Geometrical Parameters Of Molecules Research Articles

Solute solvent interaction study on 9,9-dihydroxynanoic acid by DFT, IR, Raman, UV, MEP, quantum parameters and docking studies

Density functional quantum mechanical research yield a comprehensive theoretical approach on the selected organic molecule of 9,9-dihydroxynanoic acid. The DFT approach is implemented to optimise the molecular structure. The geometrical parameters of molecule were calculated. The vibrational spectrum studies were done with FT-IR and FT-Raman and their results were investigated. VEDA software is utilised to simulate PED for the basic vibrational frequencies in order to find all the vibration modes. UV–Vis analysis is performed for the gaseous phase and on solvent phases such as water, ethanol, ethyl ethanoate, acetone, and DMSO by TD-DFT-B3LYP with 6-311++G (d,p), and band gap energies are calculated. FMO investigations reported analysing the compound energy gap, softness, hardness, and electrophilicity index in gaseous phase along with a variety solvent phase. To further understand the molecule's reactive areas, Mulliken atomic charge evaluation, Fukui functions, and dual descriptors were conceptually investigated. The electro static MEP map of the compound in distinct solvent phases is provided in order to comprehend the molecular shape, size, and reactive region. The molecule's hyperpolarizability is observed to be 201.8 a.u for gas, 146.6 a.u for acetone, 138.9 a.u for DMSO, 136.3 a.u for water, and 169.8 a.u for ethyl ethanoate, will supports the molecule is good NLO material. The donor acceptor interaction has been explored so as to explain the intramolecular hyper conjugative interaction and stability. To understand the topology Multiwfn analysis like ELF, LOL and ALIE were done. The E.coli proteins are downloaded from the PDB database and fictitiously docked with our selected ligand molecule using Auto Dock software to determine hydrogen bonding and binding energy.

The Interaction Potential of Molecules in Multicomponent Gaseous Media

To determine the transport factors in multicomponent gaseous media, the authors used an approach based on the molecular-kinetic theory of gases. A mathematical model of the interaction potential of molecules in multicomponent media is proposed. This model takes into account elastic and geometric parameters of molecules as well as an algorithm for determining the parameters in it.

Molecular Structure of 5-Methyl-2-(trifluoromethyl)furan-3-carbonitrile According to Gas-Phase Electron Diffraction and Quantum Chemistry

The mutual influence of atoms and atomic groups is one of the most important problems of structural chemistry. Gas-phase electron diffraction allows us to obtain the geometrical parameters of molecules that describe them most accurately in the free state. Such parameters constitute the basis of modern chemistry because they contain none of the contributions from intermolecular interactions that are typical of X-ray diffraction data.

The methods of optical physics as a mean of the objects’ molecular structure identification (on the base of the research of dophamine and adrenaline molecules)

Structural and dynamic models of dopamine and adrenaline are proposed on the basis of ab initio quantum calculations of the geometric and electronic structure. The parameters of the adiabatic potential are determined, a vibrational states interpretation of the test compound is proposed in this work. The analysis of the molecules conformational structure of the substance is made. A method for calculating the shifts of vibrational excitation frequencies in 1,2,4-threesubstituted of benzole is presented. It is based on second order perturbation theory. A choice of method and basis for calculation of a fundamental vibrations frequencies and intensities of the bands in the IR and Raman spectra is justified. The technique for evaluation of anharmonicity with cubic and quartic force constants is described. The paper presents the results of numerical experiments, geometric parameters of molecules, such as the valence bond lengths and angles between them. We obtain the frequency of the vibrational states and values of their integrated intensities. The interpretation of vibration of conformers is given. The results are in good agreement with experimental values. Proposed frequency can be used to identify the compounds of the vibrational spectra of molecules. The calculation was performed quantum density functional method DFT/B3LYP. It is shown that this method can be used to modeling the geometrical parameters molecular and electronic structure of various substituted of benzole. It allows us to construct the structural-dynamic models of this class of compounds by numerical calculations.

