Quantum-Chemical Study of the Biogenic Amino Acids

2021 ◽  
Author(s):  
Roman Boča ◽  
Beata Vranovičová
Keyword(s):  
Amino Acids ◽  
Ab Initio ◽  
Quantum Chemical ◽  
Probabilistic Neural Network ◽  
Pair Correlation ◽  
Quantum Chemical Study ◽  
Principal Component ◽  
Molecular Surface ◽  
Molecular Volume ◽  
Dipole Polarizability

Abstract Ten amino acids have been subjected to the quantum chemical calculations using the ab initio MO-LCAO-SCF calculations and semiempirical PM3 method. When the geometry optimization started form the X-ray structure confirming the zwitterionic form, the ab initio calculations in vacuo result in the amino acid (canonical) form with the hydrogen atom attached not to the amine but to the carboxylate group. At the optimum geometry a number of properties were evaluated: dipole moment, dipole polarizability, molecular surface, molecular volume, HOMO, LUMO, ionization energy and electron affinity using the ΔSCF approach and their values corrected for electron correlation by the 2 nd –order perturbation theory (MP2). In addition, the molecular electrostatic potential and the charge density have been drawn. These properties have been mutually correlated by employing the statistical multivariate methods: the cluster analysis, the probabilistic neural network classifier, the principal component analysis and the Pearson pair correlation.

Evaluation of Chemotherapeutic Activity of the Selected Bases’ Analogues of Nucleic Acids Supported by ab initio Various Quantum Chemical Calculations

2020 ◽  
Vol 16 (2) ◽  
pp. 93-103 ◽  
Author(s):  
Piotr Kawczak ◽  
Leszek Bober ◽  
Tomasz Bączek
Keyword(s):  
Biological Activity ◽  
Nucleic Acids ◽  
Ab Initio ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Structural Parameters ◽  
Principal Component ◽  
Polarizable Continuum Model ◽  
Activity Data ◽  
Qsar Models

Background: Pharmacological and physicochemical classification of bases’ selected analogues of nucleic acids is proposed in the study. Objective: Structural parameters received by the PCM (Polarizable Continuum Model) with several types of calculation methods for the structures in vacuo and in the aquatic environment together with the huge set of extra molecular descriptors obtained by the professional software and literature values of biological activity were used to search the relationships. Methods: Principal Component Analysis (PCA) together with Factor Analysis (FA) and Multiple Linear Regressions (MLR) as the types of the chemometric approach based on semi-empirical ab initio molecular modeling studies were performed. Results: The equations with statistically significant descriptors were proposed to demonstrate both the common and differentiating characteristics of the bases' analogues of nucleic acids based on the quantum chemical calculations and biological activity data. Conclusion: The obtained QSAR models can be used for predicting and explaining the activity of studied molecules.

AB initio quantum chemical study of the reaction mechanism of ethynide ion formation in the C2H2/MOH/DMSO system (M = Li, Na, K)

2009 ◽  
Vol 50 (1) ◽  
pp. 27-33 ◽  
Author(s):  
E. Yu. Larionova ◽  
N. M. Vitkovskaya ◽  
V. B. Kobychev ◽  
N. V. Kaempf ◽  
A. D. Skitnevskaya ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Ab Initio ◽  
Quantum Chemical ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Ion Formation ◽  
Dmso System

Quantum chemical study on the formation of isopropyl cyanide and its linear isomer in the interstellar medium

2020 ◽  
pp. 1-11
Author(s):  
Keshav Kumar Singh ◽  
Poonam Tandon ◽  
Alka Misra ◽  
Shivani ◽  
Manisha Yadav ◽  
...  
Keyword(s):  
Amino Acids ◽  
Interstellar Medium ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Density Functional ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Dark Cloud ◽  
Water Ice ◽  
Hydrocarbon Radicals

Abstract The formation mechanism of linear and isopropyl cyanide (hereafter n-PrCN and i-PrCN, respectively) in the interstellar medium (ISM) has been proposed from the reaction between some previously detected small cyanides/cyanide radicals and hydrocarbons/hydrocarbon radicals. n-PrCN and i-PrCN are nitriles therefore, they can be precursors of amino acids via Strecker synthesis. The chemistry of i-PrCN is especially important since it is the first and only branched molecule in ISM, hence, it could be a precursor of branched amino acids such as leucine, isoleucine, etc. Therefore, both n-PrCN and i-PrCN have significant astrobiological importance. To study the formation of n-PrCN and i-PrCN in ISM, quantum chemical calculations have been performed using density functional theory at the MP2/6-311++G(2d,p)//M062X/6-311+G(2d,p) level. All the proposed reactions have been studied in the gas phase and the interstellar water ice. It is found that reactions of small cyanide with hydrocarbon radicals result in the formation of either large cyanide radicals or ethyl and vinyl cyanide, both of which are very important prebiotic interstellar species. They subsequently react with the radicals CH2 and CH3 to yield n-PrCN and i-PrCN. The proposed reactions are efficient in the hot cores of SgrB2 (N) (where both n-PrCN and i-PrCN were detected) due to either being barrierless or due to the presence of a permeable entrance barrier. However, the formation of n-PrCN and i-PrCN from the ethyl and vinyl cyanide always has an entrance barrier impermeable in the dark cloud; therefore, our proposed pathways are inefficient in the deep regions of molecular clouds. It is also observed that ethyl and vinyl cyanide serve as direct precursors to n-PrCN and i-PrCN and their abundance in ISM is directly related to the abundance of both isomers of propyl cyanide in ISM. In all the cases, reactions in the ice have smaller barriers compared to their gas-phase counterparts.

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