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Chelidonic acid (4-oxo-4H-pyran-2,6-dicarboxylic acid) is present in plants of Papaveraceae family, especially in Chelidonium majus. Due to its anticancer, antibacterial, hepatoprotective, and antioxidant properties, it has been used in medical treatments. In this work, the X-ray structure of methanol solvate of chelidonic acid was determined. Layers of chelidonic acid are held by hydrogen bonds via COOH and C = O fragments and additionally bridged by methanol. The formed H-bond network between two acid units is different from typical –COOH dimers observed, e.g., in crystals of isophtalic acid. The molecular structure of 2,6-dimethyl-γ-pyrone (2Me4PN) and chelidonic acid, a 2,6-dicarboxylic derivate of γ-pyrone (4PN), was verified in silico using density functional theory (DFT-B3LYP) combined with large correlation-consistent basis sets. The impact of –CH3 and –COOH substituents on 4PN ring structure, dipole moments, geometric/magnetic indexes of aromaticity, and NBO charges was assessed following unconstrained geometry optimization in the gas phase, chloroform, methanol, DMSO, and water with solvent effect introduced using the polarized continuous model (PCM). H-bond network formed in chelidonic acid–methanol complex was analyzed and their interaction energy estimated. Theoretical modeling enabled prediction of accurate structural parameters, dipole moments, and geometric/magnetic indexes of aromaticity of the studied 4PN, 2Me4PN, and chelidonic acid molecules.

Anthropogenic ecological ecosystems create favourable conditions for the growth of the nitrophilous medicinal species Chelidonium majus in six urban parks in Southern Poland. This study focuses on the concentrations of trace elements in the soils, leaves, stems, and rhizomes of greater celandine. The soil samples were taken only in the humus horizon (A), which averaged approximately 15 cm in thickness under the clumps of Ch. majus. Regarding the reaction, the soil samples tested can be described as slightly acidic (5.6–6.8 in KCl) to alkaline (7.1–7.4 in H2O). Organic carbon content at all sites is high, ranging from 3.2% to 13.6%, while the highest total nitrogen (Nt) content is 0.664%. The average total phosphorus (Pt) content in all samples is 548.8 mg/kg (and its range is 298–940 mg/kg), such values indicating its anthropogenic origin. In terms of heavy metals, Zn has the highest content in the analysed soil samples compared to the other elements, and its range is from 394.50 mg/kg to 1363.80 mg/kg in soil. In rhizomes, Zn also has the highest values (178.7–408.3 mg/kg), whereas, in stems and leaves, it varies (from 80.6 to 227.5 and from 57.8 to 297.4 mg/kg, respectively). Spearman’s rank correlation showed high correlations between the content of Pb, Zn, Cd, and As in the soil and rhizomes of Ch. majus. Despite soil contamination with Pb, Cd, and Zn, Ch. majus does not accumulate them in its tissues. However, the translocation of Hg and Cr from rhizomes to leaves was observed. The different concentrations of metals in each park result from the degree of diversity of the parent rocks on which the soil was formed.

The problem of aromaticity in heterocyclic rings of uracil and its 5-halogenoderivatives (5XU) was analyzed theoretically by calculating modified harmonic oscillator model of aromaticity (HOMA) for Heterocycle Electron Delocalization (HOMHED), nucleus-independent chemical shift parameters (NICS) and the so-called scan experiments, using helium-3 atom as a magnetic probe. The impact of halogen electronegativity on C5 atom’s NBO charges was also investigated. Water, as a polar environment, has a negligible impact on 5XU aromaticity. The most stable diketo tautomer shows a very low aromaticity while the “rare” dihydroxy form (tautomer No 6) is aromatic and resembles benzene. This is in agreement with traditional drawing of chemical formula of uracil’s six-membered ring, directly showing three alternating single and double bonds in its tautomer No 6. No good correlation between magnetic and geometric indexes of aromaticity for the studied 5XU tautomers was found. Linear correlation between the magnitude of NICS minimum, as well as the distance of the minimum above uracil ring plane center from 3He NMR chemical shift scan plot with respect to halogen electronegativity were observed. A strong linear dependence of magnetic index of aromaticity and the electronegativity of 5X substituent was observed.

