Simulation of porphyrin-ethanol solvate shell by DFT method

2015 ◽  
Vol 19 (11) ◽  
pp. 1212-1218 ◽  
Author(s):  
Pavel V. Singin ◽  
Mikhail K. Islyaikin ◽  
Irina P. Trifonova ◽  
Vladimir A. Burmistrov ◽  
Oscar I. Koifman
Keyword(s):  
Density Functional ◽  
Dft Method ◽  
Solvation Energy ◽  
Solvation Shell ◽  
Theoretical Studies ◽  
Functional Theory ◽  
H Nmr ◽  
Ethanol Solvate ◽  
Nucleophilic Solvation ◽  
Good Agreement

Theoretical studies on porphyrin-ethanol solvates containing from 1 to 8 ethanol molecules have been carried out by density functional theory (DFT) calculations using hybrid (B3LYP) and meta-GGA (M06-L) functionals. It was established that porphirin molecule can be considered as two centered protones acceptor. Specific solvation is at the base of porphyrin-(EtOH)n interactions and results in a distortion of macrocycle planar structure. The nucleophilic solvation energy of the porphirin pyrrole demonstrates dependence on the number of molecules in the ethanol solvate, being the highest for the first two ethanol molecules and decreasing with ethanol association in the solvation shell. Results obtained by this way are in good agreement with data derived from 1H NMR.

Ab Initio Theoretical Studies of Relative Stabilities and IR Spectrum of 5-Methylcytosine Tautomers

2003 ◽  
Vol 2003 (4) ◽  
pp. 195-199 ◽  
Author(s):  
Lida Ghassemzadeh ◽  
Majid Monajjemi ◽  
Karim Zare
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Relative Energy ◽  
Theoretical Studies ◽  
Functional Theory ◽  
Relative Stabilities ◽  
B3lyp Method ◽  
Wide Range ◽  
Good Agreement

The structure and relative energies of the tautomers of 5-methylcytosine in the gasphase and in different solvents are predicted using MP2 and density functional theory methods. The order of stability for these tautomers is C3>C1>C2>C4>C5>C6 calculated by MP2 and C1>C3>C2>C4>C5>C6 calculated by the B3LYP method. Relative energy calculations are performed in wide range of solvent dielectrics and in all solvents the oxo-amino C1 is predicted as the most stable tautomer. The infrared spectra of two dominant tautomers are calculated in the gas phase using HF and density functional theory. Good agreement between calculated (DFT) and experimental harmonic vibrational frequencies is found.

scholarly journals Theoretically nanoscale study on ionization of muscimol nano drug in aqueous solution

2015 ◽  
Vol 51 (1) ◽  
pp. 213-219 ◽  
Author(s):  
Farhoush Kiani ◽  
Mehran Abbaszadeh ◽  
Mohammad Pousti ◽  
Fardad Koohyar
Keyword(s):  
Density Functional ◽  
Dft Method ◽  
Acid Dissociation ◽  
Basis Sets ◽  
Acid Dissociation Constant ◽  
Functional Theory ◽  
Hydrogen Bond Formation ◽  
Pka Values ◽  
The Density Functional Theory ◽  
Good Agreement

In the present work, acid dissociation constant (pKa) values of muscimol derivatives were calculated using the Density Functional Theory (DFT) method. In this regard, free energy values of neutral, protonated and deprotonated species of muscimol were calculated in water at the B3LYP/6-31G(d) basis sets. The hydrogen bond formation of all species had been analyzed using the Tomasi's method. It was revealed that the theoretically calculated pKa values were in a good agreement with the existing experimental pKa values, which were determined from capillary electrophoresis, potentiometric titration and UV-visible spectrophotometric measurements.

