Basis Set In Gas Phase Research Articles

Molecular structure investigation and tautomerism aspects of (E)-3-benzylideneindolin-2-one

The synthesis and spectral characterization of the (E)-3-benzylideneindolin-2-one is reported. The compound crystallized in the monoclinic system with space group P21/n with cell coordinates a= 3.9849 (2) Å, b= 22.2236 (9) Å, c= 12.2501 (5) Å, β= 95.0535 (12) ∘, V=1080.64 (8) Å 3, and Z= 4. In the crystal, molecules are packed in chains formed via weak intermolecular C13–H13A ⋯O1 and N1-H1N1 …O1 hydrogen bonding. The relative stabilities of the two tautomeric isomers of 3 are calculated by DFT/B3LYP method using 6-311G(d,p) basis set in gas phase and in solution. The quantum chemical calculations, NMR studies and the XRD analyses showed that the keto form T0 is the only form that could exist in gas, solution and solid phases respectively. The calculated geometric parameters of the dimer molecule showed better agreement with the XRD data than those obtained for single isolated molecule. This shed light on the effect of intermolecular interactions on the calculated geometric parameters. MEP study showed that, the O-atom and the NH proton are the most reactive H-acceptor and H-donor sites, respectively. The N-H...O H-bonding interactions increased the negative charge at the O-atoms and the positive charge of the NH protons compared to the monomer unit. The synthesis, X-ray single crystal structure, spectral characterizations and DFT computation of the (E)-3-benzylideneindolin-2-one 3 is reported.

Three dimethoxy-substituted luminol derivatives: A comparative study using theoretical method

In this research, geometrical optimisation, Mulliken charge, molecular electrostatic potential, and the frontier molecular orbitals of three dimethoxy-substituted luminol derivatives were investigated by ab initio, density functional, and Møller-Plesset perturbation theory with a 6-311G (d, p) basis set in gas phase, water, and dimethylsulphoxide solution. The UV–vis spectra were calculated by time dependent density functional theory method. The properties of derivatives were compared with luminol at a molecular level to investigate the change induced by the methoxy group. The three derivatives were also compared with the aim of predicting the order of chemiluminescent efficiency. The results showed that methoxy substitution significantly changed the electronic and spectral properties of luminol. Among three derivatives, structure 2 was suggested to have the highest chemiluminescent efficiency. The results may shed some light on the design and selection of chemiluminescent reagents.

Theoretical conformational study of 1,1,1-trifluoro-4-mercapto-but-3-ene-2-thione and the importance of intramolecular hydrogen bonding in ground and first electronic excited state

Quantum chemical calculations of energies, geometrical structure, intramolecular hydrogen bonding (HB) and vibrational frequencies of 1,1,1-trifluoro-4-mercapto-but-3-ene-2-thione were carried out by the ab initio Hartree–Fock, Moller–Plesset second-order perturbation (MP2) and density functional theory (DFT) methods with 6-311++G** basis set in gas phase and water solution. The nature of the intramolecular hydrogen bond in the most stable chelated conformers has been studied by using the atoms in molecules theory of Bader, which is based on topological properties of the electron density. Natural bond orbital (NBO) analysis was also performed for better understanding of the nature of intramolecular interactions. The influence of the solvent on the stability order of conformers and the strength of intramolecular HB was considered using Tomasi's polarized continuum model. The HOMA, NICS, PDI, ATI, FLU and FLU π indices as well-established aromaticity indicators are examined. The excited-state properties of intramolecular HB in hydrogen-bonded systems have been investigated theoretically using the time-dependent DFT method. The calculated highest occupied molecular orbital (MO) and lowest unoccupied MO with frontier orbital gap are presented. Further verification of the obtained transition state structures was implemented via intrinsic reaction coordinate analysis.

