Structure, energetics, and dynamics of smectite clay interlayer hydration: Molecular dynamics and metadynamics investigation of Na-hectorite

Morrow C P; Yazaydin A O; Krishnan M; Bowers G M; Kalinichev Andrey G.; Kirkpatrick R J

doi:10.1021/jp312286g

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Structure, energetics, and dynamics of smectite clay interlayer hydration: Molecular dynamics and metadynamics investigation of Na-hectorite

The Journal of Physical Chemistry C. 2013. Vol. 117. P. 5172--5187.

Morrow C. P., Yazaydin A. O., Krishnan M., Bowers G. M., Kalinichev A. G., Kirkpatrick R. J.

This paper presents a classical molecular dynamics (MD) and metadynamics investigation of the relationships between the structure, energetics, and dynamics of Na-hydroxyhectorite and serves to provide additional, molecular-scale insight into the interlayer hydration of this mineral. The computational results support a model for interlayer H2O structure and dynamics based on 2H NMR spectroscopy and indicate that H2O molecules undergo simultaneous fast librational motions about the H2O C2 symmetry axis and site hopping with C3 symmetry with respect to the surface normal. Hydration energy minima occur at one-, one-and-one-half-, and two-water-layer hydrates, which for the composition modeled correspond to 3, 5.5, and 10 H2O/Na+, respectively. Na+ ions are coordinated by basal O atoms (OMIN) at the lowest hydration levels and by H2O molecules (OH2O) in the two-layer hydrate, and H2O molecules have an average of three H-bonds at the greatest hydration levels. The metadynamics calculations yield activation energies for site hopping of H2O molecules of ~6.0 kJ/mol for the one-layer structure and ~3.3 kJ/mol for hopping between layers in the two-layer structure. Computed diffusion coefficients for water and Na+ are substantially less than in bulk liquid water, as expected in a nanoconfined environment, and are in good agreement with previous results.

Приоритетные направления: компьютерно-математическое инженерные науки

Язык: английский

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Ключевые слова: molecular modeling Nanostructured materials

Molecular structure and dynamics of nano-confined water: Computer simulations of aqueous species in clay, cement, and polymer membranes.

Kalinichev A. G. In bk.: Transport and Reactivity of Solutions in Confined Hydrosystems, NATO Science for Peace and Security Series C: Environmental Security. Dordrecht: Springer, 2014. P. 99-111.

Molecular-level knowledge of the thermodynamic, structural, and transport properties of water confined by interfaces and nanopores of various materials is crucial for quantitative understanding and prediction of many natural and technological processes, including carbon sequestration, water desalination, nuclear waste storage, cement chemistry, fuel cell technology, etc. Computational molecular modeling is capable to significantly complement the experimental investigations of such systems by providing invaluable atomic-scale information leading to improved understanding of the specific effects of the substrate structure and composition on the structure, dynamics and reactivity of interfacial and nano-confined aqueous solutions. This paper offers a brief overview of recent efforts to quantify some of these effects for individual H2O molecules and hydrated ions confined at the interfaces and in nanopores of several typical hydrophilic and hydrophobic materials. The first molecular layer of aqueous solution at all substrates is often highly ordered, indicating reduced translational and orientational mobility of the H2O molecules. This ordering cannot be simply described as “ice-like”, but rather resembles the behavior of supercooled water or amorphous ice, although with very significant substrate-specific variations.

Добавлено: 4 мая 2017

Role of dimerization efficiency of transmembrane domains in activation of fibroblast growth factor receptor 3

Volynsky P. E., Polyansky A. A., Fakhrutdinova G. N. et al. Journal of the american chemical society. 2013. Vol. 135. No. 22. P. 8105-8108.

