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    Wyświetlanie 1-6 z 6
    Tytuł:
    Właściwości czasowo-rozdzielcze słabych międzycząsteczkowych wiązań wodorowych C-H···F
    Time-resolved properties of intermolecular C-H···F hydrogen bonds
    Autorzy:
    Polańska, Marta
    Rodziewicz, Paweł
    Powiązania:
    https://bibliotekanauki.pl/articles/27310029.pdf
    Data publikacji:
    2023
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    wiązanie wodorowe
    teoria funkcjonału gęstości
    dynamika molekularna Cara i Parrinello
    hydrogen bond
    density functional theory
    Car-Parrinello molecular dynamics
    Opis:
    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.
    Źródło:
    Wiadomości Chemiczne; 2023, 77, 9-10; 899--919
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Struktura a nieelastyczne rozpraszanie neutronów przez kryształy molekularne z wiązaniami wodorowymi
    Structure and inelastic neutron scattering by the molecular crystals with the hydrogen bonds
    Autorzy:
    Rok, M.
    Bator, G.
    Sobczyk, L.
    Powiązania:
    https://bibliotekanauki.pl/articles/171492.pdf
    Data publikacji:
    2017
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    kompleksy molekularne
    wiązanie wodorowe
    struktura krystaliczna
    rozpraszanie neutronów
    dynamika cząsteczek w fazie stałej
    molecular complexes
    hydrogen bonds
    crystal structure
    neutron scattering
    molecular dynamics in the solid state
    Opis:
    The molecular crystals, which are built of organic or organic-inorganic molecules, are characterized by the weak intermolecular interactions. From the viewpoint of the potential applications in electronics or optoelectronics the electric properties of the crystals are essential. In turn these properties are related to their crystal structure as well as the dynamics of the molecules in the solid state. The existence of the hydrogen bonds in the crystal structures, conventional and unconventional, is crucial from the viewpoint of the electric properties of the crystals. The dynamics of methyl groups present in the structure can be a measure of the molecular interactions in the crystals. In this work the dynamical properties, first of all taking into account the research results concerning the neutron scattering, will be discussed. The neutron technique is very effective as regards the methyl group dynamics investigations. The relationship between a formation of the conventional and unconventional hydrogen bonds and a tunneling of the methyl groups at low temperature will be discussed. The method of the interpretation of the INS spectra will be described taking into account the theoretical model, the parameters of which are fitted to the experimental data. The examples will regard the following molecular crystals: p-N,N’-1,10-tetraacethyldiaminodurene (TADD) (Figs. 2 and 4), 2,3,5,6-tetramethylpyrazine with chloranilic acid (TMP·CLA) (Figs. 5, 6 and 7), 2,3,5,6- tetramethylpyrazine with bromanilic acid (TMP·BRA) (Figs. 5 and 6) and the crystal of 3,4,7,8-tetramethylphenantroline (Me4phen) and its complex with picric acid (Me4phen·PIC) (Figs. 8 and 9). In this paper we have shown that the surrounding of the methyl group and its interactions with the adjacent molecules has a stronger effect than the changes in the electronic charge density in the molecule.
    Źródło:
    Wiadomości Chemiczne; 2017, 71, 7-8; 533-557
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Nanopory : budowa, właściwości, modele, zastosowania
    Nanopores : structure, properties, models, app lications
    Autorzy:
    Stachiewicz, A.
    Molski, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/171558.pdf
    Data publikacji:
    2013
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    nanopory
    prąd jonowy
    translokacja biopolimerów
    równanie Poissona-Boltzmanna
    równanie Poissona-Nernsta-Plancka
    dynamika molekularna
    nanopores
    ion current
    biopolymer translocation
    Poisson-Boltzmann
    equation
    Poisson-Nernst-Planck equation
    molecular dynamics
    Opis:
    Nanopores are small (1–100 nm diameter) holes/channels formed in biological membranes (Fig. 1) or fabricated in synthetic materials (Fig. 2). Permeation of ions and small molecules through nanopores is common in biological systems. The first experiments where nanopores were used as single-molecule sensors were performed in the 90s [1, 2]. The detection principle is based on a monitoring of an ionic current passing through a nanopore as an electric field is applied across the membrane. Electrically charged particles (e.g. DNA ) move in the electric field and block the ionic current as they pass through the nanopore. A sudden drop of the ionic current signals a single-molecule translocation event (Fig. 3–5). Nanopore sensors can give an information about the analyte: its size, structure and bonds stability. Today, a major topic of interest is the possibility of nanopore DNA sequencing. In this work we present an introduction to nanopore technology and to current research related to potential nanopore applications. First, we describe biological and synthetic nanopores: their structure and methods of fabrication. Next, different modes of nanopore experiments are presented. In the third section, we focus on theoretical models and simulations of nanopores. Finally, we present future perspectives for applications with particular reference to DNA sequencing.
    Źródło:
    Wiadomości Chemiczne; 2013, 67, 3-4; 277-302
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Badanie struktury i dynamiki N-terminalnych sekwencji dermorfiny i ich analogów z wykorzystaniem spektroskopii NMR w ciele stałym i rentgenografii
    Studies on the structure and dynamics of N-terminal sequences of dermorphin and their analogs by means of solid state NMR spectroscopy and XRD
    Autorzy:
    Trzeciak-Karlikowska, K.
