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Đorđević Zlatković MR, Radulović NS, Dangalov M, Vassilev NG. Conformation Analysis and Stereodynamics of Symmetrically ortho-Disubstituted Carvacrol Derivatives. Molecules 2024; 29:1962. [PMID: 38731453 PMCID: PMC11085911 DOI: 10.3390/molecules29091962] [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: 03/22/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
The design and synthesis of analogs of natural products can be a valuable source of medicinal preparations for the pharmaceutical industry. In the present study, the structural elucidation of eleven derivatives of 2,4-dihalogeno substituted synthetic analogues of the natural compound carvacrol was carried out by means of NMR experiments, and of another thirteen by DFT calculations. By selective NOE experiments and the irradiation of CH signals of the isopropyl group, individual conformers were assigned as syn and anti. By comparing GIAO/B3LYP/6-311++G(d,p)-calculated and experimentally measured vicinal 3JCH spin-spin constants, this assignment was confirmed. An unusual relationship is reported for proton-carbon vicinal couplings: 3JCH (180°) < 3JCH (0°). The conformational mobility of carvacrols was studied by 2D EXSY spectra. The application of homonuclear decoupling technique (HOBS) to these spectra simplifies the spectra, improves resolution without reducing the sensitivity, and allows a systematic examination of the rotational barrier of all compounds via their CH signals of the isopropyl group in a wider temperature interval. The rate constants of the isopropyl rotation between syn and anti conformers were determined and the corresponding energy barriers (14-17 kcal/mol) were calculated. DFT calculations of the energy barriers in carvacrol derivatives allowed the determination of the steric origin of the restricted isopropyl rotation. The barrier height depends on the size of the 2- and 4-position substituents, and is independent of the derivatization of the OH group.
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Affiliation(s)
| | - Niko S. Radulović
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Serbia;
| | - Miroslav Dangalov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bontchev Str. Bl. 9, 1113 Sofia, Bulgaria;
| | - Nikolay G. Vassilev
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bontchev Str. Bl. 9, 1113 Sofia, Bulgaria;
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2
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Yao C, Wang T. Quantum Size-Driven Spectral Variations in Pillar[n]arene Systems: A Density Functional Theory and Wave Function Assessment. Molecules 2024; 29:1912. [PMID: 38731404 PMCID: PMC11085802 DOI: 10.3390/molecules29091912] [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: 04/01/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
This study explores the quantum size effects on the optical properties of pillar[n]arene (n = 5, 6, 7, 8) utilizing density functional theory (DFT) and wave function analysis. The mechanisms of electron transitions in one-photon absorption (OPA) and two-photon absorption (TPA) spectra are investigated, alongside the calculation of electron circular dichroism (ECD) for these systems. Transition Density Matrix (TDM) and electron-hole pair density maps are employed to study the electron excitation characteristics, unveiling a notable size dependency. Analysis of the transition electric dipole moment (TEDM) and the transition magnetic dipole moment (TMDM) reveals the electromagnetic interaction mechanism within pillar[n]arene. Raman spectra computations further elucidate vibrational modes, while interactions with external environments are studied using electrostatic potential (ESP) analysis, and electron delocalization is assessed under an external magnetic field, providing insights into the magnetically induced current phenomena within these supramolecular structures. The thermal stability of pillar[n]arene was investigated by ab initio molecular dynamics (AIMD).
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Affiliation(s)
- Cailian Yao
- College of Science, Liaoning Petrochemical University, Fushun 113001, China
| | - Tao Wang
- College of Science, Liaoning Petrochemical University, Fushun 113001, China
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3
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Pitman SJ, Evans AK, Ireland RT, Lempriere F, McKemmish LK. Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided. J Phys Chem A 2023; 127:10295-10306. [PMID: 37982604 DOI: 10.1021/acs.jpca.3c05573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Basis sets are a crucial but often largely overlooked choice in setting up quantum chemistry calculations. The choice of the basis set can be critical in determining the accuracy and calculation time of your quantum chemistry calculations. Clear recommendations based on thorough benchmarking are essential but not readily available currently. This study investigates the relative quality of basis sets for general properties by benchmarking basis set performance for a diverse set of 139 reactions (from the diet-150-GMTKN55 data set). In our analysis, we find the distributions of errors are often significantly non-Gaussian, meaning that the joint consideration of median errors, mean absolute errors, and outlier statistics is helpful to provide a holistic understanding of basis set performance. Our direct comparison of performance between most modern basis sets provides quantitative evidence for basis set recommendations that broadly align with the established understanding of basis set experts and is evident in the design of modern basis sets. For example, while zeta is a good measure of quality, it is not the only determining factor for an accurate calculation with unpolarized double- and triple-ζ basis sets (like 6-31G and 6-311G) having very poor performance. Appropriate use of polarization functions (e.g., 6-31G*) is essential to obtain the accuracy offered by double- or triple-ζ basis sets. In our study, the best performances for double- and triple-ζ basis sets are 6-31++G** and pcseg-2, respectively. However, the performances of singly polarized double-ζ and doubly polarized triple-ζ basis sets are quite similar with one key exception: the polarized 6-311G basis set family has poor parametrization, which means its performance is more like a double-ζ than a triple-ζ basis set. All versions of the 6-311G basis set family should be avoided entirely for valence chemistry calculations moving forward.
