Monte Carlo-Simulated Annealing and Machine Learning-Based Funneled Approach for Finding the Global Minimum Structure of Molecular Clusters.

Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e., global potential energy minimum) remains a challenge, especially for highly symmetric clusters. Here, we suggest a new funneled Monte Carlo-based simulated annealing (SA) approach, which includes two key steps: generation of symmetrical clusters and classification of the clusters according to their geometry using machine learning (MCSA-ML). We demonstrate the merits of the MCSA-ML method in comparison to other approaches on several Lennard-Jones (LJ) clusters and four molecular clusters-Ser8(Cl-)2, H+(H2O)6, Ag+(CO2)8, and Bet4Cl-. For the latter of these clusters, the correct structure is unknown, and hence, we compare the experimental and simulated fragmentation patterns, and the fragmentation of the proposed global minimum matches experiments closely. Additionally, based on the fragmentation of the predicted betaine cluster, we were able to identify hitherto unknown neutral fragmentation channels. In comparison to results obtained with other methods, we demonstrated a superior ability of MCSA-ML to predict clusters with high symmetry and similar abilities to predict clusters with asymmetrical structures.

Effect of Field Trial on Silymarin Complex Composition and Antioxidant Assessment of Milk Thistle (Silybum marianum L. Gaertner).

Plant foods are receiving increasing attention as a valuable source of health beneficial compounds. Understanding the impact of growing conditions on the quality of milk thistle is critical for determining appropriate agro-ecological and agro-economic parameters for its production and, subsequently, food products rich in health-beneficial compounds. For this purpose, a randomized milk thistle cultivation trial was established in the experimental field of Agritec Plant Research Plc. in Sumperk, Czech Republic, and carried out for two subsequent growing seasons in 2020 and 2021. The milk thistle achenes, variety Mirel, were sown in the row width of 12.5, 25 and 37 cm; and the qualitative parameters of each field trial such as achenes yields, silymarin complex determination and also antioxidant assessment (total phenolic content, total flavonoids content, DPPH and ABTS radical scavenging activity) were evaluated. The environmental impact of the extraction process was reduced by using pressurized liquid extraction with 60% EtOH (v/v). The weather conditions during the trial as well as the row spacing of milk thistle sowing were revealed to have a significant influence on the evaluated parameters (p ≤ 0.05). The highest yields of evaluated parameters were obtained for the growing season 2021 and the row spacing of 37 cm.

Capillary electrophoretic methods for classification of methicillin-resistant Staphylococcus aureus (MRSA) clones.

This study describes differentiation of methicillin-resistant Staphylococcus aureus (MRSA) isolates belonging to different genotype groups by the combination of electrophoretic techniques, transient isotachophoresis and micellar electrokinetic chromatography. MRSA isolates were separated in fused silica capillary with roughened inner surface prepared by etching with supercritical water. Separation temperature together with the rinsing procedure of the capillary turned out to be the key factors of successful analysis. The individual genotype groups were baseline-resolved in 40 min. Partial separation of the individual isolates within the groups was also observed. Relative standard deviations of the migration times of the isolate zones ranged from 0.32 to 0.79%. In addition, capability of the developed CE method to concentrate and separate MRSA isolates in clinical samples was proved by the analysis of blood sample.

Classification of clinical Cutibacterium acnes isolates at phylotype level by capillary electrophoretic methods in roughened fused silica capillary.

