Wyniki wyszukiwania - Biblioteka Nauki

1

Conformational studies of aliphatic secondary ozonides (propene, 1-butene and 1-heptene) by means of FTIR spectroscopy

100%

Bariseviciute R. , Ceponkus J. , Gruodis A. , Sablinskas V.

Open Chemistry

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2006

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tom 4

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nr 4

578-591

EN

Ozonization reaction of simple alkenes was studied by means of FT infrared absorption gas spectroscopy. The reaction was performed at 95 K in neat films of the reactants. IR absorption spectra of the gaseous products were recorded. The spectra were analyzed combining experimental results with theoretical calculations performed at B3LYP 6-311++G (3df, 3pd) level. We found that among all theoretically predicted conformers of propene secondary ozonide, only one which has the O-O half-chair configuration for the five membered ring and the radical attached in the equatorial position was present in the sample. Samples of 1-butene and 1-heptene secondary ozonides consist from two conformers of very similar energy (ΔH=0.3 kJ/mol). The most stable conformer for both ozonides is the one with O-O half-chair configuration of the five membered ring and the radical attached in equatorial position and the aliphatic chain in gauche position. The second stable conformer has the aliphatic chain in anti position.

2

Energy transfer in peptides based on phthalimide derivatives of aliphatic aminoacids

100%

Yukhimenko N. , Savchenko I. , Kolendo A. , Syromyatnikov V. , Błażejowski J. , Wiczk W.

Materials Science

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2002

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tom Vol. 20, No. 4

77-83

EN

Model peptides containing phthalimide derivatives of aliphatic aminoacids with various number of methylene groups in side chains have been synthesized and investigated spectroscopically. The study aimed at the creation of polymers with the intramolecular triplet-triplet excitation energy transfer. In all compounds investigated, efficient triplet-triplet energy transfer is observed, resulting in the phosphorescence only from phtalimide t-electronic system in frozen solutions at 77 K.

3

Novel Buspirone-Like 5-HT 1A Receptor Ligands

88%

Krajewski K.

Polish Journal of Chemistry

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2001

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tom Vol. 75, nr 1

71-78

EN

Four novel buspirone-like compounds were synthesized and their affinity to the serotonin 5-HT1A receptor was determined. Two compounds bind to 5-HT1A receptor with a high affinity and two other compounds exhibit a low affinity to this receptor. A simple two-parameter polynomial correlation was suggested to express the structure-activity relationships.

4

Theoretical study of structure, vibrational and electronic spectra of isomers of methyl-3-methoxy-2-propenoate

88%

Virdi A. , Gupta V. , Sharma A.

Open Chemistry

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2004

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tom 2

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nr 3

456-479

EN

A systematic quantum mechanical study of the possible conformations, their relative stabilities, vibrational and electronic spectra and thermodynamic parameters of methyl-3-methoxy-2-propenoate has been reported for the electronic ground (S0) and first excited (S1) states using time-dependent and time-independent Density Functional Theory (DFT) and RHF methods in extended basis sets. Detailed studies have been restricted to the E-isomer, which is found to be substantially more stable than the Z-isomer. Four possible conformers c′Cc, c′Tc, t′Cc, t′Tc, of which the first two are most stable, have been identified in the S0 and S1 states. Electronic excitation to S1 state is accompanied with a reversal in the relative stability of the c′Cc and c′Tc conformers and a substantial reduction in the rotational barrier between them, as compared with the S0 state. Optimized geometries of these conformers in the S0 and S1 states are being reported. Based on suitably scaled RHF/6-31G** and DFT/6-311G** calculations, assignments have been provided to the fundamental vibrational bands of both these conformers in terms of frequency, form and intensity of vibrations and potential energy distribution across the symmetry coordinates in the S0 state. A complete interpretation of the electronic spectra of the conformers has been provided.

5

Quantum chemical computational studies on bis-thiourea zinc acetate

88%

Pir H. , Günay N. , Tamer O. , Avci D. , Tarcan E. , Atalay Y.

