Adducts of free-base meso-tetraarylporphyrins with trihaloacetic acids: Structure and photostability

2020

Abstract Four diverse meso-tetraarylporphyrins in the form of diprotonated adducts with trifluoro-, trichloro-, tribromoacetic acids and acetic acid were investigated in benzene solution. Despite similar structural distortion of the chromophore system due to protonation, the respective adducts demonstrated different photostability when exposed to UV irradiation. The trifluoro- and trichloroacetic adducts, and the acetic acid one, showed some common features both molecular and in the mechanism of photodegradation. However, the tribromo-derivative decayed according to a different kinetic scheme, revealing a considerable impact of the bromine atoms upon the pyrrole units of the porphyrin macro…

Azoxybenzene rearrangement catalyzed by solid acids

2008

Abstract For the first time, the potential of acidic cation-exchange resin (sulfonated polystyrene) to catalyze the Wallach rearrangement of azoxybenzene into 4-hydroxyazobenzene has been proved. This finding reveals an alternative reaction path possible in a heterogeneous process using solid acids and may help to clear some doubts concerning the rearrangement mechanism postulated so far. The resin-induced reaction was found to proceed exclusively in a non-polar medium. Reasonable yield was obtained particularly in isooctane due to favorable distribution of azoxybenzene throughout the resin's matrix. On the contrary, the HY type zeolite did not activate the rearrangement, most probably beca…

Conformational properties of oxazoline-amino acids

2016

Abstract Oxazoline-amino acids (Xaa-Ozn) occur in natural peptides of potentially important bioactivity. The conformations of the model compounds: Ac-(S)-Ala-Ozn(4R-Me), Ac-(S)-Ala-Ozn(4S–Me), and (gauche+, gauche−, anti) Ac-(S)-Val-Ozn(4R-Me) were studied at meta-hybrid M06-2X/6–311++G(d,p) method including solvent effect. Boc- l -Ala- l -Ozn-4-COOMe and Boc- l -Val- l -Ozn-4-COOMe were synthesized and studied by FT-IR and NMR-NOE methods. The conformations in crystal state were gathered from the Cambridge Structural Data Base. The main conformational feature of the oxazoline amino acids is the conformation β2 (ϕ,ψ ∼ −161°, −6°), which predominates in weakly polar environment and still is …

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…

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

2017

The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results,…

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.

Conformational investigation of alpha,beta-dehydropeptides. VIII. N-acetyl-alpha,beta-dehydroamino acid N'-methylamides: conformation and electron de…

2009

The Fourier transform infrared spectra are analyzed in the regions of Vs(N-H), amide I, amide II and Vs(C alpha = C beta) bands for a series of Ac-delta Xaa-NHMe, where delta Xaa = delta Ala, (Z)-delta Abu, (Z)-delta Leu, (Z)-delta Phe and delta Val, to determine the predominant solution conformation of these alpha,beta-dehydropeptide-related molecules and the electron distribution perturbation in their amide bonds. The measurements were performed in dichloromethane (DCM). To confirm and rationalize the assignments, the spectra of the respective series of saturated Ac-Xaa-NHMe, recorded in DCM, and the spectra of these two series of unsaturated and saturated compounds, recorded in acetonitr…

The conformational properties of dehydrobutyrine and dehydrovaline: theoretical and solid-state conformational studies

2010

Dehydrobutyrine is the most naturally occurring dehydroamino acid. It is also the simplest dehydroamino acid having the geometrical isomers E/Z. To investigate its conformational properties, a theoretical analysis was performed on N-acetyl-α,β-dehydrobutyrine N′-methylamides, Ac-(E)-ΔAbu-NHMe and Ac-(Z)-ΔAbu-NHMe, as well as the dehydrovaline derivative Ac-ΔVal-NHMe. The ϕ, ψ potential energy surfaces and the localised conformers were calculated at the B3LYP/6-311 + + G(d,p) level of theory both in vacuo and with inclusion of the solvent (chloroform, water) effect (SCRF method). The X-ray crystal structures of Ac-(Z)-ΔAbu-NHMe and Ac-ΔVal-NHMe were determined at 85 and 100 K, respectively. …

Infrared bandshapes of intramolecularly H-bonded systems, 2,4,6-tribromophenol

1983

Abstract A detailed quantitative analysis of the IR bandshape of the ν S (OH) vibration of 2,4,6-tribromophenol in a series of solvents of varying polarity is presented. A distinct dependence of band parameters on solvent polarity has been found. Various contributions to the bandshape are discussed.

