Semiempirical Molecular Orbital Method Research Articles

Possible role of essential tyrosine on the protonation of isoalloxazine ring in the excited singlet state and the triplet state in photolyase from Escherichia coli. Molecular orbital study

Photolyases from Escherichia coli. (PLEC) function to repair UV-damaged DNA. Photolyases and cryptochromes (altogether 42 proteins) are found to contain at least one tyrosine (Tyr) residue near the isoalloxazine ring (Iso) of flavin adenine dinucleotide (FAD) within 1.2 nm, Tyr281 in PLEC. Iso in PLEC is surrounded by four Trp residues and one Tyr within 1.2 nm from Iso. Photoinduced charge transfer interactions (PCT) among these chromophores in the Iso-Tyr281-Trp277-Trp338-Trp382-Trp384 system were studied by means of a semi-empirical molecular orbital (MO) method. Structure of the system was extracted from crystal structure of PLEC. In the ground state the PCT interactions between any pairs were negligible. Upon photo-excitation almost one electron transferred from Trp382 to the excited Iso, to which an electron transport chain from Tyr residues at the protein - water interface to Iso is connected. Protonation at N1 or N5 of Iso from Tyr281 markedly stabilized the transition energy in the excited singlet state and triplet state, depending on the polarity of the medium, but not from a source other than Tyr281. In these states, nearly one electron migrates from Tyr281 to Trp382. Effects of the protonation from Tyr281 to the fully reduced Iso were also examined, where total charge of the system was −2. In the ground state the energy of the system was stabilized by the protonation, when the proton was bound to N5 of Iso, but not to N1. In the excited singlet state and triplet state of the fully reduced Iso, the transition energies of the system were also stabilized upon the protonation to N1 or N5 of Iso from Tyr281, but not from a source other than Tyr281. In the ground state almost two negative charges were located at Iso. In the excited singlet state one of two negative charges was mostly localized to Iso and another to Trp277 at the dielectric constant, 3, and to Trp384 at the dielectric constant, 10. In the triplet state without the protonation, one of two negative charges was localized to Iso and another to Trp384 at any dielectric constant. Upon protonation to N1 or N5 of Iso in the triplet state, one of the negative charges was localized to Iso and another to Tyr281 at any value of dielectric constant. Thus Tyr281 closely interacted with Iso in the excited singlet state and triplet state, and other Trp residues in the system through the proton transfer.

Relative energies of increasingly large [n]helicenes by means of high-level quantum chemical methods

We investigate the relative stability of increasingly large helicenes at the CCSD(T) level via the high-level G4(MP2) thermochemical protocol. The relative energies of [n]helicenes (n = 4–9) are obtained via the following reaction: [n]helicene + benzene → [n + 1]helicene + ethene. This reaction conserves the number of sp2-hybridized carbons, the number of aromatic rings, and the helical structures on the two sides of the reaction. We show that the reaction energy converges to an asymptotic value of ΔH298 = + 22.4 kJ/mol for increasingly large helicenes. For comparison, for [n]acenes, the same reaction converges to a much higher asymptotic reaction enthalpy of ΔH298 = + 56.8 kJ/mol. This difference between the two asymptotic reaction enthalpies sheds light on the relative thermodynamic stability of increasingly large helicenes. We proceed to use the G4(MP2) reaction energies to evaluate the performance of dispersion-corrected density functional theory (DFT) and semiempirical molecular orbital (SMO) methods for the relative energies of [n]helicenes. Nearly all DFT methods perform poorly with root-mean-square deviations (RMSDs) above 10 kJ/mol. The best-performing DFT method, BLYP-D4, attains an RMSD = 5.2 kJ/mol. Surprisingly, the advanced SMO methods, XTB and PM7, outperform the DFT methods and result in RMSDs of 3.0 and 3.1 kJ/mol, respectively.

Mechanism of photoinduced electron transfer from tryptophanes to the excited isoalloxazine in animal-like cryptochrome from Chlamydomonas reinhardtii: Molecular dynamics simulation and molecular orbital studies

