Conformational preferences of guanine-containing threose nucleic acid building blocks in B3LYP studies.

In this paper, detailed and systematic gas-phase B3LYP conformational studies of four monomers of threose nucleic acid (TNA) with guanine attached at the C1' atom and bearing different substituents (OH, OP(=O)OH2 and OCH3) in the C2' and C3' positions of the α-l-threofuranose moiety are presented. All exocyclic single-bond (χ, ε and γ) rotations, as well as the ν0-ν4 endocyclic torsion angles, were taken into consideration. Three (threoguanosines TG1-TG3) or two (TG4) energy minima were found for the rotation about the χ torsion angle. The syn orientation (the A rotamer family) is strongly privileged in geometries TG1 and TG2, whereas the anti orientation (the C rotamer family) and the syn orientation are observed to be in equilibrium (with populations of 56% and 44%, respectively) for TG3. In the case of TG4, the high-anti orientation (the B rotamer family) turned out to be by far the most favourable, with the contribution exceeding 90% in equilibrium. Such a preference can be attributed to the inability of H-bonding between sugar and nucleobase and possibly because of the steric strains. The low-energy conformers of TG1-TG4 occupy the northeastern (P âˆ¼ 40°) and/or southern (P âˆ¼ 210°) parts of the pseudorotational wheel, which fits the A- and B-type DNA helices quite well. Additionally, in the case of TG4, some relatively stable geometries have the furanoid ring in conformation lying on the northwestern part of the pseudorotational wheel (P âˆ¼ 288°).

Identification of the furanose ring conformations and the factors driving their adoption.

Three groups of furanoses with restricted freedom of rotation on the C3-C4, C2-C3, and C1-C2 bonds, respectively, are presented. Conformational analysis of these furanoses is conducted based on the proton nuclear magnetic resonance (1H NMR) spectroscopy, density functional theory (DFT) calculations, and X-ray analysis. It is shown that the particular group of the presented furanoses is locked in the specific conformation. These are the 1T2-like, the 0E-like, and the 3T4-like conformation, respectively. Characteristic 1H NMR spectra of these three conformations are presented and the factors influencing the conformational preferences of the analyzed furanoses are discussed.

Characteristic 1H NMR spectra of ß-d-ribofuranosides and ribonucleosides: factors driving furanose ring conformations.

A series of ß-d-ribofuranosides and ribonucleosides fused with 2,3-O-isopropylidene ring was synthesized and studied in terms of their conformational preferences. Based on the 1H NMR spectra, DFT calculations, and X-ray analysis the E 0-like and E 4-like conformations adopted by these furanosides are identified. The 3 E-like and 2 E-like conformations are assigned to ribonucleosides without the 2,3-O-isopropylidene group. The studies are supported by analysis of the structural data of ß-d-ribofuranosides and ribonucleosides deposited in the Cambridge Crystallographic Data Center (CCDC) database. Finally, the factors influencing the conformational preferences of the furanose ring with the ß-d-ribo configuration are indicated. These are the unfavorable ecliptic orientation of the 2-OH and 3-OH groups, the 1,3-pseudodiaxial interaction of the aglycone and terminal hydroxymethyl group and the endo-anomeric effect. It is also proved that the exo-anomeric effect acts in ß-d-ribofuranosides.

Antimicrobial, Cytotoxic and Mutagenic Activity of Gemini QAS Derivatives of 1,4:3,6-Dianhydro-l-iditol.

A series of quaternary diammonium salts derivatives of 1,4:3,6-dianhydro-l-iditol were synthesized, using isommanide (1,4:3,6-dianhydro-d-mannitol) as a starting material. Both aromatic (pyridine, 4-(N,N-dimethylamino)pyridine (DMAP), (3-carboxamide)pyridine; N-methylimidazole) and aliphatic (trimethylamine, N,N-dimethylhexylamine, N,N-dimethyloctylamine, N,N-dimethyldecylamine) amines were used, giving eight gemini quaternary ammonium salts (QAS). All salts were tested for their antimicrobial activity against yeasts, Candida albicans and Candida glabrata, as well as bacterial Staphylococcus aureus and Escherichia coli reference strains. Moreover, antibacterial activity against 20 isolates of S. aureus collected from patients with skin and soft tissue infections (n = 8) and strains derived from subclinical bovine mastitis milk samples (n = 12) were evaluated. Two QAS with octyl and decyl residues exhibited antimicrobial activity, whereas those with two decyl residues proved to be the most active against the tested pathogens, with MIC of 16-32, 32, and 8 µg/mL for yeast, E. coli, and S. aureus reference and clinical strains, respectively. Only QAS with decyl residues proved to be cytotoxic in MTT assay against human keratinocytes (HaCaT), IC50 12.8 ± 1.2 µg/mL. Ames test was used to assess the mutagenic potential of QAS, and none of them showed mutagenic activity in the concentration range 4-2000 µg/plate.

