Semiempirical Molecular Orbital Calculations Research Articles

Modeling and Optimisation of Comlexity by the β-Cyclodextrin of an Organic Pollutant Model: m-Methyl Red

Studies of cyclodextrin chemistry using quantum chemical methods are mainly adopted to investigate the formation of the inclusion complex causing changes in the physicochemical properties of the cyclodextrin guest. In this paper, we conducted a computational modeling study of the inclusion complexes of β-cyclodextrin (β-CD) with m-Methyl Red (m-MR) by using parametric method 6 (PM6), the semi empirical molecular orbital calculations and the natural bond orbital method (NBO). The inclusion process is carried out by maintaining the coordinates of the β-CD fixed and by displacing the guest molecule. The different relative positions between m-MR and β-CD are measured with respect to the distance between the reference atom (N) in the guest molecule and the origin of the coordinates from the equatorial plane of β-CD. The m-MR/β-CD (B) inclusion complex has a lower negative value of ΔG compared to another m-MR/β-CD (A) complex, highlighting the spontaneous behavior of the inclusion process. In addition, during the process of inclusion, the complexation energy is negative, which allows us to affirm that the complexation of m-MR in the β-CD is thermodynamically favorable. Among two directions A and B, the minimum energy generated from the PM6 was obtained in the orientation B and the guest molecule is partially encapsulated in the cavity of β-CD. In the NBO analysis, the stabilization energy is also usually used to characterize the hydrogen bond interaction between a lone pair (LP(Y)) of an atom Y and an anti-bonding orbital (BD٭(X-H)).

Self-Assembly of [3]Catenane and [4]Catenane Based on Neutral Organometallic Scaffolds

Transition metal-mediated templating and self-assembly have shown great potential to construct mechanically interlocked molecules. Herein, we describe the formation of the bimetallic [3]catenane and [4]catenane based on neutral organometallic scaffolds via the orthogonality of platinum-to-oxygen coordination-driven self-assembly and copper(I) template–directed strategy of a [2]pseudorotaxane. The structures of these bimetallic [3]catenane and [4]catenane were characterized by multinuclear NMR {1H and 31P} spectroscopy, electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS), and PM6 semiempirical molecular orbital theoretical calculations. In addition, single-crystal X-ray analyses of the [3]catenane revealed two asymmetric [2]pseudorotaxane units inside the metallacycle. It was discovered that tubular structures were formed through the stacking of individual [3]catenane molecules driven by the strong π–π interactions.

Energy Efficient Ultrahigh Flux Separation of Oily Pollutants from Water with Superhydrophilic Nanoscale Metal–Organic Framework Architectures

AbstractThe rising demand for clean water for a growing and increasingly urban global population is one of the most urgent issues of our time. Here, we introduce the synthesis of a unique nanoscale architecture of pillar‐like Co‐CAT‐1 metal–organic framework (MOF) crystallites on gold‐coated woven stainless steel meshes with large, 50 μm apertures. These nanostructured mesh surfaces feature superhydrophilic and underwater superoleophobic wetting properties, allowing for gravity‐driven, highly efficient oil–water separation featuring water fluxes of up to nearly one million L m−2 h−1. Water physisorption experiments reveal the hydrophilic nature of Co‐CAT‐1 with a total water vapor uptake at room temperature of 470 cm3 g−1. Semiempirical molecular orbital calculations shed light on water affinity of the inner and outer pore surfaces. The MOF‐based membranes enable high separation efficiencies for a number of liquids tested, including the notorious water pollutant, crude oil, affording chemical oxygen demand (COD) concentrations below 25 mg L−1 of the effluent. Our results demonstrate the great impact of suitable nanoscale surface architectures as a means of encoding on‐surface extreme wetting properties, yielding energy‐efficient water‐selective large‐aperture membranes.

Energy Efficient Ultrahigh Flux Separation of Oily Pollutants from Water with Superhydrophilic Nanoscale Metal-Organic Framework Architectures.

