scholarly journals Quantum-chemical study on the relative stability of sildenafil tautomers

2021 ◽  
Author(s):  
Wojciech Piotr Oziminski ◽  
Igor Wiśniewski
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Water Solution ◽  
Quantum Chemical Study ◽  
Basis Set ◽  
Steric Interaction ◽  
Free Energies ◽  
Dft Methods ◽  
Enol Tautomer ◽  
Tautomeric Mixture

AbstractThe tautomeric equilibrium of sildenafil molecule was theoretically studied using B3LYP and M06-2X density functional theory (DFT) methods in connection with aug-cc-pVDZ correlation consistent basis set. Calculations were performed for gas phase and water solution conditions modelled by polarizable continuum model (PCM). Three tautomeric forms are possible. Two keto forms: A — where the tautomeric proton in more distant from carbonyl group and B — where it is closer, and one enol form denoted, C. Both DFT methods qualitatively give similar tautomer stability order: B > A > C. The B tautomer is dominant in gas phase and water environment, whereas the C tautomer is too high in energy to be present in the tautomeric mixture. Regarding the A tautomer, it is not present in the gas phase but is present in small amounts in water solution. According to B3LYP/aug-cc-pVDZ, the relative Gibbs-free energies for A and C relative to B are 10.05 kcal/mol and 11.91 kcal/mol for gas phase and 5.49 kcal/mol and 12.49 kcal/mol for water solution. According to M06-2X/aug-cc-pVDZ, the relative Gibbs-free energies for A and C are 9.12 kcal/mol and 10.60 kcal/mol for gas phase and 4.27 kcal/mol and 10.23 kcal/mol for water solution. Therefore, for in vivo conditions, we expect that the B tautomer is dominant, and there may exist small amounts of the A tautomer. The C enol tautomer is not present at all. This picture is very different from the parent tautomeric system: 4-hydroxypyrimidine/4-pyrimidinone where the C enol tautomer is less stable than keto B only by about 1 kcal/mol in the gas phase and the A keto tautomer is the least stable and not present in the tautomeric mixture. In order to understand these differences, we performed additional calculations for a series of parent molecules starting from 4-hydroxypyrimidine/4-pyrimidinone, going through two in-between model molecules and ending at Sildenafil molecule. We found that the most important reasons of C form destabilization are dearomatization of the 6-membered ring caused by the fusion with pyrazole ring, lack of strong intramolecular hydrogen bond in C form of sildenafil and presence of destabilizing steric interaction of oxygen and nitrogen atoms of two 6-memberd rings in this tautomer.

scholarly journals Quantum-Chemical Study on the Relative Stability of Sildenafil Tautomers

2021 ◽  
Author(s):  
Wojciech Piotr Oziminski ◽  
Igor Wiśniewski
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Water Solution ◽  
Quantum Chemical Study ◽  
Basis Set ◽  
Steric Interaction ◽  
Free Energies ◽  
Dft Methods ◽  
Enol Tautomer ◽  
Tautomeric Mixture

