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Plants possess an essential ability to rapidly down-regulate light-harvesting in response to high light. This photoprotective process involves the formation of energy-quenching interactions between the chlorophyll and carotenoid pigments within the antenna of Photosystem II (PSII). The nature of these interactions is currently debated, with, among others, ‘incoherent’ or ‘coherent’ quenching models (or a combination of the two) suggested by a range of time-resolved spectroscopic measurements. In ‘incoherent quenching’, energy is transferred from a chlorophyll to a carotenoid and is dissipated due to the intrinsically short excitation lifetime of the latter. ‘Coherent quenching’ would arise from the quantum mechanical mixing of chlorophyll and carotenoid excited state properties, leading to a reduction in chlorophyll excitation lifetime. The key parameters are the energy gap, $$\Updelta \varepsilon =\varepsilon_{\rm Car}-\varepsilon_{\rm Chl},$$ Δ ε = ε Car - ε Chl , and the resonance coupling, J, between the two excited states. Coherent quenching will be the dominant process when $$-J - J < Δ ε < J , i.e., when the two molecules are resonant, while the quenching will be largely incoherent when $$\varepsilon_{\rm Chl}>(\varepsilon_{\rm Car}+J).$$ ε Chl > ( ε Car + J ) . One would expect quenching to be energetically unfavorable for $$\varepsilon_{\rm Chl} ε Chl < ( ε Car - J ) . The actual dynamics of quenching lie somewhere between these limiting regimes and have non-trivial dependencies of both J and $$\Updelta \varepsilon.$$ Δ ε . Using the Hierarchical Equation of Motion (HEOM) formalism we present a detailed theoretical examination of these excitation dynamics and their dependence on slow variations in J and $$\Updelta \varepsilon.$$ Δ ε . We first consider an isolated chlorophyll–carotenoid dimer before embedding it within a PSII antenna sub-unit (LHCII). We show that neither energy transfer, nor the mixing of excited state lifetimes represent unique or necessary pathways for quenching and in fact discussing them as distinct quenching mechanisms is misleading. However, we do show that quenching cannot be switched ‘on’ and ‘off’ by fine tuning of $$\Updelta \varepsilon$$ Δ ε around the resonance point, $$\Updelta \varepsilon =0.$$ Δ ε = 0 . Due to the large reorganization energy of the carotenoid excited state, we find that the presence (or absence) of coherent interactions have almost no impact of the dynamics of quenching. Counter-intuitively significant quenching is present even when the carotenoid excited state lies above that of the chlorophyll. We also show that, above a rather small threshold value of $$J>10\,\mathrm{cm}^{-1}$$ J > 10 cm - 1 quenching becomes less and less sensitive to J (since in the window $$-J - J < Δ ε < J the overall lifetime is independent of it). The requirement for quenching appear to be only that $$J>0.$$ J > 0 . Although the coherent/incoherent character of the quenching can vary, the overall kinetics are likely robust with respect to fluctuations in J and $$\Updelta \varepsilon.$$ Δ ε . This may be the basis for previous observations of NPQ with both coherent and incoherent features.

Immunoglobulin E (IgE) plays a central role in allergic reactions. IgE is a dynamic molecule that is capable of undergoing large conformational changes. X-ray crystal structures of the Fc region of IgE in complex with various ligands have shown that IgE-Fc can exist in extended and various bent conformations. IgE-Fc consists of three domains: Cε2, Cε3 and Cε4. While the complete NMR backbone assignments of the Cε2 and Cε3 domains have been reported previously, the Cε4 domain has not been assigned. Here, we report the complete backbone assignment of the Cε4 homodimer. Cε4 can be used as a model system to study dynamics and allostery in IgE, as both molecules exist as homodimers and exhibit similar binding properties to a number of ligands.

We introduce a 13C–2H Rotational Echo DOuble Resonance (REDOR) technique that uses the difference between on-resonance and off-resonance 2H irradiation to detect dynamic segments in deuterated molecules. By selectively inverting specific regions of the 2H magic-angle spinning (MAS) sideband manifold to recouple some of the deuterons to nearby carbons, we distinguish dynamic and rigid residues in 1D and 2D 13C spectra. We demonstrate this approach on deuterated GB1, H/D exchanged GB1, and perdeuterated bacterial cellulose. Numerical simulations reproduce the measured mixing-time and 2H carrier-frequency dependence of the REDOR dephasing of bacterial cellulose. Combining numerical simulations with experiments thus allow the extraction of motionally averaged quadrupolar couplings from REDOR dephasing values.

The exciton transfer between light-harvesting complex 1(LH1) and photosynthetic reaction center dimer is investigated theoretically. We assume a ring shape structure of the LH1 complex with dimer in the ring centre. The kinetic equations which describe the energy transfer between the antenna complex and reaction center dimer were derived. It was shown that the dimer does not act as a photon trap. There is a weak localization of the exciton on the dimer and there is relatively rapid back exciton transfer from dimer to antenna complex which depends on the number of the pigment molecules in the antenna ring. The relation between the rates of the exciton transfer from the antenna complex to dimer and back transfer from dimer to antenna complex has been derived.

