Wyniki wyszukiwania - BazTech

1

Determination of distribution of configurational- compositional sequences and simulation of carbonyl signal of poly(methyl methacrylate-co-isopropyl acrylate) based on the 13C NMR spectra

Pasich Marcin, Henzel Norbert, Matlengiewicz Marek

Farby i Lakiery

|

2019

|

nr 2

14--21

EN

A series of sampies of the poly(methyl methacrylate-co-isopropyl acrylate), PMMA/iPrA, of different composition was synthesized via free radical polymerization in solution. The copolymer composition was determined from 400 MHz 1H NMR spectra while the carbonyl region of 100 MHz 13C NMR spectra provided microstructural information on sequence distribution at the level of configurational-compositional triads and pentads. Incremental calculation of the chemical shifts of individual sequences can be performed for carbonyl signal and permit for spectral simulation and verification of the signal attribution to respective sequences.

PL

: Serię próbek kopolimeru metakrylanu metylu z akrylanem izopropylu (PMMA/iPrA) o zmiennym udziale komonomerów, zsyntezowano w wolnorodnikowej polimeryzacji w roztworze. Skład kopolimeru wyznaczono na podstawie 400 MHz widm 1H NMR, podczas gdy obszar karbonylowy 100 MHz 13C NMR widm dostarczył mikrostrukturalnych informacji o rozkładzie kompozycyjno-konfiguracyjnych sekwencji na poziomie triad i pentad. Metoda inkrementalnego obliczania przesunięć chemicznych indywidualnych sekwencji zastosowana do sygnału karbonylowego pozwala na symulację tej części widma i weryfikację przypisania poszczególnych linii odpowiednim sekwencjom.

2

Microstructural analysis of two poly(propyl acrylates): poly(n-propyl acrylate) and poly(isopropyl acrylate), based on the carbonyl signal in the 13C NMR spectra

Pasich M., Henzel N., Matlengiewicz M

Przetwórstwo Tworzyw

|

2018

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T. 24, Nr 1 (181)

56--63

EN

The samples of poly(n-propyl acrylate), PnPrA, and poly(isopropyl acrylate), PiPrA, were synthesized by free radical polymerization in solution (butan-2-one). The 100 MHz 13C NMR spectra of these homopolymers were recorded in two deuterated solvents: chloroform (CDCl3) and benzene (C6D6). In the spectra of both PnPrA and PiPrA recorded in CDCl3 the carbonyl signal was split at the level of configurational triads, while in C6D6 this signal revealed heptad splitting for PiPrA and pentad splitting for PnPrA.

PL

Próbki poli(akrylanu n-propylu), PnPrA, i poli(akrylanu izopropylu), PiPrA, otrzymano w polimeryzacji rodnikowej w roztworze butan-2-onu. Widma 100 MHz 13C NMR tych homopolimerów zarejestrowano w dwóch deuterowanych rozpuszczalnikach: chloroformie (CDCl3) i benzenie (C6D6). Na widmach PnPrA i PiPrA, zarejestrowanych w deuterowanym chloroformie, sygnał węgli karbonylowych (C=O) ulega rozszczepieniu na poziomie triad konfiguracyjnych, podczas gdy dla deuterowanego benzenu sygnał C=O PiPrA rozszczepia się na poziomie heptad, a dla PnPrA pentad konfiguracyjnych.

3

Spektroskopia magnetycznego rezonansu jądrowego (NMR)

Żylewski M.

LAB Laboratoria, Aparatura, Badania

|

2018

|

R. 23, nr 3

42--46

4

Microstructural analysis of poly(n-propyl acrylate) and poly(isopropyl acrylate) based on the backbone β-methylene carbon signal in the 13C NMR spectra

Pasich M., Siołek M., Henzel N., Matlengiewicz M.

Przetwórstwo Tworzyw

|

2016

|

T. 22, Nr 5 (173)

451--457

EN

The samples of poly(n-propyl acrylate), PnPrA, and poly(isopropyl acrylate), PiPrA, were synthesized by free radical polymerization in solution (butan-2-one). The 100 MHz 13C NMR spectra of these homopolymers were recorded in two deuterated solvents: chloroform (CDCl3) and benzene (C6D6). In the PnPrA spectra, the backbone β-methylene carbon signal (β-CH2) (33.0 - 36.5 ppm) was split up to configurational hexads for CDCl3 and C6D6. In the PiPrA spectra, the β-CH2 signal (32.5 - 36.5 ppm) was split up to configurational hexads in both solvents.

