Adsorption of sulfur mustard on clean and water-saturated ZnO(101¯0): Structural diversity from first-principles calculations.

We investigate the adsorption of a chemical warfare agent, namely sulfur mustard (SM), on clean and water-saturated ZnO(101¯0) surfaces using density functional theory calculations to understand the first step of its efficient neutralization to less toxic chemical compounds. We determine the relative stability of various SM conformers adsorbed at different sites on both ZnO surfaces. The unique hydrogen bonding patterns obtained for the idealized clean and the more realistic water-saturated ZnO surface are analyzed and their influence on the stability of the SM@ZnO structures is demonstrated. We find that absolute values of the calculated binding and interaction energies are significantly higher for the clean than for the water-saturated ZnO surface due to the formation of Cl⋯Zn and S⋯Zn contacts. The high adsorptive reactivity of the clean ZnO surface is also evident from the strong structural changes of the initial local energy minimum gas-phase conformations of the SM molecules upon adsorption. This phenomenon is not observed for the water-saturated ZnO surface, which has almost no impact on the SM conformation after adsorption, leaving it as it exists in the gas phase. The insights from the results obtained provide a missing piece toward the understanding of the complex mechanism of SM neutralization on ZnO surfaces.

Conformational diversity of the THF molecule in N2 matrix by means of FTIR matrix isolation experiment and Car-Parrinello molecular dynamics simulations.

Tetrahydrofuran (THF) is a widely used chemical compound, in particular as a solvent in organic and inorganic synthesis. The THF molecule has also an interesting property, namely, undergoes pseudorotation, similar to the case of the cyclopentane. Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. We study the influence of the molecular environment (N2) on the Cs-C2 equilibrium of tetrahydrofuran in the THF@N2 system utilizing nitrogen matrix isolation infrared spectroscopy. We observe a different ratio between envelope (Cs) and twisted (C2) conformations with respect to a change of the temperature. FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. On the basis of the THF@N2 matrix model, with explicit nitrogen molecules, the anharmonic infrared spectra are generated from the Fourier transformation of the dipole moment autocorrelation function.

Single-walled carbon nanotubes in tetrahydrofuran solution: microsolvation from first-principles calculations.

The molecular interactions between the commonly used solvent tetrahydrofuran (THF) and single-walled carbon nanotubes (SWCNT) are studied using density functional theory calculations and Car-Parrinello molecular dynamics simulations. The competitive interplay between THF-THF and THF-SWCNT interactions via C-H⋯O and C-H⋯π hydrogen bonds is analyzed in detail. The binding energies for different global and local energy minima configurations of THF monomers, dimers, trimers, and tetramers on SWCNT(10,0) were determined. The adsorbed species are analyzed in terms of their coordination to the surface via weak hydrogen bonds of the C-H⋯π type and in terms of their ability to form intermolecular C-H⋯O hydrogen bonds, which are responsible for the self-aggregation of THF molecules and a possible dimerization or tetramerization process. A special focus is put on the pseudorotation of the THF molecules at finite temperatures and on the formation of blue-shifting hydrogen bonds.

Cannabinoid synthases and osmoprotective metabolites accumulate in the exudates of Cannabis sativa L. glandular trichomes.

Cannabinoids are terpenophenolic compounds produced by Cannabis sativa L., which accumulate in storage cavities of glandular trichomes as a part of the exudates. We investigated if tetrahydrocannabinolic acid synthase and cannabidiolic acid synthase, which are involved in the last step of cannabinoid biosynthesis, are also secreted into Cannabis trichome exudates. The exudates were collected by microsuction from storage cavities of Cannabis glandular trichomes and were subjected for proteomic and metabolomic analyses. The catalytic activity of the exudates was documented by cannabigerolic acid biotransformation studies under hydrophobic conditions. Electrophoretic separations revealed protein bands at ˜65 kDa, which were further identified as tetrahydrocannabinolic acid synthase and cannabidiolic acid synthase. The accumulation of the enzymes in trichome exudates increased substantially during the flowering period in the drug-type Cannabis plants. The content of cannabinoids increased significantly after incubating hexane-diluted trichome exudates with cannabigerolic acid. In this study, we showed that Cannabis glandular trichomes secrete and accumulate cannabinoid synthases in storage cavities, and the enzymes able to convert cannabigerolic acid under hydrophobic trichome-mimicking conditions. Metabolite profiling of the exudates revealed compounds with hydrophilic, osmoprotective and amphiphilic properties, which may play a role in providing a necessary aqueous microenvironment, which enables enzyme solubility and biocatalysis under hydrophobic conditions of glandular trichomes.