5-Fluorouracil (5-FU) is one of anticancer drugs with broad activity. Due to its severe side effects, recent studies concentrate on new ways of directed 5-FU delivery and its release in ill tissue. One of selective carriers could be cyclodextrins and liposomes. The combination of novel methods, leading to formation of inclusion complexes (IC) between host molecule of β-cyclodextrin (β-CD) or 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) and 5-FU guest and its subsequent encapsulation in dipalmitoylphosphatidylcholine (DPPC) liposomes is studied experimentally in the present work. Several methods are applied to proof the encapsulation of the analysed drug and its release over time at 37 and 41 °C. The 5-FU release from complex of liposomal form of 5-fluorouracil and β-cyclodextrin (L[DPPC/5-FU]:β-CD) and complex of liposomal form of 5-fluorouracil and (2-hydroxypropyl)-β-cyclodextrin (L[DPPC/5-FU]:HP-β-CD) was followed using UV–Vis and fluorescence spectroscopy, proton nuclear magnetic resonance (1H NMR) and differential scanning calorimetry (DSC) techniques. The electronic and NMR spectra analysis were additionally supported by molecular modeling, including prediction of spectral changes in vacuum and in water using density functional theory (DFT-B3LYP-D3). From the observed changes the fastest release from liposomes (within 1 h) was observed for the 5-FU complexes with HP-β-cyclodextrin at 41 °C.

1 J(15 N,H) coupling constants for enaminones and NH-forms of intramolecularly hydrogen-bonded Schiff bases as model compounds for sp2 -hybridized nitrogen atoms are evaluated using density functional theory (DFT) to find the optimal functionals and basis sets. Ammonia is used as a test molecule and its one-bond coupling constant is compared with experiment. A methylamine Schiff base of a truncated molecule of gossypol is used for checking the performance of selected B3LYP, O3LYP, PBE, BHandH, and APFD density functionals and standard, modified, and dedicated basis sets for coupling constants. Both in vacuum and in chloroform, modeled by the simple continuum model of solvent, the modified basis sets predict significantly better the 1 J(15 N,H) value in ammonia and in the methylamine Schiff base of a truncated molecule of gossypol than the standard basis sets. This procure is then used on a broad set of intramolecularly hydrogen-bonded molecules, and a good correlation between calculated and experimental one-bond NH coupling constants is obtained. The 1 J(15 N,H) couplings are slightly overestimated. The calculated data show for hydrogen-bonded NH interatomic distances that the calculated values depend on the NH bond lengths. The shorter the bond lengths, the larger the 1 J(15 N,H). A useful correlation between 1 J(15 N,H) and NH bond length is derived that enables realistic predictions of one-bond NH coupling constants. The calculations reproduce experimentally observed trends for the studied molecules.

Glass-forming ability is one of the most desired properties of organic compounds dedicated to optoelectronic applications. Therefore, finding general structure–property relationships and other rules governing vitrification and related near-glass-transition phenomena is a burning issue for numerous compound families, such as Schiff bases. Hence, we employ differential scanning calorimetry, broadband dielectric spectroscopy, X-ray diffraction and quantum density functional theory calculations to investigate near-glass-transition phenomena, as well as ambient- and high-pressure molecular dynamics for two structurally related Schiff bases belonging to the family of glycine imino esters. Firstly, the surprising great stability of the supercooled liquid phase is shown for these compounds, also under high-pressure conditions. Secondly, atypical self-organization via bifurcated hydrogen bonds into lasting centrosymmetric dimers is proven. Finally, by comparing the obtained results with the previous report, some general rules that govern ambient- and high-pressure molecular dynamics and near-glass transition phenomena are derived for the family of glycine imino esters. Particularly, we derive a mathematical formula to predict and tune their glass transition temperature (Tg) and its pressure coefficient (dTg/dp). We also show that, surprisingly, despite the presence of intra- and intermolecular hydrogen bonds, van der Waals and dipole–dipole interactions are the main forces governing molecular dynamics and dielectric properties of glycine imino esters.