The Investigation of Sequence-dependent Interaction of Messenger RNA Binding to Carbon Nanotube

To investigate carbon nanotubes (CNTs) as gene delivery vehicles, it is essential to characterize their interactions with mRNA. Messenger RNA is a powerful tool for controlling the expression of genes in biomedical applications. In the present report, we study the interactions of single-walled CNT with three codons of mRNA(UGC,GAC,CAG) by using MM, AM1,HF and DFT (B3LYP) methods with STO-3G and 3-21G basis sets in gas phase. To estimate the stability of Nanotubes- mRNA complexes total energy of the systems were determined. The varieties of obtained energy data suggest the relation between the stability of complexes as this order: CAG > GAC > UGC. According to the ability of NMR in providing detailed information about the structure and chemical environment of molecules, this technique has been carried out by supposing gauge-included atomic orbital (GIAO). Considering on the calculated results of NMR chemical shift consist of σiso, σaniso, Δσ, δ and η that are very sensitive to small changes in molecular geometry and chemical environments and the results of energy reveal that the characteristic's variety and the stability of these complexes is depend on the specific mrna base and nucleotide sequences. We can predict that diseases with special mutation and gene sequences are the better aim for special kinds of treatment. Current observations will allow the implementation of new strategies in the development of CNT: mRNA complexes as effective gene therapy.

Formation of spiroiminodihydantoin due to the reaction between 8-oxoguanine and carbonate radical anion: A quantum computational study

Reaction of 8-oxoguanine (8OG) with carbonate radical anion (CO3·−) producing spiroiminodihydantoin has been investigated using density functional theory. Geometries of reactant complex, intermediate complexes, product complexes and transition states were optimized at the B3LYP/6-31G(d,p) level of theory in gas phase which was followed by single point energy calculations employing the B3LYP, M06-2X and WB97XD functionals along with the AUG-cc-pVDZ basis set in gas phase and aqueous media. Solvent effect was treated employing the integral equation formalism of the polarizable continuum model. Possible roles of aeration, stirring and photoirradiation of reaction media which are performed in experimental studies have been explained.

Modeling the intermolecular interactions: Molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by 1H NMR, 13C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P21/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings.

The analysis of structural and electronic properties for assessment of intramolecular hydrogen bond (IMHB) interaction: a comprehensive study into the effect of substitution on intramolecular hydrogen bond of 4-nitropyridine-3-thiol in ground and electronic excited state

The hydrogen bond strength, molecular geometry, π-electron delocalization, and physical properties such as dipole moment, chemical potential, and chemical hardness of 4-nitropyridine-3-thiol and its 29 derivatives have been studied by means of density functional method with 6-311++G** basis set in gas phase and water solution. Also, the excited-state properties of intramolecular hydrogen bonding in these systems have been investigated theoretically using the time-dependent density functional theory method. The HOMA, NICS, PDI, ATI, FLU, and FLUπ indices as well-established aromaticity indicators have been examined. Natural bond orbital analysis is also performed for better understanding the nature of intramolecular interactions. The electron density and Laplacian (∇2ρ) properties, estimated by AIM calculations, indicate that H···O bond possesses low ρ and positive ∇2ρ values, which are in agreement with electrostatic character of the HBs, whereas S–H bond has covalent character. Numerous correlations between topological, geometrical, and energetic parameters are also found.

A DFT Study on Estrone – TNT Interaction

AbstractTrinitrotoluene, known as TNT, is a widely used powerful explosive. It is a poisonous material, which injures almost all cells, especially those of liver, bone marrow, and kidney. Estrone is a sex hormone having an electron rich aromatic (phenolic) ring that is capable of forming a π complex with molecules containing an electron deficient π system. This study has focused on investigating the tendency of the complex formation of TNT with estrone. It has been thought that the formation of estrone‐TNT π complex might take place in a human body exposed to acute or prolong period of this hazardous chemical and consequently estrone activities might be impaired. The complex formation reaction was investigated mainly using DFT method with B3LYP/6‐31G(d, p) basis set in gas phase. The existence of π interaction between estrone and TNT was demonstrated by computational spectroscopic analyses (UV/Vis, IR, and 1H NMR techniques). The frontier molecular orbital (HOMO and LUMO) analyses have shown that the considered π complex is very resistant to oxidation with respect to its components, estrone and TNT.

