APPLICATIONS: Structure and Dynamics of Atomic-Molecular Systems

Systems with hydrogen bonds: inner peculiarities and the effect on solute properties


Novakovskaia Yulia
Moscow State Uiversity

DRIVER: Discovering the peculiarities of the formation of hydrogen bonds in diverse systems and the resulting properties of the systems. Predicting and judging the role of hydrophilic and hydrophobic effects.

STRATEGY: Combination of stationary and dynamic modeling (with the use of methods taking into account electron correlation) of molecular clusters and individual particles stabilized by hydrogen bonds. Distinguishing predominant structural types and the ways of their reorganization. Numerical analysis of the electron density distributions and energetic characteristics of the systems with the use of specially developed schemes of analytical approximations.

OBJECTIVE: Explain the nature and character of the cooperative effects in hydrogen-bonded systems and the physical reasons for the experimentally observed signatures of the systems. Clarify the structure peculiarities of diverse hydrogen-bonded systems and their effect on the properties of objects they solvate.

IMPACT: Clarification of the nature of hydrogen bonds and their role in the formation of certain kinds of aggregates and surface structures not only contributes to the theoretical concept of the substance structure and materials science, but also provides grounds for the founded selection of the strategy of producing supramolecular systems with the desirable properties.

USAGE: Fundamental physical chemistry; materials science; production of hydrogen-bond-based nanosystems with the desirable structure and properties; effect produced by hydrogen-bonded environment on the structure and surface properties of nanoparticles

AREA: Structure and Dynamics of Atomic-Molecular Systems



Computational methods of quantum chemistry and their application


Laikov Dmitry
Moscow State Uiversity

DRIVER: Development of new mathematical models, approximations, and computational algorithms for the predictions of properties of complex chemical systems

STRATEGY: Create new mathematical models, write computer programs, run calculations and see how is works

OBJECTIVE: Extend the limits on the complexity of chemical systems whose properties can be computed with an acceptable accuracy in a reasonable amount of time

IMPACT: The computational methods of can help the interested chemists to understand the structure and reactivity of complex molecular systems and design new materials with desired properties

USAGE: The computation of properties of molecular systems

AREA: Structure and Dynamics of Atomic-Molecular Systems



Modeling mechanisms of photochemical processes in photoreceptor and fluorescent proteins


KHrenova Maria
Moscow State Uiversity

DRIVER: Studying mechanisms of functioning of fluorescent proteins, flavin containing photoreceptor proteins and bacterial photosystem

STRATEGY: Development and application of methods of computer molecular modeling, including combined method of quantum mechanics/ molecular mechanics and modern approaches of quantum chemistry, for properties calculations of photoreceptor proteins and their chromophores

OBJECTIVE: Establishment of mechanisms of functioning of fluorescent proteins, flavin containing photoreceptor proteins and bacterial using combined method of quantum mechanics/ molecular mechanics and modern methods of quantum chemistry of high level of accuracy

IMPACT: Prediction of new fluorescent and photoreceptor proteins with the suggested properties, on the basis of mechanisms established in the project

USAGE: biosensor technologies, life sciences

AREA: Structure and Dynamics of Atomic-Molecular Systems, Physicochemical Biology



Determination of the structural and dynamic characteristics of the self-organizing media by means of EPR spectroscopy


Chumakova Natalia
Moscow State Uiversity

DRIVER: The aim of the project is investigation of structural and dynamic parameters of self-organizing media, i.e. media which spontaneously form microscopic molecular structures. In the course of the project we work out and use for concrete systems the methods for simultaneous determination of rotation and translation mobility as well as orientation ordering of the molecules. These methods are applied for analysis of ionic liquids, micelle-forming polymers (pluronics), micelle-forming dendrimers, and nematic, smectic and cholesteric liquid crystals. Structural and dynamic characteristics would allow to establish the mechanism of the structural and phase transitions in such systems.

STRATEGY: Determination of the structural and dynamic characteristics of the materials in present project is realized by means of numerical modelling of EPR spectra. In the case of orientational ordering of the sample the joint modelling of series of the spectra is performed. Hence the values under consideration are the varied parameters in the course of solving of the spectroscopic inverse task.

OBJECTIVE: The aim of the project is investigation of the dynamic characteristics and the structure of the self-forming molecular structures.