Materials Science Poland

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2013

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tom Vol. 31, No. 3

357--371

EN

In this study, quantum chemical calculations of vibrational spectra, Raman spectra, electronic properties (total energy, dipole moment, electronegativity, chemical hardness and softness), Mulliken atomic charges and thermodynamic parameters of bis-thiourea zinc acetate (BTZA) have been performed using Gaussian 09 program. Additionally, nonlinear optical (NLO), conformational, natural bond orbital (NBO) analyses of BTZA have been carried out using the same program. The structural and spectroscopic data of the molecule in the ground state have been calculated using Hartree-Fock (HF) and density functional method (DFT/B3LYP) with the 6-311++G(d,p) basis set. In addition, the molecular frontier orbital energies (HOMO, HOMO-1, LUMO and LUMO+1) of the title compound have been calculated at the HF and B3LYP levels. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Finally, the calculated results were applied to simulate infrared and Raman spectra of the title compound which showed good agreement with the experimental ones.

6

The ECEPP package for conformational analysis of polypeptides

88%

Ripoll D. R. , Liwo A. , Czaplewski C.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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1999

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tom Vol. 3, No 3

313-331

EN

We present here the ECEPPAK (developed in the laboratory of prof. H.A. Scheraga, Cornell University) and ANALYZE packages for the conformational search of polypeptides that is based on the ECEPP/3 force field. The functions of the program include energy calculation and minimization and global conformational search using the Electrostatically Driven Monte Carlo (EDMC) method. The search can be constrained using experimental information e.g., the distance constraints from NMR measurements. The sister program, ANALYZE, allows the user to classify the conformations by means of cluster analysis and fit the statistical weights of the conformations to best fit the experimental observables. The package is extensively parallelized, which allows the user to carry out the conformational search even of comparatively large polypeptides in real time.

7

Conformational studies of tachykinin peptides using NMR spectroscopy

75%

Rodziewicz S. , Xiao-Fei Q. , Rolka K.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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1998

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tom Vol. 2, No 1

47-53

EN

Conformational analysis of two tachykinin family peptides: Scyliorhinin I (ScyI) and Scyliorhinin II (ScyII) was carried out by 1D- and 2D-NMR (DQF-COSY, TOCSY, HMQC, HMBC, NOESY and ROESY) and molecular dynamics calculation methods in water and DMSO. Scyliorhinin I is an equipotent agonist of NK-1 and NK-2 tachykinin receptors and Scyliorhinin II is a selective agonist of the NK-3 tachykinin receptor. In DMSO, two groups of conformations (major and minor) were obtained for both peptides based on the experimental data. The conformations proposed for ScyI represent a folded structure, which show certain similarities to the structures reported for other NK-1 and NK-2 tachykinin agonists. In water ScyII displays a flexible, extended structure, whereas in DMSO the structure is more compact and in the fragment from the centre to the C-terminus several beta -turns may be present.

8

DFT and neutron diffraction study of 1,6-anhydro-β-D-glucopyranose (levoglucosan)

75%

Sládkovic̆ová M. , Mach P. , Smrc̆ok L. u. , Rundlöf H.

Open Chemistry

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2007

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tom 5

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nr 1

55-70

EN

Geometries of 27 generated conformers of levoglucosan were optimized in vacuo at DFT level of theory combining several functionals with high quality basis sets. For the sake of comparison a reference molecular and crystal geometry obtained from 30 K single crystal neutron diffraction data was used. Analysis of the conformers’ geometries revealed that in all stable conformers intramolecular two-or three centre hydrogen bonds were formed. Relative energy of the conformer, which approximated the molecule in the crystal structure the most, was only ∼3 kcal/mol higher, than the energy of the most stable conformer in vacuo. The largest discrepancies between the geometries calculated in vacuo and experimental geometry concentrated in the vicinity of anomeric C1. These differences were reduced by involving O1 to intermolecular hydrogen bond using a simple model of the respective hydrogen bond in the crystal. [...]

9

Conformational Stability, TGA, and Molecular Docking Investigations of p-Coumaric Acid with Special Relevance to Anti-Cancer and Antibacterial Activity

75%

Sathish M. , Meenakshi G. , Xavier S. , Sebastian S.

