair. At low to moderate temperatures, the computed reaction rates prove to be dominated by intersystem crossing.
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Affiliation(s)
- Pedro Recio
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Silvia Alessandrini
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Chimica 'Giacomo Ciamician', University of Bologna, Bologna, Italy
| | - Gianmarco Vanuzzo
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Giacomo Pannacci
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Alberto Baggioli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica 'Giulio Natta', Politecnico di Milano, Milan, Italy
| | - Demian Marchione
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Adriana Caracciolo
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- Department of Aerospace Engineering Sciences, University of Colorado, Boulder, CO, USA
| | - Vanessa J Murray
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- Montana State University, Bozeman, MT, USA
| | - Piergiorgio Casavecchia
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Nadia Balucani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy.
| | - Carlo Cavallotti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica 'Giulio Natta', Politecnico di Milano, Milan, Italy.
| | - Cristina Puzzarini
- Dipartimento di Chimica 'Giacomo Ciamician', University of Bologna, Bologna, Italy.
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25
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Rizk MG, Emara AA, Abou-Hussein A, Mahmoud NH. Novel metal complexes of N,N-bis(4-phenylthiazol-2-yl)phthalamide: Synthesis, spectroscopic, thermal and kinetic investigations, molecular modeling, computational calculations, anti-breast cancer studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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Yang Q, Kapitán J, Bouř P, Bloino J. Anharmonic Vibrational Raman Optical Activity of Methyloxirane: Theory and Experiment Pushed to the Limits. J Phys Chem Lett 2022; 13:8888-8892. [PMID: 36125432 PMCID: PMC9531246 DOI: 10.1021/acs.jpclett.2c02320] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
Combining Raman scattering and Raman optical activity (ROA) with computer simulations reveals fine structural and physicochemical properties of chiral molecules. Traditionally, the region of interest comprised fundamental transitions within 200-1800 cm-1. Only recently, nonfundamental bands could be observed as well. However, theoretical tools able to match the observed spectral features and thus assist their assignment are rather scarce. In this work, we present an accurate and simple protocol based on a three-quanta anharmonic perturbative approach that is fully fit to interpret the observed signals of methyloxirane within 150-4500 cm-1. An unprecedented agreement even for the low-intensity combination and overtone transitions has been achieved, showing that anharmonic Raman and ROA spectroscopies can be valuable tools to understand vibrations of chiral molecules or to calibrate computational models.
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Affiliation(s)
- Qin Yang
- Scuola Normale
Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Josef Kapitán
- Department
of Optics, Palacký University Olomouc, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí
2, 16610 Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale
Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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27
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Hanson-Heine MWD. Static Electron Correlation in Anharmonic Molecular Vibrations: A Hybrid TAO-DFT Study. J Phys Chem A 2022; 126:7273-7282. [PMID: 36164938 PMCID: PMC9574917 DOI: 10.1021/acs.jpca.2c05881] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hybrid thermally-assisted-occupation density functional theory is used to examine the effects of static electron correlation on the prediction of a benchmark set of experimentally observed molecular vibrational frequencies. The B3LYP and B97-1 thermally-assisted-occupation measure of static electron correlation is important for describing the vibrations of many of the molecules that make up several popular test sets of experimental data. Shifts are seen for known multireference systems and for many molecules containing atoms from the second row of the periodic table of elements. Several molecules only show significant shifts in select vibrational modes, and significant improvements are seen for the prediction of hydrogen stretching frequencies throughout the test set.