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Affiliation(s)
- Samuel J Pitman
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alicia K Evans
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Robbie T Ireland
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Felix Lempriere
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Laura K McKemmish
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
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4
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Rusakov YY, Rusakova IL. New pecJ- n ( n = 1, 2) Basis Sets for Selenium Atom Purposed for the Calculations of NMR Spin-Spin Coupling Constants Involving Selenium. Int J Mol Sci 2023; 24:ijms24097841. [PMID: 37175548 PMCID: PMC10178039 DOI: 10.3390/ijms24097841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
We present new compact pecJ-n (n = 1, 2) basis sets for the selenium atom developed for the quantum-chemical calculations of NMR spin-spin coupling constants (SSCCs) involving selenium nuclei. These basis sets were obtained at the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes (SOPPA(CCSD)) level with the property-energy consistent (PEC) method, which was introduced in our previous papers. The existing SSCC-oriented selenium basis sets are rather large in size, while the PEC method gives more compact basis sets that are capable of providing accuracy comparable to that reached using the property-oriented basis sets of larger sizes generated with a standard even-tempered technique. This is due to the fact that the PEC method is very different in its essence from the even-tempered approaches. It generates new exponents through the total optimization of angular spaces of trial basis sets with respect to the property under consideration and the total molecular energy. New basis sets were tested on the coupled cluster singles and doubles (CCSD) calculations of SSCCs involving selenium in the representative series of molecules, taking into account relativistic, solvent, and vibrational corrections. The comparison with the experiment showed that the accuracy of the results obtained with the pecJ-2 basis set is almost the same as that provided by a significantly larger basis set, aug-cc-pVTZ-J, while that achieved with a very compact pecJ-1 basis set is only slightly inferior to the accuracy provided by the former.
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Affiliation(s)
- Yuriy Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
| | - Irina L Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
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5
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Rusakova IL, Rusakov YY. On the Utmost Importance of the Basis Set Choice for the Calculations of the Relativistic Corrections to NMR Shielding Constants. Int J Mol Sci 2023; 24:ijms24076231. [PMID: 37047204 PMCID: PMC10094374 DOI: 10.3390/ijms24076231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
The investigation of the sensitivity of the relativistic corrections to the NMR shielding constants (σ) to the configuration of angular spaces of the basis sets used on the atoms of interest was carried out within the four-component density functional theory (DFT). Both types of relativistic effects were considered, namely the so-called heavy atom on light atom and heavy atom on heavy atom effects, though the main attention was paid to the former. As a main result, it was found that the dependence of the relativistic corrections to σ of light nuclei (exemplified here by 1H and 13C) located in close vicinity to a heavy atom (exemplified here by In, Sn, Sb, Te, and I) on the basis set used on the light spectator atom was very much in common with that of the Fermi-contact contribution to the corresponding nonrelativistic spin-spin coupling constant (J). In general, it has been shown that the nonrelativistic J-oriented and σ-oriented basis sets, artificially saturated in the tight s-region, provided much better accuracy than the standard nonrelativistic σ-oriented basis sets when calculating the relativistic corrections to the NMR shielding constants of light nuclei at the relativistic four-component level of the DFT theory.
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Gleeson R, Andersen CL, Rapta P, Machata P, Christensen JB, Hammerich O, Sauer SPA. A Combined Experimental and Theoretical Study of ESR Hyperfine Coupling Constants for N,N,N',N'-Tetrasubstituted p-Phenylenediamine Radical Cations. Int J Mol Sci 2023; 24:ijms24043447. [PMID: 36834859 PMCID: PMC9967363 DOI: 10.3390/ijms24043447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/26/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
A test set of N,N,N',N'-tetrasubstituted p-phenylenediamines are experimentally explored using ESR (electron spin resonance) spectroscopy and analysed from a computational standpoint thereafter. This computational study aims to further aid structural characterisation by comparing experimental ESR hyperfine coupling constants (hfccs) with computed values calculated using ESR-optimised "J-style" basis sets (6-31G(d,p)-J, 6-31G(d,p)-J, 6-311++G(d,p)-J, pcJ-1, pcJ-2 and cc-pVTZ-J) and hybrid-DFT functionals (B3LYP, PBE0, TPSSh, ωB97XD) as well as MP2. PBE0/6-31g(d,p)-J with a polarised continuum solvation model (PCM) correlated best with the experiment, giving an R2 value of 0.8926. A total of 98% of couplings were deemed satisfactory, with five couplings observed as outlier results, thus degrading correlation values significantly. A higher-level electronic structure method, namely MP2, was sought to improve outlier couplings, but only a minority of couples showed improvement, whilst the remaining majority of couplings were negatively degraded.