Despite being commensal bacterium involved in the maintenance of healthy skin, Cutibacterium acnes is also associated with inflammatory diseases. Since inflammatory and immunogenic properties vary between C. acnes phylotypes, reliable classification of clinical C. acnes isolates is important for determining their pathogenicity. Combination of optimized separation methods, polymer-enhanced transient isotachophoresis and sweeping of the charged bacterial cells in micellar electrokinetic chromatography in the roughened fused silica capillary, was used for the separation of twenty clinical C. acnes isolates. Their correct classification into the individual phylotypes was achieved in 20 min at laboratory temperature. In addition, decrease in the separation temperature to 15 °C led to the separation of the individual isolates of some phylotypes. Relative standard deviations of migration times of both intra- and inter-day analyses did not exceed 1.7%. Linearity of the proposed method in the concentration range from 5 × 105 to 1 × 107 cells mL-1 was characterized by the coefficient of determination R2 = 0.9985. Limit of detection of 5 × 105 cells mL-1 (50 cells in 100 nL of the injected sample) was determined for all the examined bacteria.

Fabrication of monolithic capillary columns with inner diameter 50-530 µm employing a mixture of pentaerythritol tetraacrylate and polyhedral oligomeric silsesquioxane-methacrylate as crosslinkers.

Highly crosslinked monolithic capillary columns with inner diameters in the range of 50-530 µm were prepared by radical polymerization of pentaerythritol tetraacrylate, polyhedral oligomeric silsesquioxane-methacrylate, and n-octadecyl methacrylate in the presence of methanol, dodecyl alcohol, and polyethylene glycol lauryl ether. Columns were evaluated by inverse size-exclusion chromatography employing a set of polystyrene standards of narrow molecular-size distribution and by scanning electron microscopy. Chromatographic performance under reversed-phase conditions was also evaluated. The combination of two effective crosslinkers as pentaerythritol tetraacrylate and polyhedral oligomeric silsesquioxane-methacrylate in the polymerization mixture allows for the preparation of robust and efficient monolithic capillary columns within a fairly wide range of internal diameters.

Sensitive identification of milk protein allergens using on-line combination of transient isotachophoresis/micellar electrokinetic chromatography and capillary isoelectric focusing in fused silica capillary with roughened part.

A method for on-line concentration of milk proteins from large sample volumes using combination of transient isotachophoresis (tITP) and micellar electrokinetic chromatography (MEKC) in fused silica capillary with an inner roughened part has been developed. The method utilizes reversible dynamic adsorption of proteins onto a thin layer of PEG 4000 on the roughened surface of the capillary. In addition, the tITP/MEKC method was combined with capillary isoelectric focusing (CIEF) for on-line concentration, separation, identification and sensitive determination of proteins in skimmed milk. The method allows analysis of up to 50 µL of sample. This study has focused on the four important whey proteins, bovine serum albumin (BSA), α-lactalbumin (α-LA), and two genetic variants of ß-lactoglobulin (ß-LG A and ß-LG B). The proteins were identified on the basis of their migration times and characteristic pI values. The pI values of BSA, α-LA, ß-LG A, and ß-LG B were determined as 4.7, 4.4, 5.1, and 5.2, respectively. Limits of detection for BSA, α-LA and both ß-LG variants were found as 1.2, 1.0 and 1.0 pg mL-1, respectively. The linearity of calibration curves was characterized by the R2 = 0.9982. The method provided highly reproducible results as the relative standard deviations of the migration times and peak areas of the examined proteins did not exceed 1.6%.

Bacteriophage replication on permissive host cells in fused silica capillary with nanostructured part as potential of electrophoretic methods for developing phage applications.

Phage therapy could offer a safe and effective alternative to antibiotic treatment of infections caused by Gram-positive bacterium Staphylococcus aureus that have emerged as a significant threat in hospital and community environment and is attracting growing interest among clinicians. The legislation process of approving the phage therapeutics by pharmaceutical authorities requires rapid analytical techniques for assessment of phage activity. Here, we present a three-step method for on-line monitoring the phage effect on bacterial cells dynamically adhered from microliter volumes of high conductivity matrix onto the inner surface of fused silica capillary with a part etched with supercritical water. Phage K1/420 particles of the Kayvirus genus generated by propagation on the host S. aureus cells together with the uninfected cells were concentrated, separated and detected using capillary electrophoretic methods. The phage interactions with selected S. aureus strains exhibiting differences in phage susceptibility were compared. The method allowed determination of the phage burst size and time of phage latent period in analyzed strains. Apart from enumeration of bacteriophages by the plaque assays, the proposed method is suitable for phage activity testing.