IMPACT: Successful realisation of the project would lead to creation of the method for determination of both structural and dynamic characteristics of the self-organizing media by means of EPR spectroscopy. Application of this method would lead to creation the materials with adjusted properties.

USAGE: Development of methodology of the EPR spectroscopy Science of materials

AREA: Structure and Dynamics of Atomic-Molecular Systems, Physical Chemistry



Mineral solid solutions structure and properties supercimputer modeling


Eremin Nicolai
Moscow State Uiversity

DRIVER: Implement a set of atomistic, molecular dynamics and quantum chemical methods for simulation of crystal structures, defects, and radiation resistance of minerals and their solid solutions in some oxide and silicate systems

STRATEGY: The authors have a number of original designs that allow, first, in the framework of representative super cell receive properties of disordered solid solution and their comprehensive review of its properties, and secondly, can physically reasonable to consider the charge transfer energy, allowing the use of strict energy basis for modeling with all values of the effective atomic charges.

OBJECTIVE: 1) The estimation of radiation resistance of mineral-like matrices; 2) Predicting of the physical properties of inorganic compounds of variable composition

IMPACT: The establishment of new technologically advanced materials with variable composition

USAGE: environmental management, ecology, earth sciences,

AREA: Geology, Structure and Dynamics of Atomic-Molecular Systems



First principle calculations of silver clusters on alpha-quartz surface


Kuramshina Gulnara
Moscow State Uiversity

DRIVER: Molecular modeling the diffusion of silver clusters on alpha-quartz surface and the formation of metal island films

STRATEGY: Application of different quantum mechanical models and methods to estimate the most approrpiate energy profiles of different physical and chemical processes on the thin film formation

OBJECTIVE: Establishment of the most probable ways of adsorption and diffusion of silver clusters on quartz surface

IMPACT: Optimal and productive prediction of the efficient thin films supported by good agreement with experimental data

USAGE: Development of effective ways of obtaining the low-cost photonic heterostructures.

AREA: Engineering Sciences and Mechanical Engineering, Structure and Dynamics of Atomic-Molecular Systems



Skeletal, Exo- and Endohedral Transfromations in Carbon Nanostructures


Ioffe Ilia
Moscow State Uiversity

DRIVER: Elucidation of pathways of skeletal transformations in fullerenes and nanotubes and of formation of non-classical carbon nanostructures, and computation of rearrangement properties of exo- and endohedral addends

STRATEGY: Computation of energetic characteristics of the possible pathways of rearrangements of addends, skeletal rearrangements and of small cluster abstraction from carbon cages by means of various realizations of the density functional theory

OBJECTIVE: Detailed description of pathways of Stone-Wales rearrangements and of abstration of small cluster from carbon cages; identification of species and media that show catalytic effect on skeletal rearrangements; understanding of connections between skeletal rearrangements and rearrangements of addends

IMPACT: Synthesis of new types of non-classical carbon nanostructures and development of a new field - chemistry of skeletal transformations

USAGE: Synthesis of novel types of carbon nanostructures for molecular electronics

AREA: Engineering Sciences and Mechanical Engineering, Structure and Dynamics of Atomic-Molecular Systems



Computational modeling of nanostructured carbon materials


Ananikov Valentin
Zelinsky Institute of Organic Chemistry of RAS

DRIVER: Computational modeling of properties and synthesis of carbon-based nanostructured materials

STRATEGY: Modeling of carbon-based nanostructured systems with quantum chemistry, molecular dynamics and quantum molecular dynamics methods

OBJECTIVE: Finding new perspective nanostructured systems based on carbon materials

IMPACT: New carbon-based materials with exceptional chemical and physical properties

USAGE: Organic, organomeallic and inorganic chemistry; chemical industry

AREA: Condensed Matter Physics, Physical Chemistry, Structure and Dynamics of Atomic-Molecular Systems, Engineering Sciences and Mechanical Engineering



Modelling systems, containing d-metals


Bezrukov Dmitry
Moscow State Uiversity

DRIVER: Studying the features of atomic clusters in inert matrices and the nature of the interaction of these systems in pi-complexes

STRATEGY: Molecular dynamics modelling and multireference nonempirical calculations

OBJECTIVE: Development technique of determination of stable vacancies in the inner matrix; obtain highly accurate description of diatomic molecules, explaining experimental data