Abstract The tautomeric equilibrium of Sildenafil molecule was theoretically studied using B3LYP and M06-2X Density Functional Theory (DFT) methods in connection with aug-cc-pVDZ correlation consistent basis set. Calculations were performed for gas phase and water solution conditions modelled by Polarizable Continuum Model (PCM). Three tautomeric forms are possible. Two keto forms: A – where the tautomeric proton in more distant from carbonyl group, B – where it is closer, and one enol form denoted C. Both DFT methods qualitatively give similar tautomer stability order: B>A>C. The B tautomer is dominant in gas phase and water environment, whereas the C tautomer is too high in energy to be present in the tautomeric mixture. Regarding the A tautomer, it is not present in the gas phase but is present in small amounts in water solution. According to B3LYP/ aug-cc-pVDZ the relative Gibbs free energies for A and C relative to B, are 10.05 kcal/mol and 11.91 kcal/mol for gas phase and 5.49 kcal/mol and 12.49 kcal/mol for water solution. According to M06-2X/aug-cc-pVDZ the relative Gibbs free energies for A and C are 9.12 kcal/mol and 10.60 kcal/mol for gas phase and 4.27 kcal/mol and 10.23 kcal/mol for water solution. Therefore, for in vivo conditions we expect that the B tautomer is dominant and there may exist small amounts of the A tautomer. The C enol tautomer is not present at all. This picture is very different from the parent tautomeric system: 4-hydroxypyrimidine/4-pyrimidinone where the C enol tautomer is less stable than keto B only by about 1 kcal/mol in the gas phase and the A keto tautomer is the least stable and not present in the tautomeric mixture. In order to understand these differences we performed additional calculations for series of parent molecules starting from 4-hydroxypyrimidine/4-pyrimidinone, going through two in-between model molecules and ending at Sildenafil molecule. We found that the most important reasons of C form destabilization are: dearomatization of the 6-membered ring caused by the fusion with pyrazole ring, lack of strong intramolecular hydrogen bond in C form of Sildenafill and presence of destabilizing steric interaction of oxygen and nitrogen atoms of two 6-memberd rings in this tautomer.

Study on Pyrrole 4-Pyrazoline Derivatives: Experimental and Quantum Chemical Approaches

2016 ◽  
Vol 69 (6) ◽  
pp. 672 ◽  
Author(s):  
R. N. Singh ◽  
Poonam Rawat ◽  
Vikas Baboo
Keyword(s):  
Dft Calculations ◽  
13C Nmr ◽  
Quantum Chemical ◽  
Density Functional ◽  
Electronic Absorption Spectra ◽  
Quantum Chemical Study ◽  
Basis Set ◽  
Dft Methods ◽  
Pyrrole Derivatives ◽  
1H And 13C Nmr

As part of a study on pyrrole derivatives we report here a combined experimental and quantum chemical study of pyrrole 4-pyrazoline biheterocyclic derivatives. The structure of the synthesised compounds have been studied using experimental IR, UV, 1H and 13C NMR spectroscopic analyses along with density functional theory (DFT) calculations using the B3LYP functional with 6–311+G (d,p) basis set. The global, local reactivity, and thermodynamic parameters support the analysis. All the experimental vibrational bands have been discussed and assigned to normal modes on the basis of our calculations. In addition, the computed 1H and 13C NMR data, obtained by DFT calculations, are found to be in good agreement with the experimental data and serve as valuable tools in identifying the products. The vibrational analysis shows red shifts in vN–H and vC=O stretching vibrations as a result of dimer formation. The theoretical electronic absorption spectra have been calculated by using time dependent-DFT methods. The static first hyperpolarizability (β0) values for the synthesized pyrrole–pyrazoline derivatives 4A–D are calculated as 16.97 × 10–30, 47.64 × 10–30, 65.40 × 10–30, 65.39 × 10–30 esu, respectively, and increase from 4A to 4C as a result of the addition of an –NO2 acceptor in 4B and two –NO2 group acceptors in 4C. However, an additional –Cl group in 4D on the phenyl ring attached to the pyrazoline moiety does not result in a clear change from 4C. The calculated static and dynamic hyperpolarizability results show that the investigated molecules might be used as non-linear optical materials.

scholarly journals Theoretical Investigation of Glycine Micro-Solvated. Energy and NMR Spin Spin Coupling Constants Calculations

Sci ◽  
2021 ◽  
Vol 3 (4) ◽  
pp. 41
Author(s):  
Maria Cristina Caputo ◽  
Patricio Federico Provasi
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Water Solution ◽  
Polarizable Continuum Model ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Basis Set ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling

Glycine in its neutral form can exist in the gas phase while its zwitterion form is more stable in water solution, but how many waters are actually necessary to stabilize the zwitterionic structure in the gas phase? Are the intramolecular isotropic spin spin coupling constants sensitive enough to accuse the change in the environment? or the conformer observed? These and related questions have been investigated by a computational study at the level of density functional theory employing the B3LYP functional and the 6-31++G**-J basis set. We found that at least two water molecules explicitly accounted for in the super-molecule structure are necessary to stabilize both conformers of glycine within a water polarizable continuum model. At least half of the SSCCs of both conformers are very stable to changes in the environment and at least four of them differ significantly between Neutral and Zwitterion conformation.

