Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes.

2014

A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported b…

DFT and experimental studies on structure and spectroscopic parameters of 3,6-diiodo-9-ethyl-9H-carbazole

2015

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 harm…

DFT calculations of structures, 13C NMR chemical shifts, and Raman RBM mode of simple models of small-diameter zigzag (4,0) carboxylated single-walle…

2012

Linearly conjugated benzene rings (acenes), belt-shaped molecules (cyclic acenes), and models of single-walled carbon nanotubes (SWCNTs) with one carboxylic group at the open end were fully optimized at the B3LYP/6-31G* level of theory. These models were selected to obtain some insight into the nuclear isotropic changes resulting from systematically increasing the basic building units of open-tip-monocarboxylated SWCNTs. In addition, the position of radial breathing mode (RBM), empirically correlated with the SWCNT diameter, was directly related with the radius of model cyclic acene rings. A regular convergence of selected structural, NMR, and Raman parameters with the molecular system size…

On the convergence of zero-point vibrational corrections to nuclear shieldings and shielding anisotropies towards the complete basis set limit in wat…

2016

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 consisten…

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

2019

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 (ro…

Extrapolation of water and formaldehyde harmonic and anharmonic frequencies to the B3LYP/CBS limit using polarization consistent basis sets

2010

The harmonic and anharmonic frequencies of fundamental vibrations in formaldehyde and water were successfully estimated using the B3LYP Kohn-Sham limit. The results obtained with polarization- and correlation-consistent basis sets were fitted with a two-parameter formula. Anharmonic corrections were obtained by a second order perturbation treatment (PT2). We compared the performance of the PT2 scheme on the two title molecules using SCF, MP2 and DFT (BLYP, B3LYP, PBE and B3PW91 functionals) methods combined with polarization consistent pc-n (n = 0, 1, 2, 3, 4) basis sets, Dunning’s basis sets (aug)-cc-pVXZ where X = D, T, Q, 5, 6 and Pople’s basis sets up to 6-311++G(3df,2pd). The influence…

Anharmonic vibrational frequency calculations for solvated molecules in the B3LYP Kohn–Sham basis set limit

2012

Abstract The solvent dependence of harmonic and anharmonic vibrational wavenumbers of water, formaldehyde and formamide was studied using the B3LYP method. The results obtained with the hierarchy of Jensen's polarization-consistent basis sets were fitted with two-parameter formula toward the B3LYP Kohn–Sham complete basis set (CBS) limit. Anharmonic corrections have been obtained by a second order perturbation treatment (VPT2) and vibrational configuration interaction (VCI) method. The solvent environment was treated according to the self-consistent reaction field polarizable continuum model (SCRF PCM) approach.

From correlation-consistent to polarization-consistent basis sets estimation of NMR spin–spin coupling constant in the B3LYP Kohn–Sham basis set limit

2008

Abstract Based on B3LYP spin–spin coupling constants (SSCC) of several molecules calculated with cc-pV x Z, cc-pCV x Z, cc-pCV x Z-sd and cc-pCV x Z-sd+ t basis sets, a reasonably fit, using the two-parameter formula, to the Kohn–Sham complete basis set limit (CBS) is shown. Improvement in the CBS values going from cc-pV x Z to the most elaborated cc-pCV x Z-sd+ t basis set family is observed: standard deviation for all data drops from 33.7 to 23.1, and from 6.0 to 4.8 Hz after excluding problematic 1 J (F,H) and 1 J (F,C). Calculation of water’s 1 J (OH) using B3LYP/cc-pCV x Z and B3LYP/pcJ- n significantly improved the FC term convergence.

Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

2015

In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of (1)H and (13)C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecu…

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

2014

The interaction of phenylalanine diamide (Ac-Phe-NHMe) with egg yolk lecithin (EYL) in chloroform was studied by 1H and 13C 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. Results of our study indicate that the interaction of peptides with lecithin occurs mainly in the polar ‘head’ of the lecithin. Additionally, the most probable lecithin site of H-bond interaction with Ac-Phe-NHMe is the negatively charged oxygen in …

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

2021

Abstract 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 repro…

Efficient Modeling of NMR Parameters in Carbon Nanosystems

2015

Rapid growth of nanoscience and nanotechnology requires new and more powerful modeling tools. Efficient theoretical modeling of large molecular systems at the ab initio and Density Functional Theory (DFT) levels of theory depends critically on the size and completeness of the basis set used. The recently designed variants of STO-3G basis set (STO-3Gel, STO-3Gmag), modified to correctly predict electronic and magnetic properties were tested on simple models of pristine and functionalized carbon nanotube (CNT) systems and fullerenes using the B3LYP and VSXC density functionals. Predicted geometries, vibrational properties, and HOMO/LUMO gaps of the model systems, calculated with typical 6-31G…

1H and 13C shielding measurements in comparison with DFT calculations performed for two 2-(acetyloamino)-N,N-dimethyl-3-phenylacrylamide isomers

2015

Abstract We present measurements of 1H and 13C shielding for (2E)- and (2Z)-2-(acetyloamino)-N,N-dimethyl-3-phenylacrylamide isomers in solutions. Practically the same values of the shielding were obtained using internal and external referencing. For the interpretation, we explore DFT calculations of shieldings performed at the rovibrationally averaged geometries. The comparison of the experimental and theoretical results is verified both for the shielding and chemical shift. It appears that some inaccuracies in the calculations of the chemical shift can be reduced due to the error compensation while subtracting the reference shielding. As shown the measurement of magnetic shielding can be …

DFT calculation of structures and NMR chemical shifts of simple models of small diameter zigzag single wall carbon nanotubes (SWCNTs)

2011

Linearly conjugated benzene rings (acenes), belt-shape molecules (cyclic acenes) and model single wall carbon nanotubes (SWCNTs) were fully optimized at the unrestricted level of density functional theory (UB3LYP/6-31G*). The models of SWCNTs were selected to get some insight into the potential changes of NMR chemical shift upon systematic increase of the molecular size. The theoretical NMR chemical shifts were calculated at the B3LYP/pcS-2 level of theory using benzene as reference. In addition, the change of radial breathing mode (RBM), empirically correlated with SWCNT diameter, was directly related with the radius of cyclic acenes. Both geometrical and NMR parameters were extrapolated t…

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

2016

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 h…

Molecular modeling and experimental studies on structure and NMR parameters of 9-benzyl-3,6-diiodo-9H-carbazole

2015

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…

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

2015

Electron spin resonance (ESR), 1H-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). This compound, being the most hydrophobic, penetrates easily through biological membranes. This was also observed in voltage an…

Solvent impact on the planarity and aromaticity of free and monohydrated zinc phthalocyanine: a theoretical study

2017

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 energ…

DFT study of zigzag (n, 0) single-walled carbon nanotubes: 13C NMR chemical shifts

2016

Abstract 13 C NMR chemical shifts of selected finite-size models of pristine zigzag single walled carbon nanotubes (SWCNTs) with a diameter of ∼0.4–0.8 nm and length up to 2.2 nm were studied theoretically. Results for finite SWCNTs models containing 1, 4 and 10 adjacent bamboo-type units were compared with data obtained for infinite tubes in order to estimate the reliability of small finite models in predicting magnetic properties of real-size nanotubes and to assess their tube-length dependence. SWCNTs were fully optimized using unrestricted density functional theory (DFT-UB3LYP/6-31G*). Cyclacenes, as the shortest models of open-ended zigzag SWCNTs, with systematically varying diameter w…

3 He NMR: from free gas to its encapsulation in fullerene

2013

The (3)He nuclear magnetic shieldings were calculated for single helium atom, its dimer, simple models of fullerene cages (He@Cn), and single wall carbon nanotubes. The performances of several levels of theory (HF, MP2, DFT-VSXC, CCSD, CCSD(T), and CCSDT) were tested. Two sets of polarization-consistent basis sets were used (pcS-n and aug-pcS-n), and an estimate of (3)He nuclear magnetic shieldings in the complete basis set limit using a two-parameter fit was established. Theoretical (3)He results reproduced accurately previously reported theoretical values for helium gas, dimer, and helium probe inside several fullerene cages. Excellent agreement with experimental values was achieved. (3)H…