IMPACT: Publications in journal with hight impact-factor

USAGE: Qualitatively new results and techniques for interpretation of experimental data for a wide range of researchers

AREA: Structure and Dynamics of Atomic-Molecular Systems, Physical Chemistry



Membrane proteins modelling


Bogdan Tatiana
Moscow State Uiversity

DRIVER: Study of the factors stabilizing active form of the b2-adrenergic receptor

STRATEGY: Molecular dynamics simulation of membrane systems with different composition

OBJECTIVE: Reveal the conformational changes in the protein structure by changing composition of the membrane. Determine the role of cholesterol molecules in stabilizing the active state of b2-adrenergic receptors.

IMPACT: Explain the mechanism of transducing chemical signals across cell membranes

USAGE: biochemistry, medicine

AREA: Structure and Dynamics of Atomic-Molecular Systems



High precision computational studies in photochemistry and excited state dynamics


Ioffe Ilia
Moscow State Uiversity

DRIVER: Description of dynamics of electronically excited systems with the use of novel efficient quantum-chemical approaches

STRATEGY: Selection of most approppriate parameters of the XMCQDPT2 technique and optimization of the most important potential energy profiles of the relevant excited states in chromophores in question, as well as vibrational calculations of the stationary points

OBJECTIVE: Detailed description of isomerization pathways in stilbenes; high precision computation of spectral properties in key organic chromophores that can be used as fluorescent probes in dielectric media and biological objects

IMPACT: Understanding of evolution pathways in different characteristic photochemical systems and improvement of computational approaches to their description

USAGE: Description of evolution of molecular systems that are of key significance in photochemistry and photobiology

AREA: Structure and Dynamics of Atomic-Molecular Systems



Computer Simulation of Hypercrosslinked Polystyrene


Lazutin Aleksey
Nesmeyanov Institute of Organoelement Compounds of RAS

DRIVER: Investigation of formation of hypercrosslinked polymer networks. Investigation of the structure of hypercrosslinked polymer networks

STRATEGY: Multi-scale computer simulation

OBJECTIVE: Determination of structural properties of hypercrosslinked polymer networks

IMPACT: Knowledge of formation of hypercrosslinked polymer networks and their structure

USAGE: Development of theory of polymer networks

AREA: Structure and Dynamics of Atomic-Molecular Systems, High Molecular Weight Compounds



Small luminescent silver clusters stabilized on DNA template


Ramazanov Ruslan
Saint Petersburg State University

DRIVER: Detecting a structural characteristics defining the luminescent properties of complexes of silver clusters with DNA.

STRATEGY: Quantum chemical calculations of the excitation spectra for the equilibrium configurations of systems and their components, as well as analysis of the relaxation of the excited state to elucidate possible luminescence.

OBJECTIVE: Estimation of influence of complexation with DNA on the excitation spectra of free small clusters.

IMPACT: Investigating a high-quality theoretical prerequisites for a rational synthesis of silver clusters on the DNA template in order to obtain the set of fluorescent characteristics.

USAGE: Creating a highly selective biotests. Local biomedical diagnostics.

AREA: Informatics, Condensed Matter Physics, Structure and Dynamics of Atomic-Molecular Systems



Multiscale atomistic simulation of hierarchical nanomaterials for optical chemical sensors


Freidzon Alexandera
Photochemistry center of RAS

DRIVER: Theoretical atomistic simulation using ab initio quantum chemistry methods is proposed for the prediction of the properties of optical molecular sensors

STRATEGY: Full geometry optimization of the indicator molecules and their supramolecular complexes with analytes is to be performed by the density functional method. The absorption spectra of the indicators and complexes are to be calculated by the time-dependent density functional method with environment taken into account through the polarizable continuum model or through effective fragment potentials. The excited-state geometry of the indicators and their complexes is to be optimized by the time-dependent density functional method, and their fluorescence spectra are to be calculated. The possibility of fluorescence quenching or enhancement due to the indicator--analyte interaction is to be estimated. The most promising chromophores for optical molecular sensors and the structure of their corresponding receptor centers will be chosen on the basis of the calculations.