Mutations in transmembrane (TM) domains of receptor tyrosine kinases are shown to cause a number of inherited diseases and cancer development. Here, we use a combined molecular modeling approach to understand molecular mechanism of effect of G370R and A391E mutations on dimerization of TM domains of human fibroblast growth factor receptor 3 (FGFR3). According to results of Monte-Carlo conformational search in the implicit membrane and further molecular dynamics simulations, TM dimer of this receptor is able to form a number of various conformations, which differ significantly by the free energy of association in a full-atom model bilayer. The aforementioned mutations affect dimerization efficiency of TM segments and lead to repopulation of conformational ensemble for the dimer. Particularly, both mutations do not change the dimerization free energy of the predominant (putative “non-active”) symmetric conformation of TM dimer, while affect dimerization efficiency of its asymmetric (“intermediate”) and alternative symmetric (putative “active”) models. Results of our simulations provide novel atomistic prospective of the role of G370 and A391E mutations in dimerization of TM domains of FGFR3 and their consecutive contributions to the activation pathway of the receptor.

Добавлено: 13 ноября 2013

Atomistic Modeling and Simulation for Solving Gas Extraction Problems

Norman G., Pisarev V., Smirnov G. et al. In bk.: Molecular Modeling and Simulation. Applications and Perspectives. Singapore: Springer, 2016. P. 137-151.

Добавлено: 5 июля 2016

A single missence mutation in a coiled-coil domain of Escherichia coli ribosomal protein S2 confers thermo-sensitive phenotype that can be suppressed by ribosomal protein S1

Aseev L. V., Chugunov A. O., Efremov R. et al. Journal of Bacteriology. 2013. Vol. 195. No. 1. P. 95-104.

Ribosomal protein S2 is an essential component of translation machinery, and its viable mutated variants conferring distinct phenotypes serve as a valuable tool in studying the role of S2 in translation regulation. One of a few available rpsB mutants, rpsB1, shows thermosensitivity and ensures enhanced expression of leaderless mRNAs. In this study, we identified the nature of the rpsB1 mutation. Sequencing of the rpsB1 allele revealed a G-to-A transition in the part of the rpsB gene which encodes a coiled-coil domain of S2. The resulting E132K substitution resides in a highly conserved site, TKKE, a so-called N-terminal capping box, at the beginning of the second alpha helix. The protruding coiled-coil domain of S2 is known to provide binding with 16S rRNA in the head of the 30S subunit and, in addition, to interact with a key mRNA binding protein, S1. Molecular dynamics simulations revealed a detrimental impact of the E132K mutation on the coiled-coil structure and thereby on the interactions between S2 and 16S rRNA, providing a clue for the thermosensitivity of the rpsB1 mutant. Using a strain producing a leaderless lacZ transcript from the chromosomal lac promoter, we demonstrated that not only the rpsB1 mutation generating S2/S1-deficient ribosomes but also the rpsA::IS10 mutation leading to partial deficiency in S1 alone increased translation efficiency of the leaderless mRNA by about 10-fold. Moderate overexpression of S1 relieved all these effects and, moreover, suppressed the thermosensitive phenotype of rpsB1, indicating the role of S1 as an extragenic suppressor of the E132K mutation.

Добавлено: 14 ноября 2013

Molecular Modeling and Simulation. Applications and Perspectives

Singapore: Springer, 2016.

Добавлено: 5 июля 2016

Chugunov A.O., Koromyslova A.D., Berkut A.A., Peigneur S., Tytgat J., Polyansky A.A., Modular Organization of α-Toxins from Scorpion Venom Mirrors Domain Structure of Their Targets - Sodium Channels

Chugunov A. O., Koromyslova A. D., Berkut A. A. et al. Journal of biological chemistry. 2013. Vol. 88. No. 26. P. 19014-19027.

To gain success in the evolutionary “arms race”, venomous animals such as scorpions produce diverse neurotoxins selected to hit targets in the nervous system of prey. Scorpion α-toxins affect insect and/or mammalian voltage-gated sodium channels (Nav’s) and thereby modify the excitability of muscle and nerve cells. Although more than a hundred α-toxins are known and a number of them have been studied into detail, the molecular mechanism of their interaction with Nav’s is still poorly understood. Here, we employ extensive molecular dynamics simulations and spatial mapping of hydrophobic/hydrophilic properties distributed over the molecular surface of α-toxins. It is revealed that in spite of the small size and relatively rigid structure, these toxins possess modular organization from structural, functional and evolutionary perspectives. The more conserved and rigid “core module” is supplemented with the “specificity module” (SM) that is comparatively flexible and variable, and determines the taxon (mammal vs. insect) specificity of α-toxin activity. We further show that SMs in mammal toxins are more flexible and hydrophilic than in insect toxins. Concomitant sequence-based analysis of Nav’s extracellular loops suggests that α-toxins recognize the channels using both modules. We propose that the core module binds to the voltage-sensing domain of repeat IV, whereas the more versatile SM interacts with the pore domain in repeat I of Nav’s. These findings corroborate and expand the hypothesis on different functional epitopes of toxins that has been reported previously. In effect, we propose that the modular structure in toxins evolved to match the domain architecture of Nav’s.