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Affiliation(s)
- Ronan Gleeson
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Cecilie L. Andersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Peter Rapta
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Peter Machata
- Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Jørn B. Christensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Ole Hammerich
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Stephan P. A. Sauer
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Correspondence:
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7
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New pecJ-n (n = 1, 2) Basis Sets for High-Quality Calculations of Indirect Nuclear Spin–Spin Coupling Constants Involving 31P and 29Si: The Advanced PEC Method. Molecules 2022; 27:molecules27196145. [PMID: 36234706 PMCID: PMC9573013 DOI: 10.3390/molecules27196145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/21/2022] Open
Abstract
In this paper, we presented new J-oriented basis sets, pecJ-n (n = 1, 2), for phosphorus and silicon, purposed for the high-quality correlated calculations of the NMR spin–spin coupling constants involving these nuclei. The pecJ-n basis sets were generated using the modified version of the property-energy consistent (PEC) method, which was introduced in our earlier paper. The modifications applied to the original PEC procedure increased the overall accuracy and robustness of the generated basis sets in relation to the diversity of electronic systems. Our new basis sets were successfully tested on a great number of spin–spin coupling constants, involving phosphorus or/and silicon, calculated within the SOPPA(CCSD) method. In general, it was found that our new pecJ-1 and pecJ-2 basis sets are very efficient, providing the overall accuracy that can be characterized by MAEs of about 3.80 and 1.98 Hz, respectively, against the benchmark data obtained with a large dyall.aae4z+ basis set of quadruple-ζ quality.
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8
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Krivdin LB. Computational 1 H and 13 C NMR in structural and stereochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:733-828. [PMID: 35182410 DOI: 10.1002/mrc.5260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Present review outlines the advances and perspectives of computational 1 H and 13 C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational 1 H and 13 C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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9
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Rusakov YY, Rusakova IL. New pecS- n ( n = 1, 2) basis sets for quantum chemical calculations of the NMR chemical shifts of H, C, N, and O nuclei. J Chem Phys 2022; 156:244112. [DOI: 10.1063/5.0096907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper demonstrates the performance of our previously suggested property-energy consistent method on the example of the generation of effective basis sets, pecS-1 and pecS-2, suited for the calculation of hydrogen, carbon, nitrogen, and oxygen chemical shifts. The new basis sets were successfully approbated in the GIAO-DFT calculations of the chemical shifts of 35 molecules using six different functionals. The pecS-1 basis set demonstrated very good accuracy, which makes this small basis set an effective means for the large-scale computations. At the same time, the pecS-2 basis set also gave very accurate results, thus putting it on a par with the other commensurate basis sets suited for the chemical shifts calculations.
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Affiliation(s)
- Yuriy Yu. Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Irina L. Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
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10
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Quantum Chemical Approaches to the Calculation of NMR Parameters: From Fundamentals to Recent Advances. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8050050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantum chemical methods for the calculation of indirect NMR spin–spin coupling constants and chemical shifts are always in progress. They never stay the same due to permanently developing computational facilities, which open new perspectives and create new challenges every now and then. This review starts from the fundamentals of the nonrelativistic and relativistic theory of nuclear magnetic resonance parameters, and gradually moves towards the discussion of the most popular common and newly developed methodologies for quantum chemical modeling of NMR spectra.
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11
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Lagostina V, Romeo E, Maria Ferrari A, Maurino V, Chiesa M. Monomeric (VO2+) and dimeric mixed valence (V2O33+) vanadium species at the surface of shape controlled TiO2 anatase nano crystals. J Catal 2022. [DOI: 10.1016/j.jcat.2021.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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San Fabián J, Ema I, Omar S, García de la Vega JM. Toward a Computational NMR Procedure for Modeling Dipeptide Side-Chain Conformation. J Chem Inf Model 2021; 61:6012-6023. [PMID: 34762416 PMCID: PMC8715507 DOI: 10.1021/acs.jcim.1c00773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Theoretical relationships between
the vicinal spin–spin
coupling constants (SSCCs) and the χ1 torsion angles
have been studied to predict the conformations of protein side chains.
An efficient computational procedure is developed to obtain the conformation
of dipeptides through theoretical and experimental SSCCs, Karplus
equations, and quantum chemistry methods, and it is applied to three
aliphatic hydrophobic residues (Val, Leu, and Ile). Three models are
proposed: unimodal-static, trimodal-static-stepped, and trimodal-static-trigonal,
where the most important factors are incorporated (coupled nuclei,
nature and orientation of the substituents, and local geometric properties).
Our results are validated by comparison with NMR and X-ray empirical
data described in the literature, obtaining successful results on
the 29 residues considered. Using out trimodal residue treatment,
it is possible to detect and resolve residues with a simple conformation
and those with two or three staggered conformers. In four residues,
a deeper analysis explains that they do not have a unique conformation
and that the population of each conformation plays an important role.
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Affiliation(s)
- Jesús San Fabián
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ignacio Ema
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Salama Omar
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Abstract
Doping compounds can be considered a perturbation to the nuclear charges in a molecular Hamiltonian. Expansions of this perturbation in a Taylor series, i.e., quantum alchemy, have been used in the literature to assess millions of derivative compounds at once rather than enumerating them in costly quantum chemistry calculations. So far, it was unclear whether this series even converges for small molecules, whether it can be used for geometry relaxation, and how strong this perturbation may be to still obtain convergent numbers. This work provides numerical evidence that this expansion converges and recovers the self-consistent energy of Hartree-Fock calculations. The convergence radius of this expansion is quantified for dimer examples and systematically evaluated for different basis sets, allowing for estimates of the chemical space that can be covered by perturbing one reference calculation alone. Besides electronic energy, convergence is shown for density matrix elements, molecular orbital energies, and density profiles, even for large changes in electronic structure, e.g., transforming He3 into H6. Subsequently, mixed alchemical and spatial derivatives are used to relax H2 from the electronic structure of He alone, highlighting a path to spatially relaxed quantum alchemy. Finally, the underlying code that allows for arbitrarily accurate evaluation of restricted Hartree-Fock energies and arbitrary order derivatives is made available to support future method development.