Identification of drought responsive proteins and related proteomic QTLs in barley.

Drought is a major abiotic stress that negatively influences crop yield. Breeding strategies for improved drought resistance require an improved knowledge of plant drought responses. We therefore applied drought to barley recombinant inbred lines and their parental genotypes shortly before tillering. A large-scale proteomic analysis of leaf and root tissue revealed proteins that respond to drought in a genotype-specific manner. Of these, Rubisco activase in chloroplast, luminal binding protein in endoplasmic reticulum, phosphoglycerate mutase, glutathione S-transferase, heat shock proteins and enzymes involved in phenylpropanoid biosynthesis showed strong genotype×environment interactions. These data were subjected to genetic linkage analysis and the identification of proteomic QTLs that have potential value in marker-assisted breeding programs.

Phenotyping the genus Hypericum by secondary metabolite profiling: emodin vs. skyrin, two possible key intermediates in hypericin biosynthesis.

A wide range of compounds that occur in the genus Hypericum are listed as effective drugs of natural origin. The main biological activities of several Hypericum representatives are due to the presence of naphthodianthrones, phloroglucinols, and other diverse groups of secondary metabolites that synergistically contribute to their therapeutic effects. The regulation of biosynthesis of hypericin as the key bioactive naphthodianthrone remains uncertain. Here, we present liquid chromatography mass spectrometry-based phenotyping of 17 Hypericum species, the results of which suggest an important role for skyrin and its derivatives in the polyketide pathway that leads to hypericin formation. Moreover, we report for the first time the presence of new metabolites in the genus Hypericum that are related to classes of anthraquinones, their derivatives, and phloroglucinols. As skyrin and other species of anthraquinones are rarely found in higher plants but frequently occur in fungal microorganisms, the obtained results suggest that further research on the synthesis pathways of hypericin and the role of anthraquinone derivatives in plant metabolism should be carried out. The fact that these compounds are commonly synthesized in endophytic fungi and perhaps there is some similarity in the metabolic pathways between these organisms should also be investigated.

Solvation of diclofenac in water from atomistic molecular dynamics simulations - interplay between solute-solute and solute-solvent interactions.

The solubility-permeability relationship of active pharmaceutical ingredients determines the efficacy of their usage. Diclofenac (DCL), which is a widely used nonsteroidal anti-inflammatory drug, is characterized by extremely good membrane permeability, but low water solubility limiting drug effectiveness. The present research focuses on the fundamental explanation of this limitation using the combination of ab initio and classical molecular dynamics simulations of different ionic forms of DCL in water, namely, ionized, un-ionized and the mixture of them both. The analysis of diclofenac solvation in an aqueous environment is used to understand the origin of drug precipitation, especially in gastric pH. The used computational approach reveals the formation of micelle-like self-associated aggregates of diclofenac in water as the result of intermolecular π-π interactions and C-Hπ hydrogen bonds. The DCL aggregation in water is shown to depend mostly on drug concentration, protonation and temperature of the aqueous environment. The detected self-association properties of the drug in water are likely to be of great importance during the development of new drug formulations and fabrication of drug adsorbents for wastewater.

Therapy-Related Changes in the Serum Proteome Patterns of Early Stage Breast Cancer Patients with Different Outcomes.

Adjuvant chemo- and/or radiotherapy is applied in a majority of patients treated for early stage breast cancer, although only a small percentage of these individuals are at high risk of metastasis or recurrence. Hence, knowledge of the biomarkers associated with the risk of disease progression might facilitate the planning of an optimal therapy and protect many patients from the toxicity of unnecessary treatment. In this study, we characterized the serum proteome of patients diagnosed with early-stage breast cancer, exhibiting either no evidence of disease five years after the end of therapy or suffering from metastasis, relapse or a second cancer during the corresponding follow-up. Samples collected before treatment and one year after the end of therapy, when no clinical symptoms of a treatment failure was evidenced, were analyzed using two classical proteomics approaches: LC-MS/MS and 2D-PAGE. A total of 42 proteins with relative quantities that were significantly different between pre- and post-treatment samples were identified in either group of patients; however, the observed changes were more frequent in the treatment-failure group. Among the posttreatment samples, 30 proteins were upregulated, and 10 proteins were downregulated, while 11 proteins were upregulated, and eight proteins were downregulated in the control group. Moreover, several proteins exhibited different patterns of changes in both groups of patients. For example, haptoglobin expression increased in the treatment-failure group but decreased in the control group (this pattern of changes was confirmed using an immunoassay). Notably, proteins affected in posttreatment samples in either group of patients could be associated with different molecular and cellular functions, including angiogenesis, blood coagulation and wound healing in the treatment-failure group and cell adhesion and cell death in the control group.

