Hydrogen Bonding and Density Functional Calculations:  The B3LYP Approach as the Shortest Way to MP2 Results

Lozynski, Marek; Rusinska-Roszak, Danuta; Mack, Hans‐Georg

doi:10.1021/jp973142x

Cited by 153 publications

(84 citation statements)

References 38 publications

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“…It is a sum of two parts, an empirical Becke 3 parameter exchange contribution (30) and a Lee-Yang-Parr correlation contribution (31) patterned upon the correlations of Colle and Salvetti (32). A reference that shows B3LYP is effective for these systems is that of Lozynski and coauthors (33). The Gaussian basis set 3-21G* (27) combined with B3LYP is expected to be adequate for representations of the protoribosome in this article.…”

Section: Methods Of Calculationsmentioning

confidence: 99%

Protoribosome by quantum kernel energy method

Huang

Krupkin

Bashan

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Experimental evidence suggests the existence of an RNA molecular prebiotic entity, called by us the "protoribosome," which may have evolved in the RNA world before evolution of the genetic code and proteins. This vestige of the RNA world, which possesses all of the capabilities required for peptide bond formation, seems to be still functioning in the heart of all of the contemporary ribosome. Within the modern ribosome this remnant includes the peptidyl transferase center. Its highly conserved nucleotide sequence is suggestive of its robustness under diverse environmental conditions, and hence on its prebiotic origin. Its twofold pseudosymmetry suggests that this entity could have been a dimer of self-folding RNA units that formed a pocket within which two activated amino acids might be accommodated, similar to the binding mode of modern tRNA molecules that carry amino acids or peptidyl moieties. Using quantum mechanics and crystal coordinates, this work studies the question of whether the putative protoribosome has properties necessary to function as an evolutionary precursor to the modern ribosome. The quantum model used in the calculations is density functional theory-B3LYP/3-21G*, implemented using the kernel energy method to make the computations practical and efficient. It occurs that the necessary conditions that would characterize a practicable protoribosome-namely (i) energetic structural stability and (ii) energetically stable attachment to substrates-are both well satisfied.bonding apparatus | puromycin | interaction energy | self-assembly | chemical model

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Section: Methods Of Calculationsmentioning

confidence: 99%

Protoribosome by quantum kernel energy method

Huang

Krupkin

Bashan

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…The density functional theory (DFT) method using the Becke's three parameter hybrid functional together with Lee-Yang-Parr correlation functional (B3LYP) was used in combination with the Pople type basis set 6-31G(d) for all the calculations [55][56][57][58]. The B3LYP functional has been widely used in literature in conjunction with different Pople's basis sets to produce satisfactory geometries at relatively less computational cost [59][60][61][62]. The optimized structures were confirmed to correspond to true energy minima with the absence of imaginary frequency in the force constant calculations.…”

Section: Quantum Chemical Studies and Quantitative Structure Activitymentioning

confidence: 99%

Some Phthalocyanine and Naphthalocyanine Derivatives as Corrosion Inhibitors for Aluminium in Acidic Medium: Experimental, Quantum Chemical Calculations, QSAR Studies and Synergistic Effect of Iodide Ions

et al. 2015

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Abstract:The effects of seven macrocyclic compounds comprising four phthalocyanines (Pcs) namely 1,4,8,11,15,18,22,2,3,9,10,16,17,23,2,9,16, and 29H,31H-phthalocyanine (Pc4), and three naphthalocyanines namely 5,9,14,18,23,27,32,2,11,20, properties of the compounds were also investigated. All the studied compounds showed appreciable inhibition efficiencies, which decrease with increasing temperature from 30 °C to 70 °C. At each concentration of the inhibitor, addition of 0.1% KI increased the inhibition efficiency compared to the absence of KI indicating the occurrence of synergistic interactions between the studied molecules and I − ions. From the potentiodynamic polarization studies, the studied Pcs and nPcs are mixed type corrosion inhibitors both without and with addition of KI. The adsorption of the studied molecules on Al surface obeys the Langmuir adsorption isotherm, while the thermodynamic and kinetic parameters revealed that the adsorption of the studied compounds on Al surface is spontaneous and involves competitive physisorption and chemisorption mechanisms. The experimental results revealed the aggregated interactions between the inhibitor molecules and the results further indicated that the peripheral groups on the compounds affect these interactions. The calculated quantum chemical parameters and the QSAR results revealed the possibility of strong interactions between the studied inhibitors and metal surface. QSAR analysis on the quantum chemical parameters obtained with B3LYP/6-31G (d,p) method show that a combination of two quantum chemical parameters to form a composite index provides the best correlation with the experimental data.

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“…The adopted DFT model comprises the Becke three parameter hybrid functional together with LeeYang-Parr correlation functional (B3LYP) (Becke, 1993;Lee et al, 1988;Parr and Yang, 1984), used in conjunction with 6-311+(d,p) basis set. Acceptable predictions of equilibrium molecular geometries and quantum chemical parameters of various organic compounds have been previously obtained by using the B3LYP functional together with different Pople-type basis sets (Dibetsoe et al, 2015;Brovarets et al, 2014;Samijlenko et al, 2010;Lozynski et al, 1998). The 6-311+(d,p) basis set has also been successfully used to describe the energies of a number of organic molecules using different basis sets (Wodrich et al, 2007).…”

Section: Computational Detailsmentioning

confidence: 99%

Synthesis, antimicrobial activities and computational studies of some oxazolone derivatives

Olomola¹,

Akinboye²,

Olasunkanmi³

et al. 2018

Ife Journal of Science

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Synthesis of the oxazolone derivatives was achieved by the condensation of aromatic aldehydes with N-acetyl glycine in the presence of acetic anhydride and anhydrous sodium acetate. A total of six oxazolones were 1 13 synthesized and characterized using H-NMR, C-NMR and FT-IR spectroscopic techniques. The synthesized compounds were screened for their in vitro antibacterial and antifungal activities using streptomycin and ampicillin as control. The result showed that some of the compounds demonstrate good antibacterial activities against specific bacterial strains and moderate activities against other bacterial strains. The compounds did not show any sensitivity against the tested fungal strains. The quantitative structure-antibacterial activity relationship was studied using some quantum chemical parameters with the aid of Spartan 10 (V1.0.1) and XLSTAT (add-in) software. A good correlation was observed between the antibacterial activity of the compounds and the calculated quantum chemical descriptors.

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Hydrogen Bonding and Density Functional Calculations: The B3LYP Approach as the Shortest Way to MP2 Results

Cited by 153 publications

References 38 publications

Protoribosome by quantum kernel energy method

Protoribosome by quantum kernel energy method

Some Phthalocyanine and Naphthalocyanine Derivatives as Corrosion Inhibitors for Aluminium in Acidic Medium: Experimental, Quantum Chemical Calculations, QSAR Studies and Synergistic Effect of Iodide Ions

Synthesis, antimicrobial activities and computational studies of some oxazolone derivatives

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