PL

Próbki poli(akrylanu n-propylu), PnPrA, i poli(akrylanu izopropylu), PiPrA, otrzymano w polimeryzacji rodnikowej w roztworze. Widma 100 MHz 13C NMR tych homopolimerów zarejestrowano w dwóch deuterowanych rozpuszczalnikach: chloroformie (CDCl3) i benzenie (C6D6). Na widmach PnPrA, zarejestrowanych w deuterowanym chloroformie i benzenie sygnał, węgli metylenowych (β-CH2) (33,0 - 36,5 ppm) ulega rozszczepieniu się na poziomie heksad konfiguracyjnych, natomiast sygnał β-CH2 (32,5 - 36,5 ppm) poli(akrylanu izopropylu) rozszczepia się na poziomie heksad konfiguracyjnych.

5

Badania strukturalne cyklicznych β-aminoketonów z wykorzystaniem metod obliczeniowych i analizy NMR

Sidorowicz K., Łaźny R.

Chemik

|

2015

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Vol. 69, nr 7

401--410

PL

Przestrzenna konfiguracja na atomie azotu w cyklicznych β-aminoketonach powoduje, że związki te mogą występować w dwóch stereoizomerycznych formach, w których podstawniki na tym atomie mogą przyjmować orientację aksjalną lub ekwatorialną w stosunku do pierścienia piperydonu. Stereochemia N-podstawionych bicyklicznych β-aminoketonów była badana za pomocą metod eksperymentalnych i teoretycznych, m.in.: spektroskopia NMR, spektroskopii mikrofalowa, rentgenografii strukturalnej i obliczeń DFT.

EN

Because of pyramidal configuration of the nitrogen atom, tropanes, granatanes, and their derivatives can exist in two stereoisomeric forms, in which N-substituents can be oriented axial or equatorial with respect to the piperidone ring. The N-invertomer stereochemistry of N-substituted bicyclic β-amino ketones has been investigated using experimental, and theoretical methods, such as NMR, microwave spectroscopy, crystallography, and DFT calculations.

6

Wykorzystanie technik NMR w ocenie surowca jajczarskiego dla przemysłu spożywczego

Jawień E., Korczyński M., Opaliński S., Młynarz P.

Przemysł Chemiczny

|

2014

|

T. 93, nr 9

1616-1620

PL

Zbadano możliwość wykorzystania spektroskopii NMR do oceny profilu metabolicznego jaj będących surowcem dla przemysłu spożywczego. Badane próbki żółtka i białka jaj pochodziły od kur niosek karmionych paszą suplementowaną fitopreparatami zawierającymi głównie lucernę i/lub pulpę z żyworódki pierzastej. Stwierdzono, że substancje małocząsteczkowe zawarte w fitopreparatach nie są bezpośrednio transportowane do jaj, ale ich zastosowanie w paszy zmieniło skład metabolomiczny żółtka. Zaobserwowane zmiany dotyczyły przede wszystkim profilu aminokwasowego.

EN

Com. phytonutrients were mixed with Lucerne and/or Kalanchoe daigremonitana pulps and added to the fodder for laying hens. Yolk and albumen samples of eggs collected were analyzed by 1H-NMR. No direct transfer of low-mol. compds. from phytonutrient components into eggs was evidenced but some changes in amino acids profile of yolk were obsd.

7

Badanie struktury i dynamiki N-terminalnych sekwencji dermorfiny i ich analogów z wykorzystaniem spektroskopii NMR w ciele stałym i rentgenografii

Trzeciak-Karlikowska K.