Exploring chemistry features of favipiravir in octanol/water solutions

2021 ◽  
pp. 1-12
Author(s):  
Halimeh Rajabzadeh ◽  
Ayla Sharafat ◽  
Maryam Abbasi ◽  
Maryam Eslami Gharaati ◽  
Iraj Alipourfard
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Partition Coefficients ◽  
Density Functional ◽  
Water Solution ◽  
Peptide Group ◽  
Functional Theory ◽  
Water Solutions ◽  
Group Rotations ◽  
Heterocyclic Structure

Favipiravir (Fav) has become a well-known drug for medication of patients by appearance of COVID-19. Heterocyclic structure and connected peptide group could make changes for Fav yielding different features from those required features. Therefore, it is indeed a challenging task to prepare a Fav compound with specific features of desired function. In this work, existence of eight Fav structures by tautomeric formations and peptide group rotations were obtained using density functional theory (DFT) optimization calculations. Gas phase, octanol solution, and water solution were employed to show impact of solution on features of Fav besides obtaining partition coefficients (LogP) for Fav compounds. Significant impacts of solutions were seen on features of Fav with the obtained LogP order: Fav-7 >  Fav-8 >  Fav-4 >  Fav-3 >  Fav-2 >  Fav-5 >  Fav-1 >  Fav-6. As a consequence, internal changes yielded significant impacts on features of Fav affirming its carful medication of COVID-19 patients.

scholarly journals Spectral properties of coumarin derivatives in various environments

2013 ◽  
Vol 11 (4) ◽  
pp. 492-501 ◽  
Author(s):  
Alzbeta Holubekova ◽  
Pavel Mach ◽  
Jan Urban
Keyword(s):  
Gas Phase ◽  
Absorption Spectra ◽  
Spectral Properties ◽  
Density Functional ◽  
Water Solution ◽  
Blue Shift ◽  
Coumarin Derivatives ◽  
Complex Environments ◽  
Td Dft ◽  
Solvent Environment

AbstractThe structural and spectral properties of coumarin derivatives in complex environments were investigated within the time-dependent density functional theory (TD DFT). Absorption spectra calculations were obtained at TD PBE0/6-31+G(d,p) level of theory for coumarin47 in the gas-phase and in various polar and non-polar organic solvents. The geometries of coumarins 6, 30, 47 and 522 in the gas phase and in inclusion complexes with the β-cyclodextrin (βCD) were determined by PM3 and DFT (HCTH/6-31G) calculations. Encapsulation of coumarin in βCD and associated changes in electronic structure produced either a red or blue shift in the absorption spectra of coumarins. A proposed cavity model for βCD-coumarin complex in water solution allowed identification of various contributions to the overall shift in the absorption spectra of coumarin upon complex formation in a solvent environment

scholarly journals Diffusion and Reptation Quantum Monte Carlo Study of the NaK Molecule

2018 ◽  
Author(s):  
Marc E. Segovia ◽  
Oscar Ventura
Keyword(s):  
Monte Carlo ◽  
Dipole Moment ◽  
Potential Energy ◽  
Dissociation Energy ◽  
Quantum Monte Carlo ◽  
Density Functional ◽  
Basis Set ◽  
Energy Curve ◽  
Dft Methods ◽  
Trial Wavefunction