Analysis of Drought-Induced Proteomic and Metabolomic Changes in Barley (Hordeum vulgare L.) Leaves and Roots Unravels Some Aspects of Biochemical Mechanisms Involved in Drought Tolerance.

In this study, proteomic and metabolomic changes in leaves and roots of two barley (Hordeum vulgare L.) genotypes, with contrasting drought tolerance, subjected to water deficit were investigated. Our two-dimensional electrophoresis (2D-PAGE) combined with matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF and MALDI-TOF/TOF) analyses revealed 121 drought-responsive proteins in leaves and 182 in roots of both genotypes. Many of the identified drought-responsive proteins were associated with processes that are typically severely affected during water deficit, including photosynthesis and carbon metabolism. However, the highest number of identified leaf and root proteins represented general defense mechanisms. In addition, changes in the accumulation of proteins that represent processes formerly unassociated with drought response, e.g., phenylpropanoid metabolism, were also identified. Our tandem gas chromatography - time of flight mass spectrometry (GC/MS TOF) analyses revealed approximately 100 drought-affected low molecular weight compounds representing various metabolite types with amino acids being the most affected metabolite class. We compared the results from proteomic and metabolomic analyses to search for existing relationship between these two levels of molecular organization. We also uncovered organ specificity of the observed changes and revealed differences in the response to water deficit of drought susceptible and tolerant barley lines. Particularly, our results indicated that several of identified proteins and metabolites whose accumulation levels were increased with drought in the analyzed susceptible barley variety revealed elevated constitutive accumulation levels in the drought-resistant line. This may suggest that constitutive biochemical predisposition represents a better drought tolerance mechanism than inducible responses.

Degeneracy Lifting Effect in the FTIR Spectrum of Fluoroform Trapped in a Nitrogen Matrix. An Experimental and Car-Parrinello Molecular Dynamics Study.

The FTIR spectra of fluoroform trapped in argon and nitrogen matrixes are studied at T ∼ 10-30 K. The bands of E symmetry show the splitting effect in a nitrogen matrix, which is absent in an argon matrix. The effect is the most prominent in the case of the ν4 CH bending vibration. It decreases slightly with increasing temperature. Both static and Car-Parrinello molecular dynamic simulations suggest that the degeneracy lifting is due to C3v symmetry lowering caused by interactions between fluoroform and all neighbor N2 matrix molecules.

Intramolecular Hydrogen Bonds in Low-Molecular-Weight Polyethylene Glycol.

We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low-molecular-weight polyethylene glycol (PEG) with two to five repeat subunits. Both red-shifted O-H⋅⋅⋅O and blue-shifting C-H⋅⋅⋅O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car-Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen-bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H⋅⋅⋅O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen-bonding patterns of low-molecular-weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C-H⋅⋅⋅O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation.

Structural flexibility of the sulfur mustard molecule at finite temperature from Car-Parrinello molecular dynamics simulations.

Sulfur mustard (SM) is one of the most dangerous chemical compounds used against humans, mostly at war conditions but also in terrorist attacks. Even though the sulfur mustard has been synthesized over a hundred years ago, some of its molecular properties are not yet resolved. We investigate the structural flexibility of the SM molecule in the gas phase by Car-Parrinello molecular dynamics simulations. Thorough conformation analysis of 81 different SM configurations using density functional theory is performed to analyze the behavior of the system at finite temperature. The conformational diversity is analyzed with respect to the formation of intramolecular blue-shifting CH⋯S and CH⋯Cl hydrogen bonds. Molecular dynamics simulations indicate that all structural rearrangements between SM local minima are realized either in direct or non-direct way, including the intermediate structure in the last case. We study the lifetime of the SM conformers and perform the population analysis. Additionally, we provide the anharmonic dynamical finite temperature IR spectrum from the Fourier Transform of the dipole moment autocorrelation function to mimic the missing experimental IR spectrum.