OBJECTIVE: Multiscale simulation of the optical response of the nanostructured chemosensor material at the molecular and supramolecular level using ab initio quantum chemistry and molecular dynamics

IMPACT: The results will be used for the prediction of sensor properties of dyes with respect to various analytes in polar solutions or in matrices. The possible ways for improving the materials for nanotechnological applications will be proposed on the basis of the atomistic simulation.

USAGE: The results can be used in the design of optical molecular sensors for medicine and environmental monitoring.

AREA: Engineering Sciences and Mechanical Engineering, Structure and Dynamics of Atomic-Molecular Systems



Molecular dynamics simulation of flaviviral envelope proteins


Osolodkin Dmitry
Moscow State Uiversity

DRIVER: Theoretical study of structural determinants of virion properties. Molecular dynamics simulation of viral fusion

STRATEGY: Molecular dynamics simulation of a series of envelope protein models differing by point substitutions and protonation state

OBJECTIVE: Point mutations introduced during virus life cycle in different hosts affect the properties of viral particles, such as the interaction with cell surface proteins and (indirectly) virulence. No obvious correlations exist between these mutations and properties, so structural study should be helpful in revealing the basis for such differences. Simulation of the viral fusion process will allow us to understand the molecular basis of this sophisticated machinery and to understand the mechanism of functioning of such sophisticated molecular machine as virus

IMPACT: Deep understanding of connection between amino acid sequence of viral proteins and the properties of a viral particle. Simulation of viral fusion process

USAGE: Design of new antiviral compounds and molecular machines

AREA: Structure and Dynamics of Atomic-Molecular Systems, Organic Chemistry



Quantum-chemical investigation reaction of propylene oxidation on gold, silver, and bimetallic gold-silver catalysts


Kuzmenko Nicolai
Moscow State Uiversity

DRIVER: Study structure of active sites on gold, silver, and bimetallic gold-silver catalysts in reaction of propylene oxidation

STRATEGY: Modeling the reaction mechanism and evaluation of activation barriers of propylene oxidation by quantum chemical methods

OBJECTIVE: Modeling the reaction mechanism and evaluation of activation barriers of propylene oxidation by quantum chemical methods

IMPACT: Creating an effective catalyst in the reaction of propylene oxidation

USAGE: Catalysis, chemical industry

AREA: Structure and Dynamics of Atomic-Molecular Systems, Physical Chemistry



Firefly 8


Granovsky Alexander
Moscow State Uiversity

DRIVER: Development of the Firefly version 8.0.0 Quantum Chemistry package

STRATEGY: Efficient parallel Implementation of key Quantum Chemistry algorithms

OBJECTIVE: Extension of the package functionality, improvements in its performance and scalability

IMPACT: Increased user's base, better efficiency and functionality, competitive advantages.

USAGE: Pure and applied Chemistry, Molecular Physics, Biology, Molecular Biology, Life Science, Geology, Soli Science, Nano-technology etc...

AREA: Algorithm and Software Development, Structure and Dynamics of Atomic-Molecular Systems



TFAA cluster properties modeling in solution


Zlenko Dmitry
Moscow State Uiversity

DRIVER: 1. Calculate a diffusion factors and correlation times of TFAA molecules. 2. Discover a time-averaged structure of aggregates. 3. Calculate energies of pair ineractions of molecules in aggregates.

STRATEGY: A molecular dynamics simulaion

OBJECTIVE: Calculate the molecular properties of TFAA aggregates in solution

IMPACT: Mechanism of gellation and single 1-D string formation in TFAA solutions explanation.

USAGE: Material science

AREA: Engineering Sciences and Mechanical Engineering, Structure and Dynamics of Atomic-Molecular Systems



Structure and properties ligand-protected gold clusters


Pichugina Daria
Moscow State Uiversity

DRIVER: creation of structure concept of thiol-protected gold clusters based on quantum-chemical calculation

STRATEGY: DFT simulation of S-H bond rupture in thiols on Aun clusters including potential energy surface study

OBJECTIVE: Understanding of the mechanism of formation of thiol-protected gold clusters prediction of catalytic properties in functionalization of C-H bond in methane

IMPACT: information obtained will allow for more effective synthesis and functionalization of size-controlled nanoparticles for potential application in catalysis, sensing, photonics

USAGE: catalysis, physical-chemistry, nanotechnology

AREA: Engineering Sciences and Mechanical Engineering, Structure and Dynamics of Atomic-Molecular Systems