Nuclear shielding, chemical shift and spin–spin coupling constants are the most important parameters in nuclear magnetic resonance (NMR) spectroscopy, which allow prediction of the structure and reactivity of both inorganic and organic compounds. NMR experiments in solution are much less difficult in terms of sample preparation and analysis of the observed results. Thus, for practical reasons, mainly isotropic NMR parameters in solution are analyzed, often supported by less challenging molecular modeling, while measurement of solid-state spectra is less popular. This chapter covers the most important reports on theoretical aspects of nuclear magnetic shielding published in 2020. Experimental studies and both non-relativistic (NR) and relativistic (R) calculations of nuclear shielding at density functional theory (DFT) and ab initio levels of theory are reviewed. Several high-level calculations (in terms of electron-correlation and basis set quality) on small molecular systems are also discussed. Improved accuracy of prediction due to inclusion of zero-point vibration and temperature correction (ZPVC and TC), and both implicit and explicit solvent effects are also discussed.

The presented study focuses on the interaction of the well-known neurotoxin muscimol with water. Two approaches for the water solvent are applied – the explicit and the implicit. The muscimol-water clusters were obtained by the molecular dynamics simulations and the first solvation shell was kept for further studies. Implicit water was mimicked via the polarized continuum model (PCM). All three tautomeric forms of the free muscimol molecule are considered in the calculations. The combined theoretical and experimental vibrational IR and Raman studies determined the stability of the prevailing zwitterion form in water. We proved that water molecules in the first solvation shell are crucial for the correct prediction of structural and spectroscopic parameters of muscimol due to its ability to form strong hydrogen bonds. We believe that our findings will shed some light on the binding preferences of muscimol with the γ-aminobutyric acid (GABA) receptor.

Exponential dependencies between locally calculated geometric and magnetic indexes of aromaticity, harmonic oscillator model of aromaticity (HOMA) and nucleus independent chemical shifts (NICS)(0), NICS(1) and NICS(1)zz, and the number of conjugated benzene rings in linear acenes, from benzene to decacene were observed at B3LYP/6-311+G** level of theory. Correlations between HOMA and NICS indexes showed exponential dependencies and were fitted with simple three-parameter function. Similar correlations between both indexes of aromaticity and proton and carbon nuclear isotropic shieldings of individual acene rings were observed. Contrary to proton data, the predicted 13 C nuclear isotropic shieldings of carbon atoms belonging to inner rings in polyacenes were less shielded, indicating lower aromaticity and therefore, higher reactivity.

Detailed studies on the stability, interaction, and microstructure of host‐guest complexes in the vacuum of 5‐fluorouracil (5FU) with β‐cyclodextrin (βCD) were performed using B3LYP with the inclusion of Grimme's dispersion correction GD3 term and 6‐31+G(d,p) basis set. Among several studied 1:1 5FU‐βCD complexes, the one placing the keto tautomer of 5FU vertically in the host cavity and forming N‐H···OCD and CO···HOCD hydrogen bonds with hydroxyl groups of the smaller rim of βCD has the highest stability (Eint = −195 kJ/mol). Interestingly, there are no interactions with the inner hydrophobic part of the βCD host cavity. The strength of the intermolecular H‐bonds to the smaller rim of βCD is comparable to those in 5FU‐water and 5FU‐methanol clusters, used as model systems characterizing the noncovalent interactions. Of several studied host‐guest complexes, the inner ones are more stable than the outer systems. Our results reveal that taking dispersion interaction in DFT into account is essential for reliable modeling of the structure, interaction, and stability of 5FU‐βCD complexes. This study is crucial for understanding the interaction of 5FU with βCD in the solid state and additionally suggests the presence of equilibrium between 5FU‐βCD complex and solvated 5FU.

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)&minus, 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)&minus, 3G basis set. The indirect spin&ndash, spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well.

In this study we report on UV-vis, IR and Raman studies of non-covalent copper phthalocyanine (CuPc) – flake graphene oxide (GO) complex in water and in the solid phase. Experimental results were supported by molecular modeling of structure, electronic and vibrational parameters for free CuPc and its 1 : 1 complexes with water, benzene, phenol, neutral and deprotonated benzoic acid. HOMO-LUMO gaps for these complexes were calculated and compared with data derived from the absorption edge of Q-band in the recorded UV-vis spectra for free CuPc and its adduct with GO in water. Small but non-negligible changes in position of spectral bands observed as result of CuPc interaction with GO were consistent with theoretical models predicted by density functional theory (DFT). Both the observed spectroscopic changes and theoretical shifts of spectral bands supported a direct interaction between CuPc and GO. The interaction site of CuPc was copper ion - small molecules were bound preferably to Cu2+ and its vicinity as an additional axial ligand forming a kind of T-shaped structure. In case of benzene and phenol sandwich type complexes were formed.