DFT studies on the structural and vibrational properties of polyenes

2015

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. BLYP/6-311++G** calculated ν(C = C) and ν(C–C) frequencies for all-trans and all-cis polyenes containing up to 14 carbon–carbon double bonds were used to estimate these values for very lo…

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

2020

In this work, the nuclear magnetic resonance (NMR) and IR spectroscopic markers of the complexation between 5-fluorouracil (5-FU) and &beta

Theoretical prediction of structural, vibrational and NMR parameters of plastic optical fiber (POF) material precursors. Cis and trans perhydro- and …

2014

Abstract Density functional theory (DFT) prediction of cis and trans perhydro- and perfluoro-2-methylene-4,5-dimethyl-1,3-dioxolanes structure, supported by vibrational analysis and calculation of multinuclear isotropic nuclear magnetic resonance (NMR) shieldings and indirect spin–spin couplings (SSCCs) was performed. The performance of the used methodology was verified on 1,3-dioxolane selected as model compound. The structures of hydrogenated and fluorinated monomers of POF materials were calculated using B3LYP and BLYP density functionals combined with 6-311 ++ G(3df,2pd) basis set. The BLYP/6-311++G(3df,2pd) level of theory was suggested for vibrational analysis. Gauge independent atomi…

Density functional theory (DFT) prediction of structural and spectroscopic parameters of cytosine using harmonic and anharmonic approximations

2015

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 harmoni…

Convergence of Nuclear Magnetic Shieldings in the Kohn-Sham Limit for Several Small Molecules.

2015

Convergence patterns and limiting values of isotropic nuclear magnetic shieldings were studied for several small molecules (N2, CO, CO2, NH3, CH4, C2H2, C2H4, C2H6, and C6H6) in the Kohn-Sham limit. Individual results of calculations using dedicated families of Jensen's basis sets (pcS-n and pcJ-n) were fitted toward the complete basis set limit (CBS) using a simple two-parameter formula. Several density functionals were used; calculated vibrational corrections (ZPV) applied; and, for comparison purposes, similar calculations performed using RHF, MP2, SOPPA, SOPPA(CCSD), and CCSD(T) methods and additionally, the aug-cc-pVTZ-J basis set. Finally, the CBS estimated results were critically com…

Modeling red coral (Corallium rubrum) and African snail (Helixia aspersa) shell pigments: Raman spectroscopyversusDFT studies

2016

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 pr…

DFT studies on armchair (5, 5) SWCNT functionalization. Modification of selected structural and spectroscopic parameters upon two-atom molecule attac…

2015

Abstract 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. Fu…

Estimation of formamide harmonic and anharmonic modes in the Kohn-Sham limit using the polarization consistent basis sets.

2010

Formamide harmonic and anharmonic frequencies of fundamental vibrations in the gas phase and in several solvents were successfully estimated in the B3LYP Kohn-Sham complete basis set limit (KS CBS). CBS results were obtained by extrapolating a power function (two-parameter formula) to the results calculated with polarization-consistent basis sets. Anharmonic corrections using the second order perturbation treatment (PT2) and hybrid B3LYP functional combined with polarization consistent pc-n (n = 0, 1, 2, 3, 4) and several Pople’s basis sets were analyzed for all fundamental formamide vibrational modes in the gas phase and solution. Solvent effects were modeled within a PCM method. The anhar…

Sensitivity of noble gas NMR parameters to the heterocyclic ring proximity. Density functional theory studies of Ne–furan and Ar–furan complexes

2014

Theoretical modeling of noble gas interaction with furan as a simple heterocyclic ring was performed. The structures of neon–furan and argon–furan complexes were calculated at the MP2, M06-2X, CAM-B3LYP, APFD, and VSXC levels of theory using 6-311++G** basis set. The predicted 21Ne and 39Ar NMR chemical shifts for the Ne–furan and Ar–furan complexes calculated with pcS-3 and aug-pcS-3 basis sets were sensitive to the presence of the aromatic furan ring. Our results indicate a higher sensitivity of the neon and argon NMR probes than the previously reported 3He NMR spectroscopic parameters in studies of small heterocyclic rings containing the oxygen atom.