Wiadomości Chemiczne

|

2012

|

[Z] 66, 9-10

867-891

EN

Deltorphin I (Tyr-d-Ala-Phe-Asp-Val-Val-Gly-NH_2) and dermorphin (Tyr-d-Ala-Phe- -Gly-Tyr-Pro-Ser-NH_2) are natural opioid peptides that have been isolated from the skin of South American frogs [1]. The presence of d-amino acid is crucial for their biological activity. The synthetic analogs of given heptapeptides containing l-alanine are not analgesics [2]. Analysis of the influence of stereochemistry on molecular packing, dynamics and biological functions of neuropeptides is still important for receptor studies and practical applications (e.g. design of new selective pain killers). Presented research is focused on the structure and dynamics of two N-terminal sequences of dermorphin: tripeptide Tyr-d-Ala-Phe 1, tetrapeptide Tyr-D-Ala-Phe-Gly 2, and their analogs with l-alanine: Tyr-Ala-Phe 3 and Tyr-Ala-Phe-Gly 4, using solid state NMR and X-ray diffraction. This study clearly demonstrates that 1 and 2 crystallized under different conditions to form exclusively one structure [3, 4]. In contrast, tripeptide and tetrapeptide with l-Ala in the sequence very easily form different crystal modifications. Tyr-Ala-Phe 3 crystallizes into two forms: 3a and 3b [5], while Tyr-Ala-Phe-Gly 4 gives three modifications: 4a, 4b and 4c [4]. It seems that one of the factors, which can be important in the preorganization mechanism anticipating the formation of crystals, is the intramolecular CH-đ interaction between aromatic rings of tyrosine and/or phenylalanine and the methyl group of alanine. Such interaction is possible only for d-Ala residue. For l-Ala in the peptide sequence, the methyl group is aligned on the opposite side with respect at least to one of the aromatic groups. It can be further speculated that such internal CH-π contacts can also occur during the interaction of ligand–receptor, making the message sequence of opioid peptides more rigid and finally selective. By employing different NMR experiments (e.g. PISEMA MAS and PILGRIM) it was proven that the main skeleton of analyzed peptides is rigid, whereas significant differences in the molecular motion of the aromatic residues were observed [4, 6]. Solid state 2H NMR spectroscopy of samples with deuterium labeled aromatic rings: Tyrd4-d-Ala-Phe 5, Tyr-d-Ala-Phed5 6, Tyrd4-Ala-Phe 7, Tyr-Ala-Phe^d5 8 was used to analyze the geometry and time scale of the molecular motion. At ambient temperature, the tyrosine ring of sample 5 is rigid and in the sample 6 the phenylalanine ring undergoes a "π -flip". The tyrosine rings of form I of 7 and 8 are static, while the phenylalanine rings of form II of 7 and 8 undergo a fast regime exchange [6]. Variable temperature 2H measurements proved that the tyrosine and phenylalanine rings of two forms of compounds 7 and 8 became more mobile with increasing temperature. In contrast, the aromatic rings of samples 5 and 6 preserve their dynamics regime (static tyrosine and "π -flip" phenylalanine) in a large range of temperatures [6]. The analysis of 13C, 15N labeled tetrapeptide Tyr-D-Ala-Phe-Gly 2’-phospholipid membrane interactions suggests that peptide 2’ is aligned on the surface of the membrane (RFDR MAS) and the sandwich-like π -CH_3-π arrangement of the pharmacophore is preserved (DARR) [7].

8

Composite polymeric electrolytes - mesoscale models and ion associations

Siekierski M.

Prace Naukowe Politechniki Warszawskiej. Chemia

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2012

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z. 82

3-145

EN

The present thesis is devoted to the development of model approaches towards understanding conductivity and ion transport phenomena in composite polymeric electrolytes. On the basis of experimental works, covering both the application of inorganic fillers and supramolecular additives, two modeling approaches were developed by the author. One of them applies a Random Resistor Network-based mesoscale model to describe and predict ionic conductivity of the composite material. The presented material also contains a comparison of the model developed with the ones known from the literature as well as with the experimental conductivity data. The advantages of the developed model are related to better prediction of the AC properties of the material around the percolation threshold and reduction of the number of the empirical parameters for prediction of both DC and AC conductivity. The second part of the thesis focuses on the other model where a unified NMR probe is developed integrating methods of determination of various equilibrium constants present in the solvent-salt-receptor system. The proposed procedure allows not only to obtain a complete image of the sample by means of only one method (thus, in consequence, all types of reactions are observed with the same or at least similar method originating limitations) but, also, to explain previously observed discrepancies between behavior of materials incorporating solid and liquid polymeric matrices. Both presented approaches should be treated as a methodological support towards practical applications of so-called binary composites containing both inorganic and supramolecular additives.

