Quantum chemical and spectroscopic investigations of 3-methyladenine

A Novel Prediction Model for Brain Glioma Image Segmentation Based on the Theory of Bose-Einstein Condensate

Background

The input image of a blurry glioma image segmentation is, usually, very unclear. It is difficult to obtain the accurate contour line of image segmentation. The main challenge facing the researchers is to correctly determine the area where the points on the contour line belong to the glioma image. This article highlights the mechanism of formation of glioma and provides an image segmentation prediction model to assist in the accurate division of glioma contour points. The proposed prediction model of segmentation associated with the process of the formation of glioma is innovative and challenging. Bose-Einstein Condensate (BEC) is a microscopic quantum phenomenon in which atoms condense to the ground state of energy as the temperature approaches absolute zero. In this article, we propose a BEC kernel function and a novel prediction model based on the BEC kernel to detect the relationship between the process of the BEC and the formation of a brain glioma. Furthermore, the theoretical derivation and proof of the prediction model are given from micro to macro through quantum mechanics, wave, oscillation of glioma, and statistical distribution of laws. The prediction model is a distinct segmentation model that is guided by BEC theory for blurry glioma image segmentation.

Results

Our approach is based on five tests. The first three tests aimed at confirming the measuring range of T and μ in the BEC kernel. The results are extended from −10 to 10, approximating the standard range to T ≤ 0, and μ from 0 to 6.7. Tests 4 and 5 are comparison tests. The comparison in Test 4 was based on various established cluster methods. The results show that our prediction model in image evaluation parameters of P, R, and F is the best amongst all the existent ten forms except for only one reference with the mean value of F that is between 0.88 and 0.93, while our approach returns between 0.85 and 0.99. Test 5 aimed to further compare our results, especially with CNN (Convolutional Neural Networks) methods, by challenging Brain Tumor Segmentation (BraTS) and clinic patient datasets. Our results were also better than all reference tests. In addition, the proposed prediction model with the BEC kernel is feasible and has a comparative validity in glioma image segmentation.

Conclusions

Theoretical derivation and experimental verification show that the prediction model based on the BEC kernel can solve the problem of accurate segmentation of blurry glioma images. It demonstrates that the BEC kernel is a more feasible, valid, and accurate approach than a lot of the recent year segmentation methods. It is also an advanced and innovative model of prediction deducing from micro BEC theory to macro glioma image segmentation.

Isolation, Identification, Spectral Studies and X-ray Crystal Structures of Two Compounds from Bixa orellana, DFT Calculations and DNA Binding Studies

4,6-Diacetylresorcinol (1) and 3-O-methylellagic acid dihydrate (2), both biologically significant compounds, were extracted from Bixa orellana and studied using IR, 1H, and 13C NMR, and UV-vis spectroscopic techniques. X-ray crystallographic techniques were also used to establish the molecular structure of the isolated compounds 1 and 2. Geometric parameters, vibrational frequencies, and gauge including atomic orbital (GIAO) 1H and 13C NMR of 1 and 2 in the ground state were computed by the density functional theory (DFT) using B3LYP/6-311G(d,p) basis set backing up experimental studies and established the correct structure of isolated compounds. The parameters obtained from the combined DFT, and X-ray diffraction studies are mutually agreed to establish correct structures of 1 and 2. In addition, an electrostatic potential map and HOMO−LUMO energy gap were made using the DFT calculation to determine the distribution of energy and the chemical reactivity region of the isolated compounds. The current study also provides further insights into the interaction of compound 2 with ct-DNA using numerous biophysical and in silico techniques. Moreover, in silico studies indicate that compound 2 binds to the DNA in the minor groove. Lipinski’s rule of five revealed a higher tendency of compound 2 towards drug-likeness. The bioavailability and synthetic accessibility score for compound 2 was found to be 0.55 and 3.21, suggesting that compound 2 could serve as an effective therapeutic candidate.

Reinvestigation of the photophysics of 3-aminobenzoic acid in neat and mixed binary solvents

The present study elucidates the reinvestigation of the photophysical behavior of 3-aminobenzoic acid (3ABA) in solvents of different polarities using the steady-state spectroscopic techniques. Kamlet-Taft and Catalan solvatochromic models have been used to analyze the solvatochromic changes in neat solvents. The hydrogen bond donating ability of the solvent was found to be the main parameter affecting the spectral behavior of 3ABA. The solvatochromic characteristics of 3ABA have also been examined in binary solvent mixtures viz. acetonitrile (ACN)-methanol (MeOH) and benzene (BEN)-MeOH using the concept of preferential solvation. The preferential solvation of 3ABA shows unusual behavior for BEN-MeOH binary mixture and described unnoticed sigmoidal behavior in the ground state and synergistic impact in the excited state. Besides, the 3ABA was studied theoretically by quantum chemical calculations using (HF) Hartree-Fock and (DFT/B3LYP) density functional theories and its electronic absorption bands have been assigned by time-dependent density functional theory (TD-DFT). The effect of solvents on 3ABA was considered using a IEF-PCM-TDDFT (integral equation formalism of the polarizable continuum model- TDDFT) method. Thus, the theoretical results were found to be closer to the experimental results.

