Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections.

Overbinding of ions is a common and well-known problem in classical molecular dynamics simulations. One of its main causes is the absence of electronic polarizability in the force fields. The current approaches for minimizing overbinding typically either retain the original charges and use an ad hoc readjustment of the Lennard-Jones parameters as done in the nonbonded fix (NBFIX) approach or rescale the charges using a theoretical framework. The goal in the latter is to include shielding produced by the missing electronic polarizability as done in the electronic continuum correction (ECC) approach. NBFIX and ECC are the most common corrections, and we compare their performance to the default parameterizations provided by five different commonly used biomolecular force fields, OPLS-AA/L, CHARMM27, CHARMM36m, CHARMM22*, and AMBER99SB-ILDN. As test systems, we use poly-α,l-glutamic and poly-α,l-aspartic amino acid molecules in explicit water together with Na+ and K+ counterions. We demonstrate that the different force fields yield results that are not only quantitatively but also qualitatively different. The resulting structures of the macroions depend strongly on the model for ions. NBFIX corrections alleviate the problem of overbinding, resulting in extended peptides. The ECC corrections depend nontrivially on the original underlying model, and despite being based on a theoretical framework, they cannot always solve the problem.

Molecular dynamics simulations of oligoester brushes: the origin of unusual conformations.

We present results from all-atom molecular dynamics simulations for the structural properties of oligomeric lactic acid chains (OLA) grafted to the surface of cellulose nanocrystals (CNCs) and immersed in the melt of polylactic acid (PLA). Earlier, we have found that the distribution of free ends of OLA molecules is bimodal [Glova et al., Polym. Int., 2016, 65(8), 892]. The results cannot be explained within the standard picture of uncharged polymer brushes exposed to the melt of a chemically identical polymer. Although the oligomeric brushes of the OLA chains are uncharged, they have partial polarization charges producing a non-zero dipole moment of the monomeric chain unit. We study the influence of partial charges on the structure of the layer of OLA chains grafted to the CNC surface. A detailed analysis of the conformations of the grafted chains shows that interaction of partial charges in the models causes bending of the OLA molecules toward the cellulose surface, forming a hairpin structure. The observed separation of the grafted chains into two populations increases with grafting density. We demonstrate that hydrogen bonds can be formed between the free ends of the grafted chains and the CNC surface, but they do not affect the brush structure significantly. Thus, dipole-dipole interactions turn out to be the key factor governing the unusual conformations of grafts.

Influence of specific intermolecular interactions on the thermal and dielectric properties of bulk polymers: atomistic molecular dynamics simulations of Nylon 6.

Specific intermolecular interactions, in particular H-bonding, have a strong influence on the structural, thermal and relaxation characteristics of polymers. We report here the results of molecular dynamics simulations of Nylon 6 which provides an excellent example for the investigation of such an influence. To demonstrate the effect of proper accounting for H-bonding on bulk polymer properties, the AMBER99sb force field is used with two different parametrization approaches leading to two different sets of partial atomic charges. The simulations allowed the study of the thermal and dielectric properties in a wide range of temperatures and cooling rates. The feasibility of the use of the three methods for the estimation of the glass transition temperature not only from the temperature dependence of structural characteristics such as density, but also by using the electrostatic energy and dielectric constant is demonstrated. The values of glass transition temperatures obtained at different cooling rates are practically the same for the three methods. By proper accounting for partial charges in the simulations, a reasonable agreement between the results of our simulations and experimental data for the density, thermal expansion coefficient, static dielectric constant and activation energy of γ and ß relaxations is obtained demonstrating the validity of the modeling approach reported.

Cellulose Nanofibrils and Mechanism of their Mineralization in Biomimetic Synthesis of Hydroxyapatite/Native Bacterial Cellulose Nanocomposites: Molecular Dynamics Simulations.

Molecular dynamics (MD) simulation of a nanofibril of native bacterial cellulose (BC) in solutions of mineral ions is presented. The supersaturated calcium-phosphate (CP) solution with the ionic composition of hydroxyapatite and CaCl2 solutions with the concentrations below, equal to, and above the solubility limits are simulated. The influence of solvation models (TIP3P and TIP4P-ew water models) on structural characteristics of the simulated nanofibril and on the crystal nucleation process is assessed. The structural characteristics of cellulose nanofibrils (in particular, of the surface layer) are found to be nearly independent of the solvation models used in the simulation and on the presence of ions in the solutions. It is shown that ionic clusters are formed in the solution rather than on the fibril surface. The cluster sizes are slightly different for the two water models. The effect of the ion-ion interaction parameters on the results is discussed. The main conclusion is that the activity of hydroxyl groups on the BC fibril surface is not high enough to cause adsorption of Ca(2+) ions from the solution. Therefore, the nucleation of CP crystals takes place initially in solution, and then the crystallites formed can be adsorbed on BC nanofibril surfaces.

Interactions binding mineral and organic phases in nanocomposites based on bacterial cellulose and calcium phosphates.

