Wyniki wyszukiwania - BazTech

1

Właściwości czasowo-rozdzielcze słabych międzycząsteczkowych wiązań wodorowych C-H···F

Polańska Marta, Rodziewicz Paweł

Wiadomości Chemiczne

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2023

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[Z] 77, 9-10

899--919

EN

The hydrogen bond is one of the most important and interesting phenomena in nature. In this publication we will shed light on the discovery of hydrogen bond and a time evolution of its definition in the last 100 years. Both structural and spectroscopic parameters of the hydrogen bond will be discussed. A special focus will be given to the latest IUPAC definition of the hydrogen bond and its consequences to scientific research. The main aim of this study is to highlight theoretical studies based on first principles calculations and molecular dynamics simulations which not only support experimental results but also provide parameters which are crucial to understand the nature of hydrogen bonds. Particular attention will be given to methods and theoretical ideas used in the computational studies of hydrogen bonds. Utilizing static DFT/ab initio calculations and molecular dynamics simulations enables comparison of different binding energies and studying time evolution of the hydrogen-bonded molecular system on the atomistic level. We will discuss time-resolved properties of weak intermolecular hydrogen bonds, using as an example C-H···F containing model systems, namely F3CH*(HF)n molecular complexes and (F3CH)2-4 aggregates.

2

Modelowanie właściwosci wiązań wodorowych na przykładzie kompleksów układ amidowy - woda

Rzepiela Kacper, Buczek Aneta, Kupka Teobald, Kar Tapas, Broda Małgorzta A.

Wiadomości Chemiczne

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2023

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[Z] 77, 7-8

629--645

EN

The energy and structure of intermolecular hydrogen bonds between water molecule and N-methylamide (NMA) or uracil (U) are discussed on the basis of DFT calculations. Theoretical methods are applied to calculate properties of cis- and trans- NMA complexes with one water molecule. Subsequently, H-bonds in six uracil – water complexes are analyzed. The influence of dispersion interactions and the polar environment on the hydrogen bond energy was analyzed. Results obtained by B3LYP functional with and without Grimme D3 dispersion correction indicate that dispersion interaction plays a significant role in an association process. In addition, the polar solvent reduces the hydrogen bond energy and this reduction is directly proportional to the hydrogen bond energy.

3

Właściwości kwasu salicylowego i jego wybranych pochodnych w świetle metod modelowania molekularnego

Kaczmarek Anna, Kizior Beata, Zierkiewicz Wiktor, Jezierska Aneta

Chemik

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2023

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Nr 1-4

66--70

PL

Salicylany są stosowane od wieków jako leki na różne dolegliwości. Wiele związków z tej grupy powstało w wyniku modyfikacji kwasu salicylowego, np. kwasu acetylosalicylowego (popularnego leku aspiryny) czy salicylanu fenylu (Salolu). Interesującym związkiem jest również kwas salicylurowy, będący głównym metabolitem salicylanów. Dla wspomnianych cząsteczek wykonano symulacje kwantowo-chemiczne w oparciu o Teorię Funkcjonału Gęstości (DFT) w fazie gazowej, a także w obecności rozpuszczalnika. Wpływ wewnątrzcząsteczkowego wiązania wodorowego, obecnego w kwasie salicylowym i salicylanie fenylu, na właściwości cząsteczek został również uwzględniony w badaniach. Analizę topologiczną i struktury elektronowej badanych cząsteczek wykonano według Kwantowej Teorii Atomów w Cząsteczkach (QTAIM) oraz Indeksu Oddziaływań Niekowalencyjnych (NCI).

EN

Salicylates have been used for centuries as medicine for various ailments. Many compounds of this group were obtained as a result of modification of salicylic acid, such as acetylsalicylic acid (a popular aspirin drug) and phenyl salicylate (Salol). Salicyluric acid, which is the main metabolite of salicylates, is also an interesting compound. Quantum-chemical simulations based on Density Functional Theory (DFT) in the gas phase, as well as in the presence of a continuum solvation model, were performed for the mentioned molecules. The effect of intramolecular hydrogen bonding, present in salicylic acid and phenyl salicylate, on the properties of the molecules was taken into account in the study. Topological and electron structure analyses of the molecules were carried out according to the Quantum Theory of Atoms in Molecules (QTAIM) and the Non-Covalent Interactions (NCI) index.

