Ab initio study of 4-monosubstituted pyrimidines in ground and excited n → π* states

Ab initio SCF and SCF -CI calculations have been performed to investigate substituent effects on ground- and excited-state properties of 4-R-pyrimidines, and to compare these with substituent effects in 2- and 4-R-pyridines, with R including the π donating and σ withdrawing groups CH₃, NH₂, OH, F, and C₂H₃ and the σ and π electron-withdrawing groups CHO and CN. Substitution leads to significant changes in the internal angles of the pyrimidine ring, which are independent of the nature of the substituent. The geometry of the pyrimidine ring is more sensitive to substitution in the 4 position than the pyridine ring geometry is to substitution in either the 2 or the 4 position. The isodesmic reaction energies for substituent transfer from the 4 position of pyrimidine to the 2 or 4 position of pyridine indicate that all R groups except CN have a relative stabilizing effect in pyrimidine. The presence of a π donating group leads to an increase in the n→π* transition energy of 4-R-pyrimidines, while the π withdrawing group CN leads to a decrease in the transition energy relative to pyrimidine. Orbital energy differences and virtual excitation energies tend to correlate with n→π* transition energies of 4-R-pyrimidines with saturated R groups, but such correlations are masked by π conjugation, n orbital interaction, and configurational mixing when the unsaturated groups C₂H₃, CHO, and CN are present. The electronic effects of a π donating group are stronger when the group is bonded to pyrimidine than to pyridine, but those of a π withdrawing group are weaker when the group is bonded to pyrimidine.     

Retention Behavior of Nucleic Acid Bases and Purine Derivatives on Titania

The retention of nucleic acid bases and purine derivatives on titania was studied using a 0.4 mM acetic acid–sodium acetate buffer (pH 6.0) and 70% aqueous methanol as mobile phases. We observed that the retention strength of tested analytes on titania was dependent on the structural differences between pyrimidine and purine skeletons and the variety and number of substituents. The retention order was purine derivatives with methyl groups, pyrimidine bases and purine derivatives with hydrophilic functional groups, which were retained most strongly on titania. We concluded that the retention of each analyte was caused by the analyte’s hydrophobicity in the case of purine derivatives with methyl groups and pyrimidine bases. In the case of purine and its derivatives with hydrophilic functional groups, it was considered that the retention was dependent on the analyte’s ability to form chelates, and the variety and number of functional groups on C6 and C2.     

Palladium(II) Schiff base complexes derived from sulfanilamides and aminobenzothiazoles

Schiff bases (HL) derived from sulfanilamides or aminobenzothiazoles add to Pd(OAc)₂ to give complexes of the type PdL₂ (1–7) in moderate to excellent yields. Reactions of Schiff bases containing pyrimidine groups, however, gave several products arising from competing coordination of the pyrimidine nitrogen. Palladium complexes and Schiff bases have been investigated as antifungal agents against Aspergillus niger and Aspergillus flavus.     

Novel pyrrolo[2,3-d]pyrimidine derivatives: Design,synthesis, structure elucidation and in vitro anti-BVDV activity

The progression of drug resistance of viral infection justifies the discovering of new anti-viral agents. Thus, a novel series of pyrrolopyrimidine derivatives 5–7 and 9–18 were designed, synthesized and fully characterized by IR, mass spectroscopy, NMR, and elemental analysis. The structure of 4,6-dichloro-pyrrolo[2,3-d]pyrimidine 10 elucidated by single crystal X-ray diffraction. Herein, we reported the first pyrrolo[2,3-d]pyrimidine compounds with trichloromethane at position 2 of the pyrimidine ring. As initial biological activity screening, evaluation of the pyrrolo[2,3-d]pyrimidine compounds as anti-BVDV (Bovine Viral Diarrhea Virus) was examined. The compounds 11, 13, 16 and 17 exhibited excellent activity as a potent inhibitor against BVDV. Structure activity relationship showed that the pyrrolo[2,3-d]pyrimidine molecules presenting hydrogen atom or trichloromethyl group on C2 and chlorine, sulfur, pyrrolidine or methoxy groups on C4 of the pyrimidine ring showed high activity as anti-BVDV in comparison with the compounds which have Cl or CH₃ on C2 position.     