New acyclic 1,2,4-triazole-based Schiff base hydrazone: Synthesis, characterization, spectrophotometric and computational studies

A new 1,2,4-triazole-based Schiff base hydrazone with N, O, S donor set of atoms, H4L, has been prepared by condensation reaction of N,N′-bis(3-formyl-5-methylsalicylidene)ethane-1,2-diamine, H2L, with 4-amino-3-(4-pyridyl)-5-mercapto-1,2,4-triazole. The structure of H4L was characterized by using FT-IR, UV–Vis and 1H NMR spectroscopic methods as well as elemental analysis data. The formation constants of copper(II), cadmium(II), mercury(II) and silver(I) complexes of H4L in DMSO were calculated using a hard model chemometrics method applying the spectrophotometric data. The protonation constants of H4L were also measured in DMSO-water (1:10) mixture. Furthermore, 1H chemical shifts of H4L were studied by the gauge independent atomic orbital (GIAO) and continuous set of gauge transformations (CSGTs) methods at the level of density functional theory using B3LYP/6-311++G* basis sets in gas phase. The computed chemical shifts are in reasonably good agreement with the experimental data.

Quantum Mechanical Studies on Interaction of Carbohydrate with Nanomaterials

The interactions between the fragment of various nanotubes (NTs) and carbohydrate (beta-D-glucose) has been investigated using quantum mechanical methods using different basis sets in gas phase. The most stable isomer of each complex favors multiple CH...pi contacts which arise due to the orientation of the hydrophobic surface of the carbohydrate with reference to the curved or planar aromatic systems. The carbohydrate recognition surface of the aromatic system referred as "three point landing surface" are important in the stabilization of carbohydrate-pi complexes.

Formation of 8-Nitroguanine Due to Reaction between Guanyl Radical and Nitrogen Dioxide: Catalytic Role of Hydration

8-Nitroguanine (8-NitroG) is known to be a potent mutagenic product obtained from the guanine base of DNA that induces GC to AT transversion mutation. Its formation by the reaction of guanyl radical with nitrogen dioxide radical (NO(2)(*)) has been observed experimentally. The reaction was studied here theoretically considering different reactant complexes, transition states, intermediate complexes, and product complexes. The solvent effect due to one, two, three, and six specific water molecules and the bulk solvent effect of aqueous media on the reaction were considered. With one, two, and three complexed water molecules, geometry optimization calculations were performed using the B3LYP and BHandHLYP functionals of density functional theory along with the 6-31G (d,p) and the AUG-cc-pVDZ basis sets in gas phase which was followed by single point energy calculations at the MP2/AUG-cc-pVDZ level. With six complexed water molecules, geometry optimization was performed at the BHandHLYP/6-31G(d,p) level of theory followed by single point energy calculations at all the other levels of theory mentioned above. Solvation in bulk aqueous media was treated at all the above-mentioned levels of theory using the polarizable continuum model (PCM). Specific water molecules were found to play catalytic roles in proton transfer processes that usually lowered the barrier appreciably.

Carbohydrate-Aromatic Interactions: The Role of Curvature on XH···π Interactions

The interaction between the fragment of carbon nanotube (CNT) and carbohydrates has been investigated using MP2 and M05-2X methods using various basis sets in gas phase. Three carbohydrates, viz., beta-d-glucose, beta-d-galactose, and beta-d-xylose with different degree of hydrophobic nature have been selected for this investigation. With a view to assess the effect of curvature on the interaction between the carbohydrates and CNT, calculations on intermolecular complexes comprising of coronene (COR) and carbohydrates have also been carried out in gas phase. Results obtained from electronic structure calculations combined with the Bader's electron density analysis reveal that CH...pi interaction is the predominant one in the stabilization of the carbohydrate-CNT and carbohydrate-COR complexes. Furthermore, the importance of OH...pi and lone pair...pi (lp...pi) interactions are also evident from the results. The calculated BEs for the various carbohydrate-CNT and carbohydrate-COR complexes at M05-2X with dual basis set [aug-cc-pVTZ for carbohydrate + cc-pVTZ for both CNT and COR] vary from -2.52 to -5.14 and from -4.14 to -8.04 kcal/mol, respectively. The corresponding BEs obtained from MP2/6-311++G(d,p)//M05-2X/6-31+G(d,p) level of calculation range from -4.92 to -9.93 and from -6.75 to -12.53 kcal/mol. Close scrutiny of the energetics of all the complexes elucidate that the electron correlation energy (dispersion energy) significantly contribute to the stability of these complexes. It is found from the analysis of geometrical parameters and BEs that the interplay of orientation of the X-H (X = C and O) bond to the pi-surface is crucial for the recognition and further stabilization. Molecular electrostatic potential (MESP) isosurfaces of curved and planar surfaces have clearly provided the difference between the pi-electron distributions. Evidences form the energy decomposition analysis elicit that the dispersive interaction plays a significant role in the overall stabilization of the complexes. And, it is possible to observe the delicate balance between the electrostatic interaction and the exchange-repulsion energy.