Local aromaticity in polyacenes manifested by individual proton and carbon shieldings: DFT mapping of aromaticity

2019

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 sh…

Toward engineering efficient peptidomimetics. Screening conformational landscape of two modified dehydroaminoacids

2013

Effective peptidomimetics should posses structural rigidity and appropriate interaction pattern leading to potential spatial and electronic matching to the target receptor site. Rational design of such small bioactive molecules could push chemical synthesis and molecular modeling toward faster progress in medicinal chemistry. Conformational properties of N-t-butoxycarbonyl-glycine-(E/Z)-dehydrophenylalanine N′,N′-dimethylamides (Boc-Gly-(E/Z)-ΔPhe-NMe2) in chloroform were studied by NMR and IR spectroscopy. The experimental findings were supported by extensive calculations at DFT(B3LYP, M06-2X) and MP2 levels of theory and the β-turn tendency for both isomers of the studied dipeptide were d…

Density functional theory studies of OH-modified open-ended single-wall zigzag carbon nanotubes (SWCNTs)

2010

Abstract Functionalized carbon nanotubes (CNTs) are often formed as result of oxidation and cleaning of raw product grown on metal catalyst. Structure and energy of ideal and OH-modified single-wall nanotubes (SWCNTs) of different length (2.8, 7.0 and 13.5 A) were obtained at the DFT-B3LYP level. From one to nine OH groups were added at the end of the nanotube and a nonadditive dependence of attachment energy on the number of substituents was observed. The energetics of SWCNT end substitution with OH groups was supported by high level MP2 and CCSD(T) determination of reaction energy: R – H + 1 / 2 O 2 → R – OH + Δ E for methane, benzene and anthracene. In addition, a vibrational analysis of…

Convergence of nuclear magnetic shieldings and one‐bond 1J(11 B 1H) indirect spin–spin coupling constants in small boron molecules

2018

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…

H2 O, H2 , HF, F2 and F2 O nuclear magnetic shielding constants and indirect nuclear spin-spin coupling constants (SSCCs) in the BHandH/pcJ-n and BHa…

2009

Good performance of segmented contracted basis sets XZP, where X = D, T, Q and 5, for obtaining H(2)O, H(2), HF, F(2) and F(2)O nuclear isotropic shielding constants in the BHandH Kohn-Sham basis set limit was shown. The results of two- and three-parameter complete basis set limit extrapolation schemes were compared with experimental results, earlier literature data and benchmark ab initio results. Similar convergence patterns of shieldings obtained from calculations using general purpose XZP basis sets and from polarization-consistent basis sets pcS-n and pcJ-n, where n = 0, 1, 2, 3 and 4, designed to accurately predict magnetic properties were observed. On the contrary, the SSCCs were mor…

Computational modeling of molecularly imprinted polymers as a green approach to the development of novel analytical sorbents

2018

Abstract 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 …

On the aromaticity of uracil and its 5-halogeno derivatives as revealed by theoretically derived geometric and magnetic indexes

2020

AbstractThe 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…

Phosphorus mononitride: A difficult case for theory

2019

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 e…

On novel magnetic probe for fullerene characterization: Theoretical studies on NMR parameters of free and confined in fullerenes HD and H2 molecules

2015

Chemical characterization and separation of individual fullerenes from a raw reaction mixture need new and efficient tools, including rapid spectroscopic techniques. Recent "molecular surgery" synthesis of endohedral complexes of fullerenes with selected atoms and small molecules has opened a new path for experimental and theoretical studies on structural and spectroscopic properties of these molecular systems. Among them are fullerenes with molecular hydrogen confined within a nanoscale cavity. In this work we report on quantum-chemical prediction of nuclear magnetic shielding (and chemical shift) and indirect spin-spin coupling constant in free HD and H2 molecules, as well as models of co…

Dynamic Polarizability and Higher-Order Electric Properties of Fluorene, Carbazole, and Dibenzofuran

2019

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 P…

One-bond 1 J (15 N,H) coupling constants at sp2 -hybridized nitrogen of Schiff bases, enaminones and similar compounds: A theoretical study