New 2p‐3d‐4f Chain Compounds [LnZn(hfac)5(NIT‐Pyrim)2] constructed from Pyrimidine based Nitronyl Nitroxides

The 1:1:2 mixture of Ln(hfac)₃, Zn(hfac)₂, and NIT‐Pyrim (hfac = hexafluoroacetylacetonate, NIT‐Pyrim = 2‐pyrimidine‐4,4,5,5‐tetramethylimidazoline‐1‐oxyl‐3‐oxide) afforded a series of 2p‐3d‐4f magnetic chains [Ln(hfac)₃Zn(hfac)₂(NIT‐Pyrim)₂] [Ln^III = Gd ( 1 ), Ho ( 2 ), Yb ( 3 )], in which Zn(hfac)₂ and Ln(hfac)₃ units are bridged by pyrimidine substituted nitronyl nitroxides through their NO moieties and pyrimidine nitrogen atoms. These complexes represent the first examples of 2p‐3d‐4f complexes with Zn^II ions. Magnetic studies show that there exist ferromagnetic exchange couplings between the coordinated NO groups of radical ligands and the Gd^III ions.     

Comparison of the mass spectra of 6-thiotheophyllines and 6-sulfinytheophyllines

Under electron impact, 6-thiotheophyllines eliminate various fragments from the pyrimidine moiety. In a retro Diels-Alder reaction, they lose the fragment X?C?NCH₃ from positions 1 and 2 of the pyrimidine ring. In 6-sulfinyltheophyllines, the sulfinyl group is the main target for fragmentation; it can lose either oxygen or sulfur, and the abundance of [M—16]⁺ and [M—32]⁺ is much higher than the abundance of the molecular ion. Elimination of the sulfur atom of the 6-sulfinyl substituent, with retention of its oxygen, may be explained by intermediate formation of a ring. All further fragmentations of the 6-sulfinyl derivatives proceed by a primary loss of oxygen or sulfur, followed by elimination of fragments from the pyrimidine moiety, similar to the primary processes, observed in the mass spectra of the 6-thiotheophyllines.     

Thermodynamic study of alkanes,alkylbenzenes and chloroalkanes retention on alkyl- and cyanoalkyl-bonded stationary phases in supercritical fluid chromatography

Summary The SFC retention behaviour of alkanes, alkylbenzenes and chloroalkane was investigated by studying solute/mobile phase/stationary phase interaction enthalpies. The methylene group and functional group contributions to solute retention were calculated in pure CO₂. It was shown that hydrophobic interactions mainly control retention in pure CO₂. Interaction between the polar extremity of C₁₀CN ligands and residual OH groups on the silica surface was suggested as an explanation of the retention obtained on such ligands. This was confirmed by experiments carried out with modified CO₂.     

Retention behaviour of 1,n-halo(alkylthio)alkanes in HPLC

The RPLC retention of 1,n-halo(alkylthio)alkanes on an ODS phase with methanol/water (95%/5%) has been investigated. Replacement of a methyl group in a dialkyl sulphide R-S-R by a halogen atom X, to yield the title compounds X-(CH₂)_n-S-R, generally results in a retention decrease. This retention loss results either from the halogen atom proper, or from its immediate vicinity, or from a reduced retention contribution of the alkyl units. The methylene groups (n) between halogen and sulphur produce somewhat greater retention than the methylene groups in the alkyl groups R.     

Reaction of esters of 2-substituted 5-pyrimidinecarboxylic acids with hydrazine hydrate

The reaction of methyl esters of 2-substituted 5-pyrimidinecarboxylic acids with hydrazine hydrate at 0–5°C results in the nucleophilic substitution of readily eliminating groups (Cl, CH₃O, CH₃S) at the position 2 of the pyrimidine ring, and, on the boiling with the 80% aqueous solution of hydrazine hydrate, the reaction is accompanied by the formation of hydrazides. The dimethylamino group at thepposition 2 of the pyrimidine ring is not substituted by hydrazine.Vilnius University, Vilnius 2006, Lithuania Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1528–1530, November, 1999.     