The rising demand for clean water for a growing and increasingly urban global population is one of the most urgent issues of our time. Here, we introduce the synthesis of a unique nanoscale architecture of pillar‐like Co‐CAT‐1 metal–organic framework (MOF) crystallites on gold‐coated woven stainless steel meshes with large, 50 μm apertures. These nanostructured mesh surfaces feature superhydrophilic and underwater superoleophobic wetting properties, allowing for gravity‐driven, highly efficient oil–water separation featuring water fluxes of up to nearly one million L m−2 h−1. Water physisorption experiments reveal the hydrophilic nature of Co‐CAT‐1 with a total water vapor uptake at room temperature of 470 cm3 g−1. Semiempirical molecular orbital calculations shed light on water affinity of the inner and outer pore surfaces. The MOF‐based membranes enable high separation efficiencies for a number of liquids tested, including the notorious water pollutant, crude oil, affording chemical oxygen demand (COD) concentrations below 25 mg L−1 of the effluent. Our results demonstrate the great impact of suitable nanoscale surface architectures as a means of encoding on‐surface extreme wetting properties, yielding energy‐efficient water‐selective large‐aperture membranes.

Bond dissociation energy and thermal stability of energetic materials

Thermal stability of energetic materials is often screened by differential scanning calorimetry and accelerating rate calorimetry measurements. On the other hand, bond dissociation energies can explain reactivity or stability of chemical compounds. Here bond dissociation energy was derived from standard enthalpies of formation estimated by semi-empirical molecular orbital calculations using the MOPAC-PM7 package. The weakest bond dissociation energies of energetic materials and their onset temperatures in differential scanning calorimetry and accelerating rate calorimetry measurements correlated well, except for molecules where decomposition was favored by effects like intermolecular interactions. Bond dissociation energies derived from molecular orbital calculations have been found useful to roughly predict onset temperatures in the calorimetric measurements for energetic materials where data may sometimes not be available.

Study of Synergistic Effect of Some Pyrazole Derivatives as Corrosion Inhibitors for Mild Steel in 1 M H2SO4

Six new pyrazole derivatives were successfully prepared and investigated as corrosion inhibitors for mild steel in 1 M H2SO4 solution by weight loss measurements for 24 h at 30°C. It was observed that at higher inhibitor concentrations, the rate of corrosion decreases, the inhibition efficiency increases as well as the surface coverage degree. The values of the standard free energy of adsorption showed that all prepared pyrazole derivatives afford physisorption effects. The correlation between experimental results and theoretical data could be concluded by using semiempirical molecular orbital calculations for the six studied inhibitors. Theoretical calculations were used to understand the interaction nature between the metal surface and the organic molecules as a corrosion inhibitors.

Propagation of Holes and Electrons in Metal-Organic Frameworks.

Charge transport in two zinc metal-organic frameworks (MOFs) has been investigated using periodic semiempirical molecular orbital calculations with the AM1* Hamiltonian. Restricted Hartree-Fock calculations underestimate the band gap using Koopmans theorem (ca. 2 eV compared to the experimental value of 2.8 eV). However, it almost doubles when the constraint on the wave function to remain spin-restricted is removed and the energies of the UHF Natural Orbitals are used. Charge-transport simulations using propagation of the electron- or hole-density in imaginary time allow charge-transport paths and mechanisms to be determined. The calculated relative mobilities in the directions of the three crystal axes agree with experimental expectations, but the absolute values are not reliable using the current technique. Hole-mobility along the crystal c-axis (along the metal stacks) is found to be 13 times higher in the zinc MOF with anthracene linker (Zn-ANMOF-74) than in the other directions, whereas the factor is far smaller (1.7) for electron mobility. Directional preferences are far less distinct in the equivalent structure with phenyl linkers (Zn-MOF-74). The imaginary-time simulation technique does not give quantitative mobilities. The simulations reveal a change in mechanism between the different directions: Coherent polaron migration is observed along the stacks but tunneling hops between them.

A Computational Study on the Stereo- and Regioselective Formation of the C4α-C6' Bond of Tethered Catechin Moieties by an Exhaustive Search of the Transition States.

We previously reported the total synthesis of procyanidin B6 by using the stereo- and regioselective C-C bond formation of tethered catechin moieties as the key step. The reaction afforded the product bearing a new C4α-C6' bond linkage instead of the inherently preferable C4α-C8' bond. However, the origin of this selectivity remained unclear due to the complex structure of the substrate. Here we report the results of computational exploration of this C-C bond formation to gain mechanistic insights into the selectivity. The computational study of highly flexible compounds was realized by an exhaustive search of transition states. A large library of candidate transition states was generated by a conformational search of constrained models using molecular mechanics simulations and semiempirical molecular orbital calculations. Subsequent DFT-based transition state calculations provided 367 transition states for C4-C6' and C4-C8' bond formations. Comparison of the geometries and energies showed that the C4α-C6' linkage is preferentially formed via two competing transition states, leading to a C6'-diastereomeric mixture. Interactive atomic distances and visualization of the nonbonding interactions suggest the importance of nonclassical hydrogen bonding and CH-π, π-π, and lone pair-π interactions in stabilizing the two transition states. The present study supports preferential C4α-C6' bond formation of the tethered catechins.

