Structural, Spectral, Thermodynamic and HOMO, LUMO Analysis of 2, 6 dithenobenzene-3-enyl 3, 5 dimethyl piperdine-4-one: A quantum chemical analysis

In the current work, the vibrational frequencies, infrared intensities, molecular geometry and Raman scattering were determined and investigated using ab initio Hartree–Fock (HF) and density functional methods with a basis set of 6-311++ G (d, p) of the organic molecule under interpretation. The FT-IR and FT-Raman spectra of titled molecule have been recorded in the region 4000-400 cm-1 and 5000-70 cm-1, respectively. The optimized geometry structures (bond lengths and bond angles) achieved using HF shows the best result with the experimental values of the titled molecule. The frontier molecular orbitals help to distinguish chemical responsiveness and molecular kinetic steadiness, thus HOMO-LUMO analysis can be done using the quantum chemistry to improve thermodynamics. The electron density mapping to electrostatic potential surfaces were involved in finding the reactivity sites of the titled compound. With the help of Gauss view 5.0 and Chemcraft packages, the obtained outputs are analyzed. Hyperpolarizability and non-linear optical effect of isolated molecules of NLO materials are observed to be an extensive tool for molecular spectroscopy research. Therefore, for industrial application, Hyperpolarizability of the molecule is also studied.

Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer’s Disease Mutations

Alzheimer’s disease manifests itself in brain tissue by neuronal death, due to aggregation of β-amyloid, produced by senile plaques, and hyperphosphorylation of the tau protein, which produces neurofibrillary tangles. One of the genetic markers of the disease is the gene that translates the presenilin-2 protein, which has mutations that favor the appearance of the disease and has no reported crystallographic structure. In view of this, protein modeling is performed using prediction and structural refinement tools followed by an energetic and stereochemical characterization for its validation. For the simulation, four reported mutations are chosen, which are Met239Ile, Met239Val, Ser130Leu, and Thr122Arg, all associated with various functional responses. From a theoretical analysis, a preliminary bioinformatic study is made to find the phosphorylation patterns in the protein and the hydropathic index according to the polarity and chemical environment. Molecular visualization was carried out with the Chimera 1.14 software, and the theoretical calculation with the hybrid quantum mechanics/molecular mechanics system from the semi-empirical method, with Spartan18 software and an AustinModel1 basis. These relationships allow for studying the system from a structural approach with the determination of small distance changes, potential surfaces, electrostatic maps, and angle changes, which favor the comparison between wild-type and mutant systems. With the results obtained, it is expected to complement experimental data reported in the literature from models that would allow us to understand the effects of the selected mutations.

On the Importance of Pnictogen and Chalcogen Bonding Interactions in Supramolecular Catalysis

In this review, several examples of the application of pnictogen (Pn) (group 15) and chalcogen (Ch) bonding (group 16) interactions in organocatalytic processes are gathered, backed up with Molecular Electrostatic Potential surfaces of model systems. Despite the fact that the use of catalysts based on pnictogen and chalcogen bonding interactions is taking its first steps, it should be considered and used by the scientific community as a novel, promising tool in the field of organocatalysis.

On the Importance of σ–Hole Interactions in Crystal Structures

Elements from groups 14–18 and periods 3–6 commonly behave as Lewis acids, which are involved in directional noncovalent interactions (NCI) with electron-rich species (lone pair donors), π systems (aromatic rings, triple and double bonds) as well as nonnucleophilic anions (BF4−, PF6−, ClO4−, etc.). Moreover, elements of groups 15 to 17 are also able to act as Lewis bases (from one to three available lone pairs, respectively), thus presenting a dual character. These emerging NCIs where the main group element behaves as Lewis base, belong to the σ–hole family of interactions. Particularly (i) tetrel bonding for elements belonging to group 14, (ii) pnictogen bonding for group 15, (iii) chalcogen bonding for group 16, (iv) halogen bonding for group 17, and (v) noble gas bondings for group 18. In general, σ–hole interactions exhibit different features when moving along the same group (offering larger and more positive σ–holes) or the same row (presenting a different number of available σ–holes and directionality) of the periodic table. This is illustrated in this review by using several examples retrieved from the Cambridge Structural Database (CSD), especially focused on σ–hole interactions, complemented with molecular electrostatic potential surfaces of model systems.

Shedding Light on the Optical and Nonlinear Optical Properties of Super-Alkali Doped Borophene

The present investigation highlights the 2-dimentional design of several interesting super alkali doped borophene derivatives for efficient nonlinear optical (NLO). Borophene (B36) and super alkali units (Li3O) whose combining effects and resulting NLO responses have been evaluated by orienting super-alkali clusters at various sites such as a hub, rim, and bridged around the B36 molecule. The charge analysis is characterized by frontier and natural bond orbital analysis, narrowed HOMO-LUMO band gap, better intramolecular charge transfers. Molecular electrostatic potential surfaces demonstrate enhanced optoelectronic features of these complexes that are viable owing to Li3O adsorption. Singly doped and doubly doped complexes have been considered and their NLO properties have been calculated. Band gap energy reduces about three times when doped with two Li3O. A considerably high figure of merit, first hyperpolarizability (bo) values up to five digits 10611 a. u. for complex A proved that these systems can be utilized as promising candidates in various NLO applications.