The choice of atomic charges calculation scheme in 3D-QSAR modelling of GSK-3β inhibition by paullones

descriptors in the nodes of the threedimensional lat� tice surrounding these molecules. The energy of van der Waals and electrostatic interactions of a probe atom ( with the charge +1) with molecules of the training set (CoMFA) or the electrostatic, van der Waals, hydrophobic, and donor/acceptor similarity indices (CoMSIA) are used as descriptors. The equa� tion for activity prediction is derived using the partial least squares (PLS) method. The ability of graphic representation of PLS model coefficients is the advan� tage of the methods and allows the user to suggest sub� stitutions affecting activity and/or selectivity of the molecules. The electrostatic field rules to the intermolecular interactions and plays major role in CoMFA and CoMSIA modeling. The contribution of the electro� static field is estimated with the help of partial atomic charges of molecules under consideration. The suc� cess of a modeling study strongly depends on proper selection of an adequate method for calculation of atomic charges. Various parameters should be taken into account, such as the calculation time, geometri� cal parameters of molecules, the accuracy and signifi� cance of modeling results, and stability upon small changes of the geometrical parameters of the mole� cule. In this study different charge calculation schemes based on different combinations of the men� tioned parameters were used to build predictive mod� els with the aim to identify one or more schemes pos� sessing an optimal set of parameters for 3DQSAR modeling. The training set comprised of the compounds pre� viously used for CoMSIA modeling (9) along with small series of epoxidecontaining analogues (10). The total number of compounds in the training set was 77. Twentyeight compounds whose inhibitory activity was determined later (11) were used as an external test set. The inhibitory activity of all compounds was determined under identical conditions and expressed as

Crystal and Molecular Structure of 17-(1-Adamantyl)amino-6,7,9,10-tetrahydro-17H-dibenzo[d, m]-[1,3,6,9,12,2]pentaoxaphosphacyclotetradecine-17-oxide

The crystal structure of 17-(1-adamantyl)amino-6,7,9,10-tetrahydro-17H-dibenzo[d, m][1,3,6,9,12,2]pentaoxaphosphacyclotetradecine-17-oxide, C26H32NO6P (I), was determined by single crystal X-ray diffraction. The monoclinic structure of I (space group P21/n; a=10.951(2), b=16.730(3), c=13.255(3) A, β=99.22(2)°, Z=4) was solved by direct methods and refined anisotropically by the full-matrix least-squares method; R=0.042 for all independent 4197 reflections (CAD-4 automatic diffractometer, MoKα). The geometrical parameters of molecule I (bond lengths and bond and torsion angles) were determined with a good accuracy.

Calculation of Pseudorotational Moments of Inertia of Cyclopentane Derivatives Using Molecular Mechanics Method

Pseudorotation (PR) of cyclic molecules is discussed. It is shown that PR can be considered as a special type of internal rotation with pseudorotational moment of inertia (PMI) as an important characteristic. The dependence of the PMI of a molecule upon the phase angle of PR and the nuclear trajectories is discussed. A method is proposed for the calculation of PMI from geometrical parameters of molecules. The moment of inertia of internal rotation for 1,2-dichloroethane in gauche conformation is calculated in order to test the proposed method. The obtained value is in good agreement with the values given by the Pitzer method. Pseudorotational moments of inertia of cyclopentane and its derivatives are calculated. Calculated values are compared with those adjusted to fit experimental entropy. The dependence of the PMI of cyclopentane derivatives upon their molecular mass is discussed.

NMR and ESR Investigation of Some Phosphorus Organic Compounds and their Free Radicals

Abstract The new methods of NMR and ESR spectroscopy are developed for investigation of the properties and the character of intramolecular interactions for three and four coordinated phosphorous containing compounds. Analytical dependences of direct, geminal and vicinal constants of spin-spin coupling in NMR spectra upon geometrical parameters of molecules of the P=O, P=S, P=Se orientation for the cyclic phosphorous compounds are established.

Comments on the correlations between geometric parameters of molecules and parameters of their 1H NMR spectra: The answer to a criticism

AbstractAn earlier paper by the authors has undergone criticism by Jankowski and Rabczenko. The arguments presented are analysed in this paper and the criticism is rejected.

Verification of the correlation between geometric parameters of molecules and the parameters of their 1H NMR spectra

AbstractThe dihedral and bond direction angles between all pairs of vicinal protons of the arabinofuranose residue were calculated from the coordinatees of the hydrogen atoms found by an X‐ray study of 3‐O‐acetyl‐β‐L‐arabinofuranose 1,2,5‐orthobenzoate. The values found were compared with those calculated with the help of correlation equations previously proposed by Karplus and recently by the authors, linking the values of those angles with the spin‐spin coupling constants of vicinal protons [3J(H,H′)]. It has been found that the best agreement between the angles found crystallographically and calculated from the 1H NMR data can be achieved using the equation which includes bond direction angles and the sum of the chemical shifts of the protons involved.