PL

Przedstawiona rozprawa poświęcona jest rozwojowi dwóch modeli półempirycznych pomocnych zrozumieniu mechanizmów transportu ładunku elektrycznego w kompozytowych elektrolitach polimerowych. Zostały one stworzone przez autora na podstawie wcześniejszych prac eksperymentalnych obejmujących zastosowanie tak napełniaczy nieorganicznych jak i supramolekularnych napełniaczy organicznych. Pierwszy z nich jest modelem mezoskalowych stosującym teorię rozproszonych sieci rezystorowych do opisu i przewidywania przewodności jonowej badanych kompozytów. Prezentowana praca zawiera także porównanie opracowanego modelu z innymi opisanymi w literaturze oraz wyniki jego weryfikacji w oparciu o dane eksperymentalne. Wskazano na zalety modelu polegające na trafniejszym przewidywaniu właściwości zmiennoprądowych materiałów o składach zbliżonych do progu perkolacji. Dodatkowo stworzony model pozwala na redukcję ilości parametrów empirycznych potrzebnych do przewidywania wartości przewodności elektrycznej tak w reżimie stało jak i zmienno prądowym. Druga część pracy koncentruje się na modelu, w którym analiza widm NMR pozwala na opracowanie zunifikowanej metody wyznaczania kompletu stałych równowagi reakcji dla układu rozpuszczalnik - sól - receptor supramolekularny. Zaproponowana metoda pozwala nie tylko na uzyskanie kompletnego obrazu próbki za pomocą jednej metody badawczej (a więc ze zbliżonymi błędami i ograniczeniami dla wszystkich obserwowanych typów reakcji, ale także na wyjaśnienie zaobserwowanych wcześniej rozbieżności eksperymentalnych. Różnice te dotyczyły zachowania próbek ze stałą i ciekłą matrycą polimerową. Oba prezentowane modele stanowią wsparcie metodyczne dla praktycznych zastosowań stałych elektrolitów polimerowych stanowiących kompozyty czteroskładnikowe zawierające zarówno dodatki nieorganiczne jak i supramolekularne.

9

Układy nanohybrydowe poliuretan/funkcjonalizowany silseskwioksan. Cz. I, Badania strukturalne z zastosowaniem FT-IR i NMR

Janowski B., Pielichowski K.

Polimery

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2012

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T. 57, nr 7-8

518-528

PL

Określono budowę chemiczną układów nanohybrydowych poliuretan/funkcjonalizowany silseskwioksan (PUR/PHIPOSS) otrzymanych metodą prepolimerową. Na widmach 1H NMR i 13C NMR stwierdzono występowanie sygnałów pochodzących od protonów i atomów węgla charakterystycznych fragmentów bocznych grup PHIPOSS. Analiza otrzymanych widm elastomerów PUR/PHIPOSS metodą ATR-FTIR pozwoliła na oszacowanie wpływu obecności bocznych grup oligosilseskwioksanowych na gęstość wiązań wodorowych oraz separację fazową. Stwierdzono, że stopień rozdziału faz wzrasta ze wzrostem zawartości PHIPOSS.

EN

A chemical structure of polyurethane/functionalized silsesquioxane (PUR/PHIPOSS) nanohybrid materials obtained by prepolymer method has been determined. In the 1H NMR and 13C NMR spectra signals from protons and carbon atoms of the characteristic fragments of the PHIPOSS pendant group have been identified. Analysis of the obtained PUR/PHIPOSS elastomers by ATR-FTIR allowed us to estimate the influence of oligosilsesquioxane side groups on the density of the hydrogen bonds and phase separation. It was found that the degree of phase separation increases with increasing PHIPOSS content.

10

Zastosowanie spektroskopii NMR do identyfikacji i ilościowych oznaczeń wybranych środków powierzchniowo czynnych

Siergiejczyk L.

LAB Laboratoria, Aparatura, Badania

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2011

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R. 16, nr 1

12-14

PL

Za pomocą spektroskopii NMR zbadano sześć (3 anionowe i 3 niejonowe) spośród najpowszechniej stosowanych surfaktantów. Wyznaczono zakresy przesunięć chemicznych charakterystyczne dla poszczególnych substancji. Wyznaczono krzywe wzorcowe pozwalające selektywnie oznaczać zawartość anionowych surfaktantów w zakresie stężeń od 0,1-20 g m-3. Skuteczność metody oznaczania ilościowego zweryfikowano badając sporządzone mieszaniny surfaktantów oraz środowiskowe próbki wody.