This article describes the structure of the inclusion complex that a β-cyclodextrin derivative 1, which includes a benzene ring tethered to a cyclodextrin moiety via a C,C-glucopyranoside spacer, forms when its concentration is 9 mM. As we have recently reported, 1 forms an intramolecular inclusion complex at a concentration of 2 mM. By contrast, detailed NMR structural analysis revealed that at a 9 mM concentration, 1 formed a symmetrical pseudo-dimer based on intermolecular inclusion complexiation between two molecules of 1. Thus, the inclusion structures of 1 varied depending on concentration, which indicates that the structure of this β-cyclodextrin derivative could be “concentration-switchable.”, This is a post-peer-review, pre-copyedit version of an article published in Journal of Inclusion Phenomena and Macrocyclic Chemistry. The final authenticated version is available online at: http://dx.doi.org/10.1007/s10847-017-0746-0

Plant cell walls consist of a mixture of polysaccharides that render the cell wall a strong and dynamic material. Understanding the molecular structure and dynamics of wall polysaccharides is important for understanding and improving the properties of this energy-rich biomaterial. So far, solid-state NMR studies of cell wall structure and dynamics have solely relied on 13C chemical shifts measured from 2D and 3D correlation experiments. To increase the spectral resolution, sensitivity and upper limit of measurable distances, it is of interest to explore 1H chemical shifts and 1H-detected NMR experiments for analyzing cell walls. Here we demonstrate 2D and 3D 1H–13C correlation experiments at both moderate and fast MAS frequencies of 10–50 kHz to resolve and assign 1H chemical shifts of matrix polysaccharides in Arabidopsis primary cell walls. Both 13C-detected and 1H-detected experiments are implemented and are shown to provide useful and complementary information. Using the assigned 1H chemical shifts, we measured long-range correlations between matrix polysaccharides and cellulose using 1H–1H instead of 13C–13C spin diffusion, and the 2D experiments can be conducted with either 13C or 1H detection.

The synthesis of a novel supramolecular system comprising of branched polyethylenimine and cyclodextrin, is presented. The synthesis route is based on the self-assembly phenomena with the inclusion of solvent molecules. The systems are formed by a hydrogen-bonding network and host–guest type interactions between the building blocks. It was found that the native cyclodextrin and polyethylenimine are able to form stable systems when the reaction medium constitutes a polar solvent forming host–guest type complexes with cyclodextrin. A special consideration was paid on the detailed spectroscopic analyses of the obtained water-soluble constructs, including ROESY and diffusion-ordered (DOSY) NMR spectroscopy studies. The versatility and significance of DOSY technique for the analysis of the cyclodextrin complexes and its non-covalent systems with branched polymers, were presented. It was also found that the guest molecules that were incorporated in the complexes exhibited enhanced thermal stability. The morphological details in the solid state were obtained by scanning electron microscope. Graphical Abstract Electronic supplementary material The online version of this article (doi:10.1007/s10847-016-0677-1) contains supplementary material, which is available to authorized users.

The coumarilate (coum?) and 1,10-phenanthroline (phen) mixed ligand complexes of Co(II) (1), Ni(II) (2) Cu(II) (3) and Zn(II) (4) were synthesized and structural characterizations were performed by using elemental analysis, magnetic susceptibility, solid-state UV–Vis, FTIR spectra, thermoanalytical TG-DTG/DTA and single-crystal X-ray diffraction methods. The Co(II) and Ni(II) complexes are salt-type compounds, and they have two moles phen ligands bound as bidentate, two moles aqua ligands in coordination sphere and two moles anionic coum? ligand outside of the coordination unit as the counter-ion of the molecular structure. At the same time, the Co(II) and Ni(II) complexes have five moles of aqua ligands as hydrated water outside of the molecules. It was obtained that Cu(II) and Zn(II) complex structures contain one mole of phen ligand, two moles coordinated (coum?) ligand and a one-mole aqua ligand, and the molecules (Cu(II) and Zn(II)) have fivefold structure and obey square pyramidal geometry. Thermal decomposition of each complex started with dehydration (the first removal is the dehydration of complex Co(II) and Ni(II) as removal of hydrate–aqua molecules), and then, the decomposition of organic parts was observed. The thermal dehydration of the complexes takes place in one (Cu(II) and Zn(II)) or two (Co(II) and Co(II)) steps. The decomposition mechanism, thermal decomposition steps and thermal stability of the investigated complexes provide useful data for the interpretation of their structures. The final decomposition products were found to be metal oxides. Some biological applications (antifungal/antibacterial) were performed using structurally characterized compounds. © 2018, Akadémiai Kiadó, Budapest, Hungary. FEF19004.15.005, SÜB-1901.14-01 Acknowledgements This study was financially supported by Sinop University in Turkey (Project No. SÜB-1901.14-01) and Hitit University Scientific Research Unit (Project No: FEF19004.15.005). The authors acknowledge Scientific and Technological Research Application and Research Center, Sinop University, Turkey, for the use of the Bruker D8 QUEST diffractometer. 2-s2.0-85061813314

Erbahar, Doğan (Dogus Author) -- Conference full title: NATO Advanced Research Workshop on Nanoscale Materials for Warfare Agent Detection, NMWAD 2017, 13-17 February, Levi: Finland. Ab initio density functional theory calculations can be used to study the electronic structure of phthalocyanines (Pcs) with different metal centers and functional groups as well as their interaction with selected organic analytes. Optimum adsorption site of the analytes can be interpreted in terms of the charge distribution of the frontier orbitals of Pc and that the Pc reactivity correlates well with the HOMO-LUMO gap. Calculated analyte-Pc interaction energies provide useful information about the suitability of specific Pc isomers to bind specific molecules, deciding about the suitability for sensing of organic pollutants in aqueous media.

