M. L. Chernavina

Molecular modeling of immersion optical clearing of biological tissues

AbstractThe interaction of six low-molecular tissue-clearing agents (1,2 and 1,3-propanediol, ethylene glycol, glycerol, xylitol, sorbitol) with the collagen mimetic peptide (GPH)3 was studied by applying the methods of classical molecular dynamics (GROMACS), molecular docking (AutoDock Vina) and quantum chemistry (PM6 and B3LYP). The spatial configurations of intermolecular complexes were determined and interaction energies calculated. The dependence of the volume occupied by the collagen peptide on the clearing agent concentration in an aqueous solution was calculated. This dependence is not linear, and has a maximum for almost all the agents in the study. The correlations between the optical clearing potential and intermolecular interactions parameters, such as the time of an agent being in a hydrogen-bonded state, and the relative probability of formation of double hydrogen bonds and interaction energies, were determined. Using the correlations determined, we predicted the numeric value of the optical clearing potential of dextrose molecules in rat skin, which correlates with experimental data. A molecular mechanism of tissue optical clearing within the post-diffusion stage is suggested. Graphical abstractThe molecular modeling of the interaction between clearing agents and collagen

Studying the mechanism of tissue optical clearing using the method of molecular dynamics

The interaction of three tissue-clearing agents (1,2-1,3-propanediol, 1,2-ethanediol) with the collagen mimetic peptide ((GPH)3)9 was studied by applying the method of classical molecular dynamics. The complete conformational analysis of the clearing agents under study was performed using the DFT/B3LYP/6-311+G method (d, p), the most energetically favorable spatial configurations were determined, the values of the Mulliken atomic charges were calculated which were used for the simulation. The research showed that there is a good correlation between the time of the hydrogen binding of a clearing agent with a collagen peptide and the potential of optical clearing. The paper also discusses that the interaction of the tissue-clearing agents with a collagen peptide in a water solution results in the 6% average enlargement of the distance between the alpha peptide chains. It has been suggested that such changes in a collagen structure can affect the refraction index and as a consequence the optical clearing of a biotissue. The dependences of the average distance changing between the alpha chains of a collagen peptide and the concentration of clearing agents in water solution were determined.

FT-IR and DFT study of lemon peel

Experimental FT-IR spectra of lemon peel are registered in the 650 - 3800 cm-1 range. The influence of peel artificial and natural dehydration on its vibrational spectrum is studied. The colored outer surface of lemon peel is proved not to have a significant impact on FT-IR spectrum. It is determined that only dehydration processes affect the FT-IR vibrational spectrum of the peel when a lemon is stored for 28 days under natural laboratory conditions. Polymer molecule models for dietary fibers, such as cellulose, hemicellulose, pectin, lignin, as well as hesperidin – flavonoid glycoside, and free moisture cluster are developed within the framework of DFT/B3LYP/6-31G(d) theoretical method. By implementing supramolecular approach, modeling of the vibrational FT-IR spectrum of lemon peel is carried out and its detailed theoretical interpretation is presented.

The experimental vibrational infrared spectrum of lemon peel and simulation of spectral properties of the plant cell wall

The experimental vibrational IR spectra of the outer part of lemon peel are recorded in the range of 3800–650 cm–1. The effect of artificial and natural dehydration of the peel on its vibrational spectrum is studied. It is shown that the colored outer layer of lemon peel does not have a noticeable effect on the vibrational spectrum. Upon 28-day storage of a lemon under natural laboratory conditions, only sequential dehydration processes are reflected in the vibrational spectrum of the peel. Within the framework of the theoretical DFT/B3LYP/6-31G(d) method, a model of a plant cell wall is developed consisting of a number of polymeric molecules of dietary fibers like cellulose, hemicellulose, pectin, lignin, some polyphenolic compounds (hesperetin glycoside-flavonoid), and a free water cluster. Using a supermolecular approach, the spectral properties of the wall of a lemon peel cell was simulated, and a detailed theoretical interpretation of the recorded vibrational spectrum is given.

Molecular modeling of the process of reversible dissolution of the collagen protein under the action of tissue-clearing agents

The interaction of glycerol immersion agent with collagen mimetic peptide ((GPH)9)3 and a fragment of the microfibril 5((GPH)12)3 was studied by the classical molecular dynamics method using the GROMACS software. The change in geometric parameters of collagen α-chains at various concentrations of an aqueous solution of glycerol is analyzed. It is shown that these changes nonlinearly depend on the concentration and are limited to a certain level, which correlates with the experimental data on optical clearing efficiency of human skin. A hypothesis on the cause of the decreased efficiency of optical skin clearing at high immersion agent concentrations is put forward. The molecular mechanism of immersion optical clearing of biological tissues is discussed.