Identification of serum proteome signatures of locally advanced and metastatic gastric cancer: a pilot study.

BACKGROUND: The gastric cancer is one of the most common and mortal cancer worldwide. The initial asymptomatic development and further nonspecific symptoms result in diagnosis at the advanced stage with poor prognosis. Yet, no clinically useful biomarkers are available for this malignancy, and invasive gastrointestinal endoscopy remains the only reliable option at the moment. Hence, there is a need for discovery of clinically useful noninvasive diagnostic and/or prognostic tool as an alternative (or complement) for current diagnostic tools. Here we aimed to search for serum proteins characteristic for local and invasive gastric cancer. METHODS: Pre-treatment blood samples were collected from patients with diagnosed gastric adenocarcinoma at the different stage of disease: 35 patients with locally advanced cancer and 18 patients with metastatic cancer; 50 healthy donors were also included as a control group. The low-molecular-weight fraction of serum proteome (i.e., endogenous peptidome) was profiled by the MALDI-ToF mass spectrometry, and the whole proteome components were identified and quantified by the LC-MS/MS shotgun approach. RESULTS: Multicomponent peptidome signatures were revealed that allowed good discrimination between healthy controls and cancer patients, as well as between patients with locally advanced and metastatic cancer. Moreover, a LC-MS/MS approach revealed 49 serum proteins with different abundances between healthy donors and cancer patients (predominantly proteins associated with inflammation and acute phase response). Furthermore, 19 serum proteins with different abundances between patients with locally advanced and metastatic cancer were identified (including proteins associated with cytokine/chemokine response and metabolism of nucleic acids). However, neither peptidome profiling nor shotgun proteomics approach allowed detecting serum components discriminating between two subgroups of patients with local disease who either developed or did not develop metastases during follow-up. CONCLUSIONS: The molecular differences between locally advanced and metastatic gastric cancer, as well as more obvious differences between healthy individuals and cancer patients, have marked reflection at the level of serum proteome. However, we have no evidence that features of pre-treatment serum proteome could predict a risk of cancer dissemination in patients treated due to local disease. Nevertheless, presented data confirmed potential applicability of a serum proteome signature-based biomarker in diagnostics of gastric cancer.

Structural, Vibrational and Electronic Properties of Defective Single-Walled Carbon Nanotubes Functionalised with Carboxyl Groups: Theoretical Studies.

Covalent sidewall functionalisation of defective zigzag single-walled carbon nanotubes [SWCNTs(10,0)] with COOH groups is investigated by using DFT. Four types of point defects are considered: vacancy (V), divacancy [V2 (5-8-5), V2 (555-777)], adatom (AA) and Stone-Wales (SW). The energetic, structural, electronic and vibrational properties of these systems are analysed. Decreasing reactivity is observed in the following order: AA>V>V2 (555-777)>V2 (5-8-5)>SW. These studies also demonstrate that the position in which a carboxyl group is attached to a defective SWCNT is of primary importance. Saturation of two-coordinate carbon atoms in systems with the vacancy V-7 and with the adatom AA-1(2) is 3.5-4 times more energetically favourable than saturation of three-coordinate carbon atoms for all studied systems. Vibrational analysis for these two systems shows significant redshifts of the ν(CO) stretching vibration of 96 and 123 cm-1 compared to that for carboxylated pristine systems. Detailed electronic-structure analysis of the most stable carboxylated systems is also presented.

A computational study of intramolecular hydrogen bonds breaking/formation: impact on the structural flexibility of the ranitidine molecule.

Ranitidine is a histamine H2-receptor antagonist that reduces gastric acid secretion. We studied the flexibility of the ranitidine molecule with the special focus on the network of diverse intramolecular hydrogen bonds: N-H⋯O, N-H⋯N, C-H⋯O, C-H⋯N and N-H⋯S. We performed static density functional theory calculations of global and local minima and analyzed their stability at finite temperature in the Car-Parrinello molecular dynamics simulations. We observed intramolecular H-bonds breaking/formation crucial for the structural rearrangements leading to the folding process. The lifetimes of the closed structures of ranitidine were also estimated. The existence of hydrogen bonds and their strength were confirmed on the basis of topological parameters in the bond critical points utilizing Quantum Theory of Atoms in Molecules.

Identification of serum proteome components associated with progression of non-small cell lung cancer.