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 …

Conformational investigation of α,β-dehydropeptides. IX. N-Acetyl-(E)-α,β-dehydrobutyrine N′-methylamide: stereoelectronic properties from infrared a…

2009

The Fourier transform infrared spectra of Ac-(E)-deltaAbu-NHMe were analyzed to determine the predominant solution conformation(s) of this (E)-alpha,beta-dehydropeptide-related compound and the electron density perturbation in its amide groups. The measurements were performed in dichloromethane and acetonitrile in the region of mode vs (N-H), amide I, amide II and vs (C(alpha)=Cbeta). The equilibrium geometrical parameters, calculated by a method based on the density functional theory with the B3LYP functional and the 6-31G* basis set, were used to support spectroscopic interpretation and gain some deeper insight into the molecule. The experimental and theoretical data were compared with th…

Effect of tin and lead chlorotriphenyl analogues on selected living cells.

2010

Three kinds of living cells, human embryonic kidney cells, Saccharomyces cerevisiae, and Escherichia coli, were tested for their sensitivity to chlorotriphenyltin and chlorotriphenyllead. The tin compound proved definitely more toxic than the lead derivative, particularly in the case of the human embryonic kidney cells devoid of any protective cell wall. Electron paramagnetic resonance (EPR) comparative studies carried out by using a natural model liposome system (egg yolk lecithin) confirmed considerable changes within the lipid bilayer upon doping by the aforementioned additives, which may be crucial to the mechanism of the observed cell cleavage. The individual dopants revealed diverse i…

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

2017

The influence of albumin and amino acids (l-serine, glycine, l-histidine, l-tryptophan, l-cysteine) on the properties of aluminum octacarboxyphthalocyanine hydroxide (Al(OH)PcOC) was investigated in a phosphate buffer (pH 8.0). Particular attention was paid to the spectroscopic properties and photostability of Al(OH)PcOC. The effect of albumin or amino acids on the photodegradation of Al(OH)PcOC was examined in water using red light: 685 nm and daylight irradiation. Analysis of kinetic curves indicated that interaction with those molecules increases the photostability of Al(OH)PcOC. The molecular structure of Al(OH)PcOC complexes (in vacuum and in water) with axially or equatorially coordin…

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…

Thecis-transisomerization ofN-methyl-α,β-dehydroamino acids

2012

Dehydroamino acids with the methylated N-terminal peptide group occur in natural small cyclic peptides. The structural analysis was used to investigate the cis-trans isomerization of the N-terminal tertiary amide group of diamides: Ac-(Z)-Δ(Me)Abu-NHMe (1), Ac-(Z)-Δ(Me)Phe-NHMe (2), Ac-(E)-Δ(Me)Phe-NHMe (3), Ac-Δ(Me)Ala-NHMe (4), and Ac-(Me)Ala-NHMe (5). The compounds were analyzed in the solid state by an X-ray crystallography (1-3), and in the solution by FTIR (MeCN and CHCl(3) ) and NMR (DMSO-d6 and CDCl(3) ) methods (1-5). In the solid state, the studied compounds adopt the cis configuration of N-terminal amide. In solution, this configuration also prevails for the dehydroamino acids 1-…

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

2017

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

Effects of side-chain orientation on the backbone conformation of the dehydrophenylalanine residue. Theoretical and X-ray study.

2011

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

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 …

Conformational investigation of α,β-dehydropeptides. XVI. β-turn tendency in Ac-Pro-ΔXaa-NHMe: crystallographic and theoretical studies

2006

The crystal structures of two diastereomeric alpha,beta-dehydrobutyrine peptides Ac-Pro-(Z)-DeltaAbu-NHMe (I) and Ac-Pro-(E)-DeltaAbu-NHMe (II) have been determined. Both dehydropeptides adopt betaI-turn conformation characterized by the pairs of (phi(i+1), psi(i+1)) and (phi(i+2), psi(i+2)) angles as -66, -19, -97, 11 degrees for I and -59, -27, -119, 29 degrees for II. In each peptide, the betaI turn is stabilized by (i + 3) --> i intramolecular hydrogen bonds with N...O distance of 3.12 A for I and 2.93 A for II. These structures have been compared to the crystal structures of homologous peptides Ac-Pro-DeltaVal-NHMe and Ac-Pro-DeltaAla-NHMe. Theoretical analyses by DFT/B3LYP/6-31 + G** …