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14
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Theoretical Investigation of Glycine Micro-Solvated. Energy and NMR Spin Spin Coupling Constants Calculations. SCI 2021. [DOI: 10.3390/sci3040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Glycine in its neutral form can exist in the gas phase while its zwitterion form is more stable in water solution, but how many waters are actually necessary to stabilize the zwitterionic structure in the gas phase? Are the intramolecular isotropic spin spin coupling constants sensitive enough to accuse the change in the environment? or the conformer observed? These and related questions have been investigated by a computational study at the level of density functional theory employing the B3LYP functional and the 6-31++G**-J basis set. We found that at least two water molecules explicitly accounted for in the super-molecule structure are necessary to stabilize both conformers of glycine within a water polarizable continuum model. At least half of the SSCCs of both conformers are very stable to changes in the environment and at least four of them differ significantly between Neutral and Zwitterion conformation.
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15
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Steinmann C, Sauer SPA. The aug-cc-pVTZ-J basis set for the p-block fourth-row elements Ga, Ge, As, Se, and Br. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:1134-1145. [PMID: 33929770 DOI: 10.1002/mrc.5166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The aug-cc-pVTZ-J basis set family is extended to include the fourth-row p-block elements Ga, Ge, As, Se, and Br. We use the established approach outlined by Sauer and coworkers (J. Chem. Phys. 115, 1324 [2001], J. Chem. Phys. 133, 054308 [2010], J. Chem. Theory Comput. 7, 4070 [2011], and J. Chem. Theory Comput. 7, 4077 [2011]) where the completely uncontracted aug-cc-pVTZ basis set is saturated with tight s-, p-, d-, and f-functions to form the aug-cc-pVTZ-Juc basis set for the tested elements. The saturation is carried out on the simplest hydrides possible for the tested elements GaH, GeH4 , AsH3 , H2 Se, and HBr until an improvement is less than 0.01% for all s-, p-, and d-functions added. f-Functions are added to an improvement less than or equal to 1.0% due to the computational expense these functions add. The saturated aug-cc-pVTZ-Juc (26s16p12d5f) is then recontracted using the molecular orbital coefficients from self-consistent field calculations on the simple hydrides to improve computational efficiency. During contraction of the basis set, we observe that the linear hydrogen bromide molecule has a slower convergence than the other tested molecules which sets a limit on the accuracy obtained. All calculations with the contracted aug-cc-pVTZ-J [17s10p7d5f] gives results that are within 1.0% of the uncontracted results at considerable computational savings.
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Affiliation(s)
- Casper Steinmann
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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16
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Rusakov YY, Rusakova IL. An efficient method for generating property-energy consistent basis sets. New pecJ- n ( n = 1, 2) basis sets for high-quality calculations of indirect nuclear spin-spin coupling constants involving 1H, 13C, 15N, and 19F nuclei. Phys Chem Chem Phys 2021; 23:14925-14939. [PMID: 34223856 DOI: 10.1039/d1cp01984h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This paper presents a new method of generating property-energy consistent (PEC) basis sets that can be applied to any arbitrary molecular property. The PEC method generates a basis set that is optimized for the molecular property under interest, providing the least possible total molecular energy. The main algorithm of the PEC approach involves Monte Carlo simulations to generate random exponents in the predetermined range. In this work, the PEC method is introduced in the example of generation of new pecJ-n (n = 1, 2) basis sets suited for high-quality correlated calculations of indirect nuclear spin-spin coupling constants involving the most popular NMR-active nuclei: 1H, 13C, 15N, and 19F.
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Affiliation(s)
- Yuriy Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation.
| | - Irina L Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation.
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17
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Rusakov YY, Rusakova IL. Efficient J-oriented tin basis sets for the correlated calculations of indirect nuclear spin-spin coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:713-722. [PMID: 33439515 DOI: 10.1002/mrc.5132] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
New J-oriented tin basis sets, acvXz-J (X = 2, 3, 4), have been developed at the level of the second-order polarization propagator approximation with the coupled-cluster single and double amplitudes, SOPPA (CCSD), for the purpose of correlated calculations of indirect nuclear spin-spin coupling constants involving tin nucleus. High-quality coupled-cluster calculations of several tin-proton and tin-carbon spin-spin coupling constants, performed with one of the newly developed basis sets, namely, the acv3z-J, taking into account relativistic, solvent, and vibrational corrections showed that the acv3z-J basis set is capable to provide reliable results, as compared with the experimental data.
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Affiliation(s)
- Yuriy Yu Rusakov
- Siberian Branch of the Russian Academy of Sciences, A. E. Favorsky Irkutsk Institute of Chemistry, Irkutsk, Russian Federation
| | - Irina L Rusakova
- Siberian Branch of the Russian Academy of Sciences, A. E. Favorsky Irkutsk Institute of Chemistry, Irkutsk, Russian Federation
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18
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Theibich YA, Sauer SP, Leggio LL, Hedegård ED. Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase. Comput Struct Biotechnol J 2020; 19:555-567. [PMID: 33510861 PMCID: PMC7807142 DOI: 10.1016/j.csbj.2020.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 11/07/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO Ls(AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for Ls(AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.
