Uracil-water interaction revisited - in search of single H-bonded secondary minima.

Monohydrated uracil (UW) complexes are stabilized by both O⋯HO and NH⋯O hydrogen bonds (H-bonds), simultaneously participating in forming three stable cyclic structures. The role and contribution of these individual H-bonds (O⋯HO and NH⋯O) to the stability of the three UW complexes are still not understood, because of the technical problems in obtaining their optimized structures by standard geometry optimization. The present study explores a non-standard approach to identify three single H-bonded local minima structures without imaginary frequency using DFT (M06-2X, B3LYP and B3LYP-D3), MP2 and CCSD(T) theories and Dunning's correlation-consistent aug-cc-pVTZ basis set, in both vacuum and aqueous media (CPCM method).

Electron Correlation or Basis Set Quality: How to Obtain Converged and Accurate NMR Shieldings for the Third-Row Elements?

The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical shieldings of the NMR-active nuclei of the third row. Here, we report on the importance of proper basis set selection to obtain accurate and reliable NMR shielding parameters for nuclei from the third row of the periodic table.

On the impact of side methyl groups on the structure and vibrational properties of β-carotenoids. The case of butadiene and isoprene.

Theoretical consideration about the impact of methyl groups on the structure and vibrational properties of β-carotenoids, using medium size molecules of trans-butadiene and trans-isoprene, are reported. Density functional theory (DFT) calculations with correlation-consistent and polarization-consistent basis sets were applied to trans-1,3-butadiene and trans-isoprene as the smallest building bricks of β-carotenoids. Their structure and harmonic vibrations were estimated in the complete basis set limit (CBS) using the non-linear least square fit.

Thiazole-amino acids: influence of thiazole ring on conformational properties of amino acid residues.

Post-translational modified thiazole-amino acid (Xaa-Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria.

Oxidation of diclofenac in the presence of iron(II) octacarboxyphthalocyanine.

This paper presents the results of the research on the influence of catalytic activity of iron(II) octacarboxyphthalocyanines (FePcOC) on the transformation of diclofenac (DCF) which is the most popular anti-inflammatory analgesic. Diclofenac poses a serious threat to the natural environment. The paper demonstrates that diclofenac, in the presence a monomeric form of iron octacarboxyphthalocyanine and hydroxyl radicals (HO) (from HO), undergoes a transformation into diclofenac-2,5-iminoquinone (DCF-2,5-IQ), causing distinct changes in the UV-Vis absorption spectrum.

On Complex Formation between 5-Fluorouracil and β-Cyclodextrin in Solution and in the Solid State: IR Markers and Detection of Short-Lived Complexes by Diffusion NMR.

In this work, the nuclear magnetic resonance (NMR) and IR spectroscopic markers of the complexation between 5-fluorouracil (5-FU) and β-cyclodextrin (β-CD) in solid state and in aqueous solution are investigated. In the attenuated total reflectance(ATR) spectra of 5-FU/β-CD products obtained by physical mixing, kneading and co-precipitation, we have identified the two most promising marker bands that could be used to detect complex formations: the C=O and C-F stretching bands of 5-FU that experience a blue shift by ca. 8 and 2 cm upon complexation.

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

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.

Hydrogen Bond-Mediated Conjugates Involving Lanthanide Diphthalocyanines and Trifluoroacetic Acid (Lnpc@TFA): Structure, Photoactivity, and Stability.

The interaction between lanthanide diphthalocyanine complexes, LnPc (Ln = Nd, Sm, Eu, Gd, Yb, Lu; Pc = CHN, phthalocyanine ligand) and trifluoroacetic acid (TFA) was investigated in benzene, and the stability of the resulting molecular system was assessed based on spectral (UV-Vis) and kinetic measurements. Structural Density Functional Theory (DFT) calculations provided interesting data regarding the nature of the bonding and allowed estimating the interaction energy between the LnPc and TFA species. Conjugates are created between the LnPc and TFA molecules via hydrogen bonds of moderate strength (>N∙∙H··) at the - -bridges of the Pc moieties, which renders the sandwich system to flatten.

What is the form of muscimol from fly agaric mushroom (Amanita muscaria) in water? An insight from NMR experiment supported by molecular modeling.