Acta Physica Polonica A

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2017

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tom 131

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nr 6

1512-1518

EN

In this work an attempt is made to analysis of the possible different conformers of p-coumaric acid (PCA) by using density functional method. The total energy of four possible conformers were calculated by using B3LYP/6-311G(d,p) method. Computational result identifies that the most stable conformer of PCA is C2. The formation of inter- and intra-molecular hydrogen bonding between -OH and -COOH group gave the evidence for dimer formation for PCA molecule. The highest occupied-lowest unoccupied molecular orbital analysis shows that the negative electrostatic region situated over the -COOH group and positive electrostatic potential region are localized on ring system and all hydrogen. The PCA has been screened to anti-microbial activity and found to exhibit anti-bacterial effects. Molecular docking results suggest that PCA may exhibit inhibitory activity against lung cancer protein and may act as potential against lung cancer.

10

Konformacyjne właściwości modyfikowanych reszt aminokwasowych

63%

Wałęsa R. , Buczek A. , Broda A.

Chemik

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2014

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tom Vol. 68, nr 4

329--334

PL

Konformacyjnie usztywnione aminokwasy są szeroko stosowane przy konstruowaniu peptydowych analogów o lepszych właściwościach farmako-kinetycznych. Jednym z sposobów modyfikacji peptydów jest wprowadzenie reszt a,b-dehydroaminokwasowych w łańcuch peptydowy. Podwójne wiązanie Ca=Cb usztywnia łańcuch boczny i umożliwia występowanie izomerii geometrycznej Z/E. Innym rodzajem modyfikacji jest zastąpienie amidowej grupy –NH grupą –NCH3, czyli tzw. N-metylowanie. Autorzy określili wpływ tych dwóch modyfikacji strukturalnych na konformację łańcucha peptydowego. Przeprowadzone badania pozwoliły ustalić, że reszta a,b-dehydrofenyloalaniny aminokwasów konformacji H. Wykazano również, że polarny rozpuszczalnik zwiększa wyraźnie udział konfiguracji cis wiązania amidowego w N-metylowanych peptydach.

EN

Conformationally constrained amino acids are widely used in the design of peptide analogues with better pharmacokinetic properties. One of the methods of peptide modification is the introduction of a, b -dehydroamino acid residues into peptide chain. The double bond Ca=Cb constrains side chain and enables occurrence of geometrical isomerism Z/E. The other type of modification is the replacement of amide group –NH with group –NCH3, i.e. so called N-methylation. The Authors have determined the impact of these two structural modifications on peptide chain conformation. Conducted research has lead to the conclusion that -dehydrophenylalanine residue has the ability to exhibit atypical for standard amino acids H conformation. It has also been shown that polar solvent clearly increase percentage of cis configuration of amide bond in N-methylated peptides.

11

Elektrooptyczny efekt Kerra w chemii

51%

Prezhdo O. , Olan K. , Zubkowa W. , Preżdo W.

Wiadomości Chemiczne

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2011

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tom [Z] 65, 1-2

1-31

EN

The electro-optical Kerr effect finds wide application in conformational analysis of molecules and molecular aggregates [1–5], particularly in cases where the standard X-ray and NMR techniques cannot be used. For instance, NMR allows to establish conformations of linear and cyclic unsaturated organic compounds. However, it is less effective in an analysis of molecular complexes, particularly of those that have several rotational symmetry axes. In such cases a combination of techniques based on molecular dipole moments, electro-optical Kerr effect, optical Kerr effect, IR spectroscopy, and Rayleigh scattering can be applied [6]. The foundations of conformational analysis of molecular complexes using several complementary physical approaches are developed in Ref. [7]. The electro-optical methods are particularly useful for an investigation of intramolecular interactions [8–18]. The strength, direction and other details of intramolecular interactions can be determined by analyzing the deviations of the experimental molar Kerr constant (mK) from its value calculated according to the tensor-additive scheme that operates with polarizability tensors of molecular cores and functional groups [19, 20]. For instance, using this approach it has been shown that weakening of conjugation in an electron donor-acceptor chain can lead to flattening of the molecular structure [21]. The Kerr constant is also very sensitive to intermolecular interactions [22–29]. In order to assess quantitatively an extent of the solvent effect on the mK values, both molecular and continuum models of solution structure have been used [30, 31]. The mK values are greatly affected by the mutual orientation of solvent and solute molecules, which interact by dispersive, inductive and dipole-dipole forces [32]. Hydrogen and donor-acceptor bonding have an even stronger influence on the mK values [33]. The equimolar mixtures approach developed in Ref. [34] allows to determine the molar Kerr constant (mK), dipole moment (m), equilibrium constant (K) and, ultimately, structure of a molecular complex based on measurements of the Kerr constant (B), dielectric permittivity (e), density (d) and refractive index (n) of a series of dilute solutions of the complex. Future trends in the development of the electro-optical methods in chemistry are discussed. Theories that relate the electric-optic proprieties of molecules with their reactivity are particularly important. Such theories should be able to predict the changes in the polarizabilities and dipole moments of bonds, molecules and molecular aggregates during the course of chemical reactions.