4

Kwas hypodifosforowy i jego sole nieorganiczne

Kinzhybalo Vasyl, Otręba Marta, Ślepokura Katarzyna, Lis Tadeusz

Wiadomości Chemiczne

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2021

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[Z] 75, 3-4

423--466

EN

Hypodiphosphoric acid is the lower oxoacid of phosphorus of H4P2O6 composition. It contains the direct P—P bond, in contrast to its closest analog - pyrophosphoric acid, H4P2O7. In comparison to other phosphates the knowledge on hypodiphosphoric acid and its inorganic salts is quite limited. Since its discovery almost 150 years ago, establishment of the proper molecular and structural formula of the acid has initiated intensive research and dispute in the literature, which was decisively ended in 1964, when the first complete X-ray crystal structure determination of diammonium hypodiphosphate was reported. Since then structural studies have led to the discovery of ferroelectric properties in the above-mentioned diammonium salt and dehydration-induced staggerer-eclipsed transformation of hypodiphosphate in tetrabutylammonium salt, experimental electron density distribution determination in cubic tetralithium hexahydrate and last but not least crystal structure elucidation of hypodiphosphate analogs of adenosine diphosphate. In this mini-review the information on synthesis techniques, chemical and physical properties, applications of hypodiphosphates along with crystallochemical description of reported up-to-date crystal structures are presented.

5

Izomery porfiryny : podobieństwa i różnice

Waluk Jacek

Wiadomości Chemiczne

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2021

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[Z] 75, 5-6

631--652

EN

Porphyrins, “pigments of life”, are extremely popular objects of fundamental research and as candidates for diverse applications. The prerequisite for a successful application is the understanding of the electronic structure. For that purpose, it is instructive to compare the properties of porphyrin with those of its isomers. To date, six such isomers have been synthesized. In this work, we compare the characteristics of all “nitrogen-in”, N-confused- and neo-confused porphyrin isomers, including three structures that have not yet been obtained. We discuss the electronic spectra, intramolecular hydrogen bonding, and tautomerism. Analysis of the energy pattern of frontier orbitals allows predicting the redox properties, as well as the pattern of electronic absorption and magnetic circular dichroism (MCD) spectra. In turn, the geometry of the inner cavity is the factor that determines the strength of hydrogen bonds and, in consequence, the kinetics of tautomerization.

6

Influence of Temperature on the Properties of Cellulose Iβ based on Molecular Dynamics Simulations

Huang Shuang, Wu Xin, Li Peixing

Fibres & Textiles in Eastern Europe

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2021

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Vol. 29, no. 6 (150)

32--36

EN

Natural plants, such as cotton and linen, are rich in cellulose Iβ. The properties of cellulose Iβ under different temperatures was studied using molecular dynamics simulations. Firstly, the crystal of cellulose Iβ was built. To verify the model, the X-ray fibre diffraction and thermal expansion coefficients were calculated, which were found to agree with experimental results. Then the Mulliken population of the bonds were computed and the movement of the centre chain and hydrogen bonds studied over the range 300-550 K using a PCFF force field. The results of the Mulliken population reveal the three steps of pyrolysis. The higher the temperature is, the more intensely the movement of the centre chain is. However, the impact of temperature on the movement of the centre chain is not obvious. From 300 K to 550 K, the total number of hydrogen bonds decreased by only 20%. Moreocer, the rupture of intrachain hydrogen bonds and the formation of interchain hydrogen bonds at 400 K~450 K temperature occurred.

7

Modeling electromagnetic nanostructures and experimenting with nanoelectric elements to form periodic structures

Steinbauer Miloslav, Pernica Roman, Zukal Jiri, Kadlec Radim, Bachorec Tibor, Fiala Pavel

Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska

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2020

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T. 10, nr 4

4--14

EN

We discuss the numerical modeling of electromagnetic, carbon-based periodic structures, including graphene, graphane, graphite, and graphyne. The materials are suitable for sub-micron sensors, electric lines, and other applications, such as those within biomedicine,photonics, nano-and optoelectronics; in addition to these domains and branches, the applicability extends into, for example, microscopic solutions for modern SMART elements. The proposed classic and hybrid numerical models are based on analyzing a periodic structure with a high repeatability, and they exploitthe concept of a carbon structure having its fundamental dimension in nanometers. The models can simulate harmonic and transient processes;are capable of evaluating the actual random motion of an electric charge as a source of spurious signals; and consider the parameters of harmonic signal propagation along the structure. The results obtained from the analysis are utilizable for the design of sensing devices based on carbon periodic structures andwere employed in experiments with a plasma generator.The aim is to provide a broader overview of specialized nanostructural modeling, or, more concretely, to outline a model utilizable in evaluating the propagation of a signal along a structure’s surface.