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Affiliation(s)
- Yusuf A. Theibich
- Department of Chemistry, University of University, Copenhagen, Denmark
| | | | - Leila Lo Leggio
- Department of Chemistry, University of University, Copenhagen, Denmark
| | - Erik D. Hedegård
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
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19
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Rusakov YY, Rusakova IL, Semenov VA, Krivdin LB. A New Basis Set for the Calculation of 13C NMR Chemical Shifts within a Non-empirical Correlated Framework. J Phys Chem A 2020; 124:7322-7330. [DOI: 10.1021/acs.jpca.0c06038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yuriy Yu. Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Irina L. Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Valentin A. Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Leonid B. Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russian Federation
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20
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Colasuonno F, Gentile FS, Mackrodt W, Ferrari AM, Platonenko A, Dovesi R. Interstitial defects in diamond: A quantum mechanical simulation of their EPR constants and vibrational spectra. J Chem Phys 2020; 153:024119. [DOI: 10.1063/5.0014368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Fabio Colasuonno
- Dipartimento di Chimica, Università di Torino and NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy
| | - Francesco Silvio Gentile
- Dipartimento di Chimica, Università di Torino and NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy
| | - William Mackrodt
- Dipartimento di Chimica, Università di Torino and NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy
| | - Anna Maria Ferrari
- Dipartimento di Chimica, Università di Torino and NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy
| | - Alexander Platonenko
- Institute of Solid State Physics, University of Latvia, 8 Kengaraga Street, LV1063 Riga, Latvia
| | - Roberto Dovesi
- Dipartimento di Chimica, Università di Torino and NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy
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21
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Dovesi R, Pascale F, Civalleri B, Doll K, Harrison NM, Bush I, D'Arco P, Noël Y, Rérat M, Carbonnière P, Causà M, Salustro S, Lacivita V, Kirtman B, Ferrari AM, Gentile FS, Baima J, Ferrero M, Demichelis R, De La Pierre M. The CRYSTAL code, 1976-2020 and beyond, a long story. J Chem Phys 2020; 152:204111. [PMID: 32486670 DOI: 10.1063/5.0004892] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
CRYSTAL is a periodic ab initio code that uses a Gaussian-type basis set to express crystalline orbitals (i.e., Bloch functions). The use of atom-centered basis functions allows treating 3D (crystals), 2D (slabs), 1D (polymers), and 0D (molecules) systems on the same grounds. In turn, all-electron calculations are inherently permitted along with pseudopotential strategies. A variety of density functionals are implemented, including global and range-separated hybrids of various natures and, as an extreme case, Hartree-Fock (HF). The cost for HF or hybrids is only about 3-5 times higher than when using the local density approximation or the generalized gradient approximation. Symmetry is fully exploited at all steps of the calculation. Many tools are available to modify the structure as given in input and simplify the construction of complicated objects, such as slabs, nanotubes, molecules, and clusters. Many tensorial properties can be evaluated by using a single input keyword: elastic, piezoelectric, photoelastic, dielectric, first and second hyperpolarizabilities, etc. The calculation of infrared and Raman spectra is available, and the intensities are computed analytically. Automated tools are available for the generation of the relevant configurations of solid solutions and/or disordered systems. Three versions of the code exist: serial, parallel, and massive-parallel. In the second one, the most relevant matrices are duplicated on each core, whereas in the third one, the Fock matrix is distributed for diagonalization. All the relevant vectors are dynamically allocated and deallocated after use, making the code very agile. CRYSTAL can be used efficiently on high performance computing machines up to thousands of cores.
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Affiliation(s)
- Roberto Dovesi
- Dipartimento di Chimica, and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino, Italy
| | - Fabien Pascale
- Université de Lorraine - Nancy, CNRS, Laboratoire de Physique et Chimie Théoriques, UMR 7019, 54506 Vandœuvre-lès-Nancy, France
| | - Bartolomeo Civalleri
- Dipartimento di Chimica, and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino, Italy
| | - Klaus Doll
- University of Stuttgart, Molpro Quantum Chemistry Software, Institute of Theoretical Chemistry, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Nicholas M Harrison
- Institute for Molecular Science and Engineering, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ London, United Kingdom
| | - Ian Bush
- Oxford e-Research Centre, University of Oxford, 7 Keble Road, Oxford OX1 3QG, United Kingdom
| | - Philippe D'Arco
- Sorbonne Université, CNRS-INSU, ISTeP UMR 7193, F-75005 Paris, France
| | - Yves Noël
- Sorbonne Université, CNRS-INSU, ISTeP UMR 7193, F-75005 Paris, France
| | - Michel Rérat
- Université de Pau et des Pays de L'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Mauro Causà
- Dipartimento di Ingengeria Chimica, dei Materiali e delle Produzioni Industriali DICMAPI, Università degli Studi di Napoli Federico II, Piazzale Vincenzo Tecchio 80, 80125 Napoli, Italy
| | - Simone Salustro
- Dipartimento di Chimica, and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino, Italy
| | - Valentina Lacivita
- Advanced Materials Lab, Samsung Research America, 3 Van de Graaff Drive, Burlington, Massachusetts 01803, USA
| | - Bernard Kirtman
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Anna Maria Ferrari
- Dipartimento di Chimica, and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino, Italy
