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Search results for: LiCs molecule
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations
PublicationWe present a complete exploration of the different fragmentation mechanisms of furan (C4H4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H2 loss...
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublicationStaphylococci are increasingly recognized as etiological agents of many opportunistic human and animal infections, emphasizing the need for a rapid and accurate identification, even to a genotypical level of these bacteria. In the recent years, there has been a significant progress in typing and phylogenetic study of Staphylococcus species. Here, we describe molecular methods used in taxonomy as well as staphylococci characterization....
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Structure of the interlayer between Au thin film and Si-substrate: Molecular Dynamics simulations
PublicationInteraction between 2, 3, 5 and 7 atomic layers of gold and a (111) silicon surface was investigated with the molecular dynamics simulation method. The simulation of the diffusion interaction between gold and silicon in the temperature range 425-925 K has been carried out. The peculiarities of the concentration changes of the interacting components and the atomic density at the boundary...
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Measurements of differential cross sections for elastic electron scattering in the backward direction by molecular oxygen.
PublicationZmierzono różniczkowe przekroje czynne na rozproszenie sprężyste elektronów na cząsteczkach tlenu w zakresie kątów rozproszenia 100-180 st., dla wybranych energii padających elektronów w przedziale 7-20eV. Do pomiarów wykorzystano metodę lokalnego pola magnetycznego.
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Molecular aspects of biogenesis of Escherichia coli Dr Fimbriae: characterization of DraB-DraE complexes
PublicationHemaglutynina Dr uropatogennych szczepów Escherichia coli jest fimbrialnym homopolimerem zbudowanym z podjednostek białkowych DraE kodowanych przez operon dra. Operon dra zawiera geny draB i draC, kodujące białka homologiczne do białek (białko opiekuńcze-białko kanałotwórcze) zaangażowanych w procesie biogenezy struktur polimerycznych eksprymowanych powierzchniowo. Białko DraB jest jednym z białek periplazmatycznych, należącym...
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Electron collisions with methyl-substituted ethylenes: Cross section measurements and calculations for 2-methyl–2-butene and 2,3-dimethyl–2-butene
PublicationWe report electron-scattering cross sections determined for 2-methyl–2-butene [(H3C)HC==C(CH3)2] and 2,3-dimethyl–2-butene [(H3C)2C=C(CH3)2] molecules. Absolute grand-total cross sections (TCSs) were measured for incident electron energies in the 0.5–300 eV range, using a linear electron-transmission technique. The experimental TCS energy dependences for the both targets appear to be very similar with respect to the shape. In each...
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L1 Cell Adhesion Molecule Overexpression Down Regulates Phosphacan and Up Regulates Structural Plasticity-Related Genes Rostral and Caudal to the Complete Spinal Cord Transection
PublicationL1 cell adhesion molecule (L1CAM) supports spinal cord cellular milieu after contusion and compression lesions, contributing to neuroprotection, promoting axonal outgrowth, and reducing outgrowth-inhibitory molecules in lesion proximity. We extended investigations into L1CAM molecular targets and explored long-distance effects of L1CAM rostral and caudal to complete spinal cord transection (SCT) in...
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Toward Mechanosynthesis of Diamondoid Structures: IX Commercial Capped CNT Scanning Probe Microscopy Tip as Nowadays Available Tool for Silylene Molecule and Silicon Atom Transfer
PublicationAccording to K. E. Drexler, advanced mechanosynthesis will employ advanced nanomachines, but advanced nanomachines will themselves be product of advanced mechanosynthesis. This circular relationship must be broken in SPM technology development. In the article, the possibility of use easy available commercial CNT tips to assembly silicon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target class...
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ABSORPCJA, METABOLIZM I ROLA BIOLOGICZNA KWASÓW NUKLEINOWYCH OBECNYCH W ŻYWNOŚCI
PublicationKwasy nukleinowe należą do niedocenianych składników żywności, szczególnie surowej lub nisko przetworzonej. W niniejszej publikacji skupiono się na omówieniu przemian, jakim podlegają kwasy nukleinowe w przewodzie pokarmowym człowieka, procesie absorpcji nukleotydów oraz nukleozydów z przewodu pokarmowego, a także przedstawiono podstawowe etapy ich metabolizmu w komórkach organizmu. Produkty trawienia kwasów nukleinowych stanowią...
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Proteomic Profiling of Ectosomes Derived from Paired Urothelial Bladder Cancer and Normal Cells Reveals the Presence of Biologically-Relevant Molecules
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Computational analysis of substituent effects on proton affinity and gas-phase basicity of TEMPO derivatives and their hydrogen bonding interactions with water molecules
PublicationThe study investigates the molecular structure of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its derivatives in the gas phase using B3LYP and M06-2X functional methods. Intermolecular interactions are analyzed using natural bond orbital (NBO) and atoms in molecules (AIM) techniques. NO2-substituted TEMPO displays high reactivity, less stability, and softer properties. The study reveals that the stability of TEMPO derivatives...