2020

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 b…

Calculation of Raman parameters of real-size zigzag (n, 0) single-walled carbon nanotubes using finite-size models

2016

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 w…

Impact of the ΔPhe configuration on the Boc-Gly-ΔPhe-NHMe conformation: experiment and theory

2019

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 sign…

Experimental and theoretical studies on corals. I. Toward understanding the origin of color in precious red corals from Raman and IR spectroscopies a…

2009

An attempt to explain the origin of the vivid red color in precious pink and red corals was undertaken. Raman and IR spectroscopies were applied to characterize white, pink and red corals. The position of the Raman signal near 1500 cm −1 of some corals and pearls was associated by several authors with the presence of the mixture of all-trans-polyenic pigments, containing 6 – 16 conjugated C C bonds or β-carotenoids. This hypothesis was examined theoretically by performing extensive B3LYP-DFT calculations of vibrational spectra of the model polyenic compounds. The B3LYP/6-311++G ∗∗ predicted positions of the dominating Raman mode depend on the number of C Cu nits (Cn parameter) and can be ac…

Experimental and theoretical characterization of chelidonic acid structure

2022

Abstract 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-dic…

Liposomes as nonspecific nanocarriers for 5-Fluorouracil in the presence of cyclodextrins

2021

Abstract 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 …

3 He NMR studies on helium-pyrrole, helium-indole, and helium-carbazole systems: a new tool for following chemistry of heterocyclic compounds

2014

The 3He nuclear magnetic shieldings were calculated for free helium atom and He–pyrrole, He–indole, and He–carbazole complexes. Several levels of theory, including Hartree–Fock (HF), Second-order Moller-Plesset Perturbation Theory (MP2), and Density Functional Theory (DFT) (VSXC, M062X, APFD, BHandHLYP, and mPW1PW91), combined with polarization-consistent pcS-2 and aug-pcS-2 basis sets were employed. Gauge-including atomic orbital (GIAO) calculated 3He nuclear magnetic shieldings reproduced accurately previously reported theoretical values for helium gas. 3He nuclear magnetic shieldings and energy changes as result of single helium atom approaching to the five-membered ring of pyrrole, indo…

Complete basis set B3LYP NMR calculations of CDCl3solvent's water fine spectral details

2008

The assignment of singlet at 1.55 ppm and the 1:1:1 triplet at 1.519 ppm to H2O and HOD in the 400 MHz 1H NMR spectrum of CDCl3 solvent were supported by complete basis set (CBS) GIAO-B3LYP calculated chemical shift and the CBS B3LYP estimated 2J(D,H) spin–spin coupling constant (SSCC). The CBS fitting of B3LYP/cc-pCVxZ and B3LYP/pcJ-n predicted SSCC values, the accurate value of 2J(D,H) = − 1.082 ± 0.030 Hz of HOD in chloroform-d1 and the H/D isotopic shift of 0.0307(1) ppm were reported for the first time. The agreement between CBS B3LYP predicted chemical shift, spin–spin values and experiment was good. Copyright © 2008 John Wiley & Sons, Ltd.

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

2018

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 o…

From CCSD(T)/aug-cc-pVTZ-J to CCSD(T) complete basis set limit isotropic nuclear magnetic shieldings via affordable DFT/CBS calculations

2011

It is shown that a linear correlation exists between nuclear shielding constants for nine small inorganic and organic molecules (N2, CO, CO2, NH3, CH4, C2H2, C2H4, C2H6 and C6H6) calculated with 47 methods (42 DFT methods, RHF, MP2, SOPPA, SOPPA(CCSD), CCSD(T)) and the aug-cc-pVTZ-J basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets. This implies that the remaining basis set error of the aug-cc-pVTZ-J basis set is very similar in DFT and CCSD(T) calculations. As the aug-cc-pVTZ-J basis set is significantly smaller, CCSD(T)/aug-cc-pVTZ-J calculations allow in combination with affordable DFT/pcS-n com…

Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble …

2015

Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton, and xenon dimers and free atoms. Relativistic corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles …

Modeling21Ne NMR parameters for carbon nanosystems

2013

The potential of nuclear magnetic resonance (NMR) technique in probing the structure of porous systems including carbon nanostructures filled with inert gases is analysed theoretically using accurate calculations of neon ((21) Ne) nuclear magnetic shieldings. The CBS estimates of (21) Ne NMR parameters were performed for single atom, its dimer and neon interacting with acetylene, ethylene and 1,3-cyclopentadiene. Several levels of theory including restricted Hartree-Fock (RHF), Moller-Plesset perturbation theory to the second order (MP2), density functional theory (DFT) with van Voorhis and Scuseria's t-dependent gradient-corrected correlation functional (VSXC), coupled cluster with single …

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

2019

Abstract 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 underestimat…

DFT studies of OH-functionalized open-ended zigzag, armchair, and chiral single wall carbon nanotubes

2011

The functionalization of single-wall carbon nanotubes (SWCNTs) by attaching various molecules or molecular groups to the exterior walls or tips has attracted much attention, because it offers a possible way to modify their electronic, chemical, optical and mechanical properties. In this contribution the results of DFT studies of pristine and OH-modified open-ended zigzag (9,0), armchair (5,5) and chiral (8,2) nanotubes are reported. The calculations have been performed for partially and fully functionalized at one end model SWCNTs with dangling bonds saturated with hydrogen atoms and a nonadditive dependence of attachment energy on the number of substituents was observed.

Halogen effect on structure and 13 C NMR chemical shift of 3,6-disubstituted-N -alkyl carbazoles

2013

Structures of selected 3,6-dihalogeno-N-alkyl carbazole derivatives were calculated at the B3LYP/6-311++G(3df,2pd) level of theory, and their 13C nuclear magnetic resonance (NMR) isotropic shieldings were predicted using density functional theory (DFT). The model compounds contained 9H, N-methyl and N-ethyl derivatives. The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin–orbit zeroth-order regular approximation (ZORA) method. Significant heavy atom shielding effects for the carbon atom directly bonded with Br and I were observed (~−10 and ~−30 ppm while the other carbon shifts were practically unaffected). The decreasing electronegativity of the haloge…

DFT studies of COOH tip-functionalized zigzag and armchair single wall carbon nanotubes

2011

Structure and energy calculations of pristine and COOH-modified model single wall carbon nanotubes (SWCNTs) of different length were performed at B3LYP/6-31G* level of theory. From 1 to 9 COOH groups were added at the end of the nanotube. The differences in structure and energetics of partially and fully functionalized SWCNTs at one end of the nanotube are observed. Up to nine COOH groups could be added at one end of (9,0) zigzag SWCNT in case of full functionalization. However, for (5,5) armchair SWCNT, the full functionalization was impossible due to steric crowding and rim deformation. The dependence of substituent attachment energy on the number of substituents at the carbon nanotube ri…

Noble Gases as Magnetic Probes in Fullerene Chemistry

2016

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

2020

ARTYKUŁ Z BADAŃ SPECJALNYCH

Spectroscopic characterization of non-covalent CuPc-GO system. Experiment and theory

2019

Abstract 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…

Prediction of water's isotropic nuclear shieldings and indirect nuclear spin–spin coupling constants (SSCCs) using correlation‐consistent and polariz…

2009

Density functional theory (DFT) was used to estimate water's isotropic nuclear shieldings and indirect nuclear spin-spin coupling constants (SSCCs) in the Kohn-Sham (KS) complete basis set (CBS) limit. Correlation-consistent cc-pVxZ and cc-pCVxZ (x = D, T, Q, 5, and 6), and their modified versions (ccJ-pVxZ, unc-ccJ-pVxZ, and aug-cc-pVTZ-J) and polarization-consistent pc-n and pcJ-n (n = 0, 1, 2, 3, and 4) basis sets were used, and the results fitted with a simple mathematical formula. The performance of over 20 studied density functionals was assessed from comparison with the experiment. The agreement between the CBS DFT-predicted isotropic shieldings, spin-spin values, and the experimenta…

Interaction of 5‐fluorouracil with β‐cyclodextrin: A density functional theory study with dispersion correction