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28
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Song Z, Wang S, Yu H, Hu W, Yao L. Calculation of the anharmonic effect on the main reactions referring to ethylbenzene combustion mechanism. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Zening Song
- Merchant Marine College Shanghai Maritime University Shanghai China
| | - Shiye Wang
- Marine Engineering College Dalian Maritime University Dalian China
| | - Hongjing Yu
- Marine Engineering College Dalian Maritime University Dalian China
| | - Wenye Hu
- Merchant Marine College Shanghai Maritime University Shanghai China
| | - Li Yao
- Merchant Marine College Shanghai Maritime University Shanghai China
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29
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Regulation of radicals by hydrogen-donor solvent in direct coal liquefaction. Front Chem Sci Eng 2022. [DOI: 10.1007/s11705-022-2186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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30
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Cheng X, Li F, Zhao Y, Cheng X, Nie K, Han Y, Yang Y. Stability, atomic charges, bond order analysis, and the directionality of lone‐electron pairs on nitriles and isocyanides. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xueli Cheng
- School of Chemistry and Chemical Engineering, Taishan University Tai’an China
| | - Feng Li
- Department of Teaching Affairs Taishan University Tai’an China
| | - Yanyun Zhao
- School of Chemistry and Chemical Engineering, Taishan University Tai’an China
| | - Xiaoyu Cheng
- School of Chemistry, Chemical Engineering and Materials Science Shandong Normal University Jinan China
| | - Kun Nie
- School of Chemistry and Chemical Engineering, Taishan University Tai’an China
| | - Yinfeng Han
- School of Chemistry and Chemical Engineering, Taishan University Tai’an China
| | - Yongjuan Yang
- School of Chemistry and Chemical Engineering, Taishan University Tai’an China
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31
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Santra G, Calinsky R, Martin JML. Benefits of Range-Separated Hybrid and Double-Hybrid Functionals for a Large and Diverse Data Set of Reaction Energies and Barrier Heights. J Phys Chem A 2022; 126:5492-5505. [PMID: 35930677 PMCID: PMC9393870 DOI: 10.1021/acs.jpca.2c03922] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
To better understand the thermochemical kinetics and
mechanism
of a specific chemical reaction, an accurate estimation of barrier
heights (forward and reverse) and reaction energies is vital. Because
of the large size of reactants and transition state structures involved
in real-life mechanistic studies (e.g., enzymatically catalyzed reactions),
density functional theory remains the workhorse for such calculations.
In this paper, we have assessed the performance of 91 density functionals
for modeling the reaction energies and barrier heights on a large
and chemically diverse data set (BH9) composed of 449 organic chemistry
reactions. We have shown that range-separated hybrid functionals perform
better than the global hybrids for BH9 barrier heights and reaction
energies. Except for the PBE-based range-separated nonempirical double
hybrids, range separation of the exchange term helps improve the performance
for barrier heights and reaction energies. The 16-parameter Berkeley
double hybrid, ωB97M(2), performs remarkably well for both properties.
However, our minimally empirical range-separated double hybrid functionals
offer marginally better accuracy than ωB97M(2) for BH9 barrier
heights and reaction energies.
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Affiliation(s)
- Golokesh Santra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Rivka Calinsky
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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32
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Gas- and liquid-phase ozonolysis of ethylene, butadiene, and perfluoro-olefins: solvation and the cage effect. MONATSHEFTE FUR CHEMIE 2022. [DOI: 10.1007/s00706-022-02946-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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33
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Zapata Trujillo JC, McKemmish LK. VIBFREQ1295: A New Database for Vibrational Frequency Calculations. J Phys Chem A 2022; 126:4100-4122. [PMID: 35723975 DOI: 10.1021/acs.jpca.2c01438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
High-throughput approaches for producing approximate vibrational spectral data for molecules of astrochemistry interest rely on harmonic frequency calculations using computational quantum chemistry. However, model chemistry recommendations (i.e., a level of theory and basis set pair) for these calculations are not yet available and, thus, thorough benchmarking against comprehensive benchmark databases is needed. Here, we present a new database for vibrational frequency calculations (VIBFREQ1295) storing 1295 experimental fundamental frequencies and CCSD(T)(F12*)/cc-pVDZ-F12 ab initio harmonic frequencies from 141 molecules. VIBFREQ1295's experimental data was complied through a comprehensive review of contemporary experimental data, while the ab initio data was computed here. The chemical space spanned by the molecules chosen is considered in-depth and is shown to have good representation of common organic functional groups and vibrational modes. Scaling factors are routinely used to approximate the effect of anharmonicity and convert computed harmonic frequencies to predicted fundamental frequencies. With our experimental and high-level ab initio data, we find that a single global uniform scaling factor of 0.9617(3) results in median differences of 15.9(5) cm-1. A far superior performance with a median difference of 7.5(5) cm-1 can be obtained, however, by using separate scaling factors (SFs) for three regions: frequencies less than 1000 cm-1 (SF = 0.987(1)), between 1000 and 2000 cm-1 (SF = 0.9727(6)), and above 2000 cm-1 (SF = 0.9564(4)). This sets a lower bound for the performance that could be reliably obtained using scaling of harmonic frequency calculations to predict experimental fundamental frequencies. VIBFREQ1295's most important purpose is to provide a robust database for benchmarking the performance of any vibrational frequency calculations. VIBFREQ1295 data could also be used to train machine-learning models for the prediction of vibrational spectra and as a reference and data starting point for more detailed spectroscopic modeling of particular molecules. The database can be found as part of the Supporting Information for this paper or in the Harvard DataVerse at https://doi.org/10.7910/DVN/VLVNU7.