Rapid Isolation, Propagation, and Online Analysis of a Small Number of Therapeutic Staphylococcal Bacteriophages from a Complex Matrix.

A method for the fast isolation, propagation, and characterization of very low count bacteriophages active against pathogenic bacterial strains is described in this study. Bacteriophages with a count of 102 phage particles were dynamically adhered from the maximum 10 mL blood plasma sample onto the nanostructured part of the fused silica capillary. One-step propagation of phage particles of genus Kayvirus inside the etched capillary on 104Staphylococcus aureus host cells increased their number to 6 × 104 phage particles. Phage particles were concentrated online and separated by capillary electrophoretic methods. No phage replication occurred when the phage-resistant S. aureus or Escherichia coli cells were used. Two-step phage propagation in the capillary allowed an increase in the total virion count to up to 6 × 105 phage particles and subsequent off-line matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of the phage zone collected after capillary electrophoresis. Relative standard deviations of the phage peak area were at most 2.3%. We expect that the method of isolating bacteriophages from blood plasma and their simultaneous identification will facilitate clinical studies of phage preparations and contribute to pharmacokinetics studies during phage therapy. This approach is also suitable for capturing and enriching new phages from the environment when a susceptible indicator strain is available.

Identification of Aspergillus Conidia in Bronchoalveolar Lavage Using Offline Combination of Capillary Electrophoresis in Supercritical Water-Treated Fused Silica Capillary and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry.

Diagnosis of fungal infection in lung parenchyma is relatively difficult. Bronchoscopy with bronchoalveolar lavage is very useful in its diagnosing. Therefore, a method for rapid online concentration and analysis of Aspergillus conidia in bronchoalveolar lavage fluid using the combination of transient isotachophoresis (tITP) and micellar electrokinetic chromatography (MEKC) with subsequent off-line identification of the separated conidia by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is described in this study. In the proposed procedure, conidia were first dynamically adhered onto the roughened part of the inner surface of a fused silica capillary prepared by etching with supercritical water. Then the adhered conidia were desorbed, concentrated, and separated using a combination of tITP and MEKC. Finally, the fractions containing the separated conidia were collected from the capillary and analyzed by MALDI-TOF MS. The adhesion efficiency under the optimized experimental conditions was about 80%. This rapid diagnosis will contribute to timely initiation of therapy and increase the patient's chances of survival.

Nano-etched fused-silica capillary used for on-line preconcentration and electrophoretic separation of bacteriophages from large blood sample volumes with off-line MALDI-TOF mass spectrometry identification.

The properties of staphylococcal phages from the Siphoviridae, Podoviridae, and Myoviridae families were monitored using capillary electrophoretic methods on fused-silica capillaries with different morphology of surface roughness. Isoelectric points of the examined phages were determined by capillary isoelectric focusing in the original, smooth fused-silica capillary, and they ranged from 3.30 to 3.85. For capillary electrophoresis of phages, fused-silica capillaries with the "pock" and "cone" roughened surface types were prepared by etching a part of the capillary with supercritical water. The best resolution of the individual phages (to range from 3.2 to 4.6) was achieved with the "cone" surface-type fused-silica capillary. Direct application of phage K1/420 at the infection site, represented by human plasma or full blood spiked with Staphylococcus aureus, was on-line monitored by micellar electrokinetic chromatography. The phage particles were dynamically adhered onto the roughened surface of the capillary from 10 µL of the prepared sample at the optimized flow rate of 6.5 µL min-1. The limit of detection was determined to be 104 phage particles. The linearity of the calibration lines was characterized by the regression coefficient, R2 = 0.998. The relative standard deviation (RSD) of the peak area, calculated from ten independent measurements, was (±) 2%. After analysis, viability of the detected phages was verified by the modified "double-layer drop assay" method, and collected phage fractions were simultaneously off-line analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Graphical abstract.