Phosphorus nitride (PN) is the simplest molecule formed solely by phosphorus and nitrogen. It represents an interesting model for materials, where phosphorus is directly attached to nitrogen. Nevertheless, both theoretical and experimental studies often provide an incomplete picture on the structural, electronic, and spectral properties of PN. Theoretical predictions often suffer from insufficient level of theory, incomplete basis set, or from neglecting several effects, for example, zero‐point vibrational correction (ZPVC). Therefore, we performed an extensive benchmark study on structural, electronic, and spectral properties of PN at the Hartree‐Fock, density functional theory (DFT), or even the coupled‐cluster levels. We paid special attention to the basis set effect. We tested three variants of Dunning's aug‐cc‐pVXZ basis sets with the size from double‐ζ to sextuple‐ζ, as well as Jensen's aug‐pc‐n, aug‐pcJ‐n, and aug‐pcSseg‐n basis sets, where n = 1‐4. Obtained energetics, PN distance, dipole moment, vibrational frequencies, and nuclear magnetic resonance (NMR) parameters were extrapolated to the complete basis set limit (CBS) using three‐ or two‐parameter formulas. The 31P NMR shieldings estimated with the aug‐cc‐pVXZ and aug‐cc‐pV(X + d)Z basis sets strongly depend on the basis set size providing scattered convergence patterns toward CBS. The Hartree‐Fock self‐consistent field (HF‐SCF) NMR parameters evinced similar behavior as the coupled‐cluster data. The only smooth convergence was achieved using the aug‐cc‐pCVXZ basis sets that include core‐valence effects. The KT3 functional underestimated the phosphorus CBS shieldings by about 12 ppm compared to coupled cluster with singles and doubles (CCSD) (T). Nevertheless, KT3 unambiguously surpasses the HF‐SCF and CCSD levels that provide 31P shieldings that are lower by about 150 ppm and 24 ppm compared to CCSD(T). The convergence of nitrogen shieldings was regular for all basis set hierarchies and all theoretical methods. Relativistic and vibrational effects on selected properties were also discussed.

Static electric properties, from the dipole moment to the second-hyperpolarizability tensor γ, of the 3-membered, isoelectronic ring molecules, fluorene (FL), carbazole (CR), and dibenzofuran (DBF), have been calculated at various levels of approximation. The electron correlation effects have been included at the coupled-cluster (CC) level, using CCSD and CC2 versions of the method. DFT calculations with the CAM-B3LYP functional have also been performed, and the results are compared to the CC values. The electric property-tailored Pol basis set and its more compact Z3Pol version have been employed in all static calculations. Differences between dipole polarizability values computed at the Pol and Z3Pol bases have been found to be almost negligible. Therefore, all components of the frequency-dependent dipole polarizability tensor α(-ω;ω) have been determined at the CAM-B3LYP/Z3Pol level. Divergence occurring at electronic resonances has been eliminated using the complex polarization propagator (CPP) formalism, explicitly introducing an imaginary iΓ parameter to account approximately for the finite lifetime of the excited state. The imaginary part of the dipole polarizability Im α(-ω;ω) has been calculated for a wide range of external radiation energies up to 10 eV, and its maxima have been compared to the calculated vertical electronic excitation energies.

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 H2 Pc, ZnPc, Al(OH)Pc, and CuPc. Similar behavior of three selected magnetic probes, Bq, 3 He, and 7 Li+ , approaching perpendicularly the ring centers, was observed. For better visualization of shielding zone over the centers of aromatic rings, we introduced a simple mathematical procedure: the first and second derivatives of scan curves with respect to magnetic probe position enabled their additional examination. It allowed an easier localization of curve minimum and discrimination between areas in space varying by the magnetic field magnitude and to illustrate local aromaticity of two different kinds of rings in MPc with better resolution. Our results supported earlier reports on very low aromaticity indexes of pyrrole ring incorporated into MPc and significant aromaticity of the central macrocycle. No direct dependence between harmonic oscillator model of aromaticity and NICS was observed. Instead, a correlation between position of scan curve minimum and its magnitude were observed. In addition, the NICS values and 3 He chemical shifts in the middle of neutral C60 and C606- anion agreed well with the reported experimental NMR values for He@C60 and He@C606- .