11

Tri-tert-butoksysilanotiolanowe kompleksy cynku(II), kadmu(II) i kobaltu(II) jako modele koordynacji jonu cynku w miejscu aktywnym dehydrogenazy alkoholowej i niektórych innych enzymów

Dołęga A.

Wiadomości Chemiczne

|

2010

|

[Z] 64, 5-6

389-411

EN

Zinc is ubiquitous in living organisms and second only to iron among the transition metals. Catalytic zinc sites have been found in all six classes of enzymes. Liver alcohol dehydrogenase (EC 1.1.1.1, LADH, Fig. 1) is a zinc enzyme, which catalyzes reversible oxidation of alcohols to aldehydes utilizing as a co-substrate NAD+. The mechanism of an action of the enzyme is summarized by an equation: R1R2CHOH + NAD+ = R1R2CO + NADH + H+ The coordination of zinc in LADH is usually described as pseudotetrahedral but there were several findings supporting penta-coordination of zinc during the catalytic cycle (Fig. 1 and 2) [1–7]. Studies on synthetic analogues of functional sites of the enzymes are used to elucidate the substrate – metal interactions [8]. Tri-tert-butoxysilanethiol which was used as a ligand to model cysteinate – metal ion centers has several advantageous features. It secures formation of mononuclear transition-metal complexes, exhibits resistance towards hydrolysis, and additionally its pKa value is close to that of cysteine mercapto group [9–11]. Over 20 tri-tertbutoxysilanethiolate complexes with MS2NO2 (M = transition metal) cores were synthesized to model the enzymatic centre of alcohol dehydrogenase, including complexes with water, methanol and ethanol (Fig. 5). Crystal structures of zinc(II), cobalt(II), cadmium(II), and manganese(II) complexes were determined and compared to the structures of LADH [12–17]. Structural features of zinc(II) and cadmium(II) complexes were analyzed (Fig. 9, Tab. 2) [15]. 113Cd CP/MAS NMR spectra of tri-tert-butoxysilanethiolate cadmium(II) complexes were determined and compared with the 113Cd NMR spectra of the cadmium-substituted alcohol dehydrogenase. Solid state 113Cd NMR shifts of five-coordinate cadmium(II) complexes with the CdNO2S2 coordination core were found to be identical to that of cadmium-substituted alcohol dehydrogenase in complex with NAD+ [15,18]. The equilibrium character of the reactions between bis(bis(tri-tert-butoxysilanethiolate) cadmium(II) and nitrogen ligands, with a low equilibrium constant of heteroleptic complex formation, were proved by 113Cd NMR studies in solution [18, 19]. The electronic absorption spectra of heteroleptic cobalt(II) complexes with tri-tert-butoxysilanethiolate and imidazole ligands were measured in methanol and solid state. The equilibrium reactions in the methanolic solutions of cobalt complexes were described on the basis of the analysis of charge transfer bands S→dCo LMCT and the molecular structures of the obtained complexes [17]. EPR spectra revealed the high-spin configuration of the studied cobalt(II) compounds [17]. Quantum mechanical calculations performed on the model zinc complex indicate ca10–20% decrease in enthalpy of ethanol deprotonation due to complexation with Zn2+ [15].

12

Zastosowanie spektroskopii magnetycznego rezonansu jądrowego do badania mikrostruktury układów metakrylowo-akrylowych

Pasich M., Matlengiewicz M.

Zeszyty Naukowe Politechniki Rzeszowskiej. Chemia

|

2009

|

z. 20 [263]

111-115

PL

Spektroskopia 13C NMR jest doskonałym narzędziem do badania mikrostruktury łańcucha polimerowego, gdyż pozwala obserwować atomy węgla oraz ich sąsiadów od "wewnątrz" makrocząsteczki. Dokładne zdefiniowanie mikrostruktury pozwala na "sterowanie" budową łańcucha, a co za tym idzie otrzymywanie polimeru o żądanych właściwościach fizykochemicznych i mechanicznych.