Online Concentration of Bacteria from Tens of Microliter Sample Volumes in Roughened Fused Silica Capillary with Subsequent Analysis by Capillary Electrophoresis and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry.

This study presents a timely, reliable, and sensitive method for identification of pathogenic bacteria in clinical samples based on a combination of capillary electrophoresis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In this respect, a part of a single-piece fused silica capillary was etched with supercritical water with the aim of using it for static or dynamic cell-surface adhesion from tens of microliter sample volumes. The conditions for this procedure were optimized. Adhered cells of Staphylococcus aureus (methicillin-susceptible or methicillin-resistant) and of Pseudomonas aeruginosa were desorbed and preconcentrated from the rough part of the capillary surface using transient isotachophoretic stacking from a high conductivity model matrix. The charged cells were swep and separated again in micellar electrokinetic chromatography using a nonionogenic surfactant. Static adhesion of the cells onto the roughened part of the capillary is certainly volumetric limited. Dynamic adhesion allows the concentration of bacteria from 100 µL volumes of physiological saline solution, bovine serum, or human blood with the limits of detection at 1.8 × 102, 1.7 × 103, and 1.0 × 103 cells mL-1, respectively. The limits of detection were the same for all three examined bacterial strains. The recovery of the method was about 83% and it was independent of the sample matrix. A combination of capillary electrophoresis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry required at least 4 × 103 cells mL-1 to obtain reliable results. The calibration plots were linear (R2 = 0.99) and the relative standard deviations of the peak area were at most 2.2%. The adhered bacteria, either individual or in a mixture, were online analyzed by micellar electrokinetic chromatography and then collected from the capillary and off-line analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry without interfering matrix components.

Immobilization of natural lipid biomembranes and their interactions with choline carboxylates. A nanoplasmonic sensing study.

The cell membrane is mainly composed of lipid bilayers with inserted proteins and carbohydrates. Lipid bilayers made of purified or synthetic lipids are widely used for estimating the effect of target compounds on cell membranes. However, the composition of such biomimetic membranes is much simpler than the composition of biological membranes. Interactions between compounds and simple composition biomimetic membranes might not demonstrate the effect of target compounds as precisely as membranes with compositions close to real organisms. Therefore, the aim of our study is to construct biomimetic membrane closely mimicking the state of natural membranes. Liposomes were prepared from lipids extracted from L-α-phosphatidylcholine, Escherichia coli, yeast (Saccharomyces cerevisiae) and bovine liver cells through agitation and sonication. They were immobilized onto silicon dioxide (SiO2) sensor surfaces using N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid buffer with calcium chloride. The biomimetic membranes were successfully immobilized onto the SiO2 sensor surface and detected by nanoplasmonic sensing. The immobilized membranes were exposed to choline carboxylates. The membrane disruption effect was, as expected, more pronounced with increasing carbohydrate chain length of the carboxylates. The results correlated with the toxicity values determined using Vibrio fischeri bacteria. The yeast extracted lipid membranes had the strongest response to introduction of choline laurate while the bovine liver lipid extracted liposomes were the most sensitive towards the shorter choline carboxylates. This implies that the composition of the cell membrane plays a crucial role upon interaction with choline carboxylates, and underlines the necessity of testing membrane systems of different origin to obtain an overall image of such interactions.

Cohesive Energy Densities Versus Internal Pressures of Near and Supercritical Fluids.