Synthesis and study of the azide-tetrazole tautomerism in 2-azido-4-(trifluoromethyl)-6-R-pyrimidines (R = H, 4-ClC<Subscript>6</Subscript>H<Subscript>4</Subscript>)

Azide-tetrazole equilibrium in azidopyrimidines bearing trifluoromethyl group on the example of 2-azidopyrimidines has been studied. The latter were synthesized via nitrosation of 2-hydrazino-4-trifluoromethylpyrimidine and reaction of NaN₃ with 4-trifluoromethyl-2- chloro-6-(4-chlorophenyl)pyrimidine. The tautomeric equilibrium 5-trifluoro methyl tetrazolo[1,5-a]pyrimidine ? 2-azido-4-trifluoromethylpyrimidine was observed in the absence of solvent and in DMSO-d₆ solution, whereas in CDCl³ only an azide form exists. For 2-azido- 4-trifluoromethyl-6-(4-chlorophenyl)pyrimidine, only an azide isomer was detected in CDCl³ solution, and in DMSO-d₆ solution it is in equilibrium with 5-(trifluoromethyl)-7-(4-chlorophenyl) tetrazolo[1,5-a]pyrimidine (the tautomer ratio is 99 : 1). Thermodynamic and kinetic parameters of 5-trifluoromethyltetrazolo[1,5-a]pyrimidine ? 2-azido-4-trifluoromethylpyri midine tautomeric rearrangement in DMSO-d₆ for 5-trifluoromethyltetrazolo[1,5-a]pyrimidine were determined using the exchange spectroscopy (EXSY) technique.     

Facile green one‐pot synthesis of novel thiazolo[3,2‐a]pyrimidine derivatives using Fe3O4@l‐arginine and their biological investigation as potent antimicrobial agents

Thiazolopyrimidine derivatives are well known because of their excellent therapeutic properties. In this investigation, an effective one‐pot three‐component method is described for the synthesis of novel 2‐[(Z )‐1‐(substituted phenyl)methylidine]‐7‐methyl‐3‐oxo‐5‐(substituted phenyl)‐2,3‐dihydro‐5H ‐thiazolo[3,2‐a]pyrimidine‐6‐carboxilic acid tert ‐butyl ester derivatives by condensation reaction of 3,4‐dihydropyrimidine‐2(1H )‐thiones, various aromatic aldehydes and chloroacetyl chloride under reflux conditions in the presence of Fe₃O₄@l ‐arginine nanoparticles as a magnetically reusable and eco‐friendly catalyst with short reaction times and moderate yields. The chemical structures of all synthesized compounds were determined using infrared, ¹H NMR and ¹³C NMR spectroscopies. In vitro antimicrobial activities of 3,4‐dihydropyrimidine‐2(1H )‐thiones and newly fused thiazolo[3,2‐a]pyrimidine derivatives were examined using the well diffusion method against diverse pathogenic strains, namely Staphylococcus aureus ATCC 6538, S. epidermidis ATCC 12228, Escherichia coli ATCC 8739 and Pseudomonas aeruginosa ATCC 9027 (bacteria), Candida albicans ATCC 10231 (yeast) and Aspergillus niger ATCC 16404 (fungus). The compounds having 2‐hydroxy, 4‐hydroxy, 2‐chloro and 4‐chloro groups attached to the phenyl ring on the pyrimidine and 4‐CH₃, 4‐OCH₃ and 3‐NO₂ groups attached to benzylidine on the thiazolo moiety showed significant antibacterial activity.     

Inheritance and correlation of nucleic acid pyrimidine bases

Valence electronic structures of pyrimidine (P, C₄N₂H₄) and nucleic acid (NA) pyrimidine bases, including cytosine (C, C₄N₃OH₅), thymine (T, C₅N₂O₂H₆), and uracil (U, C₄N₂O₂H₄), are studied using B3LYP/aug‐cc‐pVTZ, B3LYP/TZVP, SAOP/et‐pVQZ, and OVGF/TZVP. The highest occupied molecular orbital (HOMO) and the next HOMO (NHOMO) of pyrimidine are conclusively assigned as 7b₂ and 2b₁, respectively. The ionization energy spectra and valence orbital momentum distributions studies reveal that the NA bases, that is, cytosine, thymine, and uracil, exhibit a larger degree of similarity to each other than to pyrimidine, although they do inherit certain properties from pyrimidine. © 2013 Wiley Periodicals, Inc.     