The aim of the present study was to perform comparative analysis of serum from patients with different stages of non-small cell lung cancer (NSCLC) using the three complementary proteomic approaches to identify proteome components associated with the progression of cancer. Serum samples were collected before any treatment from 200 patients with NSCLC, including 103 early stage, 64 locally advanced and 33 metastatic cancer samples, and from 200 donors without malignancy. The low-molecular-weight fraction of serum proteome was MALDI-profiled in all samples. Serum proteins were characterized using 2D-PAGE and LC-MS/MS approaches in a representative group of 30 donors. Several significant differences were detected between serum samples collected from patients with early stage cancer and patients with locally advanced cancer, as well as between patients with metastatic cancer and patients with local disease. Of note, serum components discriminating samples from early stage cancer and healthy persons were also detected. In general, about 70 differentiating serum proteins were identified, including inflammatory and acute phase proteins already reported to be associated with the progression of lung cancer (serum amyloid A or haptoglobin). Several differentiating proteins, including apolipoprotein H or apolipoprotein A1, were not previously associated with NSCLC. No significant differences in patterns of serum proteome components were detected between patients with adenocarcinoma and squamous cell carcinoma. In conclusion, we identified the biomarker candidates with potential importance for molecular proteomic staging of NSCLC. Additionally, several serum proteome components revealed their potential applicability in early detection of the lung cancer.

Structural flexibility of 4,4'-methylene diphenyl diisocyanate (4,4'-MDI): evidence from first principles calculations.

A reactant used globally in the production of polyurethane is the molecule 4,4'-methylene diphenyl diisocyanate (4,4'-MDI). The structural flexibility of 4,4'-MDI is one of the most important molecular properties influencing the polymerization process and this property was therefore modeled using density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (MD) simulations. Global and local minima structures were found and confirmed by vibrational analysis. The energy barriers related to rotation of the aromatic rings were estimated by DFT calculations. The stability of global and local minima was verified by Car-Parrinello (MD) runs at finite temperature. The presence of weak C-H⋯π hydrogen bonds was confirmed by atoms in molecules analysis and found to be responsible for the low energy barriers.

Interplay between molecule-molecule and molecule-substrate interactions: first-principles study of fluoroform aggregates on a hexagonal ice (0001) surface.

The adsorption of fluoroform molecules on a hexagonal ice (0001) surface was studied using static density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (CP-MD) simulations. Extending our previous work on isolated molecules we focus in the present study on the interplay between molecule-molecule and molecule-substrate interactions. Coverages of up to a full monolayer were modeled by introducing two, three and four fluoroform molecules per unit cell of the ice (0001) substrate. Lowest-energy structures of fluoroform aggregates on the ice surface were determined in a systematic search by performing geometry optimizations from a large set of initial configurations chosen by chemical intuition and from snapshots taken from CP-MD simulations. In the vibrational analysis of the optimized geometries both conventional red- and unusual blue-shifting hydrogen bonds were found. The finite temperature stability of the lowest-energy configurations was probed by CP-MD simulations and conformational changes were analyzed in terms of transformations between the global and local minima structures.

Bis(2,2':6',2''-terpyridine)-ruthenium(II) bis-(perchlorate) hemihydrate.

The asymmetric unit of the title compound, [Ru(C(15)H(11)N(3))(2)](ClO(4))(2)·0.5H(2)O, contains one ruthenium-terpiridine complex cation, two perchlorate anions and one half-mol-ecule of water. Face-to-face and face-to-edge π-stacking inter-actions between terpyridine units [centroid-centroid distances = 3.793 (2) and 3.801 (2)  Å] stabilize the crystal lattice The partially occupied water mol-ecule inter-acts with two perchlorate ions via O-H⋯O hydrogen bonds. In the crystal lattice, the complex cations, perchlorate ion-water pairs and the second perchlorate anions are arranged into columns along b direction.

Tris(1,10-phenanthroline-κ(2) N,N')ruthenium(II) bis-(perchlorate).

The asymmetric unit of the title compound, [Ru(C12H8N2)3](ClO4)2, contains one octahedrally coordinated Ru(II) cation of the ruthenium-phenanthroline complex and three differently occupied perchlorate anions: two, denoted A and B, are located on the twofold axis while another, denoted C, is positioned in the proximity of the twofold screw axis. Perchlorate anions B and C are severely disordered. The occupancies of the two major conformers of anion B refined to 0.302 (6) and 0.198 (6). Perchlorate ion C was modeled in two alternate conformations which refined to occupancies of 0.552 (10) and 0.448 (10).