| | - Francesco Silvio Gentile
- Dipartimento di Ingengeria Chimica, dei Materiali e delle Produzioni Industriali DICMAPI, Università degli Studi di Napoli Federico II, Piazzale Vincenzo Tecchio 80, 80125 Napoli, Italy
| | - Jacopo Baima
- CNRS and Sorbonne Université, UMR 7588, Institut des Nanosciences de Paris (INSP), 4 place Jussieu, 75005 Paris, France
| | - Mauro Ferrero
- Dipartimento di Chimica, and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino, Italy
| | - Raffaella Demichelis
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Marco De La Pierre
- Pawsey Supercomputing Centre, 26 Dick Perry Avenue, Kensington, WA 6151, Australia
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22
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Rusakov YY, Rusakova IL. Hierarchical Basis Sets for the Calculation of Nuclear Magnetic Resonance Spin–Spin Coupling Constants Involving Either Selenium or Tellurium Nuclei. J Phys Chem A 2019; 123:6564-6571. [DOI: 10.1021/acs.jpca.9b05276] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuriy Yu. Rusakov
- Siberian Branch of the Russian Academy of Sciences, A. E. Favorsky Irkutsk Institute of Chemistry, Favorsky St. 1, 664033 Irkutsk, Russian Federation
| | - Irina L. Rusakova
- Siberian Branch of the Russian Academy of Sciences, A. E. Favorsky Irkutsk Institute of Chemistry, Favorsky St. 1, 664033 Irkutsk, Russian Federation
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23
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San Fabián J, Omar S, García de la Vega JM. Computational Protocol to Evaluate Side-Chain Vicinal Spin–Spin Coupling Constants and Karplus Equation in Amino Acids: Alanine Dipeptide Model. J Chem Theory Comput 2019; 15:4252-4263. [DOI: 10.1021/acs.jctc.9b00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- J. San Fabián
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - S. Omar
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - J. M. García de la Vega
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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24
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Oliveira JPC, Rivelino R. Close Relationships between NMR J-Coupling Alternation (JCA) and Molecular Properties of Carbon Chains. J Chem Theory Comput 2019; 15:1605-1615. [PMID: 30730735 DOI: 10.1021/acs.jctc.8b01141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a J-coupling alternation (JCA) value that is demonstrated to be a suitable parameter to evaluate the nuclear magnetic resonance (NMR) indirect spin-spin coupling constants (SSCCs) as a function of molecular properties of chains by increasing their length. As an application, we report a theoretical study of the SSCCs for the interactions between neighbor nuclei in increasingly patterned carbon chains within density functional theory. First, we examine the J-coupling constants between 1H and 13C nuclei ( n JHC) considering the separation distance, as well as between two adjacent 13C nuclei (1 JCC) considering their relative positions in polyynes and cumulenes. Further, we define and determine JCA in terms of the differences of 1 JCC, which is investigated as a function of several molecular properties, e.g., cohesive energy, characteristic vibrational frequency, average polarizability, and energy gap of the systems. We also determine JCA for other types of carbon chains, such as diphenyl-capped polyynes, polyacetylene and polythiophene. The behavior of JCA as a function of the energy gap may be related to highly π-conjugated low-band-gap carbon chains. Overall, JCA correlates very well with the electronic properties of these chains, especially with their energy gap, exhibiting positive values for pristine polyyne and polythiophene and negative values for pristine cumulene and plyacetylene. These findings indicate an alternative way to establish an appropriate SSCC descriptor that characterizes the electronic nature of the system, such as the proposed JCA value averaging the whole system, instead of using only the individual J-coupling values to give insights into the properties of large and extended systems.
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Affiliation(s)
- João P C Oliveira
- Instituto de Física , Universidade Federal da Bahia , 40210-340 Salvador , Bahia , Brazil.,Centro de Ciência e Tecnologia em Energia e Sustentabilidade , Universidade Federal do Recôncavo da Bahia , 44085-132 Feira de Santana , Bahia , Brazil
| | - Roberto Rivelino
- Instituto de Física , Universidade Federal da Bahia , 40210-340 Salvador , Bahia , Brazil
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25
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Lukoyanov AN, Ulivanova EA, Razborov DA, Khrizanforova VV, Budnikova YH, Makarov SG, Rumyantcev RV, Ketkov SY, Fedushkin IL. One-Electron Reduction of 2-Mono(2,6-diisopropylphenylimino)acenaphthene-1-one (dpp-mian). Chemistry 2019; 25:3858-3866. [PMID: 30570195 DOI: 10.1002/chem.201805427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 11/06/2022]
Abstract
The electrochemical characteristics of 2-mono(2,6-diisopropylphenylimino)acenaphthene-1-one (dpp-mian) have been investigated. One-electron reduction of dpp-mian involves the iminoketone fragment, which is revealed by the EPR spectrum obtained after the electrolysis of the dpp-mian solution in tetrahydrofuran (THF). The reduction of dpp-mian with one equivalent of metallic potassium leads to a similar EPR spectrum. The sodium complex [(dpp-mian)Na(dme)]2 (1) produces an EPR signal with hyperfine coupling on the nitrogen atom of the iminoketone fragment of the dpp-mian ligand. Dpp-mian can also be reduced in a one-electron process by SnCl2 ×(dioxane). In this case, complex (dpp-mian)2 SnCl2 (2) is formed, with the tin atom displaying an oxidation state of +4. Tin(II) chloride dihydrate, SnCl2 ×2(H2 O), also reduces dpp-mian, but the two ligands bound to tin in the product form a new carbon-carbon bond between the ketone moieties of the dpp-mian monoanions to form complex (bis-dpp-mian)HSnCl3 (3). Metallic tin reduces dpp-mian to form the (bis-dpp-mian)2 Sn (4) species. Compounds 1-4 were characterized by X-ray diffraction.