Dynamic Properties of Molecular Tweezers with a Bis(2‐hydroxyphenyl)pyrimidine Backbone

4,6‐Bis(2‐hydroxyphenyl)‐2‐alkylpyrimidines with two anthryl or 9‐ethylnylanthryl substituents at the positions para to the OH groups prefer a U‐shaped conformation supported by two intramolecular OH ??? N hydrogen bonds in the solid state and in CDCl₃ solution. The compound with a hexyl substituent on the pyrimidine group and two 9‐ethynylanthryl arms at the hydroxyphenyl groups forms a 1:1 complex with 2,4,7‐trinitrofluorenone. Its association constant K_a was estimated to be 2100 M ^?1 at 298 K, which is larger than those of other molecular tweezers (K_a<1000 M ^?1). DFT calculations suggested that the complex adopts a stable conformation supported by intramolecular hydrogen bonds among the OH groups and the pyrimidine ring as well as by intermolecular π–π interaction between the anthryl groups and 2,4,7‐trinitrofluorenone. Addition of nBu₄NF to a solution of the molecular tweezers or their complexes causes the cleavage of one or two OH ??? N hydrogen bonds, formation of new O ??? HF hydrogen bonds, and changes in the molecular conformation. The resulting structure of the molecular tweezers contains nonparallel anthryl groups, which do not bind the guest molecule. Photochemical measurements on 4,6‐bis(2‐hydroxyphenyl)‐2‐methylpyrimidine with two anthryl substituents showed negligible luminescence (quantum yield ?<0.01), owing to photoinduced electron transfer of the molecule with a U‐shaped structure. However, the O‐hexylated compound exhibits emission from the anthryl groups with ?=0.39.     

Theoretical Design of High‐spin Organic Molecules with —·N—N— as a Spin‐containing Fragment and Heterocycles as an End Group

Novel stable high spin molecules possessing three different arranged fashions are designed with –·N–N< as a spin‐containing (SC) fragment, various aromatic, such as benzene ( 1 ), pyridine ( 2 ), pyridazine ( 3 ), pyrimidine ( 4 ), pyrazine ( 5 ), triazine ( 6 ) as end groups (EG) and phenyl as a ferromagnetic coupling (FC) unit. The effects of a different end groups on the spin multiplicities of the ground states and their stabilities were investigated by means of AM1‐CI approach. It has been found that the spin densities on the two atoms of the SC fragment are different from delocalization resulting in the specific stability of –·N–N<. In these molecules, the stabilities of the triplet states decrease when the distance between the atoms of central SC (–N–) increases. The orders of the stability of triplet states for 1an , 1bn , 1cn [They are isomers in which SC is connected with FC in different way ( 1an , N₁NNN₁; 1bn , N₁N N₁N; 1cn , NN₁N₁N) and six heterocycles are EG] show that the stability of triplet states with heterocycles as end groups is higher than that with phenyl as end groups, and in the order:triazine (EG)>pyrimidine, pyrazine>pyridine, pyridazine.     

Transition metal complex stationary phases for the CGC analysis of ethers, thioethers and ketones

Summary The use of polysiloxanes with cyano or thiol groups as stationary phases for complexation gas chromatography is discussed. The polymers were obtained via polycondensation followed by polymerisation of the corresponding dichloro- or dimethoxy-silanes. Both the phases were modified by bonding transition metal chlorides with were modified by bonding transition metal chlorides with cyano (CuCl₂ or CoCl₂) and thiol groups (NiCl₂ or CoCl₂). The phases were examined in order to determine their application to the analysis of ethers, thioethers and ketones. Due to the presence of lone electron pairs on oxygen or sulphur atoms, the compounds should be capable of specific interacting with the electron-withdrawing centre of the liquid stationary phases. A number of retention parameters (retention indices, molecular retention indices and specific retention volume) were determined, which allowed characterisation of specific interactions between the bonded metal and the compound analysed. The results also enabled assessment of the influence of the structure of the compounds on their retention. The measurements were also carried out for the phases with free SH and CN groups as reference phases. The work demonstrates that the phases obtained may be useful for effective separations.     

