Публикации

The role of Al in aluminosilicate glasses remains somewhat a mystery: at low concentrations, it increases the resistance to hydrolysis of the glass, whereas at high concentrations an opposite effect is observed. To understand the origin of the phenomenon on a fundamental atomistic scale, we performed 577 MD simulations and applied potential mean force (PMF) calculations to estimate the activation barriers for hydrolysis and to statistically correlate them with local structural features of the glass. Models of pure silicate and aluminosilicate glasses are constructed and investigated. PMF simulation results are further validated by the experimental measurements and revealed that Al is very easy to dissociate, but it also increases the glass chemical durability through significantly increasing both the strength of Si and network connectivity of the glass. In contrast, at high Al concentration, preferential dissolution of Al weakens the silicate network, which it supposes to strengthen, and so the glass resistance becomes poor. Through PMF calculations, we evaluated the activation barriers for dissociating bonds around Al as 0.49 eV, which is less than a half of the energy to dissociate bonds around Si in pure silicate (1.22 eV) and around Si in aluminosilicate glass (1.34 eV), all these energy differences being statistically significant. Molecular structural level investigation revealed that Si with Al as a second neighbour in the glass network has a significantly higher activation energy for dissociation than Si in pure silicate glass. The proposed approach opens the way to the development of quantitative predictive models of glass durability.

We report the synthesis and antibacterial activities of a series of amphiphilic membrane-active peptides composed, in part, of various non-genetically coded hydrophobic amino acids. Lead cyclic peptides, 8C and 9C, showed broad-spectrum activity against drug-resistant Gram-positive (MIC=1.5-6.2 µg/mL) and Gram-negative (MIC=12.5-25 µg/mL) bacteria. Cytotoxicity study showed the predominant lethal action of the peptides against bacteria as compared with mammalian cells. A plasma stability study revealed approximately 2-fold higher stability of lead cyclic peptides as compared to their linear counterparts after 24 h incubation. A calcein dye leakage experiment revealed the membranolytic effect of the cyclic peptides. Nuclear magnetic resonance spectroscopy and molecular dynamics simulations studies of the interaction of the peptides with phospholipid bilayer provided a solid structural basis explaining the membranolytic action of the peptides with atomistic details. These results highlight the potential of newly designed amphiphilic peptides as the next generation of peptide-based antibiotics.

Рассмотрено течение вязкой жидкости вдоль полубесконечной пластины с малыми периодическими неровностями на поверхности при больших значениях числа Рейнольдса. Течение вблизи пластины описывается уравнениями Прандтля с индуцированным давлением, которые не являются классически ми уравнениями в частных производных, поскольку содержат предельный член. Основная цель данной работы — построение алгоритма численного решения этих уравнений с периодическими граничными условиями. Приведены результаты численного моделирования течения.

As a general-purpose force field for molecular simulations of layered materials and their fluid interfaces, Clayff continues to see broad usage in atomistic computational modeling for numerous geoscience and materials science applications due to its (1) success in predicting properties of bulk nanoporous materials and their interfaces, (2) transferability to a range of layered and nanoporous materials, and (3) simple functional form which facilitates incorporation into a variety of simulation codes. Here, we review applications of Clayff to model bulk phases and interfaces not included in the original parameter set and recent modifications for modeling surface terminations such as hydroxylated nanoparticle edges. We conclude with a discussion of expectations for future developments.

Alzheimer’s disease (AD) is a severe neurodegenerative pathology with no effective treatment known. Toxic amyloid-β peptide (Aβ) oligomers play a crucial role in AD pathogenesis. All-D-Enantiomeric peptide D3 and its derivatives were developed to disassemble and destroy cytotoxic Aβ aggregates. One of the D3-like compounds is approaching phase II clinical trials; however, high-resolution details of its disease-preventing or pharmacological actions are not completely clear. We demonstrate that peptide D3 stabilizing Aβ monomer dynamically interacts with the extracellular juxtamembrane region of a membrane-bound fragment of an amyloid precursor protein containing the Aβ sequence. MD simulations based on NMR measurement results suggest that D3 targets the amyloidogenic region, not compromising its α-helicity and preventing intermolecular hydrogen bonding, thus creating prerequisites for inhibition of early steps of Aβ conversion into β- conformation and its toxic oligomerization. An enhanced understanding of the D3 action molecular mechanism facilitates development of effective AD treatment and prevention strategies.

The Chapter is based on the material of two invited lectures given by the author at the AIPEA School for Young Scientists “Computational Modeling In Clay Mineralogy”, Granada, Spain, July 2017, and the Workshop “Argilla Studium-2019”, Moscow, Russia, November 2019.