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

2021

Abstract This paper presents the results of the research on the influence of catalytic activity of iron(II) octacarboxyphthalocyanines (FePcOC) on the transformation of diclofenac (DCF) which is the most popular anti-inflammatory analgesic. Diclofenac poses a serious threat to the natural environment. The paper demonstrates that diclofenac, in the presence a monomeric form of iron octacarboxyphthalocyanine and hydroxyl radicals (HO•) (from H2O2), undergoes a transformation into diclofenac-2,5-iminoquinone (DCF-2,5-IQ), causing distinct changes in the UV–Vis absorption spectrum. In the presence of iron octacarboxyphthalocyanine and H2O2, the previously colourless diclofenac solution becomes …

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…

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…

Structure and properties of N-methyl-N-(4-pyridyl)-nitramine and 1,4-dihydro-1-methyl-4-nitriminopyridine

2002

Abstract The molecular structure and spectral properties of N -methyl- N -(4-pyridyl)-nitramine ( 1 ) and 1,4-dihydro-1-methyl-4-nitriminopyridine ( 3 ) were investigated by the X-ray diffraction, FTIR, nuclear magnetic resonance (NMR) methods and DFT theoretical calculations. N -methyl- N -(4-pyridyl)-nitramine ( 1 ) crystallises in the orthorhombic Pbca space group. It is composed of two planar fragments; nitramino (N 2 O 2 ) group and the pirydyl ring. These two groups are twisted at about 70° with respect to each other, along the Ar–N bond. On the contrary, in compound 3 , they are coplanar to each other. Twist of the nitramino group in 1 with respect to the pirydyl ring leads to a sign…

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…

Interactions of zinc octacarboxyphthalocyanine with selected amino acids and with albumin

2015

Effect of selected amino acids (glycine, l-histidine, l-cysteine, l-serine, l-tryptophan) and albumin on the spectroscopic properties and photostability of zinc octacarboxyphthalocyanine (ZnPcOC) was explored in the phosphate buffer at a pH of 7.0. The photodegradation of ZnPcOC alone and in the presence of amino acids or albumin has been investigated in aqueous phase using UV-366 nm and daylight irradiation. Kinetic analysis showed that the interaction with amino acids or albumin enhances the photostability of ZnPcOC. To answer the question of how zinc phthalocyanine interacts with amino acids extensive DFT calculations were performed. Analysis of the optimized geometry features of ZnPcOC:…

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…

Conformational properties of N-acetyl-L-alanine N',N'-dimethylamide

2004

Ab initio/DFT analysis of the conformational properties of free Ac-Ala-NMe(2) (N-acetyl-L-alanine-N',N'-dimethylamide) in terms of the N-H.O, N-H.N, C-H.O hydrogen bonds and C(delta+) = O(delta-) dipole attractions was performed. The Ala residue combined with the C-terminal tertiary amide prefers an extended conformation and that characteristic of the (i + 1)th position of the betaVIb turn. These can be easily remodelled into a structure compatible with the (i + 1)th position of the betaII/betaVIa turn. The residue has also the potential to adopt the conformation accommodated at both central positions of the betaIII/betaIII' turn or the (i + 1)th position of the betaI/beta'I turn.

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

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…

Structural and Molecular Characterization of meso-Substituted Zinc Porphyrins: A DFT Supported Study

2011

Structural parameters of a range of over 100 meso-substituted zinc porphyrins were reviewed and compared to show how far the nature of the functional group may affect the interatomic distances and bond angles within the porphyrin core. It was proved that even despite evident deformations of the molecular structure, involving twisting of the porphyrin's central plane, the coupled π-bonding system remains flexible and stable. DFT calculations were applied to a number of selected porphyrins representative for the reviewed compounds to emphasize the relevance of theoretical methods in structural investigations of complex macrocyclic molecular systems. Experimental and DFT-simulated IR spectral …

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…

Infrared bandshapes of intramolecularly H-bonded systems—III. Vibrational dephasing of vs (OH) in 2,6-dichlorophenol

1987

Abstract The shape of the v s (OH) absorption band of intramolecularly H-bonded 2,6-dichlorophenol was measured in a series of solvents of increasing polarity and quantitatively analyzed. A distinct dependence of band positions, shape parameters, band moments, integrated intensities, correlation functions and correlation times on the polarity of solvent has been found. Vibrational dephasing due to dipole—dipole interactions seems to be an important relaxation pathway determining the bandshape in the studied systems.