PL

W artykule omówiony został procesnumerycznegomodelowaniaelektromagnetycznych, węglowych struktur okresowych, w tym grafenu, grafanu, grafitu i grafinu. Materiały te nadają się do czujników submikronowych, przewodów elektrycznych i innych zastosowań, takich jak biomedycyna, fotonika, nano-i optoelektronika.Oprócz tych dziedzin i gałęzi przemysłu, zastosowanie materiałów pokrywa się także na przykład z mikroskopijnymirozwiązaniamidla nowoczesnych elementów SMART. Proponowane klasyczne i hybrydowe modele numeryczneopierają się na analizie okresowej struktury o wysokiej powtarzalności i wykorzystują koncepcję struktury węglowej o podstawowym wymiarze w nanometrach. Modele mogą symulować procesy harmoniczne i przejściowe,potrafią ocenić rzeczywisty losowy ruch ładunku elektrycznego jako źródła fałszywych sygnałówi uwzględniająparametry propagacji sygnału harmonicznego wzdłuż konstrukcji. Rezultaty uzyskane w wyniku analizy można wykorzystać do projektowania czujników opartych na węglowych strukturach okresowych oraz do eksperymentów z generatorem plazmy. Celem jest zapewnienie szerszego przeglądu specjalistycznego modelowania nanostrukturalnego lub, bardziej konkretnie, zarysumodelu nadającego się do oceny propagacji sygnału wzdłuż powierzchnistruktury.

8

Efekt kooperatywności oddziaływań niekowalencyjnych w wybranych układach molekularnych stabilizowanych wiązaniami wodorowymi i halogenowymi

Domagała Małgorzata, Dominikowska Justyna, Palusiak Marcin

Wiadomości Chemiczne

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2019

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[Z] 73, 1-2

33--52

EN

Among various so-called weak interactions, a halogen bond [8 and references therein] is currently probably one of more explored by researchers. This is due to the fact that it has several properties in common with the hydrogen bonding, and thus, similarly as already well characterised H-bond, it may have a crucial role in different physical, chemical, and biological processes. This bond is formed due to stabilising interactions between a region of positive charge located on a surface of the halogen atom and the other atomic center possessing the electron charge surplus (e.g. a lone pair) [8]. The region of positive charge appears on the halogen atom surface due to deformation of its electron cloud resulting in its ellipsoidal shape with the short axis opposite the covalent bond and the long axis in the perpendicular direction [11]. This results in a particular distribution of local charges on the atomic surface, as shown in Figure 1. As a consequence the halogen atom may exhibit a dual character, acting as either electron charge donor or acceptor, depending on the type of interaction and the direction of the appearing interactomic contact. A good example of such situation is shown in Figure 2. Thus, one may consider the situation when two interactions are formed simultaneously and the halogen atom acts as an electron charge donor and acceptor at the same time. For such situation the synergism of both interactions may strengthen complexation. In order to analyze that case, various representative complexes were investigated [13, 17, 18, 20, 21] by means of many-body interaction approach [5, 6]. In general, it appears that as distinct to hydrogen bond [2–4], the synergism is rather weak, with some exceptions for iodine atom due to stronger halogen bonds formed by that atomic centre [13, 17, 18]. In the case of halo-amine tetramers [21] the additional stabilising effect derived from back bonding of π type was found – for the first time for a halogen bond.

