6 research outputs found
Investigation of Noncovalent Interactions in Complex Systems Using Effective Fragment Potential Method
Computational Chemistry has proven to be an effective means of solving chemical problems. The two main tools of Computational Chemistry - quantum mechanics and molecular mechanics, have provided viable avenues to probe such chemical problems at an electronic or molecular level, with varying levels of accuracy and speed. In this work, attempts have been made to combine the speed of molecular mechanics and the accuracy of quantum mechanics to work across multiples scales of time and length, effectively resulting in simulations of large chemical systems without compromising the accuracy. The primary tool utilized for methods development and application in this work is the Effective Fragment Potential (EFP) method. The EFP method is a computational technique for studying non-covalent interactions in complex systems. EFP is an accurate ab initio force field, with accuracy comparable to many Density Functional Theory (DFT) methods, at significantly lower computational cost. EFP decomposes intermolecular interactions into contributions from four terms: electrostatics, polarization, exchange-repulsion and dispersion. In the first chapter, the possibility of applying EFP method to study large radical-water clusters is probed. An approximate theoretical model in which the transition dipole moments of excitations are computed using the information from the ground state orbitals is implemented. A major challenge to broaden the scope of EFP is to overcome its limitation in describing only small and rigid molecules such as water, acetone, etc. In the second chapter, the extension of EFP method to large covalently bound biomolecules and polymers such as proteins, lipids etc., is described. Using this new method, referred to as BioEFP/mEFP, it is shown that the effect of polarization is non-negligible and must be accounted for when modeling photochemical and electron-transfer processes in photoactive proteins. Another area of interest is the development of novel drug-target binding models, in which a chemically active part of the ligand is modified via functional group modification, while the rest of the system remains intact. In the third chapter, the development and application of a drug-target binding model is explained. Lastly, in the fourth and final chapter, we show the derivation for working equations corresponding to the coupling gradient term describing the dispersion interactions between quantum mechanical and effective fragment potential regions. The primary focus of this work is to explore and expand the boundaries of multiscale QM/MM simulations applied to chemical and biomolecular systems. We believe that the work described here leads to exciting pathways in the future in terms of modeling novel systems and processes such as heterogeneous catalysis, QSAR, crystal structure prediction, etc
Simulating Redox Potentials of Biomolecules: the Case of Cryptochrome 1 from Arabidopsis thaliana
Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present the results of computational studies of the redox potential of flavin adenine dinucleotide (FAD) in cryptochrome 1 from Arabidopsis thaliana (Cry1At). The special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The theoretical estimate (0.07 V) of the midpoint reduction potential of FAD in Cry1At is reported for the first time and is in good agreement with available experimental data
Molybdenum Trioxide on Anatase TiO2(101) - Formation of Monodispersed (MoO3)1 Monomers from Oligomeric (MoO3)n Clusters
Complex oxide systems with hierarchical order are of
critical importance in material science and catalysis. Despite their immense
potential, their design and synthesis are rather difficult. In this study we
demonstrate how the deposition of small oligomeric (MoO3)1-6 clusters,
which can be formed by the sublimation of MoO3 powders,
leads to the formation of locally ordered layers of (MoO3)1 monomers
on anatase TiO2(101). Using both high-resolution imaging and
theoretical calculations, we show that at room temperature, such oligomers
undergo spontaneous dissociation to their monomeric units. In initial stages of
the deposition, this is reflected by the observation of one to six
neighboring (MoO3)1 monomers that parallel the size
distribution of the oligomers. A transient mobility of such oligomers on both
bare TiO2(101) and (MoO3)1 covered
areas is key to the formation of a complete layer with a saturation coverage of
one (MoO3)1 per two undercoordinated surface Ti
sites. We further show that such layers are stable to 500 K, making them highly
suitable for a broad range of applications. </p
Photocatalytic degradation of methyl orange dye using silver (Ag) nanoparticles synthesized from Ulva lactuca
Extension of the Effective Fragment Potential Method to Macromolecules
The
effective fragment potential (EFP) approach, which can be described
as a nonempirical polarizable force field, affords an accurate first-principles
treatment of noncovalent interactions in extended systems. EFP can
also describe the effect of the environment on the electronic properties
(e.g., electronic excitation energies and ionization and electron-attachment
energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable
embedding scheme. The original formulation of the method assumes that
the system can be separated, without breaking covalent bonds, into
closed-shell fragments, such as solvent and solute molecules. Here,
we present an extension of the EFP method to macromolecules (mEFP).
Several schemes for breaking a large molecule into small fragments
described by EFP are presented and benchmarked. We focus on the electronic
properties of molecules embedded into a protein environment and consider
ionization, electron-attachment, and excitation energies (single-point
calculations only). The model systems include chromophores of green
and red fluorescent proteins surrounded by several nearby amino acid
residues and phenolate bound to the T4 lysozyme. All mEFP schemes
show robust performance and accurately reproduce the reference full
QM calculations. For further applications of mEFP, we recommend either
the scheme in which the peptide is cut along the C<sub>α</sub>–C bond, giving rise to one fragment per amino acid, or the
scheme with two cuts per amino acid, along the C<sub>α</sub>–C and C<sub>α</sub>–N bonds. While using these
fragmentation schemes, the errors in solvatochromic shifts in electronic
energy differences (excitation, ionization, electron detachment, or
electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP
against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most
cases, the errors are 0.01–0.02 eV). The errors in the QM/molecular
mechanics calculations with standard point charges can be as large
as 0.3 eV