Geological carbon capture and sequestration (CCS) is a promising technology for curbing the global warming crisis by reduction of the overall carbon footprint. Degradation of cement wellbore casings due to carbonation reactions in the underground CO2 storage environment is one of the central issues in assessing the long-term success of the CCS operations. However, the complexity of hydrated cement coupled with extreme subsurface environmental conditions makes it difficult to understand the carbonation reaction mechanisms leading to the loss of well integrity. In this work, we use biased ab initio molecular dynamics (AIMD) simulations to explore the reactivity of supercritical CO2 with the basal and edge surfaces of a model hydrated cement phase—portlandite—in dry scCO2 and water-rich conditions. Our simulations show that in dry scCO2 conditions, the undercoordinated edge surfaces of portlandite experience a fast barrierless reaction with CO2, while the fully hydroxylated basal surfaces suppress the formation of carbonate ions, resulting in a higher reactivity barrier. We deduce that the rate-limiting step in scCO2 conditions is the formation of the surface carbonate barrier which controls the diffusion of CO2 through the layer. The presence of water hinders direct interaction of CO2 with portlandite as H2O molecules form well-structured surface layers. In the water-rich environment, CO2 undergoes a concerted reaction with H2O and surface hydroxyl groups to form bicarbonate complexes. We relate the variation of the free-energy barriers in the formation of the bicarbonate complexes to the structure of the water layer at the interface which is, in turn, dictated by the surface chemistry and the degree of nanoconfinement.

Проведено молекулярно динамическое моделирование свойств двухвалентных ионов в органических растворителях. Показано, что молекулы рассмотренных растворителей связываются с ионами через атомы кислорода. На основе этого построена теоретическая модель, описывающая координационное число иона. В данной модели координационное число определяется соотношением размера иона и атома органической молекулы, связывающегося с ионом. Показано, что координационное число слабо зависит от растворителя и существенно от сорта иона. На основе теоретической модели получено значение 0.13 нм для эффективного размера атома кислорода, связывающегося с двухвалентным ионом. Построенная теоретическая модель согласуется с результатами молекулярно динамических расчетов и имеющимися экспериментальными данными.

As global energy demand increases, natural gas recovery from source rocks is attracting considerable attention since recent development in shale extraction techniques has made the recovery process economically viable. Kerogens are thought to play an important role in gas recovery; however, the interactions between trapped shale gas and kerogens remain poorly understood due to the complex, heterogeneous microporous structure of kerogens. This study examines the diffusive behavior of methane molecules in kerogen matrices of different types (Type I, II, and II) and maturity levels (A to D for Type II kerogens) on a molecular scale. Models of each kerogen type were developed using simulated annealing. We employed grand canonical Monte Carlo simulations to predict the methane loadings of the kerogen models and then used equilibrium molecular dynamics simulations to compute the mean square displacement of methane molecules within the kerogen matrices under reservoir-relevant conditions, that is, 365 K and 275 bar. Our results show that methane self-diffusivity exhibits some degree of anisotropy in all kerogen types examined here except for Type I-A kerogens, where diffusion is the fastest and isotropic diffusion is observed. Self-diffusivity appears to correlate positively with pore volume for Type II kerogens, where an increase in diffusivity is observed with increasing maturity. Swelling of the kerogen matrix up to a 3% volume change is also observed upon methane adsorption. The findings contribute to a better understanding of hydrocarbon transport mechanisms in shale and may lead to further development of extraction techniques, fracturing fluids, and recovery predictions.

The amount and size of the charge-balancing cations on the exposed faces of clay particles are supposed to be one of the key factors affecting the specificity of adsorption of gases at clay surfaces. However, the trends characterizing the thermodynamics of gas adsorption, reported for different members of 2:1 phyllosilicate phases, do not systematically follow neither the difference in their layer charge, determining the number of charge-balancing cations, nor the nature of the latter. To better understand the specificity of CH4 and CO2 molecular interactions with different clay phases, the adsorption isotherms were measured for isoionic pure-phase illite and montmorillonite up to pressures of 9 MPa at ambient temperature. For both gases, higher adsorption capacities per unit of specific surface area for montmorillonites in comparison to illites could not be explained by the existing theory relying on the properties of exposed charge-balancing cations on the surface. Instead, the slopes of the isotherms perfectly correlate with the shape of clay particles, characterized by their basal-to-lateral faces’ aspect ratio, which is assessed by derivative isotherm summation (DIS) using argon adsorption at 77 K. Montmorillonite clays, characterized by higher fractions of high-energy hydroxylated particles’ edges (∼45%) in the total specific surface area, featured stronger adsorption interactions with CO2 and CH4 in comparison to illites, for which the contribution of edges to the surface area is only 20%. This introduces a new important factor controlling the mechanism of CH4 and CO2 adsorption by clay minerals.