Virus families have evolved different strategies for genome uncoating, which are also followed by recombinant vectors. Vectors derived from adeno-associated viruses (AAV) are considered as leading delivery tools for in vivo gene transfer, and in particular gene therapy. Using a combination of atomic force microscopy (AFM), biochemical experiments, and physical modeling, we investigated here the physical properties and stability of AAV vector particles. We first compared the morphological properties of AAV vectors derived from two different serotypes (AAV8 and AAV9). Furthermore, we triggered ssDNA uncoating by incubating vector particles to increasing controlled temperatures. Our analyses, performed at the single-particle level, indicate that genome release can occur in vitro via two alternative pathways: either the capsid remains intact and ejects linearly the ssDNA molecule, or the capsid is ruptured, leaving ssDNA in a compact entangled conformation. The analysis of the length distributions of ejected genomes further revealed a two-step ejection behavior. We propose a kinetic model aimed at quantitatively describing the evolution of capsids and genomes along the different pathways, as a function of time and temperature. This model allows quantifying the relative stability of AAV8 and AAV9 particles. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10867-018-9488-5) contains supplementary material, which is available to authorized users.

The coupling between molecular excitations and nanoparticles leads to promising applications. It is for example used to enhance the optical cross-section of molecules in surface enhanced Raman scattering, Purcell enhancement or plasmon enhanced dye lasers. In a coupled system new resonances emerge resulting from the original plasmon (ωpl) and exciton (ωex) resonances as $$\displaystyle \begin{aligned} \omega_{\pm} = \frac{1}{2}(\omega_{pl} + \omega_{ex}) \pm \sqrt{\frac{1}{4}(\omega_{pl}-\omega_{ex})^2+g^2}, {} \end{aligned} $$ (1) where g is the coupling parameter. Hence, the new resonances show a separation of Δ = ω+ − ω− from which the coupling strength can be deduced from the minimum distance between the two resonances, Ω = Δ(ω+ = ω−).

Thermodynamic and explosive properties of 1-azido-2-nitro-2-azapropane (ANAP) have been determined in a combined computational ab initio and EXPLO5 (Becker—Kistiakowsky—Wilson equation of state, BKW EOS) study. The enthalpy of formation of ANAP in the liquid phase, heat of detonation, detonation pressure and detonation velocity of ANAP were calculated. ANAP compounds were characterized using vibrational (IR and Raman) and multinuclear NMR spectroscopy, elemental analysis and low-temperature single crystal X-ray diffraction. ANAP represents a covalently bound liquid energetic material which contains both a nitramine unit and an azide group in the molecule.

FOX-7 (1,1-diamino-2,2-dinitroethylene) was first synthesized in 1998 by the FOA Defense Research Establishment (Sweden). Synthesis of the FOX-7 and its structural, spectroscopic, and explosive properties are described in this chapter. The chemical reactivity of FOX-7 towards nucleophilic substitution (transamination), electrophilic substitution, and acid-base properties, thermal behavior (phase transformations and thermal decomposition, molecular structure and physical properties, other energetic molecules that are structurally related to FOX-7 are also summarized in this chapter.

Engineered nanoparticles released into the environment may interact with natural organic matter (NOM). Surface complexation affects the surface potential, which in turn may lead to aggregation of the particles. Aggregation of synthetic TiO2 (anatase) nanoparticles in aqueous suspension was investigated at pH 2.8 as a function of time in the presence of various organic molecules and Suwannee River fulvic acid (SRFA), using dynamic light scattering (DLS) and high-resolution transmission electron microscopy (TEM). Results showed that the average hydrodynamic diameter and ζ-potential were dependent on both concentration and molecular structure of the organic molecule. Results were also compared with those of quantitative batch adsorption experiments. Further, a time study of the aggregation of TiO2 nanoparticles in the presence of 2,3-dihydroxybenzoic acid (2,3-DHBA) and SRFA, respectively, was performed in order to observe changes in ζ-potential and particle size over a time period of 9 months. In the 2,3-DHBA-TiO2 system, ζ-potentials decreased with time resulting in charge neutralization and/or inversion depending on ligand concentration. Aggregate sizes increased initially to the micrometer size range, followed by disaggregation after several months. No or very little interaction between SRFA and TiO2 occurred at the lowest concentrations tested. However, at the higher concentrations of SRFA, there was an increase in both aggregate size and the amount of SRFA adsorbed to the TiO2 surface. This was in correlation with the ζ-potential that decreased with increased SRFA concentration, leading to destabilization of the system. These results stress the importance of performing studies over both short and long time periods to better understand and predict the long-term effects of nanoparticles in the environment. Electronic supplementary material The online version of this article (doi:10.1007/s11051-017-3807-9) contains supplementary material, which is available to authorized users.