Conformational propensities of N-t-butoxycarbonyl-glycine-(E/Z)-dehydrophenylalanine N′-methylamides (Boc-Gly-(E/Z)-ΔPhe-NHMe) in chloroform were investigated by NMR and IR techniques. The low-temperature crystal structure of the E isomer was determined by single crystal X-ray diffraction and the experimental data were elaborated by theoretical calculations using DFT (B3LYP, M06-2X) and MP2 approaches. The β-turn tendencies for both isomers were determined in the gas phase and in the presence of solvent. The obtained results reveal that the configuration of ΔPhe residue significantly affects the conformations of the studied dehydropeptides. The tendency to adopt β-turn conformations is significantly lower for the E isomer (Boc-Gly-(E)-ΔPhe-NHMe), both in gas phase and in chloroform solution.

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. Optimized geometries and harmonic frequencies, obtained with B3LYP and BLYP density functionals and large basis sets, were favorably reproduced by a significantly faster approach, using a recently modified STO(1M)-3G Slater-type basis set. Selected density functionals with STO(1M)-3G and 6-311++G** basis sets were also successful in predicting β-carotene structures and harmonic vibrations. This work demonstrates the potential applicability of the proposed level of theory for larger molecules, including β-carotenoids, present in numerous natural food sources. The proposed scheme of molecular modeling, applied to biologically active compounds in food, could provide a deeper insight into their function in vivo, which is directly related to their structure and spectroscopic properties. It could also support the experimental qualitative analysis, based on peak assignment of β-carotenoids in various food sources.

The role of theory level in prediction of benzene magnetic indexes of aromaticity is analysed and compared with calculated nuclear magnetic shieldings of 3 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. Similar deviations between magnetic indexes of aromaticity were observed for values calculated with selected basis sets. Only very small effect of polar solvent on benzene aromaticity was predicted. The 3 He nuclear magnetic isotropic shielding (σ) and its zz-components (σzz ) of helium atom approaching the centre of benzene ring from above produced similar curves versus benzene-He distance to NICS parameters calculated for similarly moving Bq ghost atom. We also propose an experimental verification of NICS calculations by designing the 3 He NMR measurement for benzene saturated with helium gas or in low temperature matrices.

A theoretical investigation on the planarity of molecular structure of zinc phthalocyanine (ZnPc) and its aromaticity has been performed using B3LYP and M06-2X density functionals combined with selected Pople-type basis sets. The effect of the applied calculation method on the optimized structure of ZnPc and ZnPc∙∙∙H2O, both in the gas phase and in the polar solvent, was analyzed. To quantify the aromaticity of the ZnPc and ZnPc∙∙∙H2O complexes, both the geometric and magnetic criteria, i.e., Harmonic Oscillator Model of Aromaticity (HOMA) index and the nucleus-independent chemical shift (NICS) values at the centers or 1 A above the centers of structural subunits, were calculated. The energies of highest energy occupied molecular orbital (HOMO) and lowest energy unoccupied molecular orbital (LUMO) and energy gaps were also estimated. The results show that the free ZnPC molecule is flat in the gas phase and nonplanar in the polar environments (DMSO and water). ZnPC∙∙∙H2O is nonpolar in the gas phase and polar solvent which is in agreement with recent X-ray reports. Both HOMA and NICS indexes indicate the presence of highly aromatic macrocycle and benzene rings while these parameters for pyrrolic ring are significantly smaller than in free pyrrole. The presence of polar solvents practically does not change aromaticity of the ring subunits of the studied compounds.