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Affiliation(s)
| | - Laura K McKemmish
- School of Chemistry, University of New South Wales, 2052 Sydney, Australia
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34
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Zapata Trujillo JC, McKemmish LK. Meta‐analysis of uniform scaling factors for harmonic frequency calculations. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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35
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Viana RB, Savedra RM, da Silva AB. A mechanistic view of the reaction between phosphine and fluorine atom: insights into PH3F isomers. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Sapkota R, Marshall P. Gas-Phase Chemistry of 1,1,2,3,3,4,4-Heptafluorobut-1-ene Initiated by Chlorine Atoms. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030647. [PMID: 35163912 PMCID: PMC8839731 DOI: 10.3390/molecules27030647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 11/16/2022]
Abstract
The possibility of mitigating climate change by switching to materials with low global warming potentials motivates a study of the spectroscopic and kinetic properties of a fluorinated olefin. The relative rate method was used to determine the rate constant for the reaction of heptafluorobut-1-ene (CF2=CFCF2CF2H) with chlorine atoms in air. A mercury UV lamp was used to generate atomic chlorine, which initiated chemistry monitored by FTIR spectroscopy. Ethane was used as the reference compound for kinetic studies. Oxidation of heptafluorobut-1-ene initiated by a chlorine atom creates carbonyl difluoride (CF2=O) and 2,2,3,3 tetrafluoropropanoyl fluoride (O=CFCF2CF2H) as the major products. Anharmonic frequency calculations allowing for several low-energy conformations of 1,1,2,3,3,4,4 heptafluorobut-1-ene and 2,2,3,3 tetrafluoropropanoyl fluoride, based on density functional theory, are in good accord with measurements. The global warming potentials of these two molecules were calculated from the measured IR spectra and estimated atmospheric lifetimes and found to be small, less than 1.
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Affiliation(s)
- Ramesh Sapkota
- Department of Chemistry, University of North Texas, 1155 Union Circle, #305070, Denton, TX 76203, USA;
| | - Paul Marshall
- Center for Advanced Scientific Computing and Modeling, University of North Texas, 1155 Union Circle, #305070, Denton, TX 76203, USA
- Correspondence:
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37
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Matrix Isolation FTIR and Theoretical Study of Weakly Bound Complexes of Isocyanic Acid with Nitrogen. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020495. [PMID: 35056808 PMCID: PMC8777744 DOI: 10.3390/molecules27020495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 11/17/2022]
Abstract
Weak complexes of isocyanic acid (HNCO) with nitrogen were studied computationally employing MP2, B2PLYPD3 and B3LYPD3 methods and experimentally by FTIR matrix isolation technique. The results show that HNCO interacts specifically with N2. For the 1:1 stoichiometry, three stable minima were located on the potential energy surface. The most stable of them involves a weak, almost linear hydrogen bond from the NH group of the acid molecule to nitrogen molecule lone pair. Two other structures are bound by van der Waals interactions of N⋯N and C⋯N types. The 1:2 and 2:1 HNCO complexes with nitrogen were computationally tracked as well. Similar types of interactions as in the 1:1 complexes were found in the case of the higher stoichiometry complexes. Analysis of the HNCO/N2/Ar spectra after deposition indicates that the 1:1 hydrogen-bonded complex is prevalent in argon matrices with a small amount of the van der Waals structures also present. Upon annealing, complexes of the 1:2 and 2:1 stoichiometry were detected as well.