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…

The effect of β-methylation on the conformation of α, β-dehydrophenylalanine: a DFT study

2009

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…

The synthesis, structure and properties of N-acetylated derivatives of ethyl 3-amino-1H-pyrazole-4-carboxylate.

2007

Ethyl 3-amino-1H-pyrazole-4-carboxylate (1) was yielded through total synthesis and reacted with acetic anhydride to give the acetylated products 2-6. Compounds 1-6 were studied with HPLC, X-ray, FT-IR, (1)H-NMR, (13)C-NMR and MS. Acetylation was carried out in solvents of various polarity, namely; chloroform; dioxane; DMF; acetic anhydride, at room temperature and at boiling points; and in the presence and absence of DMAP. The acetylated products are mainly nitrogen atoms in the ring. The position of the ring proton in the solution was based on NOESY; multinuclear HMBC, HSQC spectra and calculations. For equivalent amounts (1-1.5 mol) of acetic anhydride at room temperature two products of…

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…

Molecular and crystal structure of Ac-(Z)-ΔAbu-NMe2 and Ac-DL-Abu-NMe2 as compared to those of related molecules

2004

Abstract The molecular and crystal structures of two homologous amino acid derivatives: N-acetyl-α,β-dehydro-butyrine N´,N´-dimethylamide (1) and N-acetyl-DL-butyrine N´,N´-dimethylamide (2), have been determined by X-ray crystallography. Similar solid-state association of both compounds is observed; despite different molecular conformation, they form centrosymmetric dimers linked by the intermolecular N–H…O hydrogen bonds. The conformation of two crystallographically independent molecules of 1 [with torsion angles ϕ, ψ, χ 1 ≈ (–47°, 130°, 3°), respectively] is also characteristic of other related diamides – ΔAla, ΔPhe and ΔLeu – previously studied in the solid state. To analyse whether thi…

meso-Aryl-substituted free-base porphyrins: formation, structure and photostability of diprotonated species

2015

Susceptibility to interact with trifluoroacetic acid (TFA) of selected free-base porphyrins, including a novel lipophilic 3-n-pentadecyl(phenoxy)-ethoxy-phenyl-substituted porphyrin, and photostability of their diprotonated compounds was explored in benzene and N,N-dimethylformamide (DMF). Results have been discussed in terms of the commonly applied pK a -based procedure and confronted with a simple approach derived from experimentally-determined correlations reflecting the porphyrins affinity for TFA. Density functional theory (DFT) has proved the porphyrin moiety creates stable diprotonated species involving two TFA molecules, in which the fluorine atoms effectively contribute to the over…

Conformational investigation of α,β‐dehydropeptides. XV: N‐acetyl‐α,β‐dehydroamino acid N ′N ′‐dimethylamides: conformational properties from infrare…

2005

The FTIR spectra were analysed in the region of the nu(s)(N-H), AI(C=O) and nu(s)(Calpha=Cbeta) bands for a series of Ac-DeltaXaa-NMe2, where DeltaXaa = DeltaAla, (Z)-DeltaAbu, (Z)-DeltaLeu, (Z)-DeltaPhe and DeltaVal, to determine a predominant solution conformation of these alpha,beta-dehydropeptide-related molecules. Measurements were taken in CCl4, DCM and MeCN solutions. In the same way, spectra of saturated analogues Ac-Xaa-NMe2, where Xaa = Ala, Abu, Leu, Phe and Val, were investigated. To help interpret the spectroscopic results, conformational maps were calculated by the B3LYP/6-31+G** method. Also, the relative energies of all conformers of the dehydro compounds in vacuo as well as…

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…

The Molecular and Crystal Structure of tert-Butyl N.ALPHA.-tert-Butoxycarbonyl-L-(S-trityl)cysteinate and the Conformation-Stabilizing Function of We…

2001

The title compound, C31H37NO4S [systematic name: (R)-tert-butyl-2-[(tert-butoxycarbonyl)amino]-3-(tritylsulfanyl)propanoate] is an L-cysteine derivative with three functions: NH2, COOH and SH, blocked by protecting groups tert-butoxycarbonyl, tert-butyl and trityl, respectively. The main chain of the molecule adopts the extended, nearly all-trans C5 conformation with the intramolecular N-H...O=C hydrogen bond. The urethane group is not involved in any intermolecular hydrogen bonding. Only weak intermolecular hydrogen bonds and hydrophobic contacts are observed in the crystal structure. These are C-H...O hydrogen bonds and CH/pi interactions with donor...acceptor distances, C...O ca. 3.5 A a…

Conformational investigation of alpha,beta-dehydropeptides. XIII. Conformational properties of N-acetyl-alpha,beta-dehydrovaline N',N'-dimethylamide.