Self‐consistent field Hartree–Fock (SCF‐HF), density functional theory (B3LYP, KT1, KT2, and KT3), and coupled‐cluster calculations of the nuclear magnetic shielding constants of BH and BH3 molecules have been conducted to characterize the convergence of individual results obtained with correlation‐ and polarization‐consistent basis sets. The individual 11B and 1H NMR parameters were estimated in the complete basis set limit and compared with benchmark literature results. The SCF‐HF and density functional theory B3LYP predicted boron shieldings and shielding anisotropies of BH significantly differed from the results obtained by coupled‐cluster with single, double, and perturbative treatment of triple excitations, CCSD(T) approach. The best agreement between the CCSD(T)/complete basis set limit estimated boron shieldings was obtained for KT3 density functional (~5.7 ppm). The 1H NMR parameters predicted at B3LYP and CCSD(T) levels of theory differed by less than 1 ppm, and the SCF‐HF calculated proton shieldings and shielding anisotropies also nicely agreed with our coupled‐cluster results. The 1J(11B1H) parameters, calculated with B3LYP and KT3 functionals, accurately reproduced the earlier reported benchmark value for BH molecule. The SCF‐HF, B3LYP, and KT3 calculated boron shieldings of BH3 differed from the CCSD(T) values by 13.2, −16.8, and −2.1 ppm, respectively.

The development of novel molecularly imprinted polymers (MIP) sorbents for specific chemical compounds require a lot of tedious and time-consuming laboratory work. Significant quantities of solvents and reagents are consumed in the course of the verification of appropriate configurations of polymerization reagents. Implementation of molecular modeling in the MIP sorbent development process appears to provide a solution to this problem. Appropriate simulations and computations facilitate the determination of the nature of interaction between the reagents and thus the selection of the best configuration of chemicals for the preparation of the sorbent. The article presents literature information on major computer software used for molecular modeling, its application in the development of MIP sorbents, as well as the advantages resulting from the implementation of computer-assisted techniques. The appropriate choice of polymerization reagents and conditions allows for a significant reduction of the adverse environmental impact of the entire laboratory process.

Harmonic and anharmonic frequencies of dimers and mixed dimers of water, methanol and benzene were computed and the results were critically analysed to investigate the anharmonicity of the normal mode vibrations within density functional theory (DFT) with empirically included Grimme correction for dispersion (D3). From several options, the B3LYP-D3/6-31++G* level of theory was selected as a good compromise between accuracy and calculation speed, suitable for future modeling of larger solvent clusters. The obtained raw harmonic and anharmonic second-order perturbation theory of vibrational frequencies (VPT2) were additionally scaled using a two-range procedure (below and above 2000 cm−1) and compared with available experimental values for the studied dimers. Additionally, the Morse and 4th order polynomial fittings of small normal mode deflections from the equilibrium geometry were used to model anharmonicity of the studied dimers. Compared to B3LYP-D3, the VPT2 vibrations calculated with APFD and M06-2X functionals very poorly model the anharmonicity of the H-bonded dimers. The surprising observation was related to the performance of CCSD/6-31++G* and CCSD(T)/6-31++G* in predicting harmonic frequencies of H-bonded dimers of water, water-methanol and methanol-water of similar quality, as compared to B3LYP-D3/6-31++G*. The obtained results suggest using of B3LYP-D3/6-31++G* scaled harmonic frequencies for the larger solvent clusters as a good alternative to anharmonic frequencies.

ARTYKUŁ Z BADAŃ SPECJALNYCH, SPECIAL ISSUE RESEARCH ARTICLE. The biologically active alkaloid muscimol is present in fly agaric mushroom (Amanita muscaria), and its structure and action is related to human neurotransmitter γ‐aminobutyric acid (GABA). The current study reports on determination of muscimol form present in water solution using multinuclear 1H and 13C 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. Several J‐couplings observed in proton and carbon NMR spectra, not available before, are reported. The obtained experimental spectra, supported by theoretical calculations, favor the zwitterion form of muscimol in water. This structure differs from NH isomer, previously determined in dimethyl sulfoxide (DMSO) solution. In addition, positions of signals C3 and C5 are reversed in both solvents.

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. the cardinal number of basis set, as well as the number of basis functions were analyzed and compared with one of the most extensive CCSD(T) results reported recently. The obtained results for both Jensen- and Dunning-type basis sets underestimate raw interaction energy by less than 0.136 kcal/mol with respect to the reference value of − 4.98065 kcal/mol. The use of counterpoise correction further improves (closer to the reference value) interaction energy. Asymptotic convergence of 3-parameter fitted interaction energy with respect to both cardinal number of basis set and the number of basis functions are closer to the reference value at the CBS limit than other fitting approaches considered here. Separate fits of Hartree-Fock and correlation interaction energy with 3-parameter formula additionally improved the results, and the smallest CBS deviation from the reference value is about 0.001 kcal/mol (underestimated) for CCSD(T)/aug-cc-pVXZ calculations. However, Jensen’s basis set underestimates such value to 0.012 kcal/mol. No improvement was observed for using the number of basis functions instead of cardinal number for fitting.