    Powiązania:
    https://bibliotekanauki.pl/articles/171648.pdf
    Data publikacji:
    2012
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    peptydy opioidowe
    oddziaływania CH-pi
    dynamika molekularna
    oddziaływanie peptyd–fosfolipid
    spektroskopia NMR
    1H Ultra Fast MAS NMR
    PISEMA MAS
    PILGRIM
    XRD
    opioid peptides
    CH-pi interactions
    molecular dynamics
    peptide–phospholipid interaction
    NMR spectroscopy
    Opis:
    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].
    Źródło:
    Wiadomości Chemiczne; 2012, 66, 9-10; 867-891
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Zastosowanie metod dynamiki molekularnej w badaniach nad układami z wiązaniami wodorowymi
    An application of molecular dynamics methods in investigations of systems with hydrogen bonds
    Autorzy:
    Jezierska, A.
    Panek, J. J.
    Powiązania:
    https://bibliotekanauki.pl/articles/172356.pdf
    Data publikacji:
    2017
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    CPMD
    dynamika molekularna Cara-Parrinello
    klasyczna dynamika molekularna
    wewnątrzcząsteczkowe wiązanie wodorowe
    międzycząsteczkowe wiązanie wodorowe
    zasada Schiffa
    zasada Mannicha
    N-tlenki
    białka
    Car-Parrinello molecular dynamics
    classical MD
    intramolecular HB
    intermolecular HB
    Schiff base
    Mannich base
    N-oxides
    proteins
    Opis:
    Modern computational chemistry offers a wide variety of methods allowing us to investigate very complex systems. In the current study, we would like to focus on ab initio and classical molecular dynamics to show their applications in our research. Car-Parrinello molecular dynamics (CPMD) was carried out to study compounds possessing intra- and intermolecular hydrogen bonds. Our simulations were performed in vacuum, in solvent and in crystalline phase. It is well known that intramolecular hydrogen bonding stabilizes 3D structure of molecules. The strength of the bonding and its features are influenced by inductive and steric effects. Our short overview on CPMD application to systems with intramolecular HB we start from Schiff and Mannich bases -model compounds to investigate intramolecular hydrogen bonding. Other examples reported here derive from the class of N-oxide type compounds. Special attention was devoted to another representative structure in such investigations – picolinic acid N-oxide. In some examples listed above proton transfer phenomena occurred making these compounds interesting objects for future excited state studies. Aliphatic boronic acid was used as a model example to study intermolecular hydrogen bonds based on CPMD method. Further, classical molecular dynamics was applied to investigate proteins. Here, we would like to report our results for two biomolecules. The first one is proteinase K for which the impact of mercury(II) on its catalytic center was studied. The second one is streptavidin. For the latter one its complexes with biotinylated ligands were investigated. We close our review with a paragraph describing further development and perspectives related to CPMD method.
    Źródło:
    Wiadomości Chemiczne; 2017, 71, 7-8; 473-495
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Właściwości wewnątrzcząsteczkowych wiązań wodorowych w wybranych N-tlenkach pochodnych chinoliny
    Intramolecular hydrogen bonds properties in selected N-oxides of quinoline derivatives
    Autorzy:
    Jezierska, Aneta
    Panek, Jarosław J.
    Błaziak, Kacper
    Powiązania:
    https://bibliotekanauki.pl/articles/171511.pdf
    Data publikacji:
    2019
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    DFT
    teoria funkcjonału gęstości
    MP2
    metoda rachunku zaburzeń drugiego rzędu Møllera-Plesseta
    CPMD
    dynamika molekularna Cara-Parrinello
    wewnątrzcząsteczkowe wiązanie wodorowe
    N-tlenki pochodnych chinoliny
    density functional theory
    Møller-Plesset second order perturbation method
    Car-Parrinello molecular dynamics
    intramolecular HB
    N-oxides of quinoline derivatives
    Opis:
    In the current article we would like to summarize our research shedding light onto properties of intramolecular hydrogen bonds present in N-oxide quinoline derivatives. The compounds for the current study were chosen to contain diverse types of hydrogen bonds. Therefore, in the current study we analyze three kinds of hydrogen bonding and their properties. It is well known, that the presence of intramolecular hydrogen bonds stabilizes conformations of molecules. Substituent effects (inductive and steric) influence the strength of the H-bonding as well as its features. Moreover, the intramolecular hydrogen bond in the studied N-oxides belongs to the family of resonance assisted hydrogen bonds (RAHB). Our short overview presents the summary of results obtained for twelve N-oxides of quinoline derivatives. Quantum-chemical simulations were performed on the basis of static models (classical DFT and MP2 approaches) as well as ab initio molecular dynamics (Car-Parrinello MD). The metadynamics method was applied to reproduce the maps of free energy for the motion of the bridged proton. The computations were performed in the gas and in the crystalline phases. Electronic ground state is a natural framework in which chemical compounds exist most of the time. However, in many chemical species we observe a spontaneous internal reorganization of their chemical bonds and atoms e.g. proton transfer phenomenon and the appearance of tautomeric forms already in the ground state. Therefore, it was interesting to investigate some N-oxides in the excited electron state knowing that they exhibit excited- state-induced proton transfer (ESIPT effect). At the end of the article we draw some conclusions related to the intramolecular H-bond properties present in the discussed N-oxides of quinoline derivatives.
    Źródło:
    Wiadomości Chemiczne; 2019, 73, 1-2; 75-95
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-6 z 6

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