13

N-winyloformamid - nowy ekologiczny monomer wodorozpuszczalny

Bortel E., Witek E., Pazdro M., Kochanowski A.

Polimery

|

2007

|

T. 52, nr 7-8

503-510

PL

Opisano trzy różne metody syntezy N-winyloformamidu (NVF) - nietoksycznego, izomerycznego w stosunku do akryloamidu monomeru rozpuszczalnego w wodzie, od niedawna produkowanego na skalę przemysłową. Są to technologie realizowane w koncernach BASF (Niemcy), Mitsubishi (Japonia) i Air Products & Chemicals (USA). Scharakteryzowano strukturę cząsteczki NVF, która w wyniku silnego sprzężenia może przybierać postaci czterech różnych konformerów. Opierając się na wynikach własnych badań spektroskopowych i obliczeń kwantowo-mechanicznych uzasadniono przyczynę występowania w widmach NMR sygnałów pochodzących tylko od dwóch konformerów (trans-cis i trans-trans, brak cis-trans i cis-cis). Przedstawiono reakcje towarzyszące rodnikowej i jonowej polimeryzacji NVF. Wskazano na możliwości zastosowania poli(N-winyloformamidu) i otrzymywanej z niego na drodze hydrolizy poliwinyloaminy.

EN

N-vinylformamide (NVF) is a nontoxic water-soluble monomer, isomeric in relation to acrylamide, until recently introduced into the industrial scale of production. Three various methods of N-vinylformamide synthesis were described, according to the technologies realized in BASF (Germany), Mitsubishi (Japan) and Air Products & Chemicals (USA) companies. There was described the structure of NVF molecule which can form four various conformers because of strong coupling. The reason of the presence of signals of just two conformers in NMR spectra (trans-cis and trans-trans only, cis-cis and cis-trans not present) has been justified on the basis of the results of own spectroscopic investigations (Fig. 1 and 2) and quantum-mechanical calculations (Fig. 3 and 4). The reactions accompanying the radical or ionic NVF polymerizations were presented. Possible applications of poly(N-vinylformamide) as well as of polyvinylamine, obtained by its hydrolysis, were pointed.

14

Pierwszorzędowa struktura antygenów O bakterii rodzaju Salmonella

Gajdus J., Głośnicka R., Szafranek J.

Wiadomości Chemiczne

|

2006

|

[Z] 60, 9-10

621-653

EN

Salmonella spp. are pathogenic Gram-negative bacteria that belong to Enterobacteriaceae family with lipopolysaccharide (LPS) as a constituent of cell wall. This is an integral component of the outer membrane of the wall. Salmonella smooth (S) forms produce LPS, which is composed of three parts, chemically bonded together viz. polysaccharide O-antigen, oligosaccharide core region and lipid A. Antigens O (O-PS) together with H flagella antigens are the foundation of serological classification of these bacteria. O-chain, which is built with up to 50 oligosaccharide repeating units, is one of the products of mild acidic hydrolysis of LPS. Due to the fact that polysaccharide antigens are the sites of specific antibody complexing, any difference in primary and secondary structures of O-antigens reflect serological specificity of bacteria. Taking this fact into consideration, we can distinguish about 2541 Salmonella serotypes with O and H antigenic formulas defined [4]. In this review we present 55 chemical structures of O-antigenic repeating units of Salmonella strains including their heterogeneity structures. The structures can have 22 different monosaccharide residues usually in 3 to 6 sugar repeating units. We describe here selected chemical and spectroscopic (MS, NMR) methods for primary structure examination of these bacterial O-PS. Enzymatic and immunochemical methods are also described. Cross-reactions of Salmonella spp. with any other bacteria or blood group A, B, 0 antigens are explained on the molecular level. Thus, structural assignments of somatic antigens of Salmonella spp. allow us to understand the molecular level of the classification system of these bacteria.

15

Zastosowanie spektroskopii jądrowego rezonansu magnetycznego w badaniach oddziaływań międzycząsteczkowych ligandów organicznych i biocząsteczek

Bocian W., Kozerski L.