Influence of a 4'-substituent on the efficiency of flavonol-based fluorescent indicators of ß-glycosidase activity.

This article presents novel fluorescent probes, based on the excited-state intramolecular proton transfer (ESIPT) phenomenon and flavonols, sensitive to the action of specific glycosidases. 4'-Substituted flavonols were synthesized, using various approaches, and glycosylated with d-glucose, N-acetyl-d-glucosamine and d-glucuronic acid. Evaluation of the ß-glycosidase activities was performed in neutral and acidic pH. In all the cases examined, an acidic environment accelerated enzymatic hydrolysis. It was demonstrated that the 4'-chloroflavonyl glycosides of all sugars tested, both in neutral and acidic pH, are the ones most sensitive to the presence of hydrolase. In turn, 4'-dimethylaminoflavonyl glucoside is not sensitive to glucosidase action at all. Generally, the rate of enzymatic hydrolysis increases as the electron-withdrawing nature of the 4'-substituent increases. An exception is the trifluoromethyl group which, in spite of having the most favourable Hammett constant, does not contribute enough to increase the rate of hydrolysis of its glucoside. The presented experimental results are supported by the electrostatic potential (ESP) analysis and related to the mechanisms of glycoside bond enzymatic hydrolysis.

Calculations of pKa Values of Selected Pyridinium and Its N-Oxide Ions in Water and Acetonitrile.

Pyridine, its N-oxide, and their derivatives are exciting classes of organic bases. These compounds show widespread biological activity, and they are often used in synthesis. In this work results on theoretical calculations of acid dissociation constants as pKa of pyridine, its N-oxide, and their derivatives were done based on the thermodynamic cycle in water and acetonitrile. Additionally, gas-phase basicity (GB) and proton affinity (PA) values were computed for systems studied. All pKa values were obtained using B3LYP, M06-2X, and G4MP2 methods in the gas phase, which were combined with the PCM model calculations (at the Hartree-Fock method) and with the use of four different scale factors alpha. Theoretical GB, PA, and pKa values were then compared with the available experimental ones. Results obtained from B3LYP and M06-2X methods are quite similar and compatible with experimental ones in terms of quality with correlation coefficients values R2 higher than 0.9, whereas results received from G4MP2 deviate strongly. The calculated pKa values are highly sensitive to the scale factors alpha used in the computational procedure. Root-mean-square deviations (RMSD) between both theoretically and experimentally available pKa values of systems studied were also computed. The RMSD values are lower than 0.8 for the best results, suggesting that the theoretical model presented in this work is promising for applications for pKa calculations of different classes of compounds.

5-Fluorouracil-Complete Insight into Its Neutral and Ionised Forms.

5-Fluorouracil (5FU), a common anti-cancer drug, occurs in four tautomeric forms and possesses two potential sites of both protonation and deprotonation. Tautomeric and resonance structures of the ionized forms of 5FU create the systems of connected equilibriums. Since there are contradictory reports on the ionized forms of 5FU in the literature, complex theoretical studies on neutral, protonated and deprotonated forms of 5FU, based on the broad spectrum of DFT methods, are presented. These indicate that the O4 oxygen is more willingly protonated than the O2 oxygen and the N1 nitrogen is more willingly deprotonated than the N3 nitrogen in a gas phase. Such preferences are due to advantageous charge delocalization of the respective ions, which is demonstrated by the NBO and ESP analyses. In an aqueous phase, stability differences between respective protonated and deprotonated forms of 5FU are significantly diminished due to the competition between the mesomeric effect and solvation. The calculated pKa values of the protonated, neutral and singly deprotonated 5FU indicate that 5FU does not exist in the protonated and double-deprotonated forms in the pH range of 0-14. The neutral form dominates below pH 8 and the N1 deprotonated form dominates above pH 8.

