On the convergence of zero-point vibrational corrections to nuclear shieldings and shielding anisotropies towards the complete basis set limit in water
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…
Extrapolation of water and formaldehyde harmonic and anharmonic frequencies to the B3LYP/CBS limit using polarization consistent basis sets
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
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.
On the impact of side methyl groups on the structure and vibrational properties of β-carotenoids. The case of butadiene and isoprene
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…
Effects of side-chain orientation on the backbone conformation of the dehydrophenylalanine residue. Theoretical and X-ray study.
Two E isomers of α,β-dehydro-phenylalanine, Ac-(E)-ΔPhe-NHMe (1a) and Ac-(E)-ΔPhe-NMe(2) (2a), have been synthesized and their low temperature structures determined by single-crystal X-ray diffraction. A systematic theoretical analysis was performed on these molecules and their Z isomers (1b and 2b). The ϕ,ψ potential energy surfaces were calculated at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels in the gas phase and at the B3LYP/6-31+G(d,p) level in the chloroform and water solutions with the SCRF-PCM method. All minima were fully optimized by the MP2 and DFT methods, and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds, and dipole-dipole interaction…
1H and 13C shielding measurements in comparison with DFT calculations performed for two 2-(acetyloamino)-N,N-dimethyl-3-phenylacrylamide isomers
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 …
Predicting the structure and vibrational frequencies of ethylene using harmonic and anharmonic approaches at the Kohn–Sham complete basis set limit
In this work, regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn–Sham complete basis set (KS CBS) limit are demonstrated for the first time. The performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with two Pople basis sets (6-311++G** and 6-311++G(3df,2pd)), the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, 6) was tested. The BLYP-calculated harmonic frequencies were found to be markedly closer than the B3LYP-calculated h…
DFT studies on the structural and vibrational properties of polyenes
Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increase in polyene size (chains containing 2 to 14 C = C units). The limiting values of the structural parameters for very long chains were estimated using simple three-parameter empirical formulae. 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 by Diffusion NMR
In this work, the nuclear magnetic resonance (NMR) and IR spectroscopic markers of the complexation between 5-fluorouracil (5-FU) and &beta
Modeling red coral (Corallium rubrum) and African snail (Helixia aspersa) shell pigments: Raman spectroscopyversusDFT studies
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…
Estimation of formamide harmonic and anharmonic modes in the Kohn-Sham limit using the polarization consistent basis sets.
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…
The effect of β-methylation on the conformation of α, β-dehydrophenylalanine: a DFT study
Dehydroamino acids are non-coded amino acids that offer unique conformational properties. Dehydrophenylalanine (ΔPhe) is most commonly used to modify bioactive peptides to constrain the topography of the phenyl ring in the side chain, which commonly serves as a pharmacophore. The Ramachandran maps (in the gas phase and in CHCl3 mimicking environments) of ΔPhe analogues with methyl groups at the β position of the side chain as well as at the C-terminal amide were calculated using the B3LYP/6-31 + G** method. Unexpectedly, β-methylation alone results in an increase of conformational freedom of the affected ΔPhe residue. However, further modification by introducing an additional methyl group a…
Toward engineering efficient peptidomimetics. Screening conformational landscape of two modified dehydroaminoacids
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…
Convergence of nuclear magnetic shieldings and one‐bond 1J(11 B 1H) indirect spin–spin coupling constants in small boron molecules
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…
On the aromaticity of uracil and its 5-halogeno derivatives as revealed by theoretically derived geometric and magnetic indexes
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…
Impact of the ΔPhe configuration on the Boc-Gly-ΔPhe-NHMe conformation: experiment and theory
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 characterization of chelidonic acid structure
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
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 …
Performance of polarization-consistent vs. correlation-consistent basis sets for CCSD(T) prediction of water dimer interaction energy
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…
β-turn tendency in N-methylated peptides with dehydrophenylalanine residue: DFT study.
The tendency to adopt β-turn conformation by model dipeptides with α,β-dehydrophenylalanine (ΔPhe) residue in the gas phase and in solution is investigated by theoretical methods. We pay special attention to a dependence of conformational properties on the side-chain configuration of dehydro residue and the influence of N-methylation on β-turn stability. An extensive computational study of the conformational preferences of Z and E isomers of dipeptides Ac-Gly-(E/Z)-ΔPhe-NHMe (1a / 1b) and Ac-Gly-(E/Z)-ΔPhe-NMe(2) (2a/2b) by B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) methods is reported. It is shown that, in agreement with experimental data, Ac-Gly-(Z)-ΔPhe-NHMe has a great tendency to adopt …
DFT study of N–H···O hydrogen bond between model dehydropeptides and water molecule
The strength of the hydrogen bond formed between a water molecule and two α,β-dehydroalanine derivatives including Ac-ΔAla-NMe2 (1) and Ac-ΔAla-NHMe (2) in comparison with standard amino acid Ac-Ala-NMe2 (3) is studied by density functional theory (with M06-2X and B3LYP functionals). Calculations were conducted for two different conformations of the peptides: extended (C5) and bent (β) with polyproline II backbone dihedral angles. The obtained results show that both dehydro and standard peptides in bent conformation form stronger hydrogen bonds with water than in the extended ones. Moreover, due to higher polarity of the N–H group of α,β-dehydroalanine residues, the H-bond in their complexe…
Spectroscopic characterization of non-covalent CuPc-GO system. Experiment and theory
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…
Interaction of 5‐fluorouracil with β‐cyclodextrin: A density functional theory study with dispersion correction
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 CO···HOCD 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…
Anharmonicity modeling in hydrogen bonded solvent dimers
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 …
Experimental and theoretical NMR and IR studies of the side-chain orientation effects on the backbone conformation of dehydrophenylalanine residue
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
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
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…
CCDC 1814248: Experimental Crystal Structure Determination
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CCDC 2144108: Experimental Crystal Structure Determination
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