A comparative study of amine and silver carboxylate adducts [R1COOAg-2(R2NH2)] (R1 = 1, 7, 11; R2 = 8, 12) as a key intermediate in NPs synthesis is carried out via differential scanning calorimetry, solid-state FT-infrared spectroscopy, 13C CP MAS NMR, powder X-ray diffraction and X-ray photoelectron spectroscopy, and various solution NMR spectroscopies (1H and 13C NMR, pulsed field gradient spin-echo NMR, and ROESY). It is proposed that carboxyl moieties in the presence of amine ligands are bound to silver ions via chelating bidentate type of coordination as opposed to bridging bidentate coordination of pure silver carboxylates resulting from the formation of dimeric units. All complexes are packed as lamellar bilayer structures. Silver carboxylate/amine complexes show one first-order melting transition. The evidence presented in this study shows that phase behavior of monovalent metal carboxylates are controlled, mainly, by head group bonding. In solution, insoluble silver salt is stabilized by amine molecules which exist in dynamic equilibrium. Using (bis)amine-silver carboxylate complex as precursor, silver nanoparticles were fabricated. During high-temperature thermolysis, the (bis)amine-carboxylate adduct decomposes to produce silver nanoparticles of small size. NPs are stabilized by strongly interacting carboxylate and trace amounts of amine derived from the silver precursor interacting with carboxylic acid. A corresponding aliphatic amide obtained from silver precursor at high-temperature reaction conditions is not taking part in the stabilization. Combining NMR techniques with FTIR, it was possible to follow an original stabilization mechanism. Graphical abstractThe synthesis of a series (bis)alkylamine silver(I) carboxylate complexes in nonpolar solvents were carried out and fully characterized both in the solid and solution. Carboxyl moieties in the presence of amine ligands are bound to silver ions via chelating bidentate type of coordination. The complexes form layered structures which thermally decompose forming nanoparticles stabilized only by aliphatic carboxylates.

Chemical reactivity in the solid state is an important topic with regards to the exploitation of organic solids. The relatively immobile nature of the molecules in a crystal can lead to highly selective conversions and be exploited in the area of chemical synthesis. It can also, using crystal engineering methods, be used to provide chemical stability, isolating potentially reactive molecules in an environment where conformational and configurational changes required for conversion become impossible. While such effects will be present in both amorphous and crystalline materials this chapter reviews the implications for crystalline solids. It considers the role of the perfect lattice (as revealed by conventional single crystal diffraction methods) as well as the nature and implications of defects (planar, linear and point as well as the terminating faces of a crystal) as possible nucleation sites for transformations to occur.

We describe how we developed and applied two annotation schemes for journal articles in the field of chemistry. The first involves the criteria for identifying a chemical named entity and assigning it a “type”, roughly speaking deciding whether it was a small molecular species, a process that a small molecular species might be involved in, an enzyme, or an adjective or a prefix. The second involves assigning these chemical named entities a “subtype” which describes the reference, for example whether “imidazole” refers to the imidazole molecule itself, the imidazole motif within a larger molecule, or any of a family of molecules bearing the imidazole motif. We also describe how these guidelines and the resulting corpora and software have subsequently been used.

WOS: 000411121500007 In this work, the Langmuir-Blodgett (LB) technique was applied onto the different substrates such as quartz, quartz crystals and gold coated glass for fabricating LB thin films with 25,27-(Dipropylmorpholinoacetamido)-26,28-dihydroxycalix[4]arene. The characteristics of the calix[4]arene LB films were evaluated by UV-Vis, atomic force microscopy (AFM), quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) measurements. The mass deposited on the quartz crystal per bilayer was predicted as 2028.80 ng (7.65 ng mm(-2)) for the calix[4]arene LB film. The sensing abilities of this LB film towards the development of room temperature organic vapor sensing devices were also examined. QCM and SPR systems were fixed to investigate vapor sensing performance of macrocyclic LB films during exposure to volatile organic compounds (VOCs). The macrocyclic LB thin films were more sensitive to dichloromethane than other vapors. The sensitivity and detection limit values of the calix[4]arene QCM sensor to dichloromethane vapor were calculated as 2.023 Hz ppm(-1) and 1.482 ppm, respectively. The sensitivities of the calix[4]arene LB films against organic vapors can be explained with the host-guest interaction between the cavity of molecule and the organic vapor molecules. It is determined that the calix[4]arene LB film is more sensitive to dichloromethane than other vapors at room temperature and the calix[4]arene is a promising material serving as a vapor sensing device. Research Foundation of Usak UniversityUsak University [UBAP 2017/HD-MF001]; Usak University Scientific Analysis Technological Application and Research Center (UBATAM)Usak University This work was supported by the Research Foundation of Usak University (UBAP 2017/HD-MF001). We also thank Usak University Scientific Analysis Technological Application and Research Center (UBATAM) for their support.