12

Elements of non-random structure in the unfolded states of proteins : location and possible implications for protein folding mechanisms

51%

Nikiforovicz G. V.

Polimery

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2003

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tom T. 48, nr 1

44-49

EN

This study introduces a simple computational procedure to search protein sequences for the segments with above average propensity to adopt non-random structures (which includes the native-like structure) in the unfolded state. The procedure consists of systematical conformational analysis of all overlapping hexapeptide segments in the protein sequence. The main aim of the computational approach is to determine the 3D structure most preferable for a given residue in the protein sequence, as determined by local interactions within the set of hexapeptides featuring the particular residue under consideration. Specifically, this study focuses on four types of "template" 3D structures that may be adopted by a hexapeptide, namely beta-strand, alpha-helix, beta-turn and the native-like structure of the folded state (assumed to be known). The study discusses also the possible importance of such segments for the different molecular mechanism of folding of the two prototypical proteins, namely the 65-residue barley chymotrypsin inhibitor 2 (CI2) and the 110-residue ribonuclease from Bacillus anzyloliquefaciens (barnase). The computational results suggest that dynamic equilibrium in the unfolded state for the continuous fragment 6-27 in CI2 will likely prefer the native-like structure that may be preserved during folding. For barnase, oil the contrary, dynamic equilibrium preferring the native-like structure most likely will occur in the unfolded state only at several small separate fragments, so the large non-native non-random segments of the unfolded state have to be restructured during folding.

PL

Opracowano prostą procedurę obliczeniową do badania sekwencji białek w odniesieniu do segmentów o większej niż średnia skłonności do przybierania postaci struktur uporządkowanych (które zawierają struktury takie same jak macierzyste) w stanie rozwiniętym. Procedura obejmuje systematyczną analizę konformacyjną wszystkich nachodzących na siebie segmentów heksapeptydowych w sekwencji białka. Głównym celem tego przybliżenia obliczeniowego jest określenie najbardziej uprzywilejowanej w przypadku danych reszt aminokwasowych w sekwencji białkowej struktury 3D, zgodnej z wynikami uzyskanymi na podstawie oceny lokalnych oddziaływań w układzie heksapeptydów obrazujących rozważane tu reszty aminokwasów. Skupiono się zwłaszcza na (przyjętych jako znane) czterech typach matrycowych struktur 3D, które mogą być przybierane przez heksapeptydy, mianowicie na strukturze P (fi-strand), a-helisy (a-helix), P-zgiętej ($-turn) oraz na strukturze takiej jak macierzysta w stanie rozwiniętym. Przedyskutowano także możliwy udział takich segmentów w różnych molekularnych mechanizmach zwijania dwu prototypowych białek: złożonego z 65 reszt aminokwasowych inhibitora 2-chymotrypsyny jęczmienia (C12) oraz 110-aminokwasowej rybonukleazy z Bacillus amyloliąuefaciens (barnazy). Wyniki obliczeń wskazują, że równowaga dynamiczna w stanie rozwiniętym ciągłego fragmentu 6-27 w C12 powinna preferować struktury takie jak macierzyste, które mogą zostać zachowane podczas zwijania (rys. 1 i 3). Przeciwnie, w przypadku barnazy równowaga dynamiczna uprzywilejowująca struktury podobne macierzystym najczęściej występuje w stanie rozwiniętym tylko w nielicznych małych wydzielonych fragmentach, zatem duże niemacierzys-te uporządkowane segmenty w tym stanie muszą być odtworzone podczas zwijania.