Optimized Structures and Theoretical 1H-NMR Spectral Analysis of the Methylene Protons in Dibenzyl Sulfoxide

2011 ◽  
Vol 391-392 ◽  
pp. 1368-1374 ◽  
Author(s):  
Zheng Ping Wu ◽  
Yuan Bing Sun ◽  
Ian S. Butler
Keyword(s):  
1H Nmr ◽  
Density Functional ◽  
Chemical Shifts ◽  
Dft Methods ◽  
Functional Theory ◽  
H Nmr ◽  
Effect Of Solvent ◽  
Solvent Shift ◽  
Total Energies ◽  
Good Agreement

Dibenzyl sulfoxide [C6H5CH2)2SO, DBzSO] has been studied using density functional theory (DFT) methods with a particular emphasis on the theoretical 1H-NMR spectra of the methylene protons. The 1H-NMR chemical shifts of the methylene protons of DBzSO can be divided into two main types. Four possible structures of DBzSO were considered and the total energies were calculated for both a vacuum and in CDCl3 solvent. The change of length of S-O and S-C bonds in solvent was more obvious than that of the C(CH2)-C(C6H5) bonds; The S-O bond was longer and S-C bond was shorter in CDCl3. The essence effect of solvent on the properties of dibenzyl sulfoxide should come from the change of the geometrical structure. The change of shift Δx, [shift (solvent) - shift (vacuum)] showed that the effect of solvent on methylene protons of dibenzyl sulfoxide was apparent. Except of the other H of the rings, the two ortho H which were near S-O bond appeared more sensitivity on the solvent. The optimized structures in CDCl3 were in good agreement with the experimental data. The NMR peaks of methylene protons should be split more apparently in actual circumstance and the complex split of CH2 1HNMR peaks should be explained in some degree.

A novel nitrogen-containing compound with D-π-A structure: theoretical and experimental study

2014 ◽  
Vol 92 (5) ◽  
pp. 411-416 ◽  
Author(s):  
Xiaoting Gong ◽  
Ziyan Zhou ◽  
Shuguang Zhang ◽  
Shuping Zhuo ◽  
Xiurong Huang ◽  
...  
Keyword(s):  
Density Functional ◽  
Fluorescence Spectra ◽  
Density Functional Theory Calculations ◽  
Absorption And Fluorescence Spectra ◽  
Functional Theory ◽  
H Nmr ◽  
Measured Absorption ◽  
Nmr Techniques ◽  
Good Agreement ◽  
C Nmr

2-(2-Hydroxy-styryl)-4,6-dimethyl-1,3,5-triazine (P1), a novel compound with D-π-A structure, possesses a variety of isomers. Density functional theory calculations were employed to explore the isomerization mechanisms of its various isomers at the 6-311+G** level. The calculated results show that the phenol configurations of compound P1 are more stable than the quinoid configurations, whether they exist as monomers, complexes, with methanol or dimers. The most stable structure of compound P1 was used to calculate the UV-vis and fluorescence spectra. To validate the calculated results, the title compound was synthesized and characterized by 1H NMR and 13C NMR techniques. The measured absorption and fluorescence spectra of P1 in methanol and N,N-dimethylformamide are in good agreement with the calculated ones.

scholarly journals CO interaction with Cu(I)-MCM-22 zeolite: density functional theory investigation

2014 ◽  
Vol 17 (3) ◽  
pp. 19-29
Author(s):  
Ho Thang Viet ◽  
Petr Nachtigall
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Co Adsorption ◽  
Dft Method ◽  
Local Geometry ◽  
Functional Theory ◽  
Two Peaks ◽  
Decomposition Of No ◽  
Good Agreement ◽  
Oxygen Atoms

MCM-22 zeolite has been widely used in many applications for catalysis and adsorption. Especially, this material exchanged with Cu+ cation (Cu(I)-MCM-22) is an active catalyst in green chemical reaction, such as decomposition of NO and N2O. The local geometry of Cu+ in vicinity of Al (III) replacement in six different Si (IV) sites and CO interaction with the most stable Cu+ in each Al site were explored using periodic density functional theory (DFT) method. The CO stretching frequencies were computed applying the ω/r scaling method in which frequencies were determined at high quantum level (couple cluster) and CO bond length calculated at DFT level. The results showed that Cu+ cation located in the channel wall position and intersection position coordinated with 3 or 2 framework oxygen atoms, respectively, before CO adsorption and Cu+ cation coordinated with 2 framework oxygen atoms after CO adsorption. The interaction energies between CO and Cu+ cation were in range - 148 to -195 kJ.mol-1 and CO frequencies exhibit two peaks at 2151 and 2159 cm-1 in good agreement with experimental data. This investigation brought us to understand the Cu+ location in MCM-22 and CO adsorption in Cu(I)-MCM-22 zeolite.