Cyclophosphamide and isophosphamide - DFT conformational studies in the gas phase and solution.

Cyclophosphamide and isophosphamide have been subjected to comprehensive conformational studies in the vacuum and solution using the SMD solvation model. Vacuum calculations were conducted using the B3LYP, M05-2X, M06-2X and ωB97XD functionals. Natural bond orbital (NBO) analysis has been performed for selected geometries. A preference for a chair conformation with the axial P=O bond is shown (1C4). The 5S0 conformation is 1.25-2.31 kcal/mol and 1.72-2.92 kcal/mol higher in energy than the global minimum conformations of cyclophosphamide and isophosphamide, respectively. In the gas phase, the chair conformation with the equatorial P=O bond (4C1) is of comparable stability or less stable than the skew form, depending on the method used, while it is slightly more favored than the 5S0 conformation in solution. The stereoelectronic effects do not differentiate the ring conformer stability. The steric strains between N(EtCl)1-2 and the C4 and C6 carbon atoms mainly influence the stability of cyclophosphamide and isophosphamide conformers.

Comparative conformational studies of 3,4,6-tri-O-acetyl-1,5-anhydro-2-deoxyhex-1-enitols at the DFT level.

B3LYP and M06-2X optimization and MP2 single point calculations are reported for the 4H5 and 5H4 conformations of 3,4,6-tri-O-acetyl-D-allal, 3,4,6-tri-O-acetyl-D-galactal, 3,4,6-tri-O-acetyl-D-glucal, and 3,4,6-tri-O-acetyl-D-gulal. Significant discrepancies in predictions of relative energies and conformers' population for B3LYP and M06-2X optimized geometries are observed. Generally, B3LYP overestimates the conformers' energies with respect to MP2, whereas M06-2X slightly underestimates the conformers' energies. B3LYP failed to estimate the 4H5⇄5H4 conformational equilibrium for 3,4,6-tri-O-acetyl-D-galactal and 3,4,6-tri-O-acetyl-D-glucal. The M06-2X functional showed good agreement with experimental results for all glycals studied. The 4H5⇄5H4 conformational equilibrium for 3,4,6-tri-O-acetyl-D-allal and 3,4,6-tri-O-acetyl-D-gulal is governed by the vinylogous anomeric effect (VAE), whereas competition between the VAE and quasi 1,3-diaxial interactions influence this equilibrium for 3,4,6-tri-O-acetyl-D-galactal and 3,4,6-tri-O-acetyl-D-glucal. The orientation of the 4-OAc group influences the strength of the quasi 1,3-diaxial interactions between the 3-OAc and 5-CH2OAc groups. AIM analysis shows weak bonding interaction between the 3-OAc and 5-CH2OAc groups.

Threocytidines: Insight into the Conformational Preferences of Artificial Threose Nucleic Acid (TNA) Building Blocks in B3LYP Studies.

A systematic DFT conformational studies of four building blocks of TNA with cytosine attached to the C1' atom of the α-L-threofuranose moiety are presented. Structures bearing 2'-OR and 3'-OR substituents, where R represents H, CH3 and phosphate groups, were used in the studies using a B3LYP functional in the gas phase. The χ angle (C2-N1-C1'-O4'), the ν0-ν4 endocyclic torsion angles and the exocyclic torsion angles ε (X-O2'-C2'-C1') and γ (X-O3'-C3'-C2') geometry parameter variations were taken into consideration. Three energy minima, high-anti, anti and syn, were found for the rotation about the C1'-N1 bond. The high-anti orientation of the base with respect to the sugar moiety, turned out to be preferred, regardless of the substituents at the C2' and C3' positions. Other orientations are at least 1.65 kcal/mol higher in Gibbs free energy than the high-anti one. It has been shown that intramolecular H-bonds and the anomeric effect of phosphate groups strongly affect the conformational preferences of the studied compounds. Further, the structure of substituents attached to the sugar moiety influence the pucker of the furanoid ring. The furanoid ring in the global minima of the compound with two OH groups (TC1) in the 2' and 3' positions, and the compound having a 3'-phosphate group (TC2), adopt roughly the same conformation located at the southern range of the pseudorotation wheel, and thus are close to those found in the B type DNA helix. The low-energy high-anti rotamers of the geometry with the phosphate group attached to the sugar ring in the 2' position (TC3) and the geometry with two methoxyl groups (TC4) have their furanoid rings in conformations resembling those found in A DNA and RNA helices (the northern range of the pseudorotation wheel).