Cryptochrome from a green alga Chlamydomonas reinhardtii binds flavin adenine dinucleotide (FAD) as a cofactor in a stacked form. The protein structures of the cryptochrome in solution were obtained by means of molecular dynamics simulation (MDS). Mechanisms of photoinduced electron transfer from aromatic chromophores including adenine to the excited isoalloxazine were quantitatively studied with the MDS structures and an electron transfer theory, using the reported experimental rate. The rates were fastest from Trp399, followed by Trp354, Trp332, Trp376, Trp401, Trp294, and adenine. The slower rate from Trp401 despite of the short distance was elucidated with much difference in a net electrostatic energy between the ion-pair and ionic groups in the protein, compared to that in Trp399. The static dielectric constant near isoalloxazine was quite high (7.95), which should be related to a higher number of water molecules near isoalloxazine, compared to those in other non-photoactive flavoproteins. Charge transfer (CT) interactions between isoalloxazine and Trp399 or other Trps (Trp354, Trp332, Trp376, Trp401) were studied by means of a semi-empirical molecular orbital (MO) method. The mean charges transferred from Trps to Iso* over 46 snapshots were −0.514 in Trp399, −0.042 in Trp354, and −0.216 in Trp332, −0.068 in Trp376, and −0.155 in Trp401, which were qualitatively in accordance with the results of photoinduced electron transfer rates. The effect of polarity of the medium on CT interaction was examined with the MO method. The amount of charge transferred from Trp399 to Iso* in the Iso* - Trp399 system decreased with static dielectric constant in the range of 2 to 30.

A non-self-consistent tight-binding electronic structure potential in a polarized double-ζ basis set for all spd-block elements up to Z = 86.

Existing semiempirical molecular orbital methods suffer from the usually minimal atomic-orbital (AO) basis set used to simplify the calculations. Here, a completely new and consistently parameterized tight-binding electronic structure Hamiltonian evaluated in a deeply contracted, properly polarized valence double-zeta basis set (vDZP) is described. The inner-shell electrons are accounted for by standard, large-core effective potentials and approximations to them. The primary target of this so-called density matrix tight-binding method is to reproduce the one-particle density matrix P of a molecular ωB97X-V range-separated hybrid density functional theory (DFT) calculation in exactly the same basis set. Additional properties considered are orbital energies, dipole polarizabilities and dipole moments, and dipole polarizability derivatives. The key features of the method are as follows: (a) it is non-self-consistent with an overall fixed number of only three required matrix diagonalizations; (b) only AO overlap integrals are needed to construct the effective Hamiltonian matrix; (c) new P-dependent terms emulating non-local exchange are included; and (d) only element-specific empirical parameters (about 50 per element) need to be determined. The method globally achieves a high accuracy for the target properties at a speedup compared to the ωB97X-V/vDZP reference of about 3-4 orders of magnitude. It performs robustly for difficult transition metal complexes, for highly charged or zwitterionic systems, and for chemically unusual bonding situations, indicating a generally robust approximation of the (self-consistent) Kohn-Sham potential. As an example application, the vibrational Raman spectrum of an entire protein with 327 atoms with respect to the DFT reference calculation is shown. This method may be used out-of-the-box to generate molecular/atomic features for machine learning applications or as the basis for accurate high-speed DFT methods.

Structure–antioxidant activity (oxygen radical absorbance capacity) relationships of phenolic compounds

Antioxidant capacity is the extent to which a compound can eliminate reactive oxygen species, and in vitro methods for its chemical evaluation have been proposed. Among these methods, the oxygen radical absorbance capacity (ORAC) assay comes close to the oxidation reaction in the living body because it generates radical species that mimic the lipid peroxyl radical involved in the peroxidation reaction of biological components and react in a phosphate buffer. In this study, PM7, a semi-empirical molecular orbital method, was used to calculate the thermodynamic properties (bond dissociation enthalpy, ionisation potential and proton affinity) associated with ORAC. We also applied the clusterwise linear regression analysis as a statistical method for grouping the antioxidants by structure. By analysing the data for antioxidants, the trend in the hydrophilic ORAC values was determined using the calculated structures and bond dissociation enthalpies of the groups classified according to the presence or absence of oxygen functional groups in the ortho position of phenol. Further studies of indicators other than bond dissociation enthalpy are needed to predict the ORAC of other antioxidants such as flavonoids and indoles.

Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability.