scholarly journals Mechanism, kinetics and selectivity of selenocyclization of 5-alkenylhydantoins: an experimental and computational study

2015 ◽  
Vol 11 ◽  
pp. 1865-1875 ◽  
Author(s):  
Biljana M Šmit ◽  
Radoslav Z Pavlović ◽  
Dejan A Milenković ◽  
Zoran S Marković
Keyword(s):  
Density Functional Theory ◽  
Double Bond ◽  
Density Functional ◽  
Computational Study ◽  
Theoretical Calculations ◽  
Reaction Products ◽  
Dft Methods ◽  
Functional Theory ◽  
H Nmr ◽  
Good Agreement

The mechanism and selectivity of a bicyclic hydantoin formation by selenium-induced cyclization are investigated. The proposed mechanism involves the intermediates formed by an electrophilic addition of the selenium reagent on a double bond of the starting 5-alkenylhydantoin prior the cyclization. These intermediates are readily converted into the more stable cyclic seleniranium cations. A key step of the mechanism is an intramolecular cyclization which is realized through an anti-attack of the internal nucleophile, the amidic nitrogen, to the seleniranium cation yielding the intermediate imidazolinium cations. Their deprotonation is followed by the formation of the fused bicyclic reaction products. Important intermediates and key transition states are studied by using density functional theory (DFT) methods. The pathways of the reaction are investigated in detail. There are two regioselective pathways related to 5-exo and 6-endo products. Theoretical calculations and the monitoring of the cyclization reaction using 1H NMR spectroscopy are in a good agreement with the proposed mechanism and are consistent with our experimental results. The preferred pathway for formation of 5-exo products is confirmed.

Vibrationally resolved K-shell photoionization cross sections of methane

Open Physics ◽  
2013 ◽  
Vol 11 (9) ◽  
Author(s):  
Etienne Plésiat ◽  
Piero Decleva ◽  
Fernando Martín
Keyword(s):  
Cross Sections ◽  
Density Functional ◽  
Dft Method ◽  
Chem Phys ◽  
Angular Distributions ◽  
Functional Theory ◽  
The Rich ◽  
Photoelectron Angular Distributions ◽  
Molecular Frame ◽  
Good Agreement

AbstractWe use an extension of the static-exchange density functional theory (DFT) method, previously reported in [E. Plésiat et al., Phys. Rev. A 2, 023409 (2012), E. Plésiat, P. Decleva, F. Martín, Phys. Chem. Chem. Phys. 31, 10853 (2012)], to evaluate vibrationally resolved (total and angular) K-shell photoelectron cross sections of methane. The calculated cross sections are in very good agreement with the existing experimental measurements at low photoelectron energies. We show that, in contrast with the rich interference patterns previously observed in molecular frame C(1s) photoelectron angular distributions of methane at both low and high photoelectron energy, no interference effects are observed in the calculated β parameters, even at high photon energies.

Synthesis of New α-Amino Phosphonates Containing 3-Amino-4(3H) Quinazolinone Moiety as Anticancer and Antimicrobial Agents: DFT, NBO, and Vibrational Studies

2018 ◽  
Vol 15 (2) ◽  
pp. 286-296 ◽  
Author(s):  
Mohamed K. Awad ◽  
Mahmoud F. Abdel-Aal ◽  
Faten M. Atlam ◽  
Hend A. Hekal
Keyword(s):  
Biological Activity ◽  
Cell Line ◽  
Quantum Chemical ◽  
Density Functional ◽  
Carcinoma Cell ◽  
Liver Carcinoma ◽  
Anticancer Activities ◽  
Functional Theory ◽  
Ft Ir ◽  
Good Agreement