FT-IR spectrum of grape seed oil and quantum models of fatty acids triglycerides

FT-IR spectra of grape seed oil and glycerol were registered in the 650-4000 cm-1 range. Molecular models of glycerol and some fatty acids that compose the oil under study – linoleic, oleic, palmitic and stearic acids – as well as their triglycerides were developed within B3LYP/6-31G(d) density functional model. A vibrating FT-IR spectrum of grape seed oil was modeled on the basis of calculated values of vibrating wave numbers and IR intensities of the fatty acids triglycerides and with regard to their percentage. Triglyceride spectral bands that were formed by glycerol linkage vibrations were revealed. It was identified that triglycerol linkage has a small impact on the structure of fatty acids and, consequently, on vibrating wave numbers. The conducted molecular modeling became a basis for theoretical interpretation on 10 experimentally observed absorption bands in FT-IR spectrum of grape seed oil.

Structural Parameters and Thermodynamics of the Formation of Molecular Water Clusters

The formation of molecular water clusters is simulated using the theoretical density functional theory/ B3LYP/6-311+G(d,p) method. The spatial configurations of 29 clusters with 2 to 28 water molecules are calculated. The dipole moments, the complete complex-formation enthalpy, and the enthalpy of the successive joining of water molecules are determined with the basis-set superposition error taken into account. The features of the geometric structure and the hydrogen-bond strength of water clusters are analyzed on the basis of the obtained theoretical data. The complex-formation enthalpy is revealed to depend periodically on the number of water molecules in a cluster. It is found that clusters with molecules whose number is a multiple of four are energetically most advantageous. When a molecular cluster is built starting with 17 molecules, the cluster structure is changed, resulting in that one end of the complex rolls up into a prismatic configuration.

Algorithm for solving the inverse vibronic problem on the basis of SVL fluorescence spectra

Computer methods whereby the inverse vibronic problem is solved on the basis of resonance fluorescence spectra with the use of modern quantum-mechanical methods for constructing structuraldynamic models of polyatomic molecules are discussed. An algorithm is proposed for solving the inverse vibronic problem according to resonance fluorescence spectra under laser excitation, and the corresponding calculation programs are constructed. The initial program data are acquired by means of an original software package which implements the scaling of quantum-mechanical force fields in two electronic states. The Duschinsky matrix and the initial matrix of shifts in normal coordinates caused by electron excitation are calculated in the Cartesian and natural vibrational coordinates. The program data are taken from quantum-molecular models based on calculations performed via ab initio modern quantum-mechanical methods and density functional theory. The algorithm is tested through the calculation of a model molecular system.

On algorithms for calculating the SVL-fluorescence spectra of polyatomic molecules

A software package for modeling the fluorescence spectra from a single vibrational level (SVL) of excited electron states under resonance laser excitation, in the adiabatic approximation with allowance for the “confusion” of normal coordinates under electron excitation, i.e., the Dushinsky effect, is presented. To algorithmize the calculation of the intensities in resonance fluorescence spectra, thirteen modules for the calculating Franck–Condon integrals are created. To optimize the calculation process, some simpler expressions are derived for the common terms of nested sums in the formulas for calculating Franck–Condon integrals from tone and overtone levels. To accelerate calculations, some constraints in the form of inequalities are additionally imposed on the range of vibrational quantum numbers in the ground electron state. The proposed algorithm for the modeling of SVL-fluorescence spectra of polyatomic molecules is based on quantum models of molecules in the ground and excited electron states calculated within the framework of contemporary ab initio quantum-mechanical methods and methods based on density functional theory.

Spectra-structure correlation in metalloporphyrins

The calculations of the geometrical parameters, frequencies of normal fluctuations and intensity in IR-spectrums of some metalloforbids (Mg-, Zn-, Cu-, Fe-e and Ni-forbid) have been performed by the matrix isolation technique B3LYP/6-311+G (d, p). In this article the absorption bands in IRspectra sensitive to the nature of the metal’s central ion were defined too. The correlations between the force of the interaction of the central ion of the metal with porphyrin macrocycle and the series of changes in the structural parameters have been established.