scholarly journals Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives

Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 3931 ◽  
Author(s):  
Kacper Rzepiela ◽  
Aneta Buczek ◽  
Teobald Kupka ◽  
Małgorzata A. Broda
Keyword(s):  
Electrostatic Interactions ◽  
Density Functional ◽  
Chemical Shifts ◽  
Polarizable Continuum Model ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Basis Set ◽  
Basis Sets ◽  
Nmr Parameters ◽  
Solvent Model

We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of uracil and its derivatives in the gas phase and water. The values of these parameters showed that the most stable tautomer is the least aromatic. A good performance of newly designed xOPBE density functional in combination with both large aug-cc-pVQZ and small STO(1M)−3G basis sets for predicting chemical shifts of uracil and 5-fluorouracil in vacuum and water was observed. As a practical alternative for calculating the chemical shifts of challenging heterocyclic compounds, we also propose B3LYP calculations with small STO(1M)−3G basis set. The indirect spin–spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well.

[Pt@Pb12]2– — A challenging system for relativistic density functional theory calculations of 195Pt and 207Pb NMR parameters

2011 ◽  
Vol 89 (7) ◽  
pp. 814-821 ◽  
Author(s):  
Boris Le Guennic ◽  
Jochen Autschbach
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Relativistic Effects ◽  
Magnetic Coupling ◽  
Principal Component ◽  
Density Functional Theory Calculations ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Test Case ◽  
Nmr Parameters

We report computations of NMR chemical shifts and indirect spin-spin coupling constants (J couplings) for the [Pt@Pb12]2– “superatom”. The system is strongly influenced by relativistic effects. The Pt–Pb coupling constant is predicted to be negative, with its magnitude being in reasonable agreement with experiment. Pt and Pb chemical shifts also agree reasonably well with experiment. The Pb shielding tensor is strongly anisotropic, with a large deshielding principal component dominated by magnetic coupling between frontier orbitals of the cluster that resemble atomic g orbitals. The NMR parameters are sensitive to approximations made in the computations and require the inclusion of spin-orbit coupling in the theoretical model to achieve reliable results. Computing the NMR parameters of the compact [Pt@Pb12]2– system with its many electrons proves to be a challenging test case for relativistic density functional methods.

Calculated NMR Parameters (Chemical Shifts and Coupling Constants) of Cyclic C4H2 and C4H4 Molecules Containing Carbene Centers, and of Some of their Boron Analoga, Using Density Functional Theory (DFT)

2004 ◽  
Vol 59 (1) ◽  
pp. 37-43 ◽  
Author(s):  
Bernd Wrackmeyer
Keyword(s):  
Density Functional ◽  
Singlet State ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Spin Orbital ◽  
Functional Theory ◽  
Orbital Interactions ◽  
Nmr Parameters ◽  
Spin Spin Coupling

Abstract Singlet state structures of small, cyclic hydrocarbons which can result from the addition of molecular dicarbon (C2) to ethyne (HC≡CH) or ethene (H2C=CH2) have been calculated (B3LYP/6- 311+G(d,p) level of theory), and were found to contain carbene centres. Some structures of analogous boranes (replacement of the carbene centers by BH fragments) were also calculated. The computation of NMR parameters such as chemical shifts δ 13C and δ 11B, and coupling constants 1J(13C,1H), 1J(11B,1H), J(13C,13C) and J(13C,11B) shows that these data can be used for the discussion of the bonding situation. The presence of inverted carbene centers is clearly indicated by the increased 13C nuclear magnetic shielding. Scalar 13C-13C spin-spin coupling involving carbene centers are frequently dominated by spin-dipole and spin-orbital interactions.

scholarly journals Theoretical Investigation of Glycine Micro-Solvated. Energy and NMR Spin Spin Coupling Constants Calculations

Sci ◽  
2021 ◽  
Vol 3 (4) ◽  
pp. 41
Author(s):  
Maria Cristina Caputo ◽  
Patricio Federico Provasi
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Water Solution ◽  
Polarizable Continuum Model ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Basis Set ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling

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.

scholarly journals Theoretical Investigation of Glycine Micro-solvated. Energy and NMR Spin Spin Coupling Constants Calculations

2021 ◽  
Author(s):  
Maria Cristina Caputo ◽  
Patricio Federico Provasi
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Polarizable Continuum Model ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Basis Set ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling ◽  
Polarizable Continuum

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 in the super-molecule structure are necessary to stabilize both conformers of glycine within a water polarizable continuum model. At least half of the SSCC’s of both conformers are very stable to changes in the environment and at least four of them differ significantly between Neutral and Zwitterion conformation.