2004

The crystal structure of Ac-DeltaVal-NMe(2) (DeltaVal = alpha,beta-dehydrovaline) was determined by X-ray crystallography. The found angles phi = -60 degrees and psi = 125 degrees correspond exactly to the respective values of the (i + 1)th residue in idealised beta-turn II/VIa. Ab initio/DFT studies revealed that the molecule adopts the angle psi restricted only to about |130 degrees | and very readily attains the angle phi = about -50 degrees. This is in line with its solid-state conformation. Taken together, these data suggest that the DeltaVal residue combined with a C-terminal tertiary amide is a good candidate at the (i + 1)th position in a type II/VIa beta-turn.

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…

Solvent dependence of the νs(OD) bandshape in 2,6-dichlorophenol

1994

Abstract The infrared bandshape of νs(OD) of 2,6-dichlorophenol is measured in a series of solvents of increasing polarity, and is quantitatively analysed. The bandshape is described in terms of band indices, moments, correlation functions and correlation times. A distinct solvent dependence of bandshape and relaxation parameters has been found. The changes of the νs(OD) bandshape with increasing solvent polarity are compared in detail with those obtained earlier for analogous solvents for νs(OH) of 2,6-dichlorophenol. The overall behaviour of the spectral and relaxation parameters is similar, but the changes are less distinct for the weaker OD ⋯ Cl bond.

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

2021

Abstract Post-translational modified thiazole–amino acid (Xaa–Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Conformational study of the series of model compounds containing this structural motif with alanine, dehydroalanine, dehydrobutyrine and dehydrophenylalanine were performed using DFT method in various environments. The solid-state crystal structure conformations of thiazole–amino acid residues retrieved from the Cambridge Structural Database were also analysed. The studied structural units tend to adopt the unique semi-extended β2 conformation; which is stabilised mainly by N–H⋯N…

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…

Geometrical and conformational preferences of the 9‐fluorenylmethoxycarbonyl‐amino moiety

2004

Structural parameters, originating from x-ray crystallographic data, have been compiled for 13 derivatives of amino acids, peptides and related compounds, which contain a total of 14 Fmoc-NH- moieties. For these moieties, molecular geometries and conformations--described by the omegao, theta1, theta2 and theta3' torsion angles--were analysed and compared with the corresponding parameters for the Z-NH- and Boc-NH-moieties (290 and 553, respectively). To gain a deeper insight into the conformational features of the Fmoc-NH- moiety, ab initio free molecule calculations were performed for fully relaxed minima. Also the potential energy surface as a function of the torsion angles (theta3', theta…

Conformational investigation of α, β‐dehydropeptides. XI. Molecular and crystal structure of Ac‐(Z )‐ΔPhe‐NMe2 as compared to those of related molecu…

2003

A series of three homologous dimethyldiamides Ac-(Z)-ΔPhe-NMe2, Ac-L-Phe-NMe2 and Ac-DL-Phe-NMe2 have been synthesized and their structures determined from single-crystal X-ray diffraction data. To learn more about the conformational preferences of the compounds studied, the fully relaxed ϕ, ψ conformational energy maps on the free molecules of Ac-ΔAla-NMe2 and Ac-(Z)-ΔPhe-NMe2 were obtained with the HF/3-21G method and the calculated minima re-optimized with the DFT/B3LYP/6-31G** method. The crystal state results have been compared with the literature data. The studied dimethyldiamide Ac-ΔXaa-NMe2 combines the double bond in positions α, β and the C-terminal tertiary amide within one molec…

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 …

Conformational Properties of Oxazole-Amino Acids: Effect of the Intramolecular N–H···N Hydrogen Bond

2014

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

Vibrational dephasing of νs (OH) in 2,4-dichlorophenol

1990

Abstract A quantitative analysis of the infrared bandshape of ν s (OH) in intramolecularly hydrogen-bonded 2,4-dichlorophenol in a series of solvents is presented. A distinct dependence of bandshape indices and relaxation parameters on the polarity of solvent has been found. The band shifts to lower wavenumbers, broadens and becomes more intense with increasing solvent polarity; correspondingly, the correlation function decays faster and the correlation time diminishes. The results are compared with those for previously studied systems. Factors influencing the bandshape are discussed.