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38
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Zheng RH, Wei WM. Sum-frequency vibrational spectroscopy of methanol at interfaces due to Fermi resonance. Phys Chem Chem Phys 2022; 24:27204-27211. [DOI: 10.1039/d2cp01808j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We present a theoretical method of studying sum-frequency vibrational spectroscopy for the CH3 group of methanol at interfaces due to Fermi resonance, which provides a novel and untraditional point of view with respect to traditional approaches.
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Affiliation(s)
- Ren-Hui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing, 100190, P. R. China
| | - Wen-Mei Wei
- School of Basic Medical Science, Anhui Medical University, Hefei, Anhui, 230032, P. R. China
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39
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Gu Y, Xu X. Symmetry Dilemma of Doubly Hybrid Density Functionals for Equilibrium Molecular Property Calculations. J Chem Theory Comput 2021; 17:7745-7752. [PMID: 34839668 DOI: 10.1021/acs.jctc.1c00990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In electronic structure theory, when an approximate wavefunction tends to artifactually break the symmetry of the exact Hamiltonian, the corresponding method is referred to as having a "symmetry dilemma" problem. Such types of artifacts were often reported when Hartree-Fock (HF) and the low-level post-HF methods were used, while the traditional Kohn-Sham density functional theory (KS-DFT) methods were usually found to be more resistant to this breakdown. In this work, we present a systematic study on the reliability of the doubly hybrid (DH) DFT methods for several violable cases. Almost all the commonly used B2PLYP-type (bDH) functionals are shown to have a severe "symmetry dilemma" problem and yield dramatically unreliable molecular properties, such as dipole moment, vibrational frequency, and static polarizability at the equilibrium geometry. A one-parameter bDH functional model study demonstrates that such a problem is a combined effect of the inappropriate portion of the HF exchange (over 50%) for the self-consistent field (SCF) calculation and the augmentation of the second-order perturbative contribution. It is remarkable that the XYG3-type (xDH) functionals show a good capability to resist the artifactual symmetry breaking and yield reliable molecular properties when the same critical cases are calculated. In the xDH, there are two functionals of different purposes, namely, the SCF functional and the energy functional, which have different amounts of the HF exchange and different portions of the correlation contributions. The success of the xDHs can be attributed to this flexibility in xDH construction to avoid using an improperly large portion of the HF exchange in the SCF functional. The insights gained in this work are of significance for the development of an improved DH functional.
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Affiliation(s)
- Yonghao Gu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai 200433, China
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40
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Barone V, Fusè M, Pinto SMV, Tasinato N. A Computational Journey across Nitroxide Radicals: From Structure to Spectroscopic Properties and Beyond. Molecules 2021; 26:molecules26237404. [PMID: 34885980 PMCID: PMC8659111 DOI: 10.3390/molecules26237404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Nitroxide radicals are characterized by a long-lived open-shell electronic ground state and are strongly sensitive to the chemical environment, thus representing ideal spin probes and spin labels for paramagnetic biomolecules and materials. However, the interpretation of spectroscopic parameters in structural and dynamic terms requires the aid of accurate quantum chemical computations. In this paper we validate a computational model rooted into double-hybrid functionals and second order vibrational perturbation theory. Then, we provide reference quantum chemical results for the structures, vibrational frequencies and other spectroscopic features of a large panel of nitroxides of current biological and/or technological interest.
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41
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Kumar P, Escudero D. Computational Protocol to Calculate the Phosphorescence Energy of Pt(II) Complexes: Is the Lowest Triplet Excited State Always Involved in Emission? A Comprehensive Benchmark Study. Inorg Chem 2021; 60:17230-17240. [PMID: 34702026 DOI: 10.1021/acs.inorgchem.1c02562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The reliable calculation of phosphorescence energies of phosphor materials is at the core of designing efficient phosphorescent organic light-emitting diodes (PhOLEDs). Therefore, it is of paramount importance to have a robust computational protocol to perform those calculations in a black-box manner. In this work, we use Domain-Based Local Pair Natural Orbital Coupled Cluster theory with single, double, and perturbative triple excitation (DLPNO-CCSD(T)) calculations to attain the phosphorescence energies of a large pool of Pt(II) complexes. Several approaches to incorporate relativistic effects in our calculations were tested. In addition, we have used the DLPNO-CCSD(T) values (i.e., our best theoretical values) to assess the performance of different flavors of density functional theory including pure, hybrid, meta-hybrid, and range-separated functionals. Among the tested functionals, the M06HF functional provides the best values compared with the DLPNO-CCSD(T) ones, with a mean absolute deviation (MAD) value of 0.14 eV. In its turn, and thanks to the increased accuracy achieved in the calculation of phosphorescence energies, we also demonstrate that not all of the investigated complexes emit from their lowest-lying triplet state (T1). The outlier complexes include different complex photophysical scenarios and both Kasha and anti-Kasha types of complexes. Finally, we provide a general computational protocol to pre-screen whether T1 is actually the emissive state and to accurately calculate the phosphorescence energies of Pt(II) complexes.