Over half a century ago, Wiehe and Bagley suggested that a product of the internal pressure and molar volume of a liquid measures the energy of nonspecific intermolecular interactions whereas the cohesive energy reflects the total energy of intermolecular interactions in the liquid. This conjecture, however, has never been considered in connection with near and supercritical fluids. In this contribution, the cohesive energy density, internal pressure and their ratios are calculated from high precision equations of state for eight important fluids including water. To secure conformity to the principle of corresponding states when comparing different fluids, the calculations are carried out along the line defined by equality between the reduced temperature and the reduced pressure of the fluid (Tr = Pr). The results provide additional illustration of the tunability of the solvent properties of water that stands apart from those of other near and supercritical fluids in common use. In addition, an overview is also presented of the derivatives of cohesive energy density, solubility parameter and internal pressure with respect to temperature, pressure and molar volume.

Supercritical water-treated fused silica capillaries in analytical separations: Status review.

Near- and supercritical water (SCW) has recently been shown to provide an unusual but effective tool to roughen the inner surface or manipulate the internal diameter of fused silica capillaries for analytical separation methods In this review, the to-date existing variants of instrumental arrangement for etching the fused silica capillaries with SCW are described, the currently accessible morphologies of SCW-etched capillaries are outlined, and both existing and prospective applications of the SCW-etched capillaries in analytical separations are briefly discussed. Relative merits of SCW and other agents to treat the inner surfaces of fused silica capillaries are also mentioned.

Pre-concentration and separation of bacteria by volume coupling electrophoresis on supercritical water-etched fused silica capillary with two segments of different internal diameters and inner surface roughnesses.

The transient isotachophoretic stacking and sweeping was used for the on-line large-volume sample pre-concentration of bacteria, Escherichia coli and Staphylococcus aureus cells (methicillin-susceptible or methicillin-resistant), in the initial stage of micellar electrokinetic chromatography using a non-ionogenic surfactant or of capillary electrophoresis, respectively. These procedures were employed in single-piece fused silica capillary etched with supercritical water with two different internal diameter segments featuring different inner surface roughness. Large volumes (maximum 2.8 µL) of the high conductivity sample matrices, physiological saline solution, urine or blood (with purification step), spiked with examined cells were injected into the wider end of a capillary with an inlet inner diameter 195 µm. This novel on-line combination of preconcentration strategies for cells produced an up to 680-fold increase in sensitivity for E. coli or S. aureus cells. The average calculated resolutions, R, for five selected methicillin-susceptible or methicillin-resistant strains were found to be 6.3 for the agar-cultivated and 14.9 for the blood-incubated cells. A low number of bacteria similar to those in clinical samples were also tested. The modified surface roughness step helped to significantly narrow the cell zones and to increase resolution. The migration velocities of E. coli agar-cultivated and blood-incubated cells were approximately the same as those of S. aureus, probably due to the minimal differences in their surface properties. This procedure, on-line pre-concentration and separation of bacteria, is rapid and provides good reproducibility and repeatability.

Fused silica capillaries with two segments of different internal diameters and inner surface roughnesses prepared by etching with supercritical water and used for volume coupling electrophoresis.

In this work, single-piece fused silica capillaries with two different internal diameter segments featuring different inner surface roughness were prepared by new etching technology with supercritical water and used for volume coupling electrophoresis. The concept of separation and online pre-concentration of analytes in high conductivity matrix is based on the online large-volume sample pre-concentration by the combination of transient isotachophoretic stacking and sweeping of charged proteins in micellar electrokinetic chromatography using non-ionogenic surfactant. The modified surface roughness step helped to the significant narrowing of the zones of examined analytes. The sweeping and separating steps were accomplished simultaneously by the use of phosphate buffer (pH 7) containing ethanol, non-ionogenic surfactant Brij 35, and polyethylene glycol (PEG 10000) after sample injection. Sample solution of a large volume (maximum 3.7 µL) dissolved in physiological saline solution was injected into the wider end of capillary with inlet inner diameter from 150, 185 or 218 µm. The calibration plots were linear (R2 ∼ 0.9993) over a 0.060-1 µg/mL range for the proteins used, albumin and cytochrome c. The peak area RSDs from at least 20 independent measuremens were below 3.2%. This online pre-concentration technique produced a more than 196-fold increase in sensitivity, and it can be applied for detection of, e.g. the presence of albumin in urine (0.060 µg/mL).