Diosgenyl 2-amino-2-deoxy-ß-D-galactopyranoside: synthesis, derivatives and antimicrobial activity.

The synthesis of diosgenyl 2-amino-2-deoxy-ß-D-galactopyranoside is presented for the first time. This synthetic saponin was transformed into its hydrochloride as well as N-acyl, 2-ureido, N-alkyl, and N,N-dialkyl derivatives. Antifungal and antibacterial studies show that some of the obtained compounds are active against Gram-positive bacteria and Candida type fungi.

Conformational studies of N-(α-d-glucofuranurono-6,3-lactone)- and N-(methyl ß-d-glucopyranuronate)-p-nitroanilines.

N-(α-d-Glucofuranurono-6,3-lactone)-p-nitroaniline and N-(methyl ß-d-glucopyranuronate)-p-nitroaniline were obtained as crystalline solids. The single-crystal X-ray diffraction, NMR data and DFT calculations for N-(α-d-glucofuranurono-6,3-lactone)-p-nitroaniline indicate that this N-furanoside adopts a 3T2/3E-like conformation in the crystal lattice, solution and gas phase. Thus, the structure of recorded for N-furanoside 1H NMR spectrum is indicative of the 3T2/3E region of the pseudorotational itinerary for furanose derivatives with α-d-gluco, ß-L-ido and α-d-xylo configurations. Moreover, it is concluded that the 1T2/E2/3T2/3E region of the pseudorotational itinerary for furanose derivatives with d-gluco, L-ido and d-xylo configurations should be characterised by the lack of coupling between H2 and H3 protons, irrespective of the anomeric configuration. Such a lack of vicinal coupling is characteristic for some of the trans-oriented furanose ring protons. The single-crystal X-ray diffraction and NMR data for N-(methyl ß-d-glucopyranuronate)-p-nitroaniline indicate that this N-glucuronide adopts the 4C1 conformation, both in the crystal lattice and solution. The occurrence of anomeric effects in the presented N-glycosides is discussed. The crystal structure analysis of both N-glycosides gives evidence that the amine group in p-nitroaniline is planar due to the nitrogen sp2 hybridisation.

Theoretical studies on the reaction of mono- and ditriflate derivatives of 1,4:3,6-dianhydro-D-mannitol with trimethylamine--Can a quaternary ammonium salt be a source of the methyl group?

DFT studies on the mechanism of the formation of "gemini" quaternary ammonium salts in the reaction of 1,4:3,6-dianhydro-D-mannitol ditriflate derivative with trimethylamine and its subsequent conversion to tertiary amine through the methyl-transfer reaction are discussed. Two alternative reaction pathways are presented in the gas phase and in ethanol. Additionally, the transformation of the monotriflate derivative of 1,4:3,6-dianhydro-D-mannitol into the single quaternary ammonium salt is presented. Two functionals (B3LYP, M062X) and two basis sets (6-31+G** and 6-311++G**) were used for the calculations. The effect of the substituent attached to the five-membered rings at the C2 (and/or C5) carbon atom on the activation barrier is described. The trimethylammonium group bond to the five-membered ring greatly reduces the activation barrier height. The preferred reaction pathway for the conversions was established. Including the London dispersion in the calculations increases the stabilization of all the points on the potential energy surface in relation to individual reactants.

N-Alkyl derivatives of diosgenyl 2-amino-2-deoxy-ß-D-glucopyranoside; synthesis and antimicrobial activity.

Diosgenyl 2-amino-2-deoxy-ß-D-glucopyranoside is a synthetic saponin exhibiting attractive pharmacological properties. Different pathways tested by us to obtain this glycoside are summarized here. Moreover, the synthesis of N-alkyl and N,N-dialkyl derivatives of the glucopyranoside is presented. Evaluation of antibacterial and antifungal activities of these derivatives indicates that they have no inhibitory activity against Gram-negative bacteria, whereas many of the tested N-alkyl saponins were found to inhibit the growth of Gram-positive bacteria and human pathogenic fungi.