Wiadomości Chemiczne

|

2005

|

[Z] 59, 1-2

3--22

EN

The title problem is reviewed in the three main areas of general interest to chemists, biochemists and biologists, i.e. mutual interactions of small molecules, ligand to biomolecule binding and interactions of biomolecules. Physical phenomena, specific and nonspecific, such as hydrogen bonding, self association, hydrophobic interactions, etc., are shown as being defined by NMR spectral parameters in solution and solid state. Diversity of hydrogen bonding encountered in nature is exemplified by the interaction of acetic acid with Watson-Crick vs Hoogsteen faces of adenosine, studied by DNMR in organic solvent at low temperatures. The complementarity of solid state NMR to solution studies of defining the nature of hydrogen bonding is presented in the case of genistein interaction with nitrogen bases. Application of a title method is presented for searching the geometry of complexes formed of organic ligands and biological molecules. General protocol for searching the geometry of complex is presented for the case of topotecan (TPT) interaction with duplex octamer and nicked decamer duplexes of DNA. Interaction of biomolecules is presented for the case of duplex octamer DNMR study showing effects of base pairing and stacking on the b 'H values and insulin aggregation as studied by Pulse Field Gradient NMR spectroscopy leading to relating the radius of molecular aggregate with the diffusion constants. In conclusion it is stated that various NMR techniques in solid and liquid state, coupled with X-ray and MS, constitute modern tool of structural biology in pursue of disclosing functions of biomolecules expressed by their interactions.

16

Strategie NMR wyznaczania struktur białek w roztworze

Ejchart A.

Wiadomości Chemiczne

|

2005

|

[Z] 59, 1-2

23--45

EN

A number of reasons have hindered the use of NMR spectroscopy as a tool for the protein structure determination. Recently, the advance in the NMR equipment, spectral techniques and isotope labelling has resulted in an enormous growth of NMR-determined protein structures. After a brief presentation of protein structure and conformation several types of NMR-derived constraints and the characteristic features of chemical shifts in proteins are discussed. Short-range, distance and dihedral angle constraints are valuable, but cumulative errors can appear when succesive constraints are used to determine spatial relationship of remote parts of a protein. Therefore, long-range constraints derived from residual dipolar couplings are highly complementary to the short-range constraints. Modern strategies to the NMR-based protein structure determination depend on the size of studied biomolecules. Small proteins (Mcz< 10 kDa) can be studied with the use of two-dimensional (2D) 1H NMR techniques. Medium size proteins (Mcz < 30 kDa) require double isotopic labeling 15N/13C and multidimensional (3D and 4D) heteronuclear techniques. There is no well established strategy to the structure determination of large proteins (Mcz > 30 kDa) yet. The most promising approaches take advantage of triple isotopic labeling 15N/13C/2H and the transverse relaxation optimized spectroscopy (TROSY), both resulting in the reduction of signal width.

17

Spektroskopia NMR w badaniach strukturalnych kwasów nukleinowych. Część 1.

Gdaniec Z.

Wiadomości Chemiczne

|

2005

|

[Z] 59, 1-2

47--65

EN

NMR spectroscopy is a powerful method that allows detetmination of the structure and dynamics of nucleic acids and their complexes in solution with atomic resolution. A major breakthrough in the structure determination of nucleic acids by NMR was introduction of advanced and efficient methods for the labeling of RNA and DNA with13C and 15N and development of multidimensional, heteronuclear NMR techniques analogous to those used in protein NMR spectroscopy. The resonance assignment is a crucial step in the NMR study. A spectrum must be assigned before useful structural information can be extracted. The assignment of RNA is considerably more difficult than for DNA of similar size. This is mainly due to the much narrower spectral dispersion of the H2', H3', H4' and H'/5 " ribose protons relative to DNA. The methodology for sequential assignment of nucleic acids via lomonuclear NMR techniques relies on the assumption of helical structure and therefore fails in the case of nonhelical structures, that is typical of RNA. Development of 13C/15N labeling techniques has afforded heteronuclear multidementional experiments that utilize the favorable properties of 13C and 15N nuclei such as large one-and two-bond heteronuclear scalar coupling constants and large chemical shift dispersion. These experiments provide increased sensitivity of double and triple resonance experiments and help in overcoming the problem of severe spectral overlap. Progress in novel NMR methods stimulated also a design of experiments for conformationindependent sequential assignment. In nucleic acids, experiments that correlate base resonances among themselves as well as with sugar resonances allow unambiguous spectral assignment for the structures, where the conventional NOE-based methods may not be applied. Assignments of highly overlapped sugar resonances are facilitated enormously by the application of correlated experiments based on 13C-13C transfer. Additionally, triple resonance experiments allow correlation of neighboring nucleotides through the phosphodiester backbone. The arsenal of existing methods in structure calculations of nuclcic acids by NMR spectroscopy has recently been extended. For example, NMR methods have been developed to detect and measure scalar couplings via hydrogen bonds. The information about hydrogen bonds provides very useful restraints for structural determination, especially in case of noncanonical motifs. Furthermore, the use of methods that introduce anisotropic environments for nucleic acids in solution allows the measurement of residual dipolar couplings (RDC). RDCs yield orientation, rather than distance-based constraints. The RDCs contain global structural information on nucleic acids that cannot be obtained by standard solution NMR techniques. These constraints can both improve the local structure of nucleic acids and provide novel data on the global structure. Another NMR technique, TROSY has been introduced to effectively suppress transverse relaxation of 1H-15N and 1H-13C moieties. TROSY selects exclusively the narrow line of a 1H-15N doublet or 1H-13C multiplet, yielding improved spectral resolution and increased sensitivity of NMR experiment. Recent advances in solution NMR techniques provide tools for structural studies of large (> 30 residues) nucleic acids molecules.