The term ‘chiral’ is defined as “geometrical figure, or group of points whose image in a plane mirror cannot be brought to coincide with itself.” The obvious examples are our hands and foot, as left hand (foot) becomes right hand (foot) in a mirror, and vice-versa. In this paper we shall focus on chirality of molecules particularly in the crystalline state where molecules are densely surrounded by neighbouring molecules in an ordered manner. In the crystalline state, conformational flexibility is restricted, and chiral discrimination energy is order of magnitudes larger compared with that in the solution phase. Thus, facile optical resolution during supramolecular crystallization can be achieved. Further, co-grinding of multiple crystals of different compounds produces unique co-crystals or crystals of unique compounds. We have ascribed the origin of these interesting phenomena to the memory of the original crystal structures which is at least partially retained during the solid-state crystallization processes. These novel chiral crystalline chemistries will be introduced, mainly focused on our own work.

Two new isomeric oxazolidin-2-one derivatives have been synthesized through reaction of (E)-3-styrylquinoxalin-2-one with bis-dichloroethylamine hydrochloride in presence of potassium carbonate. The structures of the formed products were established by NMR and mass spectroscopy. The fragmentation patterns of the two novel synthesized oxazolidin-2-ones (1, 2), possessing the same backbone structure, were investigated using electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS) techniques. A simple methodology, based on the use of ESI (positive ion mode) and by increasing the declustering potential in the atmospheric pressure/vacuum interface, collision induced dissociation (CID), was used to enhance the formation of the fragment ions. In general, the novel synthetic oxazolidin-2-one derivatives afforded, in the gas phase, protonated molecules leading to the confirmation of the molecular masses and chemical structures of the studied compounds. The breakdown routes of the protonated molecules were rationalized by conducting low-energy collision CID-MS/MS analyses (product ion scans) using. The structural similarity between the two studied oxazolidin-2-ones explains the similarity observed in their CID-MS/MS spectra and their fragmentation pathways. ESI-MS/MS recorded with increased collision energy values permits us to observe different product ions and allow us to differentiate the two studied isomers. ESI-MS and CID-MS/MS analyses have thus proven to be a specific and very sensitive method for the structural investigation of the two novel synthesized oxazolidin-2-one derivatives.

An understanding of the materials science of a new active pharmaceutical ingredient (API) is crucial at the interface of the chemical synthesis and drug product development. The selection of the crystallisation process and particle attributes during development is a key milestone in the conversion of a new API into a drug product. The physical and chemical properties of an API can impact product performance and process robustness and are strongly influenced by the solid state structure of the API. Product performance can only be assured when the API is delivered to the patient in a chemically and physically stable solid form. In this chapter we will attempt to integrate progress with cutting edge computational tools in academia to the best current industrial practices.

Cyclization reaction dynamics of photochromic thiol-functionalized terphenylthiazole-based diarylethene molecules was investigated by means of femtosecond pump-probe spectroscopy. Third harmonic generation (266 nm) of femtosecond Ti:Sapphire laser (Mira-900F) was used as a pump radiation. As a probe radiation we used supercontinuum generation (450–700 nm). The time constant of cyclization reaction for photochromic thiol-functionalized terphenylthiazole-based diarylethene molecules with alkyl chain is close to 1. 4 ± 0. 1 ps, and the one without alkyl chain is close to 0. 9 ± 0. 1 ps.

An introductory review is presented which places molecular scale modelling within the context of the multi-scale modelling paradigm. The link between constitutive equations for material properties and atomistic calculations is highlighted. The molecular modelling toolkit is described together with approaches for calculating the shapes of crystals and for exploring interactions between crystal surfaces and molecules in the solution environment. Similarly, approaches for the molecular modelling of solutions are described.

Single molecule measurements have shown that a muscle myosin step is driven by biased Brownian movement. Furthermore, they have also demonstrated that in response to strain in the backward direction a detached myosin head preferentially attaches to the forward direction due to an accelerated transition from a weak binding to strong binding state. Because they are consistent with the original Huxley model for muscle contraction, we have built a model that describes macroscopic muscle characteristics based on these single molecule results.

Contains fulltext : 103659.pdf (Publisher’s version ) (Open Access) A correlation has been established between the absorbed fraction of training-set molecules after oral administration in humans and the Quantum Mechanical Polar Surface Area (QMPSA). This correlation holds for the QMPSA calculated with structures where carboxyl groups are deprotonated. The correlation of the absorbed fraction and the QMPSA calculated on the neutral gas phase optimized structures is much less pronounced. This suggests that the absorption process is mainly determined by polar interactions of the drug molecules in water solution. Rules are given to derive the optimal polar/apolar ranges of the electrostatic potential. 01 maart 2012

