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1.
Molecules ; 27(9)2022 Apr 21.
Article in English | MEDLINE | ID: mdl-35566018

ABSTRACT

In this study, comparative analysis of calculated (GIAO method, DFT level) and experimental 31P NMR shifts for a wide range of model palladium complexes showed that, on the whole, the theory reproduces the experimental data well. The exceptions are the complexes with the P=O phosphorus, for which there is a systematic underestimation of shielding, the value of which depends on the flexibility of the basis sets, especially at the geometry optimization stage. The use of triple-ζ quality basis sets and additional polarization functions at this stage reduces the underestimation of shielding for such phosphorus atoms. To summarize, in practice, for the rapid assessment of 31P NMR shifts, with the exception of the P=O type, a simple PBE0/{6-311G(2d,2p); Pd(SDD)}//PBE0/{6-31+G(d); Pd(SDD)} approximation is quite acceptable (RMSE = 8.9 ppm). Optimal, from the point of view of "price-quality" ratio, is the PBE0/{6-311G(2d,2p); Pd(SDD)}//PBE0/{6-311+G(2d); Pd(SDD)} (RMSE = 8.0 ppm) and the PBE0/{def2-TZVP; Pd(SDD)}//PBE0/{6-311+G(2d); Pd(SDD)} (RMSE = 6.9 ppm) approaches. In all cases, a linear scaling procedure is necessary to minimize systematic errors.


Subject(s)
Magnetic Resonance Imaging , Palladium , Density Functional Theory , Magnetic Resonance Spectroscopy/methods , Phosphorus
2.
Bioorg Chem ; 109: 104725, 2021 04.
Article in English | MEDLINE | ID: mdl-33611139

ABSTRACT

In lumazines, deazalumazines and pyrimidines, there are extremely low-energy "rare" tautomers (<2.3 kcal/mol), this fact perfectly explains the observed mobility of usually "non-labile" protons of methyl groups in such systems. In general, the dependence of tautomeric preference on structure correlates well with experimental findings. Thus, the activity of alkyl groups during biological transformations may be due to the presence of the corresponding thermodynamically stable tautomers.


Subject(s)
Flavins/chemistry , Pteridines/chemistry , Pyrimidines/chemistry , Density Functional Theory , Molecular Structure , Thermodynamics
3.
Dalton Trans ; 46(25): 8146-8156, 2017 Jun 27.
Article in English | MEDLINE | ID: mdl-28607987

ABSTRACT

The interplay of NMR experiments and DFT calculations of NMR parameters is a reliable method for determining the relative configurations of pentacoordinate chiral spirophosphoranes bearing two six- or five-membered rings at the phosphorus atom in solution. The major product of the Betti based derivatives corresponds to the isomers with both substituents at chiral carbons being opposite to the P-H proton. The next populated product corresponds to the isomer with different chiralities at carbons. The least populated isomer is one with both substituents being at the same side of the heterocycle as the P-H bond.

4.
Dalton Trans ; 45(5): 2053-9, 2016 Feb 07.
Article in English | MEDLINE | ID: mdl-26407302

ABSTRACT

In solution, nickel phosphanido hydride complexes ([NiH{P(Ar)(H)}(dtbpe)], Ar = Dmp, Mes*) undergo a degenerate intramolecular exchange, with the Ni-H and P-H hydrogens and both halves of the dtbpe moiety interchanging. This intramolecular rearrangement was shown to occur in three steps: first, the hydride proton migrates to phosphorus, then the P-Aryl moiety rotates around the P-Ni bond, and finally the back migration of one proton to Ni completes the process. Both migration and rotation were determined to be characterized by high barriers (on the NMR time scale) and to depend on the type of aryl group at the terminal phosphorus. Compared to that observed for the Ni complexes, the same isomeric preference, but with a slower rate of intramolecular rearrangement, is predicted for the corresponding Pt complexes. An opposite isomeric preference, however, is expected for the corresponding Pd complexes. Thus, it is likely that some of the catalytic reactions of Pd and Pt complexes are driven by the relative thermodynamic stabilities of their main forms.

5.
Dalton Trans ; 44(30): 13565-72, 2015 Aug 14.
Article in English | MEDLINE | ID: mdl-26135988

ABSTRACT

A novel type of 14-membered cyclic polyphosphine, namely 1,8-diaza-3,6,10,13-tetraphosphacyclotetradecanes 2a­4ahas been synthesized by the condensation of 1,2-bis(phenylphosphino)ethane, formaldehyde and alkylamines (isopropylamine, ethylamine and cyclohexylamine) as a RRRR/SSSS-stereoisomer. The structure of macrocycle 2a was investigated by NMR-spectroscopy and X-ray crystal structure analysis. The unique reversible processes of macrocycles 2a­4a splitting onto the corresponding rac- (2b­4b) and meso- (2c­4c) stereoisomers of 1-aza-3,6-diphosphacycloheptanes were discovered.


Subject(s)
Amines/chemistry , Cycloheptanes/chemistry , Macrocyclic Compounds/chemistry , Phosphines/chemistry , Amines/chemical synthesis , Crystallography, X-Ray , Cyclization , Macrocyclic Compounds/chemical synthesis , Methylation , Models, Molecular , Phosphines/chemical synthesis , Stereoisomerism
6.
Phys Chem Chem Phys ; 17(10): 6976-87, 2015 Mar 14.
Article in English | MEDLINE | ID: mdl-25683906

ABSTRACT

The aim of this work is to convince practitioners of (31)P NMR methods to regard simple GIAO quantum chemical calculations as a safe tool in structural analysis of organophosphorus compounds. A comparative analysis of calculated GIAO versus experimental (31)P NMR chemical shifts (CSs) for a wide range of phosphorus containing model compounds was carried out. A variety of combinations (at the HF, DFT (B3LYP and PBE1PBE), and MP2 levels using 6-31G(d), 6-31+G(d), 6-31G(2d), 6-31G(d,p), 6-31+G(d,p), 6-311G(d), 6-311G(2d,2p), 6-311++G(d,p), 6-311++G(2d,2p), and 6-311++G(3df,3pd) basis sets) were tested. On the whole, it is shown that, in contrast to what is claimed in the literature, high level of theory is not needed to obtain rather accurate predictions of (31)P CSs by the GIAO method. The PBE1PBE/6-31G(d)//PBE1PBE/6-31G(d) level can be recommended for express estimation of (31)P CSs. The PBE1PBE/6-31G(2d)//PBE1PBE/6-31G(d) combination can be recommended for routine applications. The PBE1PBE/6-311G(2d,2p)//PBE1PBE/6-31+G(d) level can be proposed to obtain better results at a reasonable cost. Scaling by linear regression parameters significantly improves results. The results obtained using these combinations were demonstrated in (31)P CS calculations for a variety of medium (large) size organic compounds of practical interest. Care has to be taken for compounds that may be involved in exchange between different structural forms (self-associates, associates with solvent, tautomers, and conformers). For phosphorus located near the atoms of third period elements ((CH3)3PS and P(SCH3)3) the impact of relativistic effects may be notable.

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