Conformational investigation of ?,?-dehydropeptides.N-acetyl-(E)-dehydrophenylalanineN?-methylamide: conformational properties from infrared and theo…

2005

N-Acetyl-(E)-dehydrophenylalanine N'-methylamide [Ac-(E)-DeltaPhe-NHMe], one of a few representative (E)-alpha,beta-dehydroamino acids, was studied by FTIR in dichloromethane and acetonitrile. To support spectroscopic interpretations and to gain some deeper insight into the Ac-(E)-DeltaPhe-NHMe molecule, the Ramachandran potential energy surface was calculated by the B3LYP/6-31G*//HF/3-21G method and the conformers localized were fully optimized at the B3LYP/6-31 + G** level. The spectra and calculations were compared with those of the related molecules Ac-DeltaAla-NHMe and Ac-(Z)-DeltaPhe-NHMe. The title compound assumes two conformational states in equilibrium in dichloromethane solution …

Stereoelectronic properties ofN-acetyl-α,β-dehydroamino acidN′-methylamides

1998

α,β-Dehydroamino acids are useful peptide modifiers. However, their stereoelectronic properties still remain insufficiently recognized. Based on FTIR experiments in the range ofvs(N-H), AI, AII andvs(Cα=Cβ) and ab initio calculations with B3LYP/6–31G*, we studied the solution conformational preferences and the amide electron density perturbation of Ac-ΔXaa-NHMe, where ΔXaa=ΔAla, (E)-ΔAbu, (Z)-ΔAbu, (Z)-ΔLeu, (Z)-ΔPhe and ΔVal. Each of these dehydroamides adopts a C5 structure, which in Ac-ΔAla-NHMe is fully extended and accompanied by the strong C5 hydrogen bond. Interaction with bond Cα=Cβ lessens the amidic resonance within the flanking amide groups. TheN-terminal C=O bond is noticeably s…

Association of model peptides and dehydropeptides: N-acetyl-L-butyrine and (Z)-dehydrobutyrine N',N'-dimethylamides.

2006

These comparative studies on the aggregation behaviour of Ac-(Z)-DeltaAbu-NMe(2) and Ac-L-Abu-NMe(2) in carbon tetrachloride were performed by the analysis of their FTIR spectra and by theoretical calculations. The percentage of the monomeric form (alpha) decreased as concentration increased and this occurred to a higher degree for the (Z)-DeltaAbu derivative than for its saturated analogue. The dimerization constant K(D), calculated on the basis of the intensity of the monomer and associate bands in the nu(s)(N-H) vibration region, is by three orders of magnitude larger for Ac-(Z)-DeltaAbu-NMe(2) than for Ac-L-Abu-NMe(2). The obtained dimer geometries of the dehydro- compound were calculat…

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…

Hydrogen bond-mediated conjugates involving lanthanide diphthalocyanines and trifluoroacetic acid (Lnpc2@TFA): Structure, photoactivity, and stability

2020

The interaction between lanthanide diphthalocyanine complexes, LnPc2 (Ln = Nd, Sm, Eu, Gd, Yb, Lu

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…

Conformational analysis of α,β-dehydropeptide models at the HF and DFT levels

2004

Abstract The Ramachandran potential energy surfaces of N-acetyl-α,β-dehydroamino acid N′-monomethylamides Ac-ΔXaa-NHMe (ΔXaa=ΔAla, (Z)-ΔPhe; 1, 2) and N-acetyl-α,β-dehydroamino acid N′,N′-dimethylamides Ac-ΔXaa-NMe2 (ΔXaa=ΔAla, (Z)-ΔPhe, (Z)-ΔAbu; 3–5) were calculated at the HF/6-31G*//HF/3-21G level. The conformers localised were fully optimised at the DFT/B3LYP/6-31+G** level and their relative stabilities were analysed in terms of both π-conjugation and internal hydrogen bonding. The Ac-ΔXaa-NMe2 molecules reveal the low-energy conformer H/F, φ=−41±4°, ψ=128±4°, which is not too easily accessible for common amino acid residues. This conformer is stabilised by the bifurcated N2–CH3 O1 int…

β-turn tendency in N-methylated peptides with dehydrophenylalanine residue: DFT study.