Aim and Objective: Synthesis of new .-aminophosphonates containing quinazoline moiety through Kabachnik-Fields reaction in the presence of copper triflate catalyst [32], followed by studying their antimicrobial activities and in vitro anticancer activities against liver carcinoma cell line (HepG2) with the hope that new anticancer agents could be developed. Also, the quantum chemical calculations are performed using density functional theory (DFT) to study the effect of the changes of molecular and electronic structures on the biological activity of the investigated compounds. Materials and Method: The structures of the synthesized compounds are confirmed by FT-IR, 1H NMR, 13C NMR, 31P NMR and MS spectral data. The synthesized compounds show significant antimicrobial and also remarkable cytotoxicity anticancer activities against liver carcinoma cell line (HepG2). Density functional theory (DFT) was performed to study the effect of the molecular and electronic structure changes on the biological activity. Results: It was found that the electronic structure of the substituents affects on the reaction yield. The electron withdrawing substituent, NO2 group 3b, on the aromatic aldehydes gave a good yield more than the electron donating substituent, OH group 3c. The electron deficient on the carbon atom of the aldehydic group may increase the interaction of the Lewis acid (Cu(OTf)2) and the Lewis base (imine nitrogen), and accordingly, facilitate the formation of imine easily, which is attacked by the nucleophilic phosphite species to give the α- aminophosphonates. Conclusion: The newly synthesized compounds exhibit a remarkable inhibition of the growth of Grampositive, Gram-negative bacteria and fungi at low concentrations. The cytotoxicity of the synthesized compounds showed a significant cytotoxicity against the liver cancer cell line (HepG 2). Also, it was shown from the quantum chemical calculations that the electron-withdrawing substituent increases the biological activity of the α-aminophosphonates more than the electron donating group which was in a good agreement with the experimental results. Also, a good agreement between the experimental FT-IR and the calculated one was found.

Understanding the molecular mechanism of the stereoselective conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives

2021 ◽  
Author(s):  
Agnieszka Kącka-Zych ◽  
Radomir Jasinski
Keyword(s):  
Density Functional Theory ◽  
Molecular Mechanism ◽  
Electron Density ◽  
Density Functional ◽  
Dft Method ◽  
Functional Theory ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

Conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives has been explored using Density Functional Theory (DFT) method within the context of the Molecular Electron Density Theory (MEDT) at the B97XD(PCM)/6-311G(d,p)...

A DFT study of spherands containing five anisyl groups — Highly preorganized to bind the alkali metal

2006 ◽  
Vol 84 (8) ◽  
pp. 1045-1049 ◽  
Author(s):  
Shabaan AK Elroby ◽  
Kyu Hwan Lee ◽  
Seung Joo Cho ◽  
Alan Hinchliffe
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Ionic Radius ◽  
Binding Energies ◽  
Cavity Size ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Good Agreement

Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygens during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. We used standard B3LYP/6-31G** (5d) density functional theory (DFT) to investigate the complexation between spherands containing five anisyl groups, with CH2–O–CH2 (2) and CH2–S–CH2 (3) units in an 18-membered macrocyclic ring, and the cationic guests (Li+, Na+, and K+). Our geometric structure results for spherands 1, 2, and 3 are in good agreement with the previously reported X-ray diffraction data. The absolute values of the binding energy of all the spherands are inversely proportional to the ionic radius of the guests. The results, taken as a whole, show that replacement of one anisyl group by CH2–O–CH2 (2) and CH2–S–CH2 (3) makes the cavity bigger and less preorganized. In addition, both the binding and specificity decrease for small ions. The spherands 2 and 3 appear beautifully preorganized to bind all guests, so it is not surprising that their binding energies are close to the parent spherand 1. Interestingly, there is a clear linear relation between the radius of the cavity and the binding energy (R2 = 0.999).Key words: spherands, preorganization, density functional theory, binding energy, cavity size.

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