9

Charakterystyka mocy poszczególnych wiązań wodorowych w parach zasad DNA

Szatyłowicz Halina, Sadlej-Sosnowska Nina, Jezierska Aneta

Wiadomości Chemiczne

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2019

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[Z] 73, 1-2

53--74

EN

The main idea of the current review is to present methods useful to characterize the strength of individual hydrogen bonds in nucleic acids base-pairs. In the paper, the Authors discuss the energy definition of intermolecular interactions taking into account the presence of one intermolecular hydrogen bond (HB) as well as the situation when several intermolecular interactions (namely intermolecular hydrogen bonds) are present. In the Section 2 of the review a general overview of methods developed to estimate the strength of the individual intermolecular hydrogen bond in DNA/RNA base-pairs is presented. Thus, the reader can find detailed information on the methods used so far: the rotational method (2003), compliance constants method (2004), the EML equation application (2006), the atom replacement method (2007), the estimation of hydrogen bond energy on the basis of electron density (calculated by using the AIM theory) at BCP values (2009), the application of NBO method (2010), the comparison of HB strength based on the last two approaches (2015) and the application of coordinates interaction approach (2017). It should be emphasized, that these methods allow to estimate the strength of intermolecular interactions both in the model base-pairs and in other systems with several intermolecular hydrogen bonds. The discussion of the presented methods is supported by Tables 1-10, containing numerical values characteristics of the strength of the particular HB, and Figures 1–2. The section 3 contains a critical comparison of results based on the presented methods. Concluding remarks are given in the last Section.

10

Borowce jako centra kwasów Lewisa w oddziaływaniach międzycząsteczkowych : porównanie z wiązaniami wodorowymi

Grabowski S. J.

Wiadomości Chemiczne

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2017

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[Z] 71, 7-8

447--471

EN

The triel bonds are analyzed and compared with the hydrogen bond interaction. The triel bonds belong to the class of interactions that are named as the σ-hole and π-hole bonds. The σ-hole bond is an interaction between the σ-hole characterized by the positive electrostatic potential and the electron rich regions such as lone electron pairs, π-electron systems, in other words, centers paying a role of Lewis bases. The σ-holes may be observed for elements of the 14–18 groups of the periodic system and the corresponding interactions with Lewis bases are named; tetrel, pnicogen, chalcogen, halogen and aerogen bonds, respectively. On the other hand, π-holes also characterized by the positive electrostatic potential are observed for centers in planar molecules or planar fragments of molecules in regions above those planes. π-holes may be attributed to triel centers (13th group of the periodic system). The boron and aluminium trihydrides and trihalides are examples of molecules where triels are characterized by π-holes. The mechanism of the triel bond formation is very similar to the mechanism of the formation of the hydrogen bond. It is the Lewis acid – Lewis base interaction where the electron charge transfer from the base unit to the acid one is observed. Next there is outflow of the electron charge from the triel center to the other parts of the Lewis acid unit; in other words the positive charge of the triel center increases as a result of complexation. The triel bonds are often very strong and often they possess characteristics of typical covalent bonds; this is confirmed by the QTAIM (Quantum Theory of Atoms in Molecules) and NBO (Natural Bond Orbital) approaches. For example, for the triel bonds the bond paths between the triel center and the Lewis base center are observed with the bond critical points (BCPs) attributed to those paths. Similarly for the A-H…B hydrogen bonds the H…B bond paths are observed. The parameters of those BCPs often indicate the covalent character of the triel bonds and analogously those characteristics for H-bonds may also indicate the covalent character of the latter interactions. It is very interesting that the triel bonds are observed experimentally in the real systems; for example in crystal structures. The triel center which is trivalent and possesses the trigonal configuration is hypovalent; it means that the octet rule is not obeyed here because of the valence electrons´ deficiency (the triel center possesses six valence electrons in such species). Thus it may interact with one Lewis base ligand reaching rather stable octet and tetrahedral configuration. If the trivalent triel center interacts with two Lewis base ligands thus it may lead to the configuration of the trigonal bipyramid with the hypervalent and pentavalent triel center. These kinds of the triel species occur in crystal structures that are described here.

11

Skręty zwrotne w peptydach i białkach. Mimetyki skrętów zwrotnych. Część 1

Owińska M.