18

Podstawowe techniki eksperymentalne spektroskopii NMR w fazie ciekłej

Koźmiński W.

Wiadomości Chemiczne

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2005

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[Z] 59, 1-2

107--120

EN

General overview of most important NMR techniques and applications for organic and bioorganic molecules in liquids is given. The sensitivity of NMR experiments is discussed with regard to nuclear properties, Bo field, applied method of excitation and detection, and finally concentration. In the next chapter the principles and consequences of quadrature detection are discussed. The most important techniques of quadrature detection in directly and indirectly detected domains are exemplified. In the next point the principles, advantages and disadvantages of coherence selection techniques via phase cycling and Pulsed Field Gradients are indicated and compared with respect to various applications. In the last part of present article the most important homo- (COSY, TOCSY, NOESY, and ROESY) and heteronuclear (HSQC, HMQC/HMBC) techniques used in NMR investigations in liquids are briefly reviewed. The characteristic features and experimental problems of these methods are discussed with respect to usual applications in chemistry and biochemistry.

19

Kopolimery glikolidu z TMC, metoda wyznaczania mikrostruktury łańcucha z pomocą spektroskopii NMR

Kasperczyk J., Dobrzyński P., Bero M.

Inżynieria Biomateriałów

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2005

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R. 8, nr 47-53

143--145

20

Zastosowania spektroskopii magnetycznego rezonansu jądrowego w badaniach strukturalnych węglowodanów i ich pochodnych

Kaźmierski S.

Wiadomości Chemiczne

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2003

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[Z] 57, 5-6

339--365

EN

Carbohydrates play very important role in biological systems. Both carbohydrates and their derivatives are involved in many biological processes, such as cell-cell recognition, cell growth and energy transfer. In spite of very high importance in living processes, carbohydrates remain one of the less exploited class of biologically active molecules. There is a lot of different methods which can be used in carbohydrates analysis [1]. The Nuclear Magnetic Resonance (NMR) spectroscopy is one of the most attractive, important and powerful tool for analyzing the conformation and molecular architecture of carbohydrate molecules. This method serves the possibility of solving the majority of problems in this area, without any different methods – particularly in the liquid phase. The biggest advantage of NMR spectroscopy is that it is a nondestructive method. Both one- and two-dimensional NMR methods have provided valuable information about small and large molecules, ranging from the anomeric configuration of a monosaccharide to the sequence of monosaccharide residues in a bigger oligo- or polysaccharide compounds. After first years of applications mainly in primary carbohydrate structures, NMR spectroscopy has recently reached a level of sophistication, which allows both the structural and conformational analysis of carbohydrates in solution. This article reviews the applications and possibilities of current NMR techniques to the structural and conformational characterization of carbohydrate and its derivatives. Both 1D and 2D (COSY, HSQC, HSQC-TOCSY, HMBC) NMR spectra of the GOTCAB saponin 1 are presented as examples of utilization of NMR in the structure elucidation of the carbohydrate derivatives.