The interactions responsible for the adhesion of calcium phosphate (CP) nanocrystals and bacterial cellulose (BC) nanofibrils in the composite material obtained by mixing aqueous suspensions of presynthesized CP and BC and the dependence of these interactions on the CP morphology and chemical structure have been elucidated by molecular mechanics calculations of the CP-BC interfacial structures. The interactions between the superficial CP and BC crystal layers have been simulated. Two crystalline CP structures (i.e., hydroxyapatite (HAP) and whitlockite) with two morphologies (plate-shaped and rod-shaped) were considered. Electrostatics has been found to be the major contributor to the adhesion of the CP crystallites and BC nanofibers, and the formation of interfacial hydrogen bonds makes a minor contribution to the interaction energy. It has also been found that, in general, the energy gain resulting from whitlockite-BC binding is greater than that for HAP-BC binding, and the binding of the rod-shaped crystallites of whitlockite with BC is the most profitable. The energy loss and entropy gain upon replacement of the BC-water and CP-water contacts by the BC-CP contacts have been estimated.

Use of models of biomacromolecule separation in AMT database generation for shotgun proteomics.

Generation of a complex proteome database requires use of powerful analytical methods capable of following rapid changes in the proteome due to changing physiological and pathological states of the organism under study. One of the promising technologies with this regard is the use of so-called Accurate Mass and Time (AMT) tag peptide databases. Generation of an AMT database for a complex proteome requires combined efforts by many research groups and laboratories, but the chromatography data resulting from these efforts are tied to the particular experimental conditions and, in general, are not transferable from one platform to another. In this work, we consider an approach to solve this problem that is based on the generation of a universal scale for the chromatography data using a multiple-point normalization method. The method follows from the concept of linear correlation between chromatography data obtained over a wide range of separation parameters. The method is further tested for tryptic peptide mixtures with experimental data collected from mutual studies by different independent research groups using different separation protocols and mass spectrometry data processing tools.

[Postpericardiotomy syndrome: risk factors and methods of diagnosis].

This study was designed to identify major risk factors of PCTS and elucidate the possibility of early laboratory diagnosis of this syndrome for the choice of optimal therapeutic strategy. Retrospective analysis covered medical records of 500 patients who had experienced open heart surgery. Prospective studies included 60 patients of whom 50 had clinical manifestations of PCTS. Risk of its development depended on the severity of the underlying disease and increased after mechanical revascularization of myocardium. Urgency surgical intervention and greater extent of coronary shunting increased the probability of PCTS. Results of the measurement of serum procalcitonin by a highly sensitive method and of relative content of different protein fractions in serum and pleural/pericardial fluid suggest high informative value of these methods as diagnostic tools for PCTS. Preventive treatment with non-steriodal anti-inflammatory agents decreased the incidence of PCTS by 53%.

[Combined effects of psychoemotional stress and carbon monoxide in experiments]. / Sochetannoe deistvie nervno-émotsional'nogo stressa i monooksida ugleroda v éksperimente.

Psychoemotional stress and exposure to various concentrations of carbon monoxide are antagonists or act independently. The results necessitate changes in MAC for carbon monoxide in air of workplace.

[Use of dispersion analysis in the assessment of combined effect of low levels of carbon monoxide and psychoemotional stress in chronic experiment]. / Ispol'zovanie dispersionnogo analiza pri otsenke éffektov sochetannogo deistviia nizkikh urovnei monooksida ugleroda i psikhoémotsial'nogo stressa v khronicheskom éksperimente.

The article deals with evaluation of joint effects by means of dispersion analysis. The experimental study covered joint effects caused by low levels of carbon oxide (MAC and those 3 times lower) and specific psychoemotional stress in white rats. The studied parameters described activities of the central nervous, cardiovascular and immune systems. Dispersion analysis helped to reveal predominant role of the stress in the joint effects on the cardiovascular and central nervous systems, prevalent role of carbon oxide in the joint effects on the immune system.

[Cellular immunity indices in combined chronic exposure to stress and low concentrations of carbon monoxide (II). Experimental research]. / Pokazateli kletochnogo immuniteta pri sochetannom khronicheskom vozdeistvii stressa i malykh kontsentratsi oksida ugleroda (II). Eksperimental'noe issledovanie.

Studies of the chronic combined effects of carbon monoxide low concentrations and psychoemotional stress revealed changes in the peripheral lymphocyte subpopulation in all groups of examinees, connected with the defense activation of the humoral immunity and functional decrease of T lymphocytes. Analysis of correlations of cell subpopulations revealed disorders of their relationships, augmenting with the intensity of exposure. Combined action of carbon monoxide in the maximal of studies concentrations with stress resulted in the most severe changes of nonspecific immunity, which proves decompensated decrease of immunity.

[A method of creating the model of chronic psychoemotional stress in a toxicological experiment]. / Metodika sozdaniia modeli khronicheskogo psikhoémotsional'nogo stressa v usloviiakh toksikologicheskogo éksperimenta.

The article presents a technique and description of a device for creating psychoemotional stress conditions in toxicological experiments. The technique was based on the model of electric stimulus stress expectation. The device consisted of a block with depots for small laboratory animals. The depots had metal-covered floors connected to a generator of irregular electric impulses. The impulses were periodically proceeded by light signals. The block with animals was placed into a chamber for toxicological experiments. The technique proved its effectiveness with highly reliable results. The article contains the major technical parameters and drawings of the device.