Wiadomości Chemiczne

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2016

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[Z] 70, 9-10

598--611

EN

The secondary structure of the proteins can be divided into α-helix, βsheet and reverse turns. A reverse turn is defined as a site where a polypeptide chain reverses its overall direction. It leads the chain to fold back on itself by almost 180°. Another condition for defining this motif is the amount of amino acid residues involved in forming the turn that can not be greater then six and polypeptide chain in this region can not be in helical conformation [1]. Turns are classified as: γ-turn, β-turn, α-turn and π-turn, which are formed by 3-, 4-, 5- and 6- amino acid residues, respectively. Turns defined as “closed” are stabilized by intramolecular hydrogen bonds between the main chain carbonyl group from the first residue and the main chain amide group from the last residue in the turn. This results in formation of 7-, 10-, 13- and 16-membered pseudo-rings, respectively (Fig. 1, Fig. 2). The other group of turns also stabilized by hydrogen bond, but conversely between the main chain amide group of the first residue and the carbonyl group of the last residue, are δ-turn (2-residues, 8-membered pseudo-ring) and ε-turn (3-residues, 11-membered pseudo-ring) (Fig. 2) [10–13]. These are seldom found in proteins. Turns are considered irregular structures due to the lack of clearly defined torsion angle preferences. because of that, each of the turn types can be further divided into several different subtypes (Table 1, 2 and 3) [1, 15, 31]. The “open” type structures are not stabilized by hydrogen bonds, but Cα-Cα distance between the first and the last residue in main chain is up to 10 A [10]. As turns can be found mostly on the surface of the proteins they play the important role in folding processes, thus enabling the formation of the tertiary structure [2]. The turns are also responsible for the interactions between proteins, recognition processes and ligand-receptor interactions [3–8]. In the following article, the classification and characterization of the turn types is described. The particular attention was given to the γ and β turns, as these are most commonly found in proteins structure.

12

Propedeutyka kierunkowych oddziaływań miedzycząsteczkowych. Wiązania wodorowe, oddziaływania asocjacji warstwowej i wiązania halogenowe

Kruszyński R.

Zeszyty Naukowe. Chemia / Politechnika Łódzka

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2011

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Z. 50

5-47

EN

The review presents the typical bonding intermolecular interactions: hydrogen bonds, halogen bonds and stacking interactions. The first part describes the specific types of intermolecular interactions, including their definitions, energy and selected properties. The second part deals with the application of quantum-mechanical methods to study of intermolecular interactions, especially the appliance of the natural bond orbitals method, and usage of ab intio calculations for solving of structural problems appearing during the above mentioned studies. All above referred interactions have been presented in orbital terms. The third part describes the novel employment of graph theory to characterise the motifs formed by intermolecular interactions in the solid state.

13

Doświadczalne metody badań hydratów gazowych

Lorenc M., Warowny W.

Wiertnictwo, Nafta, Gaz

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2011

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T. 28, z. 1-2

227-251

PL

Poznanie natury hydratów gazowych opiera się głównie na badaniach doświadczalnych w skali laboratoryjnej i ćwierć-technicznej oraz na teorii popartej obliczeniami i symulacjami komputerowymi. W pracy przedstawiono metody pomiarowe dotyczące tworzenia lub/i zapobiegania tworzenia się hydratów gazowych, badania ich właściwości oraz wykorzystanie w nowych technologiach. Generalnie badania doświadczalne hydratów gazowych i hydratacji można podzielić na kilka grup tematycznych: doświadczalne i obliczeniowe wyznaczanie równowag fazowych, badania parametrów fizykochemicznych i strukturalnych, pomiary kinetyczne, w tym nukleacji i aglomeracji cząsteczek, badania wpływu na hydratację inhibitorów i surfaktantów, możliwość zastosowań technologicznych, w szczególności hydratu metanu, w tym wydobycia, przesyłu, magazynowania i oczyszczania, plus badania geologiczne i geofizyczne w celu oszacowania zasobów hydratu metanu.

EN

Knowledge of the nature gas hydrates is connected mainly with experimental studies in laboratory and pilot plant and theory supported by calculations and computer simulations. In work have been given methods of measurement dealing with: formation and/or prevention of formation gas hydrates, studies their properties, and utilization in new technologies. Generally, studies of the gas hydrates and hydratation can be divided on several thematic groups: experimental and calculated determination of phase equilibrium, studies of the physicochemical and structural parameters, kinetic measurements, including nucleation, and agglomeration of particles, studies influence of inhibitors and surfactants on the hydratation process, possibility of technological applications, especially hydrate of methane, including getting out, transport, storage and purification, plus geological and geophysical studies carried out in order to estimation methane hydrate deposits.

14

Wiązanie wodorowe i inne oddziaływania typu kwas Lewisa-zasada Lewisa

Grabowski S. J.