2020

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 βC…

Estimation of isotropic nuclear magnetic shieldings in the CCSD(T) and MP2 complete basis set limit using affordable correlation calculations

2013

A linear correlation between isotropic nuclear magnetic shielding constants for seven model molecules (CH2O, H2O, HF, F2, HCN, SiH4 and H2S) calculated with 37 methods (34 density functionals, RHF, MP2 and CCSD(T)), with affordable pcS-2 basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets is reported. This dependence was also supported by inspection of profiles of deviation between CBS estimated nuclear shieldings and shieldings obtained with the significantly smaller basis sets pcS-2 and aug-cc-pVTZ-J for the selected set of 37 calculation methods. It was possible to formulate a practical approach o…

DFT calculations of structures, 13C NMR chemical shifts and Raman RBM mode of simple models of ultra small diameter (4,0) zigzag hydroxylated single …

2012

Abstract Selected acenes, cyclic acenes and model zigzag (4,0) single wall carbon nanotubes (SWCNTs) with one hydroxylic group at the open end were fully optimized at the B3LYP/6-31G* level of theory. The impact of molecule size on the B3LYP/pcS-2 calculated 13 C NMR chemical shifts was studied to characterize pristine and tip-monofunctionalized ultra narrow SWCNTs. The harmonic frequency of Raman radial breathing mode (RBM) was determined for monohydroxylated cyclic acenes and correlated with their diameter. A regular convergence of selected CC bond lengths, RBM frequency and carbon chemical shifts upon increasing the size of the systems was observed and fitted toward very large systems wi…

From planar to nonplanar cyclotriphosphazenes

2008

Abstract A possible existence of planar (PNX 2 ) 3 cyclotriphosphazene, where X = H, F, Cl and Br, or nonplanar (PXNX) 3 was studied at the B3LYP/6-311++G ∗∗ and MP2/6-311++G ∗∗ level of calculations. A linear correlation of total electronic energy difference (Δ E  =  E nonplanar  −  E planar ) on electronegativity of the X substituent was observed. The more stable nonplanar form was predicted (Δ E  = −43.49 kcal/mol) only in case of X = H. The remaining planar halogenocyclotriphosphazenes are more stable, in agreement with a few available experimental data.

Substituent effect of nitro group on aromaticity of carbazole rings

2014

The molecular geometries of carbazole and its 17 nitro derivatives were optimized at the B3LYP/6-311++G(2d,2p) level of theory. The harmonic oscillator model of aromaticity and nucleus-independent chemical shift descriptors of π-electron delocalization were calculated to estimate the aromaticity of the carbazole five- and six-membered rings. The biggest changes in the value of both descriptors were observed for the pyrrole ring. The nitro group attached to 3 and/or 6 positions of the carbazole ring system exerts only a slight influence on the benzene ring aromaticity.

Basis Set Convergence of Indirect Spin-Spin Coupling Constants in the Kohn-Sham Limit for Several Small Molecules

2012

The performance of more than 40 density functionals in predicting indirect spin-spin coupling constants (SSCCs) in the Kohn-Sham basis set limit was tested. For comparison, similar calculations were performed using the RHF, SOPPA, SOPPA(CC2), and SOPPA(CCSD) methods, and the results were estimated toward the complete basis set (CBS) limit. The SSCCs of nine small molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6), and C(6)H(6)) were calculated using the dedicated Jensen pcJ-n polarization-consistent basis sets and used for the CBS limit estimations within the Kohn-Sham limit. These CBS results were compared with calculations using the aug-cc-pVTZ-J basis set. Among the 4…

Complete basis set prediction of methanol isotropic nuclear magnetic shieldings and indirect nuclear spin-spin coupling constants (SSCC) using polari…

2009

Efficient B3LYP and BHandH density functionals were used to estimate methanol's nuclear magnetic isotropic shieldings and spin–spin coupling constants in the basis set limit. Polarization-consistent pcS-n and pcJ-n (n = 0, 1, 2, 3 and 4), and segmented contracted XZP, where X = D, T, Q and 5, basis sets were used and the results fitted with simple mathematical formulas. The performance of the methods was assessed from comparison with experiment and higher level calculations. 1J(CH) and 3J(HH) values were determined from very diluted solutions in deuterochloroform and compared with theoretical predictions. The agreement between complete basis set (CBS) density functional theory (DFT) predict…