Design and quantum chemical study of electronic structures of new intermetallic compounds and derivatives


KuzneTcov Aleksey
Moscow State Uiversity

DRIVER: Representation of electronic structures of metal-metal bond based unconventional systems, the development of the fundamentals of computational design of such compounds

STRATEGY: The use of advanced methods of the evaluation of band structures of solids (DFT/LAPW; DFT/APW+lo; DFT/LDA+U) for calculating electronic structures of intermetallics and their derivatives, theoretical evaluation of electric and magnetic properties. Evaluation of the applicability and performance of various direct-space bond analysis schemes (electron density laplacian, ELF, ELI, QTAIM) for the description of metal-metal bond systems of varying dimensionality.

OBJECTIVE: The development of an effective approach for describing the bonding and properties of complex intermetallics-based systems.

IMPACT: Scientific impact, i.e. the deeper insight into the fundamental concepts of metal-metal bonding in complex systems and different aproaches to their visualization. The development of the low-dimensional metallic fragment stabilizations concepts for chemical solids and materials.

USAGE: Fundamental science - inorganic chemistry, solid state chemistry, materials science

AREA: Inorganic Chemistry, Physical Chemistry, Structure and Dynamics of Atomic-Molecular Systems



Mathematical modeling of mitotic cell division at molecular level in order to find new targets for anticancer treatment


Zaharov Pavel
Center for Theoretical Problems of Physicochemical Pharmacology of RAS

DRIVER: Study of molecular mechanisms of protein interactions in mitotic system

STRATEGY: Integration of experimental data from mechano-molecular system of cell division using methods of molecular dynamics and coarse grained models for proteins

OBJECTIVE: Creation new type of anticancer drugs

IMPACT: Scientific: new information about cell division. Commercial: new effective anti-cancer drugs. The market for such medicines is hundreds billions of dollars. Social: increasing length of the life for millions of people

USAGE: Pharmacology, medicine, molecular and cell biology

AREA: Medical Physics, Structure and Dynamics of Atomic-Molecular Systems, Physicochemical Biology



Modeling and estimation of thermodynamic characteristics of surface segregation in binary alloys.


Doronin Sergey
Institute of Problems of Chemical Physics of RAS

DRIVER: The influence of cluster composition on segregation parameters is to be evaluated by quantum chemistry methods (DFT plane wave). The influence of a number of adsorbents (atomic oxygen, water and products of water decomposition) on segregation is to be considered.

STRATEGY: The solution of the problem is to be performed using the following steps: - analysis of optimal calculation parameters (selection of pseudopotential, supercell size, comparability with the experimental data); - effect of cluster composition on energy of segregation; - effect of surface adsorbents on energy of segregation; - behavior of atoms of segregated metal in the surface layer. Additionally: - show the influence of the atomic composition of the surface on the adsorption of water - estimate the activation energy of segregation processes in the bulk and the activation energy of surface atoms migration

OBJECTIVE: The influence of surface adsorbents and cluster composition on thermodynamics and kinetics of segregation is to be shown.

IMPACT: The effect of water medium on thermodynamics and kinetics of segregation is to be clearly shown.

USAGE: The results can be used in theoretical and experimental study of catalysis on monolayer- and adatoms- covered surfaces, in particular for core-shell catalysts.

AREA: Engineering Sciences and Mechanical Engineering, Structure and Dynamics of Atomic-Molecular Systems



Nanoordering in polymer systems


Larin Sergey
Institute of Macromolecular Compounds of RAS

DRIVER: Investigation of formation and stability of nanoscale ordered structures in polymer materials

STRATEGY: Long time scale computer simulation of polymeric systems containing ordered nanostructures or ordered and disordered (amorphous) parts

OBJECTIVE: The goal is to study processes of ordered nanostructures formation in polymer systems which could occur either in bulk or near the interface of ordered and amorphous regions of the systems considered. Additional goal is an investigation of various factors influence on stability of the ordered nanostructures including influence of temperature, system composition, and filler particles.

IMPACT: Further understanding of ordered nanostructures formation processes in polymeric systems on atomistic level and understanding of various factors influence on their stability

USAGE: Development of new polymeric materials with controlled microstructure

AREA: Structure and Dynamics of Atomic-Molecular Systems



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