In Silico Studies of The Human IAPP In Presence of Osmolytes

The human islet amyloid polypeptide or amylin is secreted along with insulin by pancreatic islets. Under the drastic environmental conditions, amylin can aggregate to form amyloid fibrils. This amyloid plaque of hIAPP in the pancreatic cells is the cause of Type II diabetes. Early stages of amylin aggregates are more cytotoxic than the matured fibrils. Here, we have used the all-atom molecular dynamic simulation to see the effect of water, TMAO, urea and urea:TMAO having ratio 2:1 of different concentrations on the amylin protein. Our study suggest that the amylin protein forms β-sheets in its monomeric form and may cause the aggregation of protein through the residue 13-17 and the C-terminal region. α-helical content of protein increases with an increase in TMAO concentration by decreasing the SASA value of protein, increase in intramolecular hydrogen bonds and on making the short range hydrophobic interactions. Electrostatic potential surfaces shows that hydrophobic groups are buried and configurational entropy of backbone atoms is lesser in presence of TMAO, whereas opposite behaviour is obtained in case of urea. Counteraction effect of TMAO using Kast model towards urea is also observed in ternary solution of urea:TMAO.

Investigating the Effect of Nitro Groups on the Electronic Properties of Phenanthrene Compound

Theoretical study for calculating the electronic structure of phenanthrene compound and its simplest derivatives with nitro groups in different positions was performed using density functional theory (DFT) based on the hybrid function of three parameters. Lee-Yang-Parr [B3LYP] with 6-31 [d, p] basis set was used to investigate the effect of nitro groups on the electronic properties of phenanthrene compound. All calculations were obtaind by employing the used method using the Gaussian 09 package of programs. The energy gaps, total energies, the energy of HOMO and LUMO, softness, dipole moment, Fermi level, molecular symmetry, electrochemical hardness, electron density, electrostatic potential surfaces and infrared spectra were calculated. The results showed that the electronic properties of phenanthrene molecule are affected by the added nitro group. The total energy, energy gap and the HOMO and LUMO energy decreased compared with the original molecule. The ionization potential (IP), electron affinity (EA) and Fermi level (Ef) are increased compared with the original molecule. Keywords: B3LYP/DFT calculations, Phenanthrene molecule, Nitro group, Energy gap, Ionization potential.

Tetrabromoethane as σ-Hole Donor toward Bromide Ligands: Halogen Bonding between C2H2Br4 and Bromide Dialkylcyanamide Platinum(II) Complexes

The complexes trans-[PtBr2(NCNR2)2] (R2 = Me21, (CH2)52) were cocrystallized with 1,1,2,2-tetrabromoethane (tbe) in CH2Cl2 forming solvates 1·tbe and 2·tbe, respectively. In both solvates, tbe involved halogen bonding, viz. the C–Br···Br–Pt interactions, were detected by single-crystal X-ray diffractions experiments. Appropriate density functional theory calculations (M06/def2-TZVP) performed for isolated molecules and complex-tbe clusters, where the existence of the interactions and their noncovalent nature were confirmed by electrostatic potential surfaces (ρ = 0.001 a.u.) for isolated molecules, topology analysis of electron density, electron localization function and HOMO-LUMO overlap projections for clusters.

Solution and Solid-State Photophysical Properties of Positional Isomeric Acrylonitrile Derivatives with Core Pyridine and Phenyl Moieties: Experimental and DFT Studies

The compounds I (Z)-2-(phenyl)-3-(2,4,5-trimethoxyphenyl)acrylonitrile with one side (2,4,5-MeO-), one symmetrical (2Z,2′Z)-2,2′-(1,4-phenylene)bis(3-(2,4,5-trimethoxyphenyl)acrylonitrile), II (both sides with (2,4,5-MeO-), and three positional isomers with pyridine (Z)-2-(pyridin-2- 3, or 4-yl)-3-(2,4,5-trimethoxyphenyl)acrylonitrile, III–V were synthetized and characterized by UV-Vis, fluorescence, IR, H1-NMR, and EI mass spectrometry as well as single crystal X-ray diffraction (SCXRD). The optical properties were strongly influenced by the solvent (hyperchromic and hypochromic shift), which were compared with the solid state. According to the solvatochromism theory, the excited-state (μe) and ground-state (μg) dipole moments were calculated based on the variation of Stokes shift with the solvent’s relative permittivity, refractive index, and polarity parameters. SCXRD analyses revealed that the compounds I and II crystallized in the monoclinic system with the space group, P21/n and P21/c, respectively, and with Z = 4 and 2. III, IV, and V crystallized in space groups: orthorhombic, Pbca; triclinic, P-1; and monoclinic, P21 with Z = 1, 2, and 2, respectively. The intermolecular interactions for compounds I–V were investigated using the CCDC Mercury software and their energies were quantified using PIXEL. The density of states (DOS), molecular electrostatic potential surfaces (MEPS), and natural bond orbitals (NBO) of the compounds were determined to evaluate the photophysical properties.