Structural Characterization of Natural Products By Means of Quantum Chemical Calculations of NMR Parameters: New insights

2021 ◽  
Author(s):  
Fabio Luiz Paranhos Costa ◽  
Ana Carolina Ferreira de Albuquerque ◽  
Rodolfo Goetze Fiorot ◽  
Luciano Morais Lião ◽  
Lucas Haidar Martorano ◽  
...  
Keyword(s):  
Natural Products ◽  
Structural Characterization ◽  
Quantum Chemical ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Nmr Parameters ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling

The calculation of NMR parameters for natural products was pioneered by Bifulco and coworkers in 2002. Since then, modelling 1H and 13C chemical shifts and spin-spin coupling constants for this...

A density functional approach toward structural features and properties of C20…N2X2 (X = H, F, Cl, Br, Me) molecules

2014 ◽  
Vol 13 (04) ◽  
pp. 1450023 ◽  
Author(s):  
Reza Ghiasi ◽  
Morteza Zaman Fashami ◽  
Amir Hossein Hakimioun
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Geometry Optimization ◽  
Structural Features ◽  
Nbo Analysis ◽  
Basis Set ◽  
Basis Sets ◽  
Basis Set Superposition Error ◽  
Homo And Lumo ◽  
Lowest Unoccupied Molecular Orbitals

In this work, the interaction of C 20 with N 2 X 2 ( X = H , F , Cl , Br , Me ) molecules has been explored using the B3LYP, M062x methods and 6-311G(d,p) and 6-311+G(d,p) basis sets. The interaction energies (IEs) obtained with standard method were corrected by basis set superposition error (BSSE) during the geometry optimization for all molecules at the same levels of theory. It was found C 20… N 2 H 2 interaction is stronger than the interaction of other N 2 X 2 ( X = F , Cl , Br , Me ) with C 20. Highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) levels are illustrated by density of states spectra (DOS). The nucleus-independent chemical shifts (NICSs) confirm that C 20… N 2 X 2 molecules exhibit aromatic characteristics. Geometries obtained from DFT calculations were used to perform NBO analysis. Also, 14 N NQR parameters of the C 20… N 2 X 2 molecules are predicted.

Molecular orbital and 1H nuclear magnetic resonance studies of the inversion potentials of thianthrene and thioxanthene

1991 ◽  
Vol 69 (6) ◽  
pp. 927-933 ◽  
Author(s):  
Ted Schaefer ◽  
Rudy Sebastian ◽  
Christian Beaulieu
Keyword(s):  
Long Range ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Basis Set ◽  
Basis Sets ◽  
Inversion Barrier ◽  
H Nmr ◽  
Methylene Groups ◽  
Spin Spin Coupling ◽  
Split Valence

The inversion potentials, obtained from STO-3G, STO-3G(*), 3-21G, 3-21G(*), and 4-31G basis sets, are reported for thianthrene and thioxanthene, molecules in which both or only one of the methylene groups have been replaced by sulfur in 9,10-dihydroanthracene. Comparison with the available experimental data suggests that the split-valence bases lead to an overestimate, possibly by about 10 kJ/mol, of the inversion barrier in the crystal, whereas the STO-3G and STO-3G* basis sets underestimate this barrier. It appears that the inversion barrier for thianthrene is much lower in solution than in the crystal. The long-range coupling constants between the methylene and ring protons for thioxanthene in solution are consistent with an inversion barrier somewhat smaller than those obtained with the split-valence bases but rather larger than those predicted with the STO-3G basis set. The bond lengths and angles in the equilibrium structures of the two molecules, as computed with the 3-21G(*) basis, agree reasonably well with those in their crystals, except that the theoretical folding angles are smaller than measured. These discrepancies become less marked when expectation values are calculated from the theoretical inversion potentials at finite temperatures. Key words: MO calculations, inversion potentials of thianthrene and thioxanthene; 1H NMR, thioxanthene; spin–spin coupling constants, long range, in thioxanthene.

scholarly journals Hyperfine Coupling Constants in Local Exact Two-Component Theory

2021 ◽  
Author(s):  
Yannick J. Franzke ◽  
Jason M. Yu
Keyword(s):  
Single Molecule ◽  
Density Functional ◽  
Hyperfine Coupling ◽  
Scalar Potential ◽  
Coupling Constants ◽  
Basis Set ◽  
Basis Sets ◽  
Spin Orbit ◽  
Finite Nucleus ◽  
Two Component