In the current work we present some pharmacological characteristics of ten new analogues of bradykinin (Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg) modified in the N-terminal part of the molecule with a variety of acyl substituents. Of the many acylating agents used previously with B(2) receptor antagonists, the following residues were chosen: 1-adamantaneacetic acid (Aaa), 1-adamantanecarboxylic acid (Aca), 4-tert-butylbenzoic acid (t-Bba), 4-aminobenzoic acid (Aba), 12-aminododecanoic acid (Adc), succinic acid (Sua), 4-hydroxybenzoic acid, 4-hydroxy-3-methoxybenzoic acid, 3-(4-hydroxyphenyl)propionic acid and 6-hydroxy-2-naphthoic acid. Biological activity of the compounds was assessed in the in vivo rat blood pressure test and the in vitro rat uterus test. Surprisingly, N-terminal substitution of the bradykinin peptide chain itself with aforementioned groups resulted in antagonists of bradykinin in the pressor test and suppressed agonistic potency in the uterotonic test. These interesting findings need further studies as they can be helpful for designing more potent B(2) receptor blockers.

Glycosaminoglycans (GAGs) are anionic polysaccharides, which participate in key processes in the extracellular matrix by interactions with protein targets. Due to their charged nature, accurate consideration of electrostatic and water-mediated interactions is indispensable for understanding GAGs binding properties. However, solvent is often overlooked in molecular recognition studies. Here we analyze the abundance of solvent in GAG-protein interfaces and investigate the challenges of adding explicit solvent in GAG-protein docking experiments. We observe PDB GAG-protein interfaces being significantly more hydrated than protein–protein interfaces. Furthermore, by applying molecular dynamics approaches we estimate that about half of GAG-protein interactions are water-mediated. With a dataset of eleven GAG-protein complexes we analyze how solvent inclusion affects Autodock 3, eHiTs, MOE and FlexX docking. We develop an approach to de novo place explicit solvent into the binding site prior to docking, which uses the GRID program to predict positions of waters and to locate possible areas of solvent displacement upon ligand binding. To investigate how solvent placement affects docking performance, we compare these results with those obtained by taking into account information about the solvent position in the crystal structure. In general, we observe that inclusion of solvent improves the results obtained with these methods. Our data show that Autodock 3 performs best, though it experiences difficulties to quantitatively reproduce experimental data on specificity of heparin/heparan sulfate disaccharides binding to IL-8. Our work highlights the current challenges of introducing solvent in protein-GAGs recognition studies, which is crucial for exploiting the full potential of these molecules for rational engineering. Electronic supplementary material The online version of this article (doi:10.1007/s10822-011-9433-1) contains supplementary material, which is available to authorized users.

A compound exhibits tautomerism if it can be represented by two structures that are related by an intramolecular movement of hydrogen from one atom to another. The different tautomers of a molecule usually have different molecular fingerprints, hydrophobicities and pKa’s as well as different 3D shape and electrostatic properties; additionally, proteins frequently preferentially bind a tautomer that is present in low abundance in water. As a result, the proper treatment of molecules that can tautomerize, ~25% of a database, is a challenge for every aspect of computer-aided molecular design. Library design that focuses on molecular similarity or diversity might inadvertently include similar molecules that happen to be encoded as different tautomers. Physical property measurements might not establish the properties of individual tautomers with the result that algorithms based on these measurements may be less accurate for molecules that can tautomerize—this problem influences the accuracy of filtering for library design and also traditional QSAR. Any 2D or 3D QSAR analysis must involve the decision of if or how to adjust the observed K i or IC50 for the tautomerization equilibria. QSARs and recursive partitioning methods also involve the decision as to which tautomer(s) to use to calculate the molecular descriptors. Docking virtual screening must involve the decision as to which tautomers to include in the docking and how to account for tautomerization in the scoring. All of these decisions are more difficult because there is no extensive database of measured tautomeric ratios in both water and non-aqueous solvents and there is no consensus as to the best computational method to calculate tautomeric ratios in different environments.

Cobalt(II) complexes of 2,2′-dipyridylamine (dpamH) and substituted salicylaldehyde ligands (X-saloH, where X = 5-NO2, CH3, Br and Cl) with the general formula [Co(X-salo)2(dpamH)] (1–4), were synthesized and characterized by physicochemical methods and by spectroscopy (IR and UV–Vis). The octahedral geometry around Co2+ ion and the bidentate chelating mode of the anion X-salo− were proved by single-crystal X-ray diffraction analysis for the complexes [Co(5-CH3-salo)2(dpamH)] (2) and [Co(5-Cl-salo)2(dpamH)] (4). The variable-temperature (76–303 K) magnetic susceptibility measurements showed a paramagnetic nature of the complexes, in accordance with their molecular structure. The simultaneous TG/DTG–DTA technique was used to analyze their thermal behavior under inert atmosphere, with particular attention to determine their thermal degradation pathways, which was found to have a multi-step nature, accompanied by the release of the ligand molecules, as it is partially confirmed by analyzing the amount of gases evolved during heating under experimental conditions comparable with those of TG by using a TG–MS device. Finally, the decomposition kinetics, analyzed by applying the Vyazovkin’s advanced isoconversional method and referred to the elimination of the ligand molecules in the range 200–400 °C (process that was found to be common in all four complexes), confirmed the stability order assessed on the basis of the decomposition temperatures only.