Добавлено: 13 ноября 2013

Вопросы оптимизации проектирования РЭС с учетом ЭМС

Грачев Н. Н., Лазарев Д. В. Современная наука: актуальные проблемы теории и практики. Серия: Естественные и технические науки. 2012. № 3. С. 31-39.

В статье рассматриваются вопросы оптимизации приектирования радиоэлектронных средств с учетом электромагнитной совместимости. В зависимости от наличия и вида ограничений, количества этапов в модели, ее вида находят применение аналитические или численные методы математического программирования. Рассматриваются и анализируются алгоритмы оптимизации на графах и сетях.

Добавлено: 10 ноября 2012

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Соколова А. Г. М.: Издательство ИНЭП, 1998.

Добавлено: 25 января 2013

Управление качеством информационных систем в экономике

Черников Б. В., Ильин В. В. М.: Издательский дом «Форум», 2010.

Рассмотрены концептуальные вопросы моделирования бизнеса, проектного управления, роли управления персоналом в оптимизации бизнеса. Изложены концептуальные подходы к определению путей повышения эффективности управления. Дана характеристика особенностей внедрения информационных систем в экономике, значения систем управления качеством. Пособие предназначено для студентов очной и очно-заочной форм обучения по специальности «Менеджмент организации», однако может быть полезно и студентам других специальностей, изучающим дисциплины «Информационные технологии управления», «Автоматизированные информационные системы», «Информационные системы в экономике», «Управление качеством».

Добавлено: 29 ноября 2012

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Shutov V. V., Yehia M., Vavilova E. et al. Journal of Low Temperature Physics. 2010. Vol. 159. No. 1-2. P. 96-100.

Добавлено: 7 апреля 2015

Generically transitive actions on multiple flag varieties

Deviatov R. arxiv.org. math. Cornell University, 2010. No. arXiv:1007.1353v1.

Пусть G — полупростая алгебраическая группа, разложение которой в произведение простых групп не содержит групп типа A, и P⊆G — параболическая подгруппа. Дополняя результаты Попова [7], мы перечисляем все тройки (G, P, n), такие что (а) в кратном многообразии флагов G/P × G/P × . . . × G/P (n множителей) существует открытая G-орбита, (б) число G-орбит на кратном многообразии флагов конечно.

Добавлено: 28 июня 2012

System of Resultants as a collection of coefficients of a unique Resultant

Abramov Y. V. arxiv.org. math. Cornell University, 2011. No. arXiv:1111.4974v1.

Я выписываю точную формулу для (теоретико-множественной) системы результантов как набора коэффициентов одного результанта.

Добавлено: 28 июня 2012

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Ч. 1. М.: Энергоатомиздат, 2011.

Добавлено: 7 февраля 2013

Асимптотические разложения решений пятого уравнения Пенлеве

Парусникова А. В., Брюно А. Д. Институт прикладной математики им. М.В. Келдыша Российской академии наук, 2010. № 39.

В данной работе рассматривается пятое уравнение Пенлеве, которое имеет 4 комплексных параметра α, β, γ, δ. Методами степенной геометрии ищутся асимптотические разложения его решений при x → ∞. При α≠0 найдено 10 степенных разложений с двумя экспоненциальными добавками каждое. Шесть из них - по целым степеням x (они были известны), и четыре по полуцелым (они новые). При α=0 найдено 4 однопараметрических семейства экспоненциальных асимптотик y(x) и 3 однопараметрических семейства сложных разложений x=x(y). Все экспоненциальные добавки, экспоненциальные асимптотики и сложные разложения найдены впервые. Также уточнена техника вычисления экспоненциальных добавок.

Добавлено: 18 апреля 2012