A major shortcoming of semiempirical (SE) molecular orbital methods is their severe underestimation of molecular polarizability compared with experimental and ab initio (AI) benchmark data. In a combined quantum mechanical and molecular mechanical (QM/MM) treatment of solution-phase reactions, solute described by SE methods therefore tends to generate inadequate electronic polarization response to solvent electric fields, which often leads to large errors in free energy profiles. To address this problem, here we present a hybrid framework that improves the response property of SE/MM methods through high-level molecular-polarizability fitting. Specifically, we place on QM atoms a set of corrective polarizabilities (referred to as chaperone polarizabilities), whose magnitudes are determined from machine learning (ML) to reproduce the condensed-phase AI molecular polarizability along the minimum free energy path. These chaperone polarizabilities are then used in a machinery similar to a polarizable force field calculation to compensate for the missing polarization energy in the conventional SE/MM simulations. Because QM atoms in this treatment host SE wave functions as well as classical polarizabilities, both polarized by MM electric fields, we name this method doubly polarized QM/MM (dp-QM/MM). We demonstrate the new method on the free energy simulations of the Menshutkin reaction in water. Using AM1/MM as a base method, we show that ML chaperones greatly reduce the error in the solute molecular polarizability from 6.78 to 0.03 Å3 with respect to the density functional theory benchmark. The chaperone correction leads to ∼10 kcal/mol of additional polarization energy in the product region, bringing the simulated free energy profiles to closer agreement with the experimental results. Furthermore, the solute-solvent radial distribution functions show that the chaperone polarizabilities modify the free energy profiles through enhanced solvation corrections when the system evolves from the charge-neutral reactant state to the charge-separated transition and product states. These results suggest that the dp-QM/MM method, enabled by ML chaperone polarizabilities, provides a very physical remedy for the underpolarization problem in SE/MM-based free energy simulations.

Ultrafast photoinduced electron transfer in o-aminobenzoate – d-Amino acid oxidase complex

Absorption spectrum of ortho-amino benzoate (oAB) – D-amino acid oxidase complex (ODC) displays a charge transfer (CT) band around 570 nm. The fluorescence decays of the second lowest electronic state of ODC were measured using a fluorescence up-conversion technique. The lifetimes were 100 fs and 130 fs at 500 nm and 514 nm fluorescence emission wavelengths, respectively. These ultrafast lifetimes are ascribed to the photoinduced electron transfer (PET) from the oAB to the excited isoalloxazine (Iso*) in the ODC. The PET mechanism in ODC was studied with Marcus-Kakitani-Mataga (MKM) theory. The protein structures were obtained by molecular dynamics simulation (MDS). Mean distances between Iso and oAB over 12,500 MDS snapshots were 0.60 in subunit A (Sub A) and 0.58 nm in Sub B. The calculated lifetimes at 514 nm-emission were 97 and 179 fs in Sub A and Sub B, while at 500 nm there were 97 and 101 fs, respectively. Solvent reorganization energy was quite different between Sub A and Sub B, which is main reason for difference in the calculated lifetimes. Electrostatic (ES) energies between the photoproducts of donor -acceptor, and net ES energies between the photoproducts and ionic groups in the protein were calculated with MDS structures. These ES energies were evaluated with charge densities of neutral radical of oAB produced after PET and anion radical of Iso obtained by semi-empirical molecular orbital (MO) method. The logarithmic PET rate did not display any clear dependence on Rc, despite the ultrafast scale of the PET rates. Most of the logarithmic PET rates in Sub A displayed in the inverted region of the standard free energy gap in the energy gap law. The transition dynamics among local excited states of Iso, CT state and the ion-pair state were discussed.

Interactions between isoalloxazine and o-aminobenzoate in o-aminobenzoate−d-amino acid oxidase complex. Molecular dynamics and molecular orbital studies

Molecular interactions between o-aminobenzoate (oAB) and isoallxazine (Iso) in o-aminobenzoate - d-amino acid oxidase complex (ODC) were studied by means of molecular dynamics simulation (MDS) and molecular orbital (MO) method. The distances between oAB and Iso were 0.60 in subunit A (Sub A) and 0.58 nm in Sub B. Four of six heteroatoms of Iso ring formed hydrogen bonding (HB) with nearby amino acids. The oxygen atom and nitrogen atom of oAB also formed HB with amino acids. The ODC displays a broad absorption band around 570 nm, which is considered to be charge transfer (CT) band between oAB and Iso in the complex. The ODC displayed fluorescence at around 520 nm, which is different from that of DAAO (emission peak at 535 nm) without oAB. The emission is from a local excited state (LE) without CT interaction. The CT interaction was studied by a semi-empirical molecular orbital (MO) method, using the structures of oAB and Iso obtained by MDS. The CT state did not form in the ground state of Iso, but formed in the excited state of Iso (Iso*), when the both cannot move appreciably from the MDS structures. The CT states formed both in the oAB – Iso and oAB – Iso* (excited state of Iso) systems when the both molecules can move so as to attain the minimum energy state. It is concluded that a part of oAB could move to form CT complex with Iso in the ground state, which displays the CT absorption band, but others could not move in the protein without CT interaction, which displays the fluorescence.