Study of Active Center Structures for Fe/N/C Type Oxygen Reduction Catalyst Using Semi-Empirical Molecular Orbital Calculations

Polymer electrolyte fuel cells (PEFCs) are one of the most important devices in realizing hydrogen society. Platinum, which is used as the catalyst of PEFCs, is expensive and less abundant. Thus, the development of a non-platinum oxygen reduction catalyst is required for the wide-spread use of PEFCs. Fe/N/C non-platinum oxygen reduction catalysts are promising platinum alternative catalyst candidates. We have reported new metal/nitrogen/carbon-electrocatalysts synthesized by the pyrolysis of precursors consisting of Ketjenblack®, a Zn complex with 4,4’-bipyridine, 1,10-phenanthroline (phen), and iron(II) chloride1)．The density of active sites on the catalysts need to be increased for the improvement of for oxygen reduction reaction (ORR). Although we obtained that pyridine type nitrogen is related to the ORR activity, the chemical structure of the active center is still unknown. The conclusion does not match whether Fe atoms function as activity centers2-3．In this study, the structures of active center for Fe/N/C ORR catalysts were studied using semi-empirical molecular orbital calculations． Assuming that four electrons were injected into the compound, the distance between an O2 molecule and atoms was stepwise shortened with the parameters4 using MOPAC 20165. The result of the calculation was visualized by Jmol6. We used model compounds modeling a part of the edge of a graphite layer (Fig. 1(a)). Fig. 1(b) shows the dependence of ΔH on the distance between O and target atoms during shortening distance. The activation energies of route (i) was the smallest of the four routes. The cleavage of O-O bond occurred at routes (i) and (iv). The supply of further proton via H3O+ is necessary in the route (ii) and (iii). References and Notes Shimbori, H. Shiroishi, R. Ono, S. Kosaka, M. Saito, T. Yoshida, H. Katagiri, K. Miyazawa, Y. Tanaka, Mat. Sci. Eng. B, 228, 190 (2018). Lefèvre, J.P. Dodelet, P. Bertrand, J. Phys. Chem. B , 106, 8705 (2002). Guo, R. Shibuya, C. Akiba, S. Saji, T. Kondo, J. Nakamura, Science, 351, 361 (2016).Typical calculation parameters of MOPAC used in the simulations: PM6-DH2 EF PRECISE PULAY CAMP ITRY=9999 SHIFT=50 SYMMETRY STEP=-0.025 POINT=74 NOINTER GRAPHF EPS=78.5 NSPA=200 (UHF) CHARGE=(2 to -2).MOPAC2016, James J. P. Stewart, Stewart Computational Chemistry, Colorado Springs, CO, USA, HTTP://OpenMOPAC.net (2016).Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/ Figure 1

Structural investigation of sparfloxacin drug using mass spec-trometry and MNDO semi-empirical molecular orbital calcu-lations

Sparfloxacin is a broad spectrum antibacterial fluoroquinolone against some microorganisms including gram-positive and gram-negative bacteria and exhibits moderate activity against anaerobes and mycobacteria. Sparfloxacin is well tolerated and the intake of food has no adverse effect on the pharmacokinetic features (Blondeau 1999, Stahlmann et al. 1998). For the medical important of this drug author have been study its structure by recording and investigate its electron ionization (EI) mass spectra at different electron energies 70 and 15 eV. Also, the chemical ionization (CI) mass spectrum has been recorded and investigated. The main fragmentation processes in EI and CI have elucidated and discussed. The main fragment ions in EI mass spectra are [M-C4H8N] + and fragment [M- C4H8N- CO2] +, while [MH- CO2]+ ion are the most fragment ion in CI mass spectrum. On the other hand, the molecular structure optimization of sparfloxacin was calculated using the modified neglect of diatomic overlap (MNDO) semi-empirical molecular orbital method. Also, the thermochemical data such as heat of formations, total energy, ionization energy, electron affinity and dipole moment have been calculated and discussed.

Effect of Structure and Disorder on the Charge Transport in Defined Self-Assembled Monolayers of Organic Semiconductors.