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Cross-sections for electron-scattering from 2-methyl-1-buten-3-yne, C 5 H 6 , molecules
PublicationtCross-sections for electron collisions with the 2-methyl-1-buten-3-yne [H2C C(CH3)C CH] moleculewere measured and calculated. Absolute grand-total electron-scattering cross-section (TCS) was takenat impact energies from 0.6 to 300 eV in the linear electron-transmission experiment. The TCS energydependence for the electron–C5H6collision has two prominent enhancements separated with a deepminimum located near 1.8 eV. In addition,...
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Electron impact iozization of CCl4 and SF6 embedded in superfluid helium droplets
PublicationElectron impact ionization of helium nano-droplets containing several 104 He atoms and doped with CCl4 or SF6 molecules is studied with high-mass resolution. The mass spectra show significant clustering of CCl4 molecules, less so for SF6 under our experimental conditions. Positive ion efficiency curves as a function of electron energy indicate complete immersion of the molecules inside the helium droplets in both cases. For CCl4...
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Chapter 32. Method to predict the critical micelle concentration of ionic liquids from the molecular volume
PublicationAmfifilowość wielu imidazoliowych cieczy jonowych powoduje, że zjawiska powierzchniowe mają znaczny wpływ na właściwości układów zawierających te związki. Dotychczas przeprowadzono wiele badań w celu wyznaczenia krytycznego stężenia micelizacji cieczy jonowych o różnej budowie. Ze względu na możliwość modyfikacji budowy kationu i wyboru anionu oraz ich kombinacji, podjęto próbę opracowania empirycznego równania pozwalajacego na...
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The anion [Mg6Cl8Cp*5]-: a final intermediate on the way to the molecular donor-free Grignard compound MgClCp*?
PublicationOtrzymano i scharakteryzowano strukturalnie rzadki przypadek związku Grignarda pozbawionego donora. Struktura krystaliczna [Mg6Cl8Cp*5][AlCp*2] C6H6 zawiera zarówno metallocen (Cp*AlCp*) jak i odwrócony metallocen (MgCp*Mg).
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Bacterial SSB-like proteins of family Deinococcaceae - indentification, isolation, obtaining, purification and molecular characteristic
PublicationWiększość poznanych białek SSB jest aktywna w formie homotetramerycznej. Od 2002 roku znane są białka organizmów ekstremofilnych. Scharakteryzowano białka mikroorganizmów rodziny Deinococaceae. Uzyskane termostabilne białka stanowią atrakcyjną alternatywę w stosunku do znanych białek SSB w metodach diagnostyki molekularnej, technikach biologii molekularnej i analityce.
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Molecular dynamics study on the influence of C-terminal sugar substitution on dynamics and conformation of vancomycin derivatives
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Structure of the twist-bend nematic phase with respect to the orientational molecular order of the thioether-linked dimers
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Molecular mechanism(s) of regulation(s) of c-MET/HGF signaling in head and neck cancer
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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Classical to Path-Integral Adaptive Resolution in Molecular Simulation: Towards a Smooth Quantum-Classical Coupling
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Solubility of dapsone in deep eutectic solvents: Experimental analysis, molecular insights and machine learning predictions
PublicationBackground. Dapsone (DAP) is an anti-inflammatory and antimicrobial active pharmaceutical ingredient used to treat, e.g., AIDS-related diseases. However, low solubility is a feature hampering its efficient use. Objectives. First, deep eutectic solvents...
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Positional Scanning Identifies the Molecular Determinants of a High Affinity Multi-Leucine Inhibitor for Furin and PACE4
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Molecular modeling and evaluation of novel dibenzopyrrole derivatives as telomerase inhibitors and potential drug for cancer therapy
PublicationDuring previous years, many studies on synthesis, as well as on anti-tumor, anti-inflammatory and anti-bacterial activities of the pyrazole derivatives have been described. Certain pyrazole derivatives exhibit important pharmacological activities and have proved to be useful template in drug research. Considering importance of pyrazole template, in current work the series of novel inhibitors were designed by replacing central...
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Isolation and molecular characterization of Fowl adenovirus strains in Black grouse: First reported case in Poland
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Application of gas chromatographic data and 2D molecular descriptors for accurate global mobility potential prediction
PublicationMobility is a key feature affecting the environmental fate, which is of particular importance in the case of persistent organic pollutants (POPs) and emerging pollutants (EPs). In this study, the global mobility classification artificial neural networks-based models employing GC retention times (RT) and 2D molecular descriptors were constructed and validated. The high usability of RT was confirmed based on the feature selection...