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. The predicted 13 C and 1 H chemical shieldings of 5FC and cytosine, selected as parent molecule, were acceptable (root mean square for 13 C chemical shifts in DMSO of about 5 ppm and less) though less accurate than those calculated with large basis sets, dedicated for prediction of nuclear magnetic resonance parameters.

The method and basis set dependence of zero-point vibrational corrections (ZPVCs) to nuclear magnetic resonance shielding constants and anisotropies has been investigated using water as a test system. A systematic comparison has been made using the Hartree–Fock, second-order Møller–Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)) and Kohn–Sham density functional theory with the B3LYP exchange-correlation functional methods in combination with the second-order vibrational perturbation theory (VPT2) approach for the vibrational corrections. As basis sets, the correlation consistent basis sets cc-pVXZ, aug-cc-pVXZ, cc-pCVXZ and aug-cc-pCVXZ with X = D, T, Q, 5, 6 and the polarisation consistent basis sets aug-pc-n and aug-pcS-n with n = 1, 2, 3, 4 were employed. Our results show that basis set convergence of the vibrational corrections is not monotonic and that very large basis sets are needed before a reasonable extrapolation to the basis set limit can be performed. Furthermore, our results suggest that coupled cluster methods and a decent basis set are required before the error of the electronic structure approach is lower than the inherent error of the VPT2 approximation.

Pigments from red coral (Corallium rubrum) and African snail (Helixia aspersa) shell were studied non-invasively using Raman spectroscopy with 1064-nm laser beam. The two observed bands because of organic pigments confined in biomineralized CaCO3 matrix at about 1500 and 1100 cm−1 were assigned to ν(CC) and ν(C―C), respectively. Both signals originate from polyene(s) of largely unknown structure, containing several conjugated CC bonds. The small peak at 1016 cm−1 in the Raman spectrum of coral pigment was assigned to in-plane ―CH3 rocking or structural deformation of polyene chain because of spatial confinement in the mineral matrix. The organic pigments in red coral and snail shell were present in inorganic matrix containing aragonite (shell) and calcite (coral). In addition, using Raman spectroscopy, it was observed that aragonite was replaced by calcite as result of healing damaged parts of snail shell. This is an important finding which indicates a great potential of nondestructive Raman spectroscopy instead of X-ray technique, as a diagnostic tool in environmental studies. To support analysis of the observed Raman spectra detailed calculations using density functional theory (DFT with B3LYP and BLYP density functionals) on structure and vibrations of model all-trans polyenes were undertaken. DFT calculated CC and C―C stretching frequencies for all-trans polyenes containing from 2 to 14 CC units were compared with the observed ν(CC) and ν(C―C) band positions of the studied coral and shell. Individual correction factors were used to better match theoretical wavenumbers with observed band positions in red coral and African snail. It was concluded that all-trans polyene pigments of red coral and dark parts of African snail shell contain 11–12 and 14 CC double bond units, respectively. However, Raman spectroscopy cannot produce any clear information on the presence and nature of the end-chain substituents in the studied pigments. Copyright © 2016 John Wiley & Sons, Ltd.

Structural and selected Raman features of pristine single-walled carbon nanotubes (SWCTNs) with diameters from 0.4 to 1.2 nm and total lengths up to 2.15 nm were studied using the density functional theory (DFT) at the UB3LYP/6-31G* level. Models of different lengths (1, 4, 6 and 10 adjacent bamboo-units) of zigzag (n, 0) SWCNTs, for n ranging from 5 to 15, were studied. Highly systematic changes of individual CC bond lengths and angles along the nanotube axis were observed and described for the longest models. Predicted Raman active radial breathing mode (RBM) vibrational frequencies regularly decreased upon increasing the nanotube diameter and only a negligible effect of the tube length was observed. The changes in calculated RBM frequencies with increasing diameter were close to values estimated using empirical formulas. The experimental G-mode characteristics were reasonably well reproduced using the 4-unit model, especially for tubes with the diameter d > 1 nm. Raman features were also determined for cyclacenes representing the shortest models of SWCNTs. Calculated RBM frequencies of cyclacenes match closely the values for longer SWCNT models but are too inaccurate in the case of the G-mode. For the first time, the Raman properties of SWCNTs were also determined using the Cartesian coordinate tensor (CCT) transfer technique, thus providing reasonable frequencies of Raman active bands for long tubes consisting of 10 bamboo-units.