<p>Diffusion Monte Carlo (DMC) and Reptation Monte Carlo (RMC) methods, have been applied to study some properties of the NaK molecule. Hartree-Fock (HF), Density Functional (DFT) and single and double configuration interaction (SDCI) wavefunctions with a valence quadruple zeta atomic natural orbital (VQZ/ANO) basis set were used as trial wavefunctions. Values for the potential energy curve, dissociation energy and dipole moment were calculated for all methods and compared with experimental results and previous theoretical derivations. Quantum Monte Carlo (QMC) calculations were shown to be useful methods to recover correlation in NaK, essential to obtain a reasonable description of the molecule. The equilibrium distance—interpolated from the potential energy curves—yield a value of 3.5 Å, in agreement with the experimental value. The dissociation energy, however, is not as good. In this case, a conventional CCSD(T) calculation with an extended aug-pc-4 basis set gives a much better agreement to experiment. On the contrary, the CCSD(T), other MO and DFT methods are not able to reproduce correctly the large dipole moment of this molecule. Even DMC methods with a simple HF trial wavefunction are able to give a better agreement to experiment. RMC methods are even better, and the value obtained with a B3LYP trial wavefunction is very close to the experimental one.</p>

Donor Functionalized Perylene and Different π-Spacers Based Sensitizers for DSSC Applications - A Theoretical Approach

2021 ◽  
Author(s):  
D. Nicksonsebastin ◽  
P. Pounraj ◽  
Prasath M
Keyword(s):  
Density Functional Theory ◽  
Solar Cell ◽  
Gas Phase ◽  
Density Functional ◽  
Basis Set ◽  
Dye Sensitized Solar Cell ◽  
Functional Theory ◽  
Dye Sensitized ◽  
Td Dft ◽  
Organic Sensitizers

Abstract Perylene based novel organic sensitizers for the Dye sensitized solar cell applications are investigated by using Density functional theory (DFT) and time dependant density functional theory (TD-DFT).The designed sensitizers have perylene and dimethylamine (DM) and N-N-dimethylaniline(DMA) functionalized perylene for the dssc applications.π-spacers are thiophene andcyanovinyl groups and cyanoacrylic acid is chosen as the acceptor for the designed sensitizers. The studied sensitizers were fully optimized by density functional theory at B3LYP/6-311G basis set on gas phase and DMF phase. The electronic absorption of the sensitizers is analyzed by TD-DFT at B3LYP/6-311G basis set in both gas and DMF phase.

SOLVENT EFFECTS ON THE ELECTRONIC STRUCTURE AND NON-LINEAR OPTICAL PROPERTIES OF PYRENE AND SOME OF ITS DERIVATIVES BASED ON DENSITY FUNCTIONAL THEORY

2021 ◽  
Vol 4 (4) ◽  
pp. 236-251
Author(s):  
A. S. Gidado ◽  
L. S. Taura ◽  
A. Musa
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Energy Gap ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Lumo Energy ◽  
Functional Theory ◽  
Organic Optoelectronic ◽  
Homo Lumo

Pyrene (C16H10) is an organic semiconductor which has wide applications in the field of organic electronics suitable for the development of organic light emitting diodes (OLED) and organic photovoltaic cells (OPV). In this work, Density Functional Theory (DFT) using Becke’s three and Lee Yang Parr (B3LYP) functional with basis set 6-311++G(d, p) implemented in Gaussian 03 package was  used to compute total energy, bond parameters, HOMO-LUMO energy gap, electron affinity, ionization potential, chemical reactivity descriptors, dipole moment, isotropic polarizability (α), anisotropy of polarizability ( Δ∝) total first order hyper-polarizability () and second order hyperpolarizability (). The molecules used are pyrene, 1-chloropyrene and 4-chloropyrene  in gas phase and in five different solvents: benzene, chloroform, acetone, DMSO and water. The results obtained show that solvents and chlorination actually influenced the properties of the molecules. The isolated pyrene in acetone has the largest value of HOMO-LUMO energy gap of and is a bit closer to a previously reported experimental value of  and hence is the most stable. Thus, the pyrene molecule has more kinetic stability and can be described as low reactive molecule. The calculated dipole moments are in the order of 4-chloropyrene (1.7645 D) < 1-chloropyrene (1.9663 D) in gas phase. The anisotropy of polarizability ( for pyrene and its derivatives were found to increase with increasing polarity of the solvents.  In a nutshell, the molecules will be promising for organic optoelectronic devices based on their computed properties as reported by this work.