2010

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

2013

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…

N-Acetyl-α, β-dehydroamino acid N’-methylamides and N’, N’-Dimethylamides

1997

Association of model peptides and dehydropeptides: N-acetyl-l-alanine- and dehydroalanine N′,N′-dimethylamides

2005

Abstract The comparative studies on the association of Ac-ΔAla-NMe 2 and Ac- l -Ala-NMe 2 in carbon tetrachloride were performed by the analysis of their average molecular weight, dipole moments and FTIR spectra. To aid spectroscopic interpretation and gain some deeper insight into the nature of associates, the geometries of the minimum energy of the dimers of Ac-ΔAla-NMe 2 and Ac- l -Ala-NMe 2 were calculated by the B3LYP/6-31+G** method. The average molecular weight in the studied concentration range, for the ΔAla and l -Ala peptide, as determined by the osmometric method, did not exceed 1.5 and 1.2 of the monomeric mass, respectively. Accordingly, the percentage of the monomeric form (α)…

The conformational properties ofα,β-dehydroamino acids with aC-terminal ester group

2011

α,β-Dehydroamino acid esters occur in nature. To investigate their conformational properties, a systematic theoretical analysis was performed on the model molecules Ac-ΔXaa-OMe [ΔXaa = ΔAla, (E)-ΔAbu, (Z)-ΔAbu, ΔVal] at the B3LYP/6-311+ + G(d,p) level in the gas phase as well as in chloroform and water solutions with the self-consistent reaction field-polarisable continuum model method. The Fourier transform IR spectra in CCl(4) and CHCl(3) have been analysed as well as the analogous solid state conformations drawn from The Cambridge Structural Database. The ΔAla residue has a considerable tendency to adopt planar conformations C5 (ϕ, ψ ≈ - 180°, 180°) and β2 (ϕ, ψ ≈ - 180°, 0°), regardless…

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…

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…

Conformational preferences and synthesis of isomersZandEof oxazole-dehydrophenylalanine

2016

Dehydrophenylalanine, ΔPhe, is the most commonly studied α,β-dehydroamino acid. In nature, further modifications of the α,β-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isomers Z and E, were investigated. To determine all possible conformations, theoretical calculations were performed using Ac-(Z/E)-ΔPhe-Ozl(4-Me) model compounds at M06-2X/6-31++G(d,p) level of theory. Ac-(Z/E)-ΔPhe-Ozl-4-COOEt compounds were synthesized and the conformational preferences of each isomer, Z and E, were investigated using FTIR and NMR-NOE in solutions of increasing p…

Conformational investigation of α,β‐dehydropeptides Part VI. Molecular and crystal structure of benzyloxycarbonylglycyl‐(Z )‐dehydrophenylalanine

1994

The structure of a peptide containing C-terminal dehydrophenylalanine, Z-Gly-(Z)-delta Phe (C19H18N2O5, MW = 354) was determined from single-crystal X-ray diffraction data. Needle-shaped crystals were grown from a 1:1 mixture of methanol-acetone in the monoclinic space group P2(1) with a = 14.717(4), b = 4.941(2), c = 12.073(4) A, beta = 103.72(4) degrees; V = 852.86(8) A3, Z = 2 and Dc = 1.32 g cm-3. The structure was solved by direct methods using SHELXS-86 and refined to a final R-index of 0.032 for 1714 observed reflections. The peptide adopts a conformation folded at the glycine residue, and principal torsion angles are omega 0 = -167.6(2) degrees, phi 1 = -71.8(3) degrees, psi 1 = -31…

Novel meso-substituted porphyrins: Synthesis, characterization and photocatalytic activity of their TiO2-based composites

2009

Abstract Two series of novel meso-substituted porphyrins, namely 5,10,15,20-tetra[4-(3-phenoxy)-propoxy]phenyl porphyrin, the structural analogue 5,10,15,20-tetra[2-(3-phenoxy)-propoxy]phenyl porphyrin and their Co(II) Cu(II) and Zn(II) complexes were synthesized. The compounds were characterized using various spectroscopic techniques and their molecular structure was proposed based on density functional theory calculations. The diverse properties of the porphyrin derivatives result from the different stereochemistry of the particular substituents at the meso site on the macrocycle and are controlled also by the coordinated metal. The 1H NMR spectrum of the free-base porphyrin showed a comp…