The biologically active alkaloid muscimol is present in fly agaric mushroom (Amanita muscaria), and its structure and action is related to human neurotransmitter -aminobutyric acid (GABA). The current study reports on determination of muscimol form present in water solution using multinuclear H and C nuclear magnetic resonance (NMR) experiments supported by density functional theory molecular modeling. The structures of three forms of free muscimol molecule both in the gas phase and in the presence of water solvent, modeled by polarized continuous model, and nuclear magnetic isotropic shieldings, the corresponding chemical shifts, and indirect spin-spin coupling constants were calculated.

Performance of polarization-consistent vs. correlation-consistent basis sets for CCSD(T) prediction of water dimer interaction energy.

Detailed study of Jensen's polarization-consistent vs. Dunning's correlation-consistent basis set families performance on the extrapolation of raw and counterpoise-corrected interaction energies of water dimer using coupled cluster with single, double, and perturbative correction for connected triple excitations (CCSD(T)) in the complete basis set (CBS) limit are reported. Both 3-parameter exponential and 2-parameter inverse-power fits vs.

Local aromaticity mapping in the vicinity of planar and nonplanar molecules.

We report on nucleus-independent magnetic shielding (NICS) scans over the centers of six- and five-membered rings in selected metal phthalocyanines (MPc) and fullerene C60 for more accurate characterization of local aromaticity in these compounds. Detailed tests were conducted on model aromatic molecules including benzene, pyrrole, indole, isoindole, and carbazole and subsequently applied to H Pc, ZnPc, Al(OH)Pc, and CuPc. Similar behavior of three selected magnetic probes, Bq, He, and Li , approaching perpendicularly the ring centers, was observed.

Performance of revised STO(1M)-3G basis set for prediction of 5-fluorocytosine chemical shifts.

Nuclear shieldings and chemical shifts of 5-fluorocytosine (5FC) were predicted in the gas phase and DMSO solution modeled by polarizable continuum model using B3LYP density functional and revised STO(1M)-3G basis set. For comparison, eight arbitrary selected basis sets including STO-3G and medium-size Pople-type and larger dedicated Jensen-type ones were applied. The former basis sets were significantly smaller, but the calculated structural parameters, harmonic vibrational frequencies, were very accurate and close to those obtained with larger, polarization-consistent ones.

Convergence of nuclear magnetic shieldings and one-bond J( B H) indirect spin-spin coupling constants in small boron molecules.

Self-consistent field Hartree-Fock, density functional theory, and coupled-cluster calculations of the nuclear magnetic shielding constants of BH and BH molecules have been conducted to characterize the convergence of individual results obtained with correlation-consistent and polarization-consistent basis sets. The individual B and H NMR parameters were estimated in the complete basis set limit and compared with benchmark results. Only the KT3 density functional accurately reproduced B shielding in BH molecule.

Method and basis set dependence of the NICS indexes of aromaticity for benzene.

The role of theory level in prediction of benzene magnetic indexes of aromaticity is analysed and compared with calculated nuclear magnetic shieldings of He used as NMR probe. Three closely related nucleus-independent chemical shift (NICS) based indexes were calculated for benzene at SCF-HF, MP2, and DFT levels of theory and the impact of basis set on these quantities was studied. The changes of benzene NICS(0), NICS(1), and NICS(1)zz parameters calculated using SCF-HF, MP2 and several density functionals were within 1 to 3 ppm.

The influence of solvent on conformational properties of peptides with Aib residue-a DFT study.

The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect.

Pyrazole amino acids: hydrogen bonding directed conformations of 3-amino-1H-pyrazole-5-carboxylic acid residue.

A series of model compounds containing 3-amino-1H-pyrazole-5-carboxylic acid residue with N-terminal amide/urethane and C-terminal amide/hydrazide/ester groups were investigated by using NMR, Fourier transform infrared, and single-crystal X-ray diffraction methods, additionally supported by theoretical calculations. The studies demonstrate that the most preferred is the extended conformation with torsion angles ϕ and ψ close to ±180°. The studied 1H-pyrazole with N-terminal amide/urethane and C-terminal amide/hydrazide groups solely adopts this energetically favored conformation confirming rigidity of that structural motif.

Interactions of amino acids with aluminum octacarboxyphthalocyanine hydroxide. Experimental and DFT studies.

The influence of albumin and amino acids (L-serine, glycine, L-histidine, L-tryptophan, L-cysteine) on the properties of aluminum octacarboxyphthalocyanine hydroxide (Al(OH)PcOC) was investigated in a phosphate buffer (pH 8.0). Particular attention was paid to the spectroscopic properties and photostability of Al(OH)PcOC.

Conformational preferences and synthesis of isomers Z and E of oxazole-dehydrophenylalanine.