DFT studies of the formation of furanoid derivatives of ammonium chlorides.

B3LYP/6-31+G** level computations were performed on the formation of ammonium salts during the reaction of (S)-1,4-anhydro-5-chloro-2,3,5-trideoxypentitol (1) (2S,5S)-2,5-anhydro-6-chloro-1,3,4,6-tetradeoxyhexitol (2) and methyl 5-chloro-2,3,5-trideoxy-ß-D-pentofuranoside (3) with ammonia in order to describe the reaction pathway in detail. All the structures were fully optimized in the gas phase, in chloroform and water. In addition, the gas phase activation barrier heights were estimated at B3LYP/6-311++G**, MPWIK/6-31+G**, MPWIK/6-311++G** and MP2/6-311++G(2d,2p)//MPWIK/6-31+G** levels of theory. All the calculations in solvents were performed the using polarizable continuum model (PCM) and the B3LYP functional with the 6-31+G** basis set. A detailed description of all the stationary points is presented, and the conformational behavior of the five-membered ring is discussed in the gas phase and in the solvents. The conversion of the reactant complexes into ion pairs is accompanied by a strong energy decrease in the gas phase and in all the solvents. The overall process is strongly unfavorable in the gas phase, but takes place readily in high-polarity solvents.

The conformational behavior, geometry and energy parameters of Menshutkin-like reaction of O-isopropylidene-protected glycofuranoid mesylates in view of DFT calculations.

The formation of pyridinium salts in the transformation of three O-isopropylidene-protected mesylates of furanoid sugar derivatives under pyridine action is considered at the B3LYP/6-31+G** computation level. All the structures were optimized in the gas phase, in chloroform and water. Activation barrier heights in the gas phase were also estimated at the B3LYP/6-311++G**, MPW1K/6-31+G** and MPW1K/6-311++G** levels. The conducted calculations, both in the gas phase (regardless of the computation level) and in solvents, revealed the barrier height increasing order as follows: 1>2>3 for the three reactions studied. The conformational behavior of the five-membered ring is discussed in the gas phase and in solvents. The fused dioxolane ring makes the furanoid ring less likely to undergo conformational changes. In the case of reaction 3, the furanoid ring shape does not change either in the gas phase or in solvents. All conformers are close to E0 or (0)E.

DFT studies of conversion of methyl chloride and three substituted chloromethyl tetrahydrofuran derivatives during reaction with trimethylamine.

B3LYP/6-31+G level computations were performed for the formation of four trimethylammonium salts in the reaction of methyl chloride (1a), (S)-1,4-andydro-5-chloro-2,3,5-trideoxypentitol (2a), (2S,5S)-2,5-andydro-6-chloro-1,3,4,6-tetradeoxyhexitol (3a) and methyl 5-chloro-2,3,5-trideoxy-ß-D-pentofuranoside (4a) with trimethylamine. All the structures were fully optimized in the gas phase, in chloroform and water. In addition, B3LYP/6-311++G and MPW1K/6-31+G level calculations were carried out to estimate activation barrier heights in the gas phase. A detailed description of all stationary points is presented, and the conformational behavior of the THF ring is discussed. B3LYP and MPW1K activation barriers indicate the reaction between methyl chloride and trimethylamine to be the fastest, whereas reaction 4 is the slowest one, both in the gas phase and in solvents. THF ring conformation changes were observed for reactions 2 and 3 along the reaction pathway, whereas it was almost unchanged for reaction 4, in the gas phase. In the case of reactions 2 and 3, different shapes of the THF ring were found for the transition state geometry in the gas phase and in water. The (5) E→E 4 and (3) E→E 5 conformational changes were observed for reactions 2 and 3, respectively.

Conformational studies of diosgenyl 2-amino-2-deoxy-ß-D-glucopyranosides at the PM3 and DFT levels of theory.