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Affiliation(s)
- Anton N Lukoyanov
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russian Federation
| | - Elena A Ulivanova
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russian Federation
| | - Danila A Razborov
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russian Federation
| | - Vera V Khrizanforova
- A.E.Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, Arbuzov, 8, Kazan, 420088, Russian Federation
| | - Yulia H Budnikova
- A.E.Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, Arbuzov, 8, Kazan, 420088, Russian Federation
| | - Sergey G Makarov
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russian Federation
| | - Roman V Rumyantcev
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russian Federation
| | - Sergey Y Ketkov
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russian Federation
| | - Igor L Fedushkin
- G. A. Razuvaev Institute of Organometallic Chemistry, Russian Academy of Sciences, Tropinina, 49, Nizhny Novgorod, 603950, Russian Federation
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26
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On the development of the exact two-component relativistic method for calculating indirect NMR spin-spin coupling constants. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.09.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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A DFT investigation exploring the influence of lone electron pair on hyperfine structures of N-centered radicals. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Zhou L, Zhao C, Liu W, Li Y, Li Y, Shen R, Wang M, Wu Y, Wang M. ESR study of free radicals in polysilazane irradiated by gamma rays. Radiat Phys Chem Oxf Engl 1993 2018. [DOI: 10.1016/j.radphyschem.2018.05.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Krivdin LB. Theoretical calculations of carbon-hydrogen spin-spin coupling constants. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 108:17-73. [PMID: 30538048 DOI: 10.1016/j.pnmrs.2018.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.
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Affiliation(s)
- Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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30
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Aggelund PA, Sauer SPA, Jensen F. Development of polarization consistent basis sets for spin-spin coupling constant calculations for the atoms Li, Be, Na, and Mg. J Chem Phys 2018; 149:044117. [PMID: 30068157 DOI: 10.1063/1.5034109] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The pcJ-n basis set, optimized for spin-spin coupling constant calculations using density functional theory methods, are expanded to also include the s-block elements Li, Be, Na, and Mg, by studying several small molecules containing these elements. This is done by decontracting the underlying pc-n basis sets, followed by augmentation with additional tight functions. As was the case for the p-block elements, the convergence of the results can be significantly improved by augmentation with tight s-functions. For the p-block elements, additional tight functions of higher angular momentum were also needed, but this is not the case for the s-block elements. A search for the optimum contraction scheme is carried out using the criterion that the contraction error should be lower than the inherent error of the uncontracted pcJ-n relative to the uncontracted pcJ-4 basis set. A large search over possible contraction schemes is done for the Li2 and Na2 molecules, and based on this search contracted pcJ-n basis sets for the four atoms are recommended. This work shows that it is more difficult to contract the pcJ-n basis sets, than the underlying pc-n basis sets. However, it also shows that the pcJ-n basis sets for Li and Be can be more strongly contracted than the pcJ-n basis sets for the p-block elements. For Na and Mg, the contractions are to the same degree as for the p-block elements.
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Affiliation(s)
- Patrick A Aggelund
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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31
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Faber R, Sauer SPA. On the convergence of the ccJ-pVXZ and pcJ-n basis sets in CCSD calculations of nuclear spin–spin coupling constants: some difficult cases. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2217-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Adamson J, Nazarski RB, Jarvet J, Pehk T, Aav R. Shortfall of B3LYP in Reproducing NMR J
CH
Couplings in Some Isomeric Epoxy Structures with Strong Stereoelectronic Effects: A Benchmark Study on DFT Functionals. Chemphyschem 2018; 19:631-642. [DOI: 10.1002/cphc.201701125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/17/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Jasper Adamson
- National Institute of Chemical Physics and Biophysics; Akadeemia tee 23 12618 Tallinn Estonia
| | - Ryszard B. Nazarski
- Theoretical and Structural Chemistry Group; Department of Physical Chemistry; Faculty of Chemistry; University of Lodz; Pomorska 163/165 90-236 Łódź Poland
| | - Jüri Jarvet
- National Institute of Chemical Physics and Biophysics; Akadeemia tee 23 12618 Tallinn Estonia
- Current address: Department of Biochemistry and Biophysics; Arrhenius Laboratories; Stockholm University; Svante Arrhenius väg 16 10691 Stockholm Sweden
| | - Tõnis Pehk
- National Institute of Chemical Physics and Biophysics; Akadeemia tee 23 12618 Tallinn Estonia
| | - Riina Aav
- Department of Chemistry and Biotechnology; Tallinn University of Technology; Akadeemia tee 15 12618 Tallinn Estonia
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33
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Helgaker T, Jaszuński M, Świder P. Calculation of NMR Spin–Spin Coupling Constants in Strychnine. J Org Chem 2016; 81:11496-11500. [DOI: 10.1021/acs.joc.6b02157] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Trygve Helgaker
- Centre
for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O.