Inhomogeneities of charge distribution in porous graphitic carbon nitride g-CxNy nanosheets

Porous graphitic carbon nitrides g-CxNy (g-CN, g-C2N and g-C3N4) were studied computationally using semi-empirical molecular orbital method to obtain insights into charge distribution in them. It is found that the charge distribution is inhomogeneous but has good symmetry in the symmetrical structure. And sheet boundary has significant effect on the charge distribution. All N atoms have negative charge due to electrons enrichment. The absolute charge value of the edge atoms is significantly larger than that of the internal atoms in g-CN and g-C2N, which is opposite in g-C3N4. For the C atom, all C atoms show positive charge in g-CN. However, in g-C2N, the double-bond and triple-bond C atoms at the boundary have different gain and loss electrons. The internal triple-bond C atoms show the same positive charge value.

Fast Evaluation of Two-Center Integrals over Gaussian Charge Distributions and Gaussian Orbitals with General Interaction Kernels.

We present efficient algorithms for computing two-center integrals and integral derivatives, with general interaction kernels K(r12), over Gaussian charge distributions of general angular momenta l. While formulated in terms of traditional ab initio integration techniques, full derivations and required secondary information, as well as a reference implementation, are provided to make the content accessible to other fields. Concretely, the presented algorithms are based on an adaption of the McMurchie-Davidson Recurrence Relation (MDRR) combined with analytical properties of the solid harmonic transformation; this obviates all intermediate recurrences except the adapted MDRR itself, and allows it to be applied to fully contracted auxiliary kernel integrals. The technique is particularly well-suited for semiempirical molecular orbital methods, where it can serve as a more general and efficient replacement of Slater-Koster tables, and for first-principles quantum chemistry methods employing density fitting. But the formalism's high efficiency and ability of handling general interaction kernels K(r12) and multipolar Gaussian charge distributions may also be of interest for modeling electrostatic interactions and short-range exchange and charge penetration effects in classical force fields and model potentials. With the presented technique, a 4894 × 4894 univ-JKFIT Coulomb matrix JAB = (A|1/r12|B) (183 MiB) can be computed in 50 ms on a Q2'2018 notebook CPU, without any screening or approximations.

Erratum to "Toward a Quantum-Chemical Benchmark Set for Enzymatically Catalyzed Reactions: Important Steps and Insights".

We present steps toward the construction of a quantum-chemical benchmark set for enzymatically catalyzed reactions comprising different-quite sizable-model systems for five reactions. Our work is inspired by a study of semiempirical molecular-orbital theory methods against B3LYP-based structures and energies [ Kromann et al. PeerJ 2016 , 4 , e1994 ]. Taking the same model systems, we herein demonstrate first how adequate treatments of London dispersion and basis-set superposition error lead to structural differences compared to structures obtained at the popular B3LYP/6-31G(d,p) level. The changes observed by us have a significant influence on the final reaction barrier heights (BHs) and energies (REs), which are our main focus herein. We then proceed and carefully investigate different strategies to obtain either exact or estimated complete-basis-set BHs and REs with the help of the DLPNO-CCSD(T) approach, which offers an exciting path into exploring larger biochemically relevant structures at the coupled cluster level. On the basis of our analysis, we present three strategies for obtaining reliable values. While these recommendations constitute our main findings and are meant to be used as useful guidelines for others in the field, we demonstrate their applicability in a preliminary benchmark set comprising 16 BHs and 12 REs on which we assess 35 density functional theory (DFT) approximations. This preliminary benchmark study was used as an indicator for the validity of our approach toward generating such a benchmark set, based on the fact that we were able to reproduce major recommendations in the field of modern DFT, such as the reproduction of the famous Jacob's Ladder scheme, while also pointing out subtle differences to previous benchmark studies. We end our study by critically assessing the still popular choice to gauge the accuracy of low-level methods against B3LYP data, and we show the risks of such a strategy, adding to the ever-growing list of calls to move away from B3LYP as a standard black-box approach.

Quantitative Structure-Activity Relationship Studies Of Amino Acids Conjugated 2-Amnio-Arylthiazole As Antifungal

Thiazole derivatives as fungi-inhibitors belonging to 16 amino acids conjugated 2-amnio-arylthiazole was subjected computationally to quantitative structure-activity relationship (QSAR) analysis by optimization of chemical structures at minimum energy using molecular mechanics (MM+) theory and the semi-empirical molecular orbital (AM1) method. Correlation of their experimental inhibitory zones against three types of fungi, namely, Fusarium monoliforme, Aspergillus Flavus, and Aspergillus niger with obtained physiochemical parameters was carried out using multiple linear regression (MLR) analysis. As a result, there excellent out of 12 models were correlated with numerous descriptors having correlation coefficient rang (0.967-0.843). discriminant models were selected depending on their correlation coefficients (R2), Fisher ratios (F), and standard errors (S).These QSAR results and the probable pharmacophore features identified in this study offer important structural insight into designing novel amino acids conjugated 2-amnio-arylthiazole. Other 15 thiazole derivatives was proposed and it found that they are in good inhibitory zones.