scholarly journals DEVELOPMENT OF MOLECULAR IMPRINTED POLYMER SOLID PHASE EXTRACTION (MISPE) FOR SEPARATION NITROFURANTOIN RESIDUE IN CHICKEN EGGS

2017 ◽  
Vol 10 (6) ◽  
pp. 108
Author(s):  
Sophi Damayanti ◽  
Untung Gunawan ◽  
Slamet Ibrahim
Keyword(s):  
Solid Phase Extraction ◽  
Analytical Methods ◽  
Density Functional ◽  
Solid Phase ◽  
Basis Set ◽  
Phase Extraction ◽  
Molecular Imprinted Polymer ◽  
Imprinted Polymer ◽  
Dft Methods ◽  
The Matrix

Background: The use of nitrofurantoin and other nitrofuran antibiotics in food which produced from animals is prohibited by European Union because of potentially carcinogenic and mutagenic. Various methods for analysis of residues of nitrofurantoin has been developed, but because of the interference of the matrix, it is necessary to separate the matrix therefore, the matrix effect will not interfere the analysis. Nowadays, molecular imprinted polymer (MIP) is a well-developed tool in the analytical field, mainly for separating substances in relatively complex matrices.Objective: The purpose of this study is to obtain MISPE that is selective for the separation of nitrofurantoin residues in chicken eggs.Methods: Analytical methods development of nitrofurantoin were optimization of HPLC system and validation of analytical methods performed to obtain the suitable system for nitrofurantoin detection. In silico study used for MIP design by observing the difference Gibbs free energy using Gaussview 5.08 software with Density Functional Theory (DFT) methods using 6-311G as basis set. MIP synthesis was done using bulk method use nitrofurantoin as template, acrylamide as functional monomer, ethyleneglycoldimethacrylate (EGDMA) as crosslinker, and azobisisobutyronitrile (AIBN) as an initiator reaction inside dimethylformamide (DMF) as solvent. Non imprinted polymer (NIP) was synthesized as comparison. MIP and NIP which has been synthesized was inserted into SPE cartridge and characterized using Infrared spectroscopy and HPLC.Result: MISPE that has been synthesized was characterized and compared to non-imprinted polymer solid phase extraction (NISPE) and marketed Solid Phase Extraction (SPE) C18. Sensitivity of MIP, NIP, and SPE C-18 to nitrofurantoin was 84.54 %, 37.73 %, and 33.95 % respectively, based on recovery of nitrofurantoin.Conclusion: Based on the result it was obtained MISPE has high selectivity toward nitrofurantoin compared to NISPE and either marketed SPE.  

Studies on the structure and conformational flexibility of secondary structures in amyloid beta — A quantum chemical study

2020 ◽  
Vol 19 (06) ◽  
pp. 2050014
Author(s):  
Mahendiraprabu Ganesan ◽  
Selvarengan Paranthaman
Keyword(s):  
Gas Phase ◽  
Amyloid Beta ◽  
Density Functional ◽  
Conformational Transition ◽  
Intermolecular Hydrogen Bond ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Secondary Structures ◽  
Conformational Flexibility ◽  
Solution Phase

Density functional theory (DFT) calculations are performed to study the conformational flexibility of secondary structures in amyloid beta (A[Formula: see text]) polypeptide. In DFT, M06-2X/6-31[Formula: see text]G(d, p) method is used to optimize the secondary structures of 2LFM and 2BEG in gas phase and in solution phase. Our calculations show that the secondary structures are energetically more stable in solution phase than in gas phase. This is due to the presence of strong solvent interaction with the secondary structures considered in this study. Among the backbone [Formula: see text] and [Formula: see text] dihedral angles, [Formula: see text] varies significantly in sheet structure. This is due to the absence of intermolecular hydrogen bond (H-bond) interactions in sheets considered in this study. Our calculations show that the conformational transition of helix/coil to sheet or vice-versa is due to the floppiness of the amino acid residues. This is observed from the Ramachandran map of the studied secondary structures. Further, it is noted that the intramolecular H-bond interactions play a significant role in the conformational transition of secondary structures of A[Formula: see text].

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