Box 1033, Blindern, N-0315 Oslo, Norway
| | - Michał Jaszuński
- Institute
of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44, 01-224 Warszawa, Poland
| | - Paweł Świder
- Institute
of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44, 01-224 Warszawa, Poland
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34
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Faber R, Buczek A, Kupka T, Sauer SPA. On the convergence of zero-point vibrational corrections to nuclear shieldings and shielding anisotropies towards the complete basis set limit in water. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1210831] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Rasmus Faber
- Department of Chemistry, University of Copenhagen, Copenhagen Ø, Denmark
| | - Aneta Buczek
- Faculty of Chemistry, University of Opole, Opole, Poland
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Opole, Poland
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35
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Reid DM, Kobayashi R, Collins MA. Systematic Study of Locally Dense Basis Sets for NMR Shielding Constants. J Chem Theory Comput 2015; 10:146-52. [PMID: 26579898 DOI: 10.1021/ct4007579] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper presents a systematic study of partitioning schemes for locally dense basis sets in the context of NMR shielding calculations. The partitionings explored were based exclusively on connectivity and utilized the basis sets from the pcS-n series. Deviations from pcS-4 shieldings were calculated for a set of 28 organic molecules at the HF, B3LYP, and KT3 levels of theory, with the primary goal being the determination of an efficient scheme that achieves maximal deviations of 0.1 ppm for (1)H and 1 ppm for (13)C. Both atom based and group based divisions of basis sets were examined, with the latter providing the most promising results. It is demonstrated that for the systems studied, at least pcS-1 is required for all parts of the molecule. This, coupled with pcS-3 on the group of interest and pcS-2 on the adjacent groups, is sufficient to achieve the desired level of accuracy at a minimal computational expense. In addition, the suitability of the pcS-n basis sets for post-SCF methods was confirmed through a comparison with other standard basis sets at the MP2 level.
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Affiliation(s)
- David M Reid
- Research School of Chemistry, The Australian National University , Acton ACT 0200, Australia
| | - Rika Kobayashi
- Australian National University Supercomputer Facility, The Australian National University , Acton ACT 0200, Australia
| | - Michael A Collins
- Research School of Chemistry, The Australian National University , Acton ACT 0200, Australia
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Garbacz P, Makulski W, Jaszuński M. The NMR spin–spin coupling constant1J(31P,1H) in an isolated PH3molecule. Phys Chem Chem Phys 2014; 16:21559-63. [DOI: 10.1039/c4cp02973a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Hedegård ED, Kongsted J, Sauer SPA. Improving the calculation of Electron Paramagnetic Resonance hyperfine coupling tensors for d-block metals. Phys Chem Chem Phys 2012; 14:10669-76. [PMID: 22785432 DOI: 10.1039/c2cp40969k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Calculation of hyperfine coupling constants (HFCs) of Electron Paramagnetic Resonance from first principles can be a beneficial complement to experimental data in cases where the molecular structure is unknown. We have recently investigated basis set convergence of HFCs in d-block complexes and obtained a set of basis functions for the elements Sc-Zn, which were saturated with respect to both the Fermi contact and spin-dipolar components of the hyperfine coupling tensor [Hedegård et al., J. Chem. Theory Comput., 2011, 7, 4077-4087]. Furthermore, a contraction scheme was proposed leading to very accurate, yet efficient basis sets for the elements Sc-Zn. Here this scheme is tested against a larger test set of molecules and a wider range of DFT functionals. We further investigate the regular aug-cc-pVTZ and core-valence correlation aug-cc-pCVTZ basis sets as well as another core-property basis set, CP(PPP). While aug-cc-pVTZ-J provides hyperfine coupling constants that are almost identical to the converged series (aug-cc-pVTZ-Juc), we observe that not only the regular but also the core-valence correlation basis sets provide results far from the converged results. The usage of specialized core-basis sets leads to a large and highly significant improvement of the calculated hyperfine couplings in comparison with experimental data.
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Affiliation(s)
- Erik D Hedegård
- University of Southern Denmark, Institute for Physics, Chemistry and Pharmacy, Campusvej 55, Odense, Denmark.
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Helgaker T, Jaszuński M, Garbacz P, Jackowski K. The NMR indirect nuclear spin–spin coupling constant of the HD molecule. Mol Phys 2012. [DOI: 10.1080/00268976.2012.729097] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Trygve Helgaker
- a Centre for Theoretical and Computational Chemistry, Department of Chemistry , University of Oslo , P.O.B. 1033 Blindern, N-0315 Oslo , Norway
| | - Michał Jaszuński
- b Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44, 01224 Warsaw , Poland
| | - Piotr Garbacz
- c Laboratory of NMR Spectroscopy, Department of Chemistry , University of Warsaw , Pasteura 1, 02-093 Warsaw , Poland
| | - Karol Jackowski
- c Laboratory of NMR Spectroscopy, Department of Chemistry , University of Warsaw , Pasteura 1, 02-093 Warsaw , Poland
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Faber R, Sauer SPA. On the discrepancy between theory and experiment for the F–F spin–spin coupling constant of difluoroethyne. Phys Chem Chem Phys 2012; 14:16440-7. [DOI: 10.1039/c2cp42198d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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