Anharmonicity modeling in hydrogen bonded solvent dimers

2021

Abstract 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 …

OH-functionalized open-ended armchair single-wall carbon nanotubes (SWCNT) studied by density functional theory

2011

The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 A for C40H20, C80H20, and C140H20) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21G level, and in some cases at the B3LYP/6-31G* level, and the energy associated with the attachment of the OH substituent was determined. The OH-group attachment energy was compared with the OH functionalization of phenanthrene and picene models and with previous results for zigzag (9.0) SWCNT systems. In comparison to zigzag SWCNTs, the armchair form is more (by about 5 to 10 kcal mol−1) reactive toward hydroxylation. Figure The structures of ide…

Experimental and theoretical NMR and IR studies of the side-chain orientation effects on the backbone conformation of dehydrophenylalanine residue

2011

Conformation of N-acetyl-(E)-dehydrophenylalanine N', N'-dimethylamide (Ac-(E)-ΔPhe-NMe(2)) in solution, a member of (E)-α, β-dehydroamino acids, was studied by NMR and infrared spectroscopy and the results were compared with those obtained for (Z) isomer. To support the spectroscopic interpretation, the Φ, Ψ potential energy surfaces were calculated at the MP2/6-31 + G(d,p) level of theory in chloroform solution modeled by the self-consistent reaction field-polarizable continuum model method. All minima were fully optimized by the MP2 method and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds and dipole interactions between carbonyl groups. The obtained…

Local aromaticity mapping in the vicinity of planar and nonplanar molecules

2019

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 a…

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

2020

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 ur…

From small to medium and beyond: a pragmatic approach in predicting properties of Ne containing structures

2013

In this study, we outlined a pragmatic approach for structural studies leading to better understanding of polycarbon structures using 21Ne as a nuclear magnetic resonance (NMR) probe. 21Ne NMR parameters of a single neon atom and its dimer were predicted at the CCSD(T) level in combination with large basis sets. At a lower level of theory, an interaction of neon atom with 1,3-cyclopentadiene ring and with five- and six-membered rings in carbazole was studied using the restricted Hartree–Fock (RHF) and density functional theory (DFT) combined with smaller basis sets. The RHF and DFT modelling of neon interaction with nanosized objects were performed on cyclacenes and selected fullerenes.

Molecular modeling and experimental studies on structure and NMR parameters of 9-benzyl-3,6-diiodo-9<i>H</i>-carbazole

2016

CCDC 990604: Experimental Crystal Structure Determination

2015

Related Article: Klaudia Radula-Janik, Teobald Kupka, Krzysztof Ejsmont, Zdzisław Daszkiewicz, Stephan P. A. Sauer|2015|Struct.Chem.|26|997|doi:10.1007/s11224-014-0554-8

CCDC 1051894: Experimental Crystal Structure Determination

2016

Related Article: Klaudia Radula-Janik, Teobald Kupka , Krzysztof Ejsmont, Zdzisław Daszkiewicz, Stephan P. A. Sauer|2016|Struct.Chem.|27|199|doi:10.1007/s11224-015-0711-8

CCDC 1814248: Experimental Crystal Structure Determination

2019

Related Article: Aneta Buczek, Dawid Siodłak, Maciej Bujak, Maciej Makowski, Teobald Kupka, Małgorzata A. Broda|2019|Struct.Chem.|30|1685|doi:10.1007/s11224-019-01387-w

CCDC 2144108: Experimental Crystal Structure Determination

2022

Related Article: Natalina Makieieva, Teobald Kupka, Grzegorz Spaleniak, Oimahmad Rahmonov, Agata Marek, Alfred Błażytko, Leszek Stobiński, Nataliya Stadnytska, Danuta Pentak, Aneta Buczek, Małgorzata A. Broda, Piotr Kuś, Joachim Kusz, Maria Książek|2022|Struct.Chem.|33|2133|doi:10.1007/s11224-022-02026-7