Dehydrophenylalanine, ΔPhe, is the most commonly studied α,β-dehydroamino acid. In nature, further modifications of the α,β-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isomers Z and E, were investigated.

DFT studies on the structural and vibrational properties of polyenes.

Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increase in polyene size (chains containing 2 to 14 C = C units). The limiting values of the structural parameters for very long chains were estimated using simple three-parameter empirical formulae.

Predicting the structure and vibrational frequencies of ethylene using harmonic and anharmonic approaches at the Kohn-Sham complete basis set limit.

In this work, regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit are demonstrated for the first time. The performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with two Pople basis sets (6-311++G** and 6-311++G(3df,2pd)), the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, 6) was tested.The BLYP-calculated harmonic frequencies were found to be markedly closer than the B3LYP-calculated harmonic frequencies to the experimentally derived values, while the calculated anharmonic frequencies consistently underestimated the observed wavenumbers.

Interactions of zinc octacarboxyphthalocyanine with selected amino acids and with albumin.

Effect of selected amino acids (glycine, l-histidine, l-cysteine, l-serine, l-tryptophan) and albumin on the spectroscopic properties and photostability of zinc octacarboxyphthalocyanine (ZnPcOC) was explored in the phosphate buffer at a pH of 7.0. The photodegradation of ZnPcOC alone and in the presence of amino acids or albumin has been investigated in aqueous phase using UV-366nm and daylight irradiation.

The impact of model peptides on structural and dynamic properties of egg yolk lecithin liposomes - experimental and DFT studies.

Electron spin resonance (ESR), (1) H-NMR, voltage and resistance experiments were performed to explore structural and dynamic changes of Egg Yolk Lecithin (EYL) bilayer upon addition of model peptides. Two of them are phenylalanine (Phe) derivatives, Ac-Phe-NHMe (1) and Ac-Phe-NMe2 (2), and the third one, Ac-(Z)-ΔPhe-NMe2 (3), is a derivative of (Z)-α,β-dehydrophenylalanine. The ESR results revealed that all compounds reduced the fluidity of liposome's membrane, and the highest activity was observed for compound 2 with N-methylated C-terminal amide bond (Ac-Phe-NMe2 ).

Experimental and theoretical NMR studies of interaction between phenylalanine derivative and egg yolk lecithin.

The interaction of phenylalanine diamide (Ac-Phe-NHMe) with egg yolk lecithin (EYL) in chloroform was studied by (1)H and (13)C NMR. Six complexes EYL-Ac-Phe-NHMe, stabilized by N-H···O or/and C-H···O hydrogen bonds, were optimized at M06-2X/6-31G(d,p) level. The assignment of EYL and Ac-Phe-NHMe NMR signals was supported using GIAO (gauge including atomic orbital) NMR calculations at VSXC and B3LYP level of theory combined with STO-3Gmag basis set.

Conformational properties of oxazole-amino acids: effect of the intramolecular N-H···N hydrogen bond.

Oxazole ring occurs in numerous natural peptides, but conformational properties of the amino acid residue containing the oxazole ring in place of the C-terminal amide bond are poorly recognized. A series of model compounds constituted by the oxazole-amino acids occurring in nature, that is, oxazole-alanine (L-Ala-Ozl), oxazole-dehydroalanine (ΔAla-Ozl), and oxazole-dehydrobutyrine ((Z)-ΔAbu-Ozl), was investigated using theoretical calculations supported by FTIR and NMR spectra and single-crystal X-ray diffraction. It was found that the main feature of the studied oxazole-amino acids is the stable conformation β2 with the torsion angles φ and ψ of -150°, -10° for L-Ala-Ozl, -180°, 0° for ΔAla-Ozl, and -120°, 0° for (Z)-ΔAbu-Ozl, respectively.

Solvent effects on the conformational preferences of model peptoids. MP2 study.

The influence of aqueous environment on the main-chain conformation (ω0 , ϕ, and ψ dihedral angles) of two model peptoids: N-acetyl-N-methylglycine N'-methylamide (Ac-N(Me)-Gly-NHMe) (1) and N-acetyl-N-methylglycine N',N'-dimethylamide (Ac-N(Me)-Gly-NMe₂) (2) was investigated by MP2/6-311++G(d,p) method. The Ramachandran maps of both studied molecules with cis and trans configuration of the N-terminal amide bond in the gas phase and in water environment were obtained and all energy minima localized. The polarizable continuum model was applied to estimate the solvation effect on conformation.