We present a highly efficient implementation of the electron-nucleus hyperfine coupling matrix within one-electron exact two-component (X2C) theory. The complete derivative of the X2C Hamiltonian is formed, i.e. the derivatives of the unitary decoupling transformation are considered. This requires solution of the response and Sylvester equations, consequently increasing the computational costs. Therefore, we apply the diagonal local approximation to the unitary decoupling transformation (DLU). The finite nucleus model is employed for both the scalar potential and the vector potential. Two-electron picture-change effects are modeled with the (modified) screened-nuclear spin--orbit approach. Our implementation is fully integral direct and OpenMP-parallelized. An extensive benchmark study regarding the Hamiltonian, the basis set, and the density functional approximation is carried out for a set of 12--17 transition-metal compounds. The error introduced by DLU is negligible and the DLU-X2C Hamiltonian accurately reproduces its four-component ``fully'' relativistic parent results. Functionals with a large amount of Hartree--Fock exchange such as CAM-QTP-02 and omega-B97X-D are generally favorable. The pure density functional r2SCAN performs remarkably and even outperforms the common hybrid functionals TPSSh and CAM-B3LYP. Fully uncontracted basis sets or contracted quadruple-zeta bases are required for accurate results. The capability of our implementation is demonstrated for [Pt(C6Cl5)4]- with more than 4700 primitive basis functions and four rare-earth single molecule magnets: [La(OAr*)3]-, [Lu(NR2)3]-, [Lu(OAr*)3]-, and [TbPc2]-. Here, the spin--orbit DLU-X2C Hamiltonian results in an excellent agreement with the experimental findings of all Pt, La, Lu, and Tb molecules.

scholarly journals Estudo do tautomerismo ceto-enólico da 7-epi-clusianona através de cálculos teóricos de deslocamentos químicos de RMN

2020 ◽  
Author(s):  
Ana Carolina Ferreira de Albuquerque ◽  
José Walkimar de Mesquita Carneiro ◽  
Fernando Martins dos Santos Junior
Keyword(s):  
Natural Products ◽  
Structural Characterization ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Spectroscopic Techniques ◽  
Chemical Structures ◽  
Nmr Parameters

The properties of natural products, including their biological and pharmacological activities, are directly correlated with their chemical structures. Thus, a correct structural characterization of these compounds is a crucial step to the understanding of their biological activities. However, despite the recent advances in spectroscopic techniques, structural studies of natural products can be challenging. This way, theoretical calculations of Nuclear Magnetic Resonance (NMR) parameters (such as chemical shifts and coupling constants) have proven to be a powerful and low-cost tool for the aid to experimental techniques traditionally used for the structural characterization of natural products. One of the several applications of quantum-mechanical calculations of NMR parameters is the study of tautomerism. Since chemical shifts are sensitive to the tautomeric equilibrium, this technique can provide crucial informations. In this work, it was applied a protocol for theoretical calculations of ¹³C chemical shifts in order to study the tautomerism of the natural product 7-epi-clusianone, isolated from Rheedia gardneriana. This protocol consists in a Monte Carlo conformational search, followed by geometry optimization and shielding tensors calculations, both using a density functional level of theory. After comparison of theoretical and experimental data, it was possible to confirm the two tautomers present in equilibrium in the experimental solution. Furthermore, this study highlights how this theoretical protocol can be an effective method in identifying the preferred tautomeric form in solution.

scholarly journals Quantum-chemical study of C— H bond dissociation enthalpies of various small non-aromatic organic molecules

2013 ◽  
Vol 6 (1) ◽  
pp. 64-72 ◽  
Author(s):  
Peter Poliak ◽  
Adam Vagánek
Keyword(s):  
13C Nmr ◽  
Linear Correlation ◽  
Density Functional ◽  
Chemical Shifts ◽  
Basis Set ◽  
Basis Sets ◽  
Nmr Chemical Shifts ◽  
Bond Dissociation ◽  
13C Nmr Chemical Shifts ◽  
Experimental Values

Abstract In this work, C-H bond dissociation enthalpies (BDE) and vertical ionization potentials (IP) for various hydrocarbons and ketones were calculated using four density functional approaches. Calculated BDEs and IPs were correlated with experimental data. The linearity of the corresponding dependences can be considered very good. Comparing two used functionals, B3LYP C-H BDE values are closer to experimental results than PBE0 values for both used basis sets. The 6-31G* basis set employed with both functionals, gives the C-H BDEs closer to the experimental values than the 6-311++G** basis set. Using the obtained linear dependences BDEexp = f (BDEcalc), the experimental values of C-H BDEs for some structurally related compounds can be estimated solely from calculations. As a descriptor of the C-H BDE, the IPs and 13C NMR chemical shifts have been investigated using data obtained from the B3LYP/6-31G* calculations. There is a slight indication of linear correlation between IPs and C-H BDEs in the sets of simple alkanes and alkenes/ cycloalkenes. However, for cycloalkanes and aliphatic carbonyl compounds, no linear correlation was found. In the case of the 13C NMR chemical shifts, the correlation with C-H BDEs can be found for the sets of alkanes and cycloalkanes, but for the other studied molecules, no trends were detected.

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