Crystals consist of atoms in a lattice, which are so regularly arrayed as to be diffracted by X-ray. After such an extraordinary regularity of atoms was discovered in crystals by X-ray diffraction, it is quite natural to believe that the building block of crystals should be individual ions, atoms or molecules.

Glycoproteins are formed as the result of enzymatic glycosylation or chemical glycation in the body, and produced in vitro in industrial processes. The covalently attached carbohydrate molecule(s) confer new properties to the protein, including modified stability. In the present study, the structural stability of a glycoprotein form of myoglobin, bearing a glucose unit in the N-terminus, has been compared with its native form by the use of molecular dynamics simulation. Both structures were subjected to temperatures of 300 and 500 K in an aqueous environment for 10 ns. Changes in secondary structures and RMSD were then assessed. An overall higher stability was detected for glycomyoglobin, for which the most stable segments/residues were highlighted and compared with the native form. The simple addition of a covalently bound glucose is suggested to exert its stabilizing effect via increased contacts with surrounding water molecules, as well as a different pattern of interactions with neighbor residues.

If an element deserves praise, then this element is carbon. Its nucleus, along with N and O, catalyzes the fusion of H into He in the sun and sun-like stars. Its minor stable isotope allows chemical structure to be elucidated by 13C-NMR, along with 1H-NMR. Its long-lived radioisotope 14C allows radiocarbon dating, and reaction mechanisms or bioactivities of medicines to be understood by isotopic labeling. Its short-lived radioisotope 11C is used for PET scans. The 16th part of its atomic weight serves as unified atomic mass unit, also called “dalton”. Its allotropes (diamond, graphite, fullerenes) have extremely useful properties. And this above all: it is the element that life is based upon, the central element of organic chemistry, and the element that is present in most of the 7 × 107 substances registered till now. Due to this fact and to the multiple uses of carbon compounds, although it is now known that they do not differ from inorganic compounds, Organic Chemistry is still a distinct part of chemistry. Because carbon atoms form molecules with covalent bonds that can be represented by hydrogen-depleted molecular graphs, this makes molecular structure search the best scientific documentation among all sciences. Substantial consideration is dedicated to carbon allotropes and to derived hydrocarbon fragments such as diamondoids and benzenoids, emphasizing the author’s theoretical contributions to these research fields.

The modern drug discovery scientist is bathed in structural information – structures of target proteins, candidate drug molecules and complexes of the two. Whilst the value of protein-ligand complexes is evident from many reports and reviews of the area, the use and impact of small molecule structures can, however, be more difficult to appreciate. Information about molecular conformations and interactions derived from these structures is such an integrated part of drug discovery that it is hard to tease out the particular value they bring. This chapter attempts to do just that.

(Bio)chemical kinetics seems to be overshadowed by enzyme kinetics, the latter being of extreme importance in biochemistry. The main laws of it were established at the beginning of the last century. The derivation of the main relationships in the textbooks usually follows the old tradition not taking into account the modern developments including computers and software. Here the modeling is based on the present understanding. The interaction of a ligand molecule with another (macro)molecule being of major interest of (bio)chemical kinetics, the interaction is not confined solely to enzyme kinetics. Besides, the ligand is not necessarily inhibitor. (Likewise, the other participant of the interaction is not necessarily the enzyme.) It is easy to see that keeping that in mind make the analysis more general Only basic mathematical knowledge is required to understand and model the processes. Mathematics should be considered here as a tool. Similarly should be considered computers and computer programs.

Only the models with multiple ligand-binding sites (if the concentration of the enzyme or receptor is assumed to be low) are known to yield non-classical kinetics. A qualitative non-classic model of Rabin (1967) in which four conformational (non-structural) states are considered has been presented in a quantitative form. The model contains three extra (compared to the classical one) parameters. It can be reduced to the classical one by changing the parameters. Khl’s Recovery Model (1994) has been simplified, assuming the duration of the (obligatory) recovery phase of the receptor or enzyme (macro)molecule to be a random value distributed exponentially like the other model parameters; the model contains two extra parameters; it can be reduced to the classical one. The modified Khl’s model has been shown to retain all the essential properties of the original one, except for the ability to yield asymmetric doseresponse curves (if plotted in semi-logarithmic scale). Both models yield a diversity of non-classical dose response curves both with a higher and lower steepness. The bi-state model in which the protein concentration is assumed to be high, yields non-hyperbolic kinetics as well; the model is reduced to hyperbolic one if the protein concentration is assumed to be low.