Geometry optimizations at the PM3 level were performed for diosgenyl 2-amino-2-deoxy-ß-D-glucopyranoside and its N-protonated form. Next, B3LYP/6-311++G(**) level geometry optimizations were carried out, albeit on a simpler model. The relative Gibbs free energies and geometry parameters are presented for the optimized structures. Conformational analysis concerning the clockwise (cw) and counterclockwise (ccw) arrangements of the OH groups as well as the three orientations of the NH2 and CH2OH groups was performed. Furthermore, a full scan of all the possible locations of the diosgenyl moiety in relation to the sugar ring in the target compounds was done. The PM3 optimization results indicate that diosgenyl 2-amino-2-deoxy-ß-D-glucopyranoside exists as a mixture of many rotamers. Of these, ccw conformers as well as the -ac orientation of the aglycone (ca -100° for torsion angle φ) are preferred. In the case of the N-protonated glucoside one rotamer is dominant in the mixture (population>60%). Only the cw arrangement is stable in the protonated form, because of steric and electronic repulsion between the charged ammonium group and the hydrogen atom of the neighbouring 3-OH group. The gauche-trans (gt) orientation of the CH2OH group is favourable to both neutral and protonated forms of diosgenyl glucosides at the PM3 level. DFT studies also predict conformational mixtures for both neutral and protonated forms of simplified diosgenyl 2-amino-2-deoxy-ß-D-glucopyranosides. These investigations showed unequivocally the preference for the ccw arrangement over cw, and that values of angle φ concur with the exo-anomeric effect. The B3LYP functional predicts the greater stability of the gt and tg orientations for the neutral and protonated analogues respectively. According to both PM3 and B3LYP calculations, torsion angle ψ has only a minor influence on the conformational energy. The importance of the geometry parameters affecting the stability of these conformers appears to be as follows: angle φ≈NH2/ccw/cw>gg/gt/tg>angle ψ.

DFT studies of the conversion of four mesylate esters during reaction with ammonia.

The energetics of the Menshutkin-like reaction between four mesylate derivatives and ammonia have been computed using B3LYP functional with the 6-31+G** basis set. Additionally, MPW1K/6-31+G** level calculations were carried out to estimate activation barrier heights in the gas phase. Solvent effect corrections were computed using PCM/B3LYP/6-31+G** level. The conversion of the reactant complexes into ion pairs is accompanied by a strong energy decrease in the gas phase and in all solvents. The ion pairs are stabilized with two strong hydrogen bonds in the gas phase. The bifurcation at C2 causes a significant activation barrier increase. Also, bifurcation at C5 leads to noticeable barrier height differentiation. Both B3LYP/6-31+G** and MPW1K/6-31+G** activation barriers suggest the reaction 2 (2a + NH3) to be the fastest in the gas phase. The reaction 4 is the slowest one in all environments.

Acetylated methyl 1,2-dideoxyhex-1-enopyranuronates in density functional theory conformational studies.

Geometry optimizations at the B3LYP level and single point calculations at the MP2 level are reported for the (4)H(5) and (5)H(4) conformations of methyl 3,4-di-O-acetyl-1,2-dideoxy-d-arabino-hex-1-enopyranuronate (methyl 3,4-di-O-acetyl-D-glucuronal), and methyl 3,4-di-O-acetyl-1,2-dideoxy-D-lyxo-hex-1-enopyranuronate (methyl 3,4-di-O-acetyl-D-galacturonal). Energy and geometry parameters are presented for the most stable optimized geometries. Conformational analysis of the acetoxy and methoxycarbonyl groups as well as the 1,2-unsaturated pyranoid ring is performed. It is demonstrated that both the acetoxy and methoxycarbonyl groups are planar and prefer cis over trans orientations with respect to the CO-O bond rotations. With regard to the AcO-R bond rotations some of the orientations are forbidden. The (4)H(5)⇌(5)H(4) conformational equilibrium in both methyl 3,4-di-O-acetyl-D-glucuronal (shifted towards (5)H4) and methyl 3,4-di-O-acetyl-D-galacturonal (shifted towards (4)H(5)) is the outcome of the competition between the vinylogous anomeric effect and quasi 1,3-diaxial interactions. It is demonstrated that the orientation of the 4-OAc group influences the strength of the quasi 1,3-diaxial interactions between 3-OAc and 5-COOCH(3) groups. Theoretical results are compared with assignments based on (1)H NMR studies.