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Effect of bio-polyol molecular weight on the structure and properties of polyurethane-polyisocyanurate (PUR-PIR) foams
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Virtual screening for small molecular non-covalent binders of the SARS-CoV-2 main protease
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Municipal landfill leachate nitrification in RBC biofilm – Process efficiency and molecular analysis of microbial structure
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublicationIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
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Synthesis, Molecular Structure, Metabolic Stability and QSAR Studies of a Novel Series of Anticancer N-Acylbenzenesulfonamides
PublicationA series of novel N-acyl-4-chloro-5-methyl-2-(R1-methylthio)benzenesulfonamides 18–47 have been synthesized by the reaction of N-[4-chloro-5-methyl-2-(R1-methylthio) benzenesulfonyl]cyanamide potassium salts with appropriate carboxylic acids. Some of them showed anticancer activity toward the human cancer cell lines MCF-7, HCT-116 and HeLa, with the growth percentages (GPs) in the range from 7% to 46%. Quantitative structure-activity relationship...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Coordination polymers and molecular structures among complexes of mercury(II) halides with selected 1-benzoylthioureas
PublicationSix new 1-benzoyl-3-phenylthiourea and 1-benzoyl-3-(2-methylphenyl)thiourea complexes of mercury( II) were obtained in the reactions of the ligands with HgX2 in methanol (X = Cl, Br, I). Their structures, determined by single-crystal X-ray diffraction analysis, exhibit different stoichiometries and molecular organization. Coordination centers adopt more or less distorted tetrahedral geometry (five structures) or distorted trigonal...
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New PCR test for detection of Candida glabrata based on the molecular target chosen by the RAPD technique
PublicationRapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. #e paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted...
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Crystal and molecular structure of bis(O,O'-diethyldithiophosphato-S,S')nickel(II): A redetermination
PublicationDoniesienie przedstawia ponownie wyznaczoną strukturę tytułowego, centrosymetrycznego kompleksu, [Ni{S2P(OC2H5)2}2]. Centralny rdzeń (S2P)2 jest płaski, co potwierdza wcześniejsze wyniki uzyskane przez McConnell'a i Kastalsky'ego, przy czym odchylenia standardowe są około siedmiokrotnie mniejsze oraz wyznaczono wszystkie pozycje atomów wodoru. W strukturze krystalicznej zaobserwowano róznież parę krótkich kontaktów HH (2.33 Å).
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A DSC and NMR-Relaxation study of the molecular mobility of water protons interacting with chemically modified starches
PublicationChanges in the mobility of water protons in the chemically modified starches (CMS)–water system are studied by differential scanning calorimetry and NMR relaxation. The amounts of unfrozen water at negative temperatures and additional (after gelation) unfrozen for CMS are lower than those for native starch. The proton spin–spin relaxation time T2 for CMS samples, conventionally attributed to the water fraction in starch granules,...
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Selected symmetrically substituted carbazoles: Investigation of anticancer activity and mechanisms of action at the cellular and molecular levels
PublicationDNA topoisomerases play a critical role as essential enzymes in controlling alterations in the topology of DNA. They achieve this by orchestrating the coordinated process of breaking and rejoining DNA strands, which is crucial for maintaining the proper structure of DNA during regular cellular development. The search for and development of new potential anticancer drugs is a challenging yet immensely important area of research...
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Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents
PublicationDeep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Effect of bio-polyol molecular weight on the structure and properties of polyurethane-polyisocyanurate (PUR-PIR) foams
PublicationThe increasing interest in polyurethane materials has raised the question of the environmental impact of these materials. For this reason, the scientists aim to find an extremely difficult balance between new material technologies and sustainable development. This work attempts to validate the possibility of replacing petrochemical polyols with previously synthesized bio-polyols and their impact on the structure and properties...
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The exposure to UV filters: Prevalence, effects, possible molecular mechanisms of action and interactions within mixtures
PublicationSubstances that can absorb sunlight and harmful UV radiation such as organic UV filters are widely used in cosmetics and other personal care products. Since humans use a wide variety of chemicals for multiple purposes it is common for UV filters to co-occur with other substances either in human originating specimens or in the environment. There is increasing interest in understanding such co-occurrence in form of potential synergy, antagonist,...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling
PublicationUnderstanding the mechanisms underlying the carbon dioxide (CO2) absorption in ionic liquids (ILs) is the key to their efficient utilization in industrial flue gas treatment. One of the parameters considered substantially important in the process is the Free Volume. In this study, the Fractional Free Volume (FFV) of 73 ILs was calculated using Molecular Dynamics (MD). A quantitative Structure-Property Relationship (QSPR) study...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Are the short cationic lipopeptides bacterial membrane disruptors? Structure-Activity Relationship and molecular dynamic evaluation
PublicationShort cationic lipopeptides are amphiphilic molecules that exhibit antimicrobial activity mainly against Grampositives. These compounds bind to bacterial membranes and disrupt their integrity. Here we examine the structure-activity relation (SAR) of lysine-based lipopeptides, with a prospect to rationally design more active compounds. The presented study aims to explain how antimicrobial activity of lipopeptides is affected by...
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Multi-state multi-reference Møller-Plesset second-order perturbation theory for molecular calculations
PublicationThis work presents multi‐state multi‐reference Møller–Plesset second‐order perturbation theory as a variant of multi‐reference perturbation theory to treat electron correlation in molecules. An effective Hamiltonian is constructed from the first‐order wave operator to treat several strongly interacting electronic states simultaneously. The wave operator is obtained by solving the generalized Bloch equation within the first‐order...
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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublicationMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...