Self-assembled monolayer field-effect transistors (SAMFETs) are not only a promising type of organic electronic device but also allow detailed analyses of structure-property correlations. The influence of the morphology on the charge transport is particularly pronounced, due to the confined monolayer of 2D-π-stacked organic semiconductor molecules. The morphology, in turn, is governed by relatively weak van-der-Waals interactions and is thus prone to dynamic structural fluctuations. Accordingly, combining electronic and physical characterization and time-averaged X-ray analyses with the dynamic information available at atomic resolution from simulations allows us to characterize self-assembled monolayer (SAM) based devices in great detail. For this purpose, we have constructed transistors based on SAMs of two molecules that consist of the organic p-type semiconductor benzothieno[3,2-b][1]benzothiophene (BTBT), linked to a C11 or C12 alkylphosphonic acid. Both molecules form ordered SAMs; however, our experiments show that the size of the crystalline domains and the charge-transport properties vary considerably in the two systems. These findings were confirmed by molecular dynamics (MD) simulations and semiempirical molecular-orbital electronic-structure calculations, performed on snapshots from the MD simulations at different times, revealing, in atomistic detail, how the charge transport in organic semiconductors is influenced and limited by dynamic disorder.

Study of Thermal Analysis Behavior of Fenbendazole and Rafoxanide.

Purpose: Thermal analysis techniques have been applied to study the thermal behavior of fenbendazole (Fen) and rafoxanide (Raf). Semi-empirical molecular orbital calculations were used to confirm these results. Methods: Thermogravimetric analysis, derivative thermogravimetry, differential thermal analysis and differential scanning calorimetry were used to determine the thermal behavior and purity of the drugs under investigation. Results: Thermal behavior of Fen and Raf were augmented using semi-empirical molecular orbital calculations. The purity values were found to be 99.17% and 99.60% for Fen and Raf, respectively. Conclusion: Thermal analysis techniques gave satisfactory results to obtain quality control parameters such as melting point and degree of purity at low cost, furthermore, its simplicity and sensitivity justifies its application in quality control laboratories.

Assessment of semi-empirical molecular orbital calculations for describing magnetic interactions

We report a thorough comparison between the spin-unrestricted semi-empirical molecular orbital (SE-UMO) and density functional theory (UDFT) calculations for a variety of π-conjugated diradical molecules which exhibit through-bond magnetic exchange interactions. The spin-unrestricted neglect of diatomic differential overlap (NDDO)-based methods (UPM6 and UrPM6) and self-consistent charge density functional tight-biding (UDFTB) are examined. The UCAM-B3LYP method is used as a representative of UDFT. We have found that NDDO-based and UDFTB methods give different performances with respect to the results of UCAM-B3LYP. The degree of diradical character in the target systems decreases in the order of UPM6>UrPM6≈UCAM-B3LYP>UDFTB. The conventional UPM6 and UDFTB calculations tend to overestimate and underestimate the diradical character, respectively, whereas UrPM6 is able to provide much the same results as UCAM-B3LYP. This is convincing evidence that UrPM6 will be useful for in silico screening of materials science at much lower computational cost.

Greener solid state synthesis of nano-sized mono and homo bi-nuclear Ni(II), Co(II), Mn(II), Hg(II), Cd(II) and Zn(II) complexes with new sulfa ligand as a potential antitumour and antimicrobial agents

Abstract New nano-sized mono and homo bi-nuclear Ni(II), Co(II), Mn(II), Hg(II), Cd(II) and Zn(II) complexes with 4-[(2-hydroxybenzylidene)amino]- N -(1,3-thiazol-2-yl)benzenesulfonamide (H 2 L) were synthesized by solid-solid reaction at room temperature. The complexes were structurally characterized using MS, FT-IR, UV–Vis, ESR, 1 H and 13 C NMR, spectra, thermal analyses, X-ray powder diffraction, SEM, conductance and magnetic measurements. FT-IR and NMR studies denoted that H 2 L coordinates to the metallic centers in a di-basic tetra-dentate mode using both the Schiff base center and the sulfonamide part. UV–Vis, ESR spectra and thermo-gravimetric analysis revealed that whole complexes attain tetrahedral geometry. Coats-Redfern method was applied in calculating the activation thermo-kinetic parameters ( E* , ∆ H* , ∆ S* , and ∆ G* ) for the diverse thermal decomposition stages from TGA curves. The data obtained from XRD and SEM images unequivocally asserted the nano-sized metal chelates. The inspected structures were propped using 3-D molecular modeling of some complexes employing molecular mechanics (MM +) and semi-empirical molecular orbital calculations (PM3). The recently inspected compounds were scrutinized for antimicrobial activities towards assorted species of bacteria and fungi. Also, the anticancer efficiency versus human liver Carcinoma cell line ( HEPG2 ) was examined. The results are very promising for their enforcements in therapeutic uses.