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Affiliation(s)
- Prashant Kumar
- Quantum Chemistry and Physical Chemistry Section, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Daniel Escudero
- Quantum Chemistry and Physical Chemistry Section, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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42
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Ceselin G, Barone V, Tasinato N. Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry. J Chem Theory Comput 2021; 17:7290-7311. [PMID: 34666488 PMCID: PMC8582257 DOI: 10.1021/acs.jctc.1c00788] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The determination
of accurate equilibrium molecular structures
plays a fundamental role for understanding many physical–chemical
properties of molecules, ranging from the precise evaluation of the
electronic structure to the analysis of the role played by dynamical
and environmental effects in tuning their overall behavior. For small
semi-rigid systems in the gas phase, state-of-the-art quantum chemical
computations rival the most sophisticated experimental (from, for
example, high-resolution spectroscopy) results. For larger molecules,
more effective computational approaches must be devised. To this end,
we have further enlarged the compilation of available semi-experimental
(SE) equilibrium structures, now covering the most important fragments
containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new
SE100 database. Next, comparison with geometries optimized by methods
rooted in the density functional theory showed that the already remarkable
results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals
can be further improved by a linear regression (LR) approach. Use
of template fragments (taken from the SE100 library) together with
LR estimates for the missing interfragment parameters paves the route
toward accurate structures of large molecules, as witnessed by the
very small deviations between computed and experimental rotational
constants. The whole approach has been implemented in a user-friendly
tool, termed nano-LEGO, and applied to a number of demanding case
studies.
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Affiliation(s)
- Giorgia Ceselin
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
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43
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Viana RB, Machado ACP, Marques LDS, Modolo MZ, Santos DDO. Unravelling the diarsenic hydrides: Reactivity and spectroscopic properties. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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44
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Krupa J, Wierzejewska M, Lundell J. Structure and IR Spectroscopic Properties of HNCO Complexes with SO 2 Isolated in Solid Argon. Molecules 2021; 26:molecules26216441. [PMID: 34770850 PMCID: PMC8587861 DOI: 10.3390/molecules26216441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/13/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
FTIR spectroscopy was combined with the matrix isolation technique and quantum chemical calculations with the aim of studying complexes of isocyanic acid with sulfur dioxide. The structures of the HNCO⋯SO2 complexes of 1:1, 1:2 and 2:1 stoichiometry were optimized at the MP2, B3LYPD3, B2PLYPD3 levels of theory with the 6-311++G(3df,3pd) basis set. Five stable 1:1 HNCO⋯SO2 complexes were found. Three of them contain a weak N-H⋯O hydrogen bond, whereas two other structures are stabilized by van der Waals interactions. The analysis of the HNCO/SO2/Ar spectra after deposition indicates that mostly the 1:1 hydrogen-bonded complexes are present in argon matrices, with a small amount of the van der Waals structures. Upon annealing, complexes of the 1:2 stoichiometry were detected, as well.
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Affiliation(s)
- Justyna Krupa
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, 50-383 Wroclaw, Poland;
- Correspondence: (J.K.); (J.L.); Tel.: +358-40-744-5270 (J.L.)
| | - Maria Wierzejewska
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, 50-383 Wroclaw, Poland;
| | - Jan Lundell
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
- Correspondence: (J.K.); (J.L.); Tel.: +358-40-744-5270 (J.L.)
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45
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Sheng M, Silvestrini F, Biczysko M, Puzzarini C. Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case. J Phys Chem A 2021; 125:9099-9114. [PMID: 34623165 DOI: 10.1021/acs.jpca.1c06993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm-1, has been obtained by combining CCSD(T)/(CBS+CV)MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.