Wiadomości Chemiczne

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2011

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[Z] 65, 11-12

975-1001

EN

Hydrogen bond is analyzed very often since its importance in numerous chemical, physical and biological processes is very well known. It covers the broad range of various interactions; sometimes this is the subject of discussions and polemics if some of them may be classified as hydrogen bonds. This is because there are numerous definitions of hydrogen bond interaction, often they are hardly accepted since they are not univocal. For example one can mention different types of the proton acceptors for hydrogen bonds; one center electronegative atoms, multi-center acceptors such as đ-electrons or even ó-electrons. There are the other interactions which play the key role in various processes and phenomena. All are often named as no-covalent interactions but the other term, Lewis acid–Lewis base interactions seems to be more accurate. One can mention halogen bond, hydride bond or dihydrogen bond. These interactions may be treated as counterparts or competitors of hydrogen bond. The common characteristic for them, including hydrogen bond, is the electron charge transfer from the Lewis base to the Lewis acid. It was found that the amount of this transfer corresponds roughly to the strength of the interaction. In recent years the ó-hole concept was introduced and developed and it was applied to the Lewis base–Lewis acid interactions. According to this concept the atomic centers are characterized by the presence of the regions of positive and negative electrostatic potentials; very often both regions are detected even for atoms which are commonly known as electronegative ones. In such a way halogen atoms, especially if connected by covalent bond with carbon, may act as Lewis acids and also as Lewis bases. In the first case the halogen bond is formed, recently extensively studied. In this review the characteristics of different Lewis base–Lewis acid interactions are given as well as their common features are presented.

15

Keratyna : źródła, właściwości, zastosowanie

Staroń P., Banach M., Kowalski Z.

Chemik

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2011

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Vol. 65, nr 10

1019-1026

PL

Celem artykułu jest scharakteryzowanie keratyny. Należy ona do rodziny białek fibrylarnych. Głównym źródłem naturalnego występowania keratyny są odpadowe pióra z przemysłu drobiarskiego. W skali globalnej powstaje ponad 4 mln ton tego odpadu w ciągu roku i należy go unieszkodliwiać. Keratyna charakteryzuje się dużą odpornością na czynniki fizyczne i chemiczne, dlatego niezwykle ważne jest poszukiwanie nowych metod przerobu odpadów keratynowych. Pozwoli to uniknąć problemu składowania odpadowego pierza. W pracy przedstawiono ponadto sposoby otrzymywania, degradacji oraz zastosowania keratyny.

EN

The aim of the article is the keratin characterization. Keratin belongs to the group of fibril proteins. The main source of natural occurrence of keratin are feathers from poultry industry. In the whole world there are 4 M tones a year of feathers, which should be utilized. Keratin has a high immunity to physical and chemical factors and it is the reason of searching for a new methods of keratin waste conversion. It would help to avoid a problem with storage of feather waste. The scientific work represents also methods of receiving, degradation and application of keratin.

16

Hydrogen-bond puzzle

Grodzka J., Pomianowski A.

Physicochemical Problems of Mineral Processing

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2010

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Vol. 44

35-40

EN

A scientist creating the models of material structures works in a way similar to the artist painting from the nature. Various models, similarly as different images may describe the same reality in a better or worse way. We think that it is the time to admit that the models of the percolating lattice and dynamic clusters are two images of the same structure of water, viewed from different perspectives. We believe that the most important will be such improvement of the basic model of the structure of water molecule that both ways of its modeling would give practically the same consistency with experimental results.

PL

Uczony - tworząc modele struktur materialnych - postępuje jak artysta malujący obrazy z natury. Podobnie jak różne obrazy, tak też różne modele mogą lepiej lub gorzej opisywać tę samą rzeczywistość. Sądzimy, że nadszedł czas aby uznać, że modele, zarówno perkolującej sieci, jak też dynamicznych klasterów to dwa obrazy tej samej struktury wody, lecz oglądanej z innych perspektyw. Odnosimy wrażenie, że środek ciężkości zagadnienia przenosi się wyraźnie na takie udoskonalenie podstawowego modelu molekuły wody, aby obie drogi modelowania jej struktury, dawały praktycznie taką samą zgodność z wynikami prac doświadczalnych.

17

Theoretical and Spectroscopic Study of Infrared Spectra of Hydrogen-Bonded 2,4-Dithiouracil Crystal and Its Deuterated Derivative

Kwiendacz J., Boczar M., Boda Ł., Wójcik M. J.

Polish Journal of Chemistry

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2009

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Vol. 83, nr 5

895-915

EN

Theoretical simulation of the bandshape and fine structure of the N–H(D) stretching bands is presented for 2,4-dithiouracil and its deuterated derivative taking into account an harmonic coupling between the high-frequency N–H(D) stretching and the low-frequency NźźźS stretch ingvibrations, resonance interaction between two equivalent hydro gen bonds in the dimer, anharmonicity of the potentials for the low-frequency vibrations in the ground and excited state of the N–H(D) stretching mode, Fermi resonance between the N–H(D) stretching and the first over tone of the N–H(D) bending vibrations, and electrical anharmonicity. The effect of deuteration has been successfully reproduced by our model calculations. In fra red, far-in fra red, Raman and low-frequency Raman spectra of the polycrystalline 2,4-dithiouracil have been recorded. The geometry and experimental frequencies are compared with the results of harmonic and an harmonic DFT calculations.