Metalloporphyrin intercalation in liposome membranes: ESR study

2010

Liposomes characterized by membranes featuring diverse fluidity (liquid-crystalline and/or gel phase), prepared from egg yolk lecithin (EYL) and dipalmitoylphosphatidylcholine (DPPC), were doped with selected metalloporphyrins and the time-related structural and dynamic changes within the lipid double layer were investigated. Porphyrin complexes of Mg(II), Mn(III), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), and the metal-free base were embedded into the particular liposome systems and tested for 350 h at 24°C using the electron spin resonance (ESR) spin probe technique. 5-DOXYL, 12-DOXYL, and 16-DOXYL stearic acid methyl ester spin labels were applied to explore the interior of the lipid bila…

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 …

Orthorhombic polymorphs of twotrans-4-aminoazoxybenzenes

2002

The two isomeric compounds 4-amino-ONN-azoxybenzene [or 1-(4-aminophenyl)-2-phenyldiazene 2-oxide], i.e. the alpha isomer, and 4-amino-NNO-azoxybenzene [or 2-(4-aminophenyl)-1-phenyldiazene 2-oxide], i.e. the beta isomer, both C(12)H(11)N(3)O, crystallized from a polar solvent in orthorhombic space groups, and their crystal and molecular structures have been determined using X-ray diffraction. There are no significant differences in the bond lengths and valence angles in the two isomers, in comparison with their monoclinic polymorphs. However, the conformations of the molecules are different due to rotation along the Ar-N bonds. In the alpha isomer, the benzene rings are twisted by 31.5 (2)…

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…

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

2014

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

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…

Conformational investigation of α,β-dehydropeptides. X. Molecular and crystal structure of Ac-ΔAla-NMe2 compared with those of Ac-L-Ala-NMe2, Ac-DL-A…

2002

A series of three homologous dimethyldiamides Ac-DeltaAla-NMe2, Ac-L-Ala-NMe2 and Ac-DL-Ala-NMe2 has been synthesized and the structures of these amides determined from single-crystal X-ray diffraction data. To learn more about the conformational preferences of compounds studied, the fully relaxed (phi-psi) conformational energy maps in vacuo (AM1) of Ac-DeltaAla-NMe2 and Ac-L-Ala-NMe2 were obtained, and the calculated minima reoptimized with the DFT/B3LYP/6-31G** method. The crystal-state results have been compared with the literature data. Ac-DeltaAla-NMe2 and other alpha,beta-dehydroamino acid dimethyldiamides, Ac-DeltaXaa-NMe2 adopt the conservative conformation of the torsion angles ph…

CCDC 1534810: Experimental Crystal Structure Determination

2017

Related Article: Anna Kusakiewicz-Dawid, Monika Porada, Wioletta Ochędzan-Siodłak, Małgorzata A. Broda, Maciej Bujak, Dawid Siodłak|2017|J.Pept.Sci.|23|716|doi:10.1002/psc.3018

CCDC 1451706: Experimental Crystal Structure Determination

2016

Related Article: Monika Staś, Maciej Bujak, Małgorzata A. Broda, Dawid Siodłak|2016|Biopolymers|106|283|doi:10.1002/bip.22852

CCDC 862034: Experimental Crystal Structure Determination

2017

Related Article: Dawid Siodłak, Agnieszka Macedowska-Capiga, Małgorzata A. Broda, Anna E. Kozioł, Tadeusz Lis|2012|Biopolymers|98|466|doi:10.1002/bip.22082

CCDC 862033: Experimental Crystal Structure Determination

2017

Related Article: Dawid Siodłak, Agnieszka Macedowska-Capiga, Małgorzata A. Broda, Anna E. Kozioł, Tadeusz Lis|2012|Biopolymers|98|466|doi:10.1002/bip.22082

CCDC 862035: Experimental Crystal Structure Determination

2017

Related Article: Dawid Siodłak, Agnieszka Macedowska-Capiga, Małgorzata A. Broda, Anna E. Kozioł, Tadeusz Lis|2012|Biopolymers|98|466|doi:10.1002/bip.22082

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 1451707: Experimental Crystal Structure Determination

2016

Related Article: Monika Staś, Maciej Bujak, Małgorzata A. Broda, Dawid Siodłak|2016|Biopolymers|106|283|doi:10.1002/bip.22852

CCDC 2144108: Experimental Crystal Structure Determination

2022

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