A quantum chemical study of repair of O6-methylguanine to guanine by tyrosine: Evaluation of the winged helix-turn-helix model

The winged helix-turn-helix model for the repair of O6-MeG to guanine involving the reaction of O6-MeG with a tyrosine residue of the protein O6-alkylguanine-DNA alkyltransferase (AGT) was examined by studying the reaction mechanism and barrier energies. Molecular geometries of the species and complexes involved in the reaction, i.e. the reactant, intermediate and product complexes as well as transition states, were optimized employing density functional theory in gas phase. It was followed by single point energy calculations using density functional theory along with a higher basis set and second order M(phi)ller-Plesset perturbation theory (MP2) along with two different basis sets in gas phase and aqueous media. For the solvation calculations in aqueous media, the integral equation formalism of the polarizable continuum model (IEF-PCM) was employed. Vibrational frequency analysis was performed for each optimized structure and genuineness of transition states was ensured by visualizing the vibrational modes. It is found that tyrosine can repair O6-MeG to guanine by a two-step reaction. The present results have been compared with those obtained considering the helix-turn-helix model where the repair reaction primarily involves cysteine and occurs in a single-step. It is concluded that the repair through tyrosine envisaged in the winged helix-turn-helix model would be less efficient than that through cysteine envisaged in the helix-turn-helix model.

Reactions of NO2Cl with Imidazole: A Model Study for the Corresponding Reactions of Guanine

Reactions of nitryl chloride NO(2)Cl with imidazole, taken as a model for the guanine base of DNA, leading to the formation of 2-oxoimidazole (2-oxoIm), 2-chloroimidazole (2-chloroIm), and 2-nitroimidazole (2-nitroIm) corresponding to the 8-oxo, 8-chloro, and 8-nitro derivatives of guanine were studied at the B3LYP and MP2 levels of theory employing the 6-31+G* and AUG-cc-pVDZ basis sets in gas phase. In order to incorporate solvent effect, all the B3LYP/AUG-cc-pVDZ optimized structures were solvated in aqueous media at the B3LYP/AUG-cc-pVDZ and MP2/AUG-cc-pVDZ levels of theory using the polarizable continuum model (PCM). A single mechanism was found for the formation of 2-oxoIm, while two and three mechanisms were found for the formation of 2-nitroIm and 2-chloroIm respectively. Each of these reaction mechanisms involves two steps. The calculated barrier energies show that the formation of 2-nitroIm would occur more efficiently than those of 2-oxoIm and 2-chloroIm. It suggests that formation of 8-nitroguanine would be the main DNA lesion caused by NO(2)Cl, which is consistent with experimental observations.

Hartree-Fock, Møller-Plesset calculations and dynamic NMR study of 3,3-dimethoxy-1-(imidazolidin-2-ylidene)propan-2-one

The experimental 1H, 13C NMR spectra of 3,3-dimethoxy-1-(imidazolidin-2-ylidene)propan-2-one were recorded in CDCl 3 at temperature range 213–323 K. The variable temperature spectra revealed a dynamic NMR effect which is attributed to restricted rotation around the C C double bond. Fast exchange processes of deuterium atoms between CDCl 3 and 3,3-dimethoxy-1-(imidazolidin-2-ylidene)propan-2-one or fast exchange of proton between nitrogen and oxygen atoms of carbonyl group is also revealed by broadening of N–H (singlet) proton NMR signals. Proton and carbon theoretical chemical shifts of the title molecule were calculated by using RHF and MP2-GIAO levels and different basis sets in gas phase at 298 K. The calculated proton chemical shifts show that the experimental values have no agreement with theoretical values, but for carbon chemical shifts a good agreement achieved by using RHF with 6-31G basis set and MP2/3-21G, 6-31G basis sets. Discrepancies are attributed to either the limitations of calculating program, because the change of the structure while rotation are not considered. The results showed that to select of basis set has more important rule, because RHF–GIAO level calculation with 6-31G basis set in gas phase can excellently reproduce the 13C NMR spectrum. Moreover, MP2/3-21G, 6-31G calculation has not significant influence on 13C NMR chemical shifts with respect to RHF–6-31G.