18

The Nature of Hydrogen Bonding in Selected Hydrazide Derivatives Investigated via Static Models and Car-Parrinello Molecular Dynamics

Jezierska A., Novič M., Panek J. J.

Polish Journal of Chemistry

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2009

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Vol. 83, nr 5

799-819

EN

The geometric and spectrocopic properties of 2-hydroxy-thiobenzhydrazide and 2-hydroxy-benzhydrazide were investigated within the frame work of Density Functional Theory (DFT). Special attention was devoted to the description and analysis of intra- and intermolecular hydrogen bonds. The choice of the compounds was dictated by their structural similarity and the presence of two types of hydrogen bridges: O–H...S (in 2-hydroxy-thiobenzhydrazide, less common) and O–H...O (in 2-hydroxy-benzhydrazide). The latter could be classified as a low-barrier hydrogen bond (LBHB). First the DFT method was used to obtain the geometric parameters for the monomeric and dimeric forms of the compounds at various levels of theory. Then the binding energy was calculated for the dimeric forms to estimate the strength of the intermolecular hydrogen bonds. Atoms in Molecules (AIM) theory was applied to show quantitatively how the formation of the intermolecular hydrogen bonds affects the strength of the intramolecular hydrogen bonds. The electron density and its Laplacian were calculated for the bond critical points defining the H-bridges. Car-Parrinello molecular dynamics (CPMD) was then used to investigate the changes in the geometric parameters as a function of simulation time. This part of the computational study was performed in vacuo and in the solid state. The vibrational properties of the investigated hydrazides were obtained via Fourier transform of the autocorrelation functions of the dipole moment and atomic velocity. It was found that the formation of the intermolecular H-bonds does not significantly affect the strength of the intramolecular H-bonds. There fore inductive and steric effects out side the immediate vicinity of the intramolecular bridge have minor influence on its investigated properties. The application of CPMD gave a more detailed picture of the bridged protons’ dynamics. The computational results agree with available experimental data. The influence of the intermolecular hydrogen bonding net work and non-bonded crystal field interactions on the vibrational features of the investigated molecules is demonstrated and discussed.

19

Nonconventional Hydrogen Bonding and Vertical Electron Detachment in Anionic Complexes of Gold with DNA Bases: Few Essayistic Fragments

Kryachko E. S.

Polish Journal of Chemistry

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2009

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Vol. 83, nr 5

917-931

EN

The present work performs the computational Gedanken experiments on an ion photo-electron spectroscopy for the complexes [Au-DNA base]– established between the auride anion Au- and the DNA bases thanks to the nonconventional hydrogen bond where Au- casts as the nonconventional proton acceptor. The fascinating phenomenon of the proton acceptor character of Au- to form a variety of nonconventional hydrogen bonds with the DNA bases is computationally unveiled in the present work which also shed a light on the mechanism of the vertical electron detachments of [Au-DNA base]– and their further access of the ground electronic states of the neutral parent hood complexes [Au-DNA base].

20

Hydrogen Bonds and Electrostatic Interactions in N-(Ethoxycarbonylmethyl)-quinuclidinium Chloride Dihydrate

Dega-Szafran Z., Katrusiak A., Szafran M.

Polish Journal of Chemistry

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2009

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Vol. 83, nr 5

723-735

EN

N-(Ethoxycarbonylmethyl)-quinuclidinium chloride crystallizes as dihydrate, QNBEźClź2H2O. The crystals are monoclinic, space group C2/c. Water molecules interact with the chloride an ions and form a cyclic oligomer, through the O–HźźźCl and O–HźźźO hydrogen bonds. The chloride an ions and water molecules addition ally interact electrostically with the positively charged nitrogen atom of the quinuclidinium moiety. The optimized structure of QNBEźClź2H2O by the B3LYP/6-31G(d,p) level of the ory reproduces well the molecular aggregation observed in the crystal. The FTIR spectrum of the solid compound is consistent with the X-ray structure.