The first report on crystal and molecular structure of 3,6-diiodo-9-ethyl-9H-carbazole is presented. Experimental room-temperature X-ray and 13C chemical shift studies were supported by advanced theoretical calculations using density functional theory (DFT). The 13C nuclear magnetic shieldings were predicted at the non-relativistic and relativistic level of theory using the zeroth-order regular approximation (ZORA). Theoretical relativistic calculations of chemical shifts of carbons C3 and C6, directly bonded to iodine atoms, produced a reasonable agreement with experiment (initial deviation from experiment of 44.3 dropped to 4.25 ppm). The changes in ring aromatic character via simple harmonic oscillator model of aromaticity (HOMA) and the nucleus independent chemical shift indexes (NICS) calculations were estimated. A good linear correlation between experimental and theoretically predicted structural and NMR parameters was observed.

The applicability of popular and efficient B3LYP hybrid density functional and medium-size Pople-type basis set in combination with computationally expensive anharmonic model to obtain more accurate theoretical structure, vibrational frequencies and GIAO NMR parameters of cytosine was tested. We report on prediction of cytosine equilibrium (R e ) and rovibrationally averaged (R v ) structures and vibrational frequencies in the gas phase and DMSO solution using density functional theory combined with 6-311++G** basis set. The harmonic and anharmonic vibrational frequencies (using second-order vibrational perturbation theory, VPT2) were critically discussed. In comparison with initial harmonic data, a significantly better agreement between scaled and anharmonic frequencies and experiment was observed. Proton and carbon nuclear magnetic shieldings were calculated at R e and R v structures of cytosine in the gas phase and DMSO solution using BHandH and B3LYP density functionals combined with 6-311++G**, aug-cc-pVTZ-J and STO-3Gmag basis sets. The obtained NMR results were compared with available experimental data and discussed at length.

Density functional theory (DFT) studies on adsorption of several gaseous homo- and hetero-diatomic molecules (AB) including H2, O2, N2, NO and CO on external surface of H-capped pristine armchair (5, 5) single-walled carbon nanotube (SWCNT) were conducted. Structures of C70H10 and the corresponding C70H10–AB adducts were fully optimized at the B3LYP/6-311G* level of theory. Calculated HOMO/LUMO energy gaps (Eg), 13C NMR chemical shifts and IR/Raman parameters were analyzed and critically compared with available experimental data. Significant changes of carbon NMR atom chemical shifts (up to −100 ppm) and shielding anisotropies (up to −180 ppm) at sites of addition were observed. Functionalized SWCNTs produced IR and Raman spectra different from the pristine nanotube model. The selective changes in vibrational spectra will help in assigning the topology of functionalization at the nanotube wall.

A combined experimental and theoretical study has been performed on 9-benzyl-3,6-diiodo-9H-carbazole. Experimental X-ray (100.0 K) and room-temperature 13C NMR studies were supported by advanced density functional theory (DFT) calculations. The non relativistic structure optimization was performed and the 13C nuclear magnetic shieldings were predicted at the relativistic level of theory using the Zeroth Order Regular Approximation (ZORA). The changes in the benzene and pyrrole rings compared to the unsubstituted carbazole or the parent molecules were discussed in terms of aromaticity changes using the harmonic oscillator model of aromaticity (HOMA) and the nucleus independent chemical shift (NICS) indexes. Theoretical relativistic calculations of chemical shifts of carbons C3 and C6, directly bonded to iodine atoms, produced a reasonable agreement with experiment (initial deviation from experiment of 41.57 ppm dropped to 5.6 ppm). A good linear correlation between experimental and theoretically predicted structural and NMR parameters was observed.