Three novel bolaamphiphiles as corrosion inhibitors for carbon steel in hydrochloric acid: Experimental and computational studies

Three novel bolaamphiphiles were synthesized and investigated as corrosion inhibitors for carbon steel in 1M HCl using chemical and electrochemical techniques. The results revealed that the synthesized bolaamphiphiles have good inhibitive effect. The adsorption of bolaamphiphiles on the carbon steel surface in 1M HCl was found to obey Langmuir isotherm. Polarization results showed that these inhibitors act as mixed-type inhibitors. The inhibition efficiency of the investigated bolaamphiphiles against the corrosion of carbon steel surface was studied by means of semi empirical molecular orbital AM1 calculations. The calculations showed a good correlation between the calculated quantum chemical parameters and the experimental data.

Changes in diad sequence distribution by preferential chain scission during the thermal hydrolysis of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate)

Specific hydrolysis properties of microbial copolyester P(3HB-co-6%-3HHx) was found during super-heated steam treatment in a temperature range of 130–190 °C. From changes in diad sequences on 13C nuclear magnetic resonance spectra, preferential and suppressive chain scission of HHx*HB and HB*HHx sequences, respectively, were determined. These specific reaction properties were considered to be contributed by higher steric propyl group in HHx unit than methyl group in HB unit, that is, promoting effect due to the concentration of HHx units in amorphous regions and suppressive effect due to steric hindrance and hydrophobicity of propyl group. Further, it was validated by the lowest-unoccupied molecular orbital analysis using a semi-empirical molecular orbital calculation method.

Thermal Analysis Investigation of Dapoxetine and Vardenafil Hydrochlorides using Molecular Orbital Calculations.

Thermal analysis techniques have been used to study the thermal behavior of dapoxetine and vardenafil hydrochlorides and confirmed using semi-empirical molecular orbital calculations. Thermogravimetric analysis, derivative thermogravimetry, differential thermal analysis and differential scanning calorimetry were used to determine the thermal behavior and purity of the drugs under investigation. Thermodynamic parameters such as activation energy, enthalpy, entropy and Gibbs free energy were calculated. Thermal behavior of DAP and VAR were confirmed using by semi-empirical molecular orbital calculations. The purity values were found to be 99.97% and 99.95% for dapoxetine and vardenafil hydrochlorides, respectively. The purity of dapoxetine and vardenafil hydrochlorides is similar to that found by reported methods according to DSC data. Thermal analysis justifies its application in quality control of pharmaceutical compounds due to its simplicity, sensitivity and low operational costs.

Crystal structure of 4-(4-chloro-phen-yl)-6-(morpholin-4-yl)pyridazin-3(2H)-one.

In the title compound, C14H14ClN3O2, the morpholine ring adopts a chair conformation, with the exocyclic N-C bond in an equatorial orientation. The 1,6-di-hydro-pyridazine ring is essentially planar, with a maximum deviation of 0.014 (1) Å, and forms a dihedral angle of 40.16 (7)° with the plane of the benzene ring. In the crystal, pairs of centrosymmetrically related mol-ecules are linked into dimers via N-H⋯O hydrogen bonds, forming R 2 (2)(8) ring motifs. The dimers are connected via C-H⋯O and C-H⋯Cl hydrogen bonds, forming a three-dimensional network. Aromatic π-π stacking inter-actions [centroid-centroid distance = 3.6665 (9) Å] are also observed. Semi-empirical mol-ecular orbital calculations were carried out using the AM1 method. The calculated dihedral angles between the pyridizine and benzene rings and between the pyridizine and morpholine (all atoms) rings are 34.49 and 76.96°, respectively·The corresponding values obtained from the X-ray structure determination are 40.16 (7) and 12.97 (9)°, respectively. The morpholine ring of the title compound in the calculated gas-phase seems to have a quite different orientation compared to that indicated by the X-ray structure determination.

Photochemical Property and Photodynamic Activity of Tetrakis(2-naphthyl) Porphyrin Phosphorus(V) Complex

Photochemical Property and Photodynamic Activity of Tetrakis(2-naphthyl) Porphyrin Phosphorus(V) Complex

Structure Characterization of Terazosin Drug using Mass Spectrometry and Thermal Analyses Techniques in Comparison with Semi-Empirical Molecular Orbital (MO) Calculations

Structure Characterization of Terazosin Drug using Mass Spectrometry and Thermal Analyses Techniques in Comparison with Semi-Empirical Molecular Orbital (MO) Calculations