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Affiliation(s)
- Mingzhu Sheng
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Filippo Silvestrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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46
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Barone V, Lupi J, Salta Z, Tasinato N. Development and Validation of a Parameter-Free Model Chemistry for the Computation of Reliable Reaction Rates. J Chem Theory Comput 2021; 17:4913-4928. [PMID: 34228935 PMCID: PMC8359010 DOI: 10.1021/acs.jctc.1c00406] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
A recently developed
model chemistry (jun-Cheap) has been slightly
modified and proposed as an effective, reliable, and parameter-free
scheme for the computation of accurate reaction rates with special
reference to astrochemical and atmospheric processes. Benchmarks with
different sets of state-of-the-art energy barriers spanning a wide
range of values show that, in the absence of strong multireference
contributions, the proposed model outperforms the most well-known
model chemistries, reaching a subchemical accuracy without any empirical
parameter and with affordable computer times. Some test cases show
that geometries, energy barriers, zero point energies, and thermal
contributions computed at this level can be used in the framework
of the master equation approach based on the ab initio transition-state
theory for obtaining accurate reaction rates.
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Affiliation(s)
- Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Jacopo Lupi
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Zoi Salta
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Nicola Tasinato
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56125 Pisa, Italy
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47
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Barone V, Puzzarini C, Mancini G. Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy. Phys Chem Chem Phys 2021; 23:17079-17096. [PMID: 34346437 DOI: 10.1039/d1cp02507d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible. Some of the key tools (e.g., continuous molecular perception model and virtual multifrequency spectrometer) and theoretical developments (e.g., non-periodic boundaries, joint variational-perturbative models) are shortly sketched and their application illustrated by means of representative case studies taken from recent work by the authors. Some of the results presented are already well beyond the state of the art in the field of computational spectroscopy, thereby also providing a proof of concept for other research fields.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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48
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Metal-free visible-light-catalyzed synthesis of 3-methyl-3,4-dihydroisoquinolin-1(2H)-one: mechanism, DFT calculation and optical properties. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01639-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mendolicchio M, Bloino J, Barone V. General Perturb-Then-Diagonalize Model for the Vibrational Frequencies and Intensities of Molecules Belonging to Abelian and Non-Abelian Symmetry Groups. J Chem Theory Comput 2021; 17:4332-4358. [PMID: 34085530 PMCID: PMC8280743 DOI: 10.1021/acs.jctc.1c00240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 11/29/2022]
Abstract
In this paper, we show that the standard second-order vibrational perturbation theory (VPT2) for Abelian groups can be used also for non-Abelian groups without employing specific equations for two- or threefold degenerate vibrations but rather handling in the proper way all the degeneracy issues and deriving the peculiar spectroscopic signatures of non-Abelian groups (e.g., l -doubling) by a posteriori transformations of the eigenfunctions. Comparison with the results of previous conventional implementations shows a perfect agreement for the vibrational energies of linear and symmetric tops, thus paving the route to the transparent extension of the equations already available for asymmetric tops to the energies of spherical tops and the infrared and Raman intensities of molecules belonging to non-Abelian symmetry groups. The whole procedure has been implemented in our general engine for vibro-rotational computations beyond the rigid rotor/harmonic oscillator model and has been validated on a number of test cases.
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Affiliation(s)
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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Hanson-Heine MWD. Reduced Two-Electron Interactions in Anharmonic Molecular Vibrational Calculations Involving Localized Normal Coordinates. J Chem Theory Comput 2021; 17:4383-4391. [PMID: 34087068 DOI: 10.1021/acs.jctc.1c00314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spatially localized vibrational normal mode coordinates are shown to reduce the importance of calculating the full set of two-electron terms in the molecular electronic Schrödinger equation. Electron correlation and dispersion interactions become less significant in (E,E)-1,3,5,7-octatetraene vibrational self-consistent field calculations when displacing remote atoms along multiple coordinates. Electron correlation interactions between spatially remote modes are also found to be less important compared to their corresponding uncorrelated interaction terms. Attenuation of the Coulomb operator indicates that the two-electron terms between remote electrons become less important for accurately describing the strongly contributing mode-coupling terms between sets of localized vibrational modes.
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