Anharmonic vibrational spectra and mode-mode couplings analysis of 2-aminopyridine

Vibrational spectra of 2-aminopyridine (2AP) have been analyzed using the vibrational self-consistence field theory (VSCF), correlated corrected vibrational self-consistence field theory (CC-VSCF) and vibrational perturbation theory (VPT2) at B3LYP/6-311G(d,p) framework. The mode-mode couplings affect the vibrational frequencies and intensities. The coupling integrals between pairs of normal modes have been obtained on the basis of quartic force field (2MR-QFF) approximation. The overtone and combination bands are also assigned in the FTIR spectrum with the help of anharmonic calculation at VPT2 method. A statistical analysis of deviations shows that estimated anharmonic frequencies are closer to the experiment over harmonic approximation. Furthermore, the anharmonic correction has also been carried out for the dimeric structure of 2AP. The fundamental vibration bands have been assigned on the basis of potential energy distribution (PED) and visual look over the animated modes. Other important molecular properties such as frontier molecular orbitals and molecular electrostatics potential mapping have also been analyzed.

Biomarkers of cigarette smoking and DNA methylating agents: Raman, SERS and DFT study of 3-methyladenine and 7-methyladenine

3-Methyladenine and 7-methyladenine are biomarkers of DNA damage from exposure to methylating agents. For example, the concentration of 3-methyladenine increases significantly in the urine of cigarette smokers. Surface-enhanced Raman spectroscopy (SERS) has shown much potential for detection of biomolecules, including DNA. Much work has been dedicated to the canonical nucleobases, with comparatively fewer investigations of modified DNA and modified DNA nucleobases. Herein, Raman spectroscopy and SERS are used to examine the adsorption orientations of 3-methyladenine and 7-methyladenine on Ag nanoparticles. Density functional theory (DFT) calculations at the B3LYP level are used to support the conclusions via simulated spectra of the nucleobases and of Ag⁺/nucleobase complexes. The results herein show that 7-methyladenine adsorbs upright via its N3 and N9 atoms side, similarly to adenine. 3-Methyladenine adsorbs in a very tilted or flat orientation on the Ag nanoparticles. These findings will be useful for future SERS or other nanoparticle-based bioanalytical assays for detection of these methyladenines or other modified nucleobases.

Quantum chemical and spectroscopic investigations of 4-Hydroxy-7-methyl-1,8-naphthyridine-3-carboxylic acid

The FTIR (4000–400[Formula: see text]cm[Formula: see text]) and the FT-Raman spectra (4000–50[Formula: see text]cm[Formula: see text]) of 4-Hydroxy-7-methyl-1,8-naphthyridine-3-carboxylic acid are recorded and investigated. The spectra are interpreted using anharmonic frequency computations by VPT2, VSCF and PT2-VSCF methods within DFT/6-311G(d,p) framework. The root mean square (RMS) values indicate that VSCF computed frequencies are in close agreement with the observed frequencies. The combination and overtone bands are also identified in the FTIR spectrum. The intermolecular O-H[Formula: see text]O hydrogen bonding interactions are discussed in the dimer structure of the molecule. The magnitudes of the coupling between pair of modes are also computed. The electronic spectra in water and ethanol solvents are analyzed using TD-B3LYP/6-311[Formula: see text]G(d,p) level of theory. Molecular electrostatic potential (MEP) and HOMO-LUMO analysis are also performed.

FT-IR and FT-Raman spectra, MEP and HOMO-LUMO of 2,5-dichlorobenzonitrile: DFT study

The experimental FT-IR and FT-Raman spectra of 2,5-dichlorobenzonitrile molecule were recorded at room temperature, and the results compared with quantum chemical theoretical values using MP2 and DFT methods. Molecular geometry, vibrational wavenumbers and thermodynamic parameters were calculated. With the help of specific scaling procedures for the computed wavenumbers, the experimentally observed FTIR and FT-Raman bands were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range and the error obtained was in general very low. Several general conclusions were deduced. The NBO analysis has been done and Molecular Electrostatic Potential (MEP) has been plotted.

FTIR, FT-Raman, UV-Visible spectra and quantum chemical calculations of allantoin molecule and its hydrogen bonded dimers

FTIR, FT-Raman and electronic spectra of allantoin molecule are recorded and investigated using DFT and MP2 methods with 6-311++G(d,p) basis set. The molecular structure, anharmonic vibrational spectra, natural atomic charges, non-linear optical properties, etc. have been computed for the ground state of allantoin. The anharmonic vibrational frequencies are calculated using PT2 algorithm (Barone method) as well as VSCF and CC-VSCF methods. These methods yield results that are in remarkable agreement with the experiment. The coupling strengths between pairs of modes are also calculated using coupling integral based on 2MR-QFF approximation. The simulations on allantoin dimers have been also performed at B3LYP/6-311++G(d,p) level of theory to investigate the effect of the intermolecular interactions on the molecular structure and vibrational frequencies of the monomer. Vibrational assignments are made with the great accuracy using PED calculations and animated modes. The combination and overtone bands have been also identified in the FTIR spectrum with the help of anharmonic computations. The electronic spectra are simulated in gas and solution at TD-B3LYP/6-311++G(d,p) level of theory. The important global quantities such as electro-negativity, electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO, LUMO energy eigenvalues are also computed. NBO analysis has been performed for monomer and dimers of allantoin at B3LYP/6-311++G(d,p) level of theory.