Bridged polysilsesquioxane-based wide-bore monolithic capillary columns for hydrophilic interaction chromatography.

The synthesis and characterization of large-bore silica-based monolithic capillary columns (0.32mm×150mm) are presented. Columns were prepared by acidic hydrolysis of a mixture containing tetramethoxysilane (TMOS) and 1,2-bis(trimethoxysilyl)ethane (BTME) in different molar ratios in the presence of polyethylene glycol and urea. The monoliths were modified by zwitterionic monomer [2-(methacryloyloxy)ethyl]-dimethyl-(3-sulfopropyl)-ammonium hydroxide via 3-(trimethoxysilyl)propyl methacrylate. Prepared stationary phases were evaluated by scanning electron microscopy and chromatographic separation of nucleobases and their derivatives in the HILIC mode. The best chromatographic results were obtained with the column prepared from the reaction mixture containing BTME and TMOS in a 1:4 molar ratio. The permeability of such column reached 1.68×10-14m2 and the efficiency, expressed as a height equivalent of the theoretical plate, did not exceed 10.5µm for the tested compounds. The columns were successfully applied to HILIC separation of native and labeled oligosaccharides and glycans released from bovine ribonuclease B and human immunoglobulin G.

Partition Coefficients of Organics between Water and Carbon Dioxide Revisited: Correlation with Solute Molecular Descriptors and Solvent Cohesive Properties.

High-pressure phase behavior of systems containing water, carbon dioxide and organics has been important in several environment- and energy-related fields including carbon capture and storage, CO2 sequestration and CO2-assisted enhanced oil recovery. Here, partition coefficients (K-factors) of organic solutes between water and supercritical carbon dioxide have been correlated with extended linear solvation energy relationships (LSERs). In addition to the Abraham molecular descriptors of the solutes, the explanatory variables also include the logarithm of solute vapor pressure, the solubility parameters of carbon dioxide and water, and the internal pressure of water. This is the first attempt to include also the properties of water as explanatory variables in LSER correlations of K-factor data in CO2-water-organic systems. Increasing values of the solute hydrogen bond acidity, the solute hydrogen bond basicity, the solute dipolarity/polarizability, the internal pressure of water and the solubility parameter of water all tend to reduce the K-factor, that is, to favor the solute partitioning to the water-rich phase. On the contrary, increasing values of the solute characteristic volume, the solute vapor pressure and the solubility parameter of CO2 tend to raise the K-factor, that is, to favor the solute partitioning to the CO2-rich phase.

Capillary electrophoresis in a fused-silica capillary with surface roughness gradient.

The electro-osmotic flow, a significant factor in capillary electrophoretic separations, is very sensitive to small changes in structure and surface roughness of the inner surface of fused silica capillary. Besides a number of negative effects, the electro-osmotic flow can also have a positive effect on the separation. An example could be fused silica capillaries with homogenous surface roughness along their entire separation length as produced by etching with supercritical water. Different strains of methicillin-resistant and methicillin-susceptible Staphylococcus aureus were separated on that type of capillaries. In the present study, fused-silica capillaries with a gradient of surface roughness were prepared and their basic behavior was studied in capillary zone electrophoresis with UV-visible detection. First the influence of the electro-osmotic flow on the peak shape of a marker of electro-osmotic flow, thiourea, has been discussed. An antifungal agent, hydrophobic amphotericin B, and a protein marker, albumin, have been used as model analytes. A significant narrowing of the detected zones of the examined analytes was achieved in supercritical-water-treated capillaries as compared to the electrophoretic separation in smooth capillaries. Minimum detectable amounts of 5 ng/mL amphotericin B and 5 µg/mL albumin were reached with this method.