Graphite-like carbon nitride (g-C3N4) is the most perspective material for nanosensors creation used in nanodimensional systems that aid in the chemical and biological protection of human health and environment. Carbon nitride has an extremely wide interval of region of homogeneity (0.55 < C/N

Hydrostatic pressure leads to nonuniform compression of proteins. The structural change is on average only about 0.1 A kbar−1, and is therefore within the range of fluctuations at ambient pressure. The largest changes are around cavities and buried water molecules. Sheets distort much more than helices. Hydrogen bonds compress about 0.012 A kbar−1, although there is a wide range, including some hydrogen bonds that lengthen. In the presence of ligands and inhibitors, structural changes are smaller. Pressure has little effect on rapid fluctuations, but with larger scale slower motions, pressure increases the population of excited states (if they have smaller overall volume), and slows the fluctuations. In barnase, pressure is shown to be a useful way to characterise fluctuations on the timescale of microseconds, and helps to show that fluctuations in barnase are hierarchical, with the faster fluctuations providing a platform for the slower ones. The excited states populated at high pressure are probably functionally important.

Intensive 25 year attempts of researchers with use of superhigh pressures and temperatures to receive maximum saturated by hydrogen fullerane (С60Н60) by means of heterophases reactions of hydrogenation of fullerite (or fullerene) have appeared completely unsuccessful. This fact from the chemical point of view was quite predicted: in heterophase reactions limiting always is the stage of diffusion of one of reagents (in particular, hydrogen) through a layer of the resultant product (in particular, fullerane) therefore the particle of a final product (fullerane) is always non-uniform on composition. Moreover, defullerenization of molecules С60 and С60Нх at temperatures higher 400 °C is observed as at hydrogenation of first, and dehydrogenation of second. Herein is described a new (author method) method of pyrolysis as process of fullerenization (transformation of organic molecules in the closed molecules of carbon and their hydrides) of molecules of benzene, toluene and pyridine, which has allowed to obtain simultaneously and carbon molecules, and them hydrides. Еquiatomic composition fullerane С60Н60, quasi-fulleranes (CnHn-6–CnHn−2 (n = 20–46)) and quasi-fullerenes (C48, C40, C42) as well as small carbon molecules (C3–C11) are detected only in mass spectra of products of fullerenization of organic molecules. In products of fullerenization of pyridine molecules (C5H5N) are detected new heteroatomic molecules such as hydrogenated and hydroxylated azafullerenes (С35N5)H9, (С45N5)(ОН)3Н14 and (С49N11)(ОН)5Н18 as well as homoatomic molecules С60, С48 and С3–С18. This method allows obtain fulleranes and quasi-fulleranes in gramme quantities.

Mathematical models based on the current understanding of co-operativity in ligand binding to the (macro)molecule and relating the dose response (saturation) curve of the (macro)molecule ligation to intrinsic dissociation constants characterizing the affinities of ligand for binding sites of both unliganded and partly liganded (macro)molecule have been developed. The simplified models disregarding the structural properties and considerations concerning conformational changes of the (macro)molecule retain the ability to yield a sigmoid curves of ligand binding and reflect the co-operativity. Model 1 contains only three parameters, parameter f (a dimensionless multiplier characterising the change in the affinity) reflects also the existence and type of co-operativity of ligand binding: f 1, to the negative, and f = 1 to the absence of any co-operativity. Model 2 contains an extra parameter, s, for the equilibrium of T0 ↔ R0 is incapable to produce dose response which would suggest negative co-operativity. For any fixed n > 1, the deviation of the dose response (saturation) curve from the Henri hyperbola depends either solely on parameter f (Model 1) or also on parameter s (Model 2). The (macro)molecule being a receptor, both models yield a diversity of dose response curves due to possible variety of efficacies of the (macro)molecule. The models may be considered as extensions of the Henri model: in case the dissociation constants remain unchanged, the proposed models are reduced to the latter.

A molecular graph is the graph of a molecule in which the vertices are atoms and edges are chemical bonds. We review the recent results on computing symmetry of series of armchair polyhex, zig-zag polyhex and C4C8(R/S) nanotubes and nanotori. The topological properties of these nanostructures are also investigated.

The subject of our work is the investigation of boron doped nanocrystalline diamond (NCD) layers functionalized with photosensitive molecules of manganese phthalocyanine. The functionalized NCD sample was used as a working electrode in a three electrode cell and electrochemically studied. The two methods applied were stationary volt-ampere (VA) measurements and cyclic voltammetry (CV) in dark and under illumination. The VA and CV measurements showed that the electrode has a wide potential range and a high photosensitivity. The results obtained are promising for future application of functionalized diamond electrodes in light conversion systems.

The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the Poisson-Boltzmann (PB) model and first solvation water molecules, the influence of solvent effect is also discussed. Benefiting from the fragmentation algorithm, the AF-QM/MM approach is computationally efficient, linear-scaling with a low pre-factor, and thus can be applied to routinely calculate the ab initio NMR chemical shifts for proteins of any size. The results calculated using Density Functional Theory (DFT) show that when the solvent effect is included, this method can accurately reproduce the experimental 1H NMR chemical shifts, while the 13C NMR chemical shifts are less affected by the solvent. However, although the inclusion of solvent effect shows significant improvement for 15N chemical shifts, the calculated values still have large deviations from the experimental observations. Our study further demonstrates that AF-QM/MM calculated results accurately reflect the dependence of 13Cα NMR chemical shifts on the secondary structure of proteins, and the calculated 1H chemical shift can be utilized to discriminate the native structure of proteins from decoys.