Proximity effect in spin sublevel dynamics: Possible influence of a low-lying3 A2 (nπ*) state: On singlet → triplet intersystem crossing of Pyrimidine

Comparison of spin sublevel population rates in pyrimidine and 5-methylpyrimidine suggests that the vibronic perturbation of ³B₂ and/or ³A₁ ππ* states by a higher-lying ³A₂nπ* state plays an important role in S₁ → T₁ intersystem crossing of pyrimidine. The result also implies that the n₊π*—n_?π* splitting in pyrimidine is significantly smaller than the corresponding gap in pyrazine. The appearance of the 0.0 band in the τ_x spectrum indicates that the triplets state symmetry is lower tha C_2v.     

Hydrogen‐bonding patterns in pyrimethaminium dinitrate

The title compound, 2,4‐diamino‐5‐(4‐chloro­phen­yl)‐6‐ethyl­pyrimidine‐1,3‐diium dinitrate, C₁₂H₁₅ClN₄²⁺·2NO₃⁻, contains two crystallographically independent pyrimethamine (PMN) mol­ecules, which differ in the relative orientations of the pyrimidine and benzene rings and of the eth­yl substitutents. In both pyrimethamine mol­ecules, all the pyrimidine N atoms are protonated, unlike most related compounds, in which only one pyrimidine N atom is protonated. The two pyrimethamine moieties are bridged by a variety of N—H⋯O(nitrate) inter­actions, including some three‐centre hydrogen bonds.     

Novel macrocyclic uracil derivatives: Structure in solid and solution

Isomeric pyrimidinophanes containing uracil moieties and nitrogen atoms in bridges have been synthesized and characterized by a variety of methods both in solid and in solution. Unambiguous assignment of mutual arrangement of C(4)_pyrO groups at different pyrimidine rings in isomers is made by X-ray diffraction. In solutions the arrangement of C(4)_pyrO groups of the isomeric pyrimidinophanes results in different dipole moments. Based on dipole moments simulations mutual orientation of uracil units in isomers is analysed. UV-data are discussed in terms of hypo- or hyperchromic effect.     

catena‐Poly­[[bis­(nitrato)(pyrimidine)­copper(II)]‐μ‐pyrimidine‐N:N′]

The title compound, [Cu(NO₃)₂(C₄H₄N₂)₂]_n, crystallizes as a linear polymeric compound with one pyrimidine ligand bridging between two Cu^II atoms and a second pyrimidine ligand coordinated in a monodentate manner. The distorted octahedral geometry around the Cu^II atom consists of two pyrimidine N atoms at distances of 2.033 (4) and 2.025 (4) Å, and two nitrate O atoms at distances at 1.987 (3) and 1.973 (3) Å. The apical positions are occupied by an N atom of a bridging pyrimidine ligand [2.291 (4) Å] and a nitrate O atom at a long distance of 2.781 (3) Å. The basal plane is almost planar, with trans angles of 176.23 (14) and 165.34 (15)°.     

Hydrogen‐bonding and C—H⋯π interactions in 7‐hydroxy‐3‐methoxy‐4‐methyl‐5,6,7,8‐tetrahydro­pyrido­[1,2‐c]pyrimidin‐1(9H)‐one

In the title compound, C₁₀H₁₄N₂O₃, a pyrimidine ring is fused with a piperidine ring. The pyrimidine ring is planar, whereas the piperidine ring adopts a half‐chair conformation. The molecules of the title compound are connected via O—H⋯O intermolecular hydrogen bonds into infinite zigzag chains. The pyrimidine ring is involved in three C—H⋯π interactions, which link the hydrogen‐bonded chains into a three‐dimensional framework.