Toward a Quantum-Chemical Benchmark Set for Enzymatically Catalyzed Reactions: Important Steps and Insights.

We present steps toward the construction of a quantum-chemical benchmark set for enzymatically catalyzed reactions comprising different-quite sizable-model systems for five reactions. Our work is inspired by a study of semiempirical molecular-orbital theory methods against B3LYP-based structures and energies [ Kromann et al. PeerJ 2016 , 4 , e1994 ]. Taking the same model systems, we herein demonstrate first how adequate treatments of London dispersion and basis-set superposition error lead to structural differences compared to structures obtained at the popular B3LYP/6-31G(d,p) level. The changes observed by us have a significant influence on the final reaction barrier heights (BHs) and energies (REs), which are our main focus herein. We then proceed and carefully investigate different strategies to obtain either exact or estimated complete-basis-set BHs and REs with the help of the DLPNO-CCSD(T) approach, which offers an exciting path into exploring larger biochemically relevant structures at the coupled cluster level. On the basis of our analysis, we present three strategies for obtaining reliable values. While these recommendations constitute our main findings and are meant to be used as useful guidelines for others in the field, we demonstrate their applicability in a preliminary benchmark set comprising 16 BHs and 12 REs on which we assess 35 density functional theory (DFT) approximations. This preliminary benchmark study was used as an indicator for the validity of our approach toward generating such a benchmark set, based on the fact that we were able to reproduce major recommendations in the field of modern DFT, such as the reproduction of the famous Jacob's Ladder scheme, while also pointing out subtle differences to previous benchmark studies. We end our study by critically assessing the still popular choice to gauge the accuracy of low-level methods against B3LYP data, and we show the risks of such a strategy, adding to the ever-growing list of calls to move away from B3LYP as a standard black-box approach.

A procedure combining molecular docking and semiempirical method PM7 for identification of selective Shp2 inhibitors

Shp2 and Shp1 make up a small family of protein tyrosine phosphatases. Finding selective inhibitors for Shp2 is useful because although its inhibition is advantageous for the treatment of some types of cancer, inhibition of Shp1 may have the opposite effect, since it acts as a suppressor of tumors. We combined molecular docking and semiempirical molecular orbital-based calculations to produce data that were effective for the identification of selective inhibitors for Shp2. After definition of the interaction modes of the inhibitors with Shp2 and Shp1 by molecular docking, the resulting interaction enthalpy values were calculated following refinement of the enzyme/inhibitor complexes' geometries with the PM7 semiempirical molecular orbital method. Despite the complexity of the thermodynamics involved in the enzyme/inhibitor interaction, the selectivity for Shp2 of a series of 76 inhibitors, divided in two groups, could be effectively correlated with the difference in their interaction enthalpy values with both enzymes. For the first group, composed by 52 Shp2-selective indoline inhibitors for which only Shp2 inhibition activity data are available, we demonstrated that the interaction enthalpy can be used as a criterion for identification of selective Shp2 inhibitors, as it is significantly more favorable for Shp2 than Shp1 at a 99% confidence level. For the second group, composed by 24 oxindole derivatives with available Shp2 and Shp1 inhibition activity data, a satisfactory correlation (R = 0.70) could be obtained between the selectivity, based on the IC50 data, and the relative percentage difference of the calculated interaction enthalpies with the two enzymes.

Self-assembly of Pt(II) based nanoscalar ionic hexagons and their anticancer potencies

Two nanoscalar and supramolecular metallacycles were self-assembled by employing a predesigned pyrazine based molecular “acceptor” clip with two different ditopic pyridyl “donor” tectons. The platina macrocycles were characterized by multinuclear NMR spectroscopy, mass spectrometry (ESI-MS), and elemental analyses. Molecular modelling using PM6 semiempirical molecular orbital method suggested these metallacycles having nanoscalar dimensions with hexagonal cavities. Additionally, interactions of these macrocycles were studied with three carcinoma cell lines. Results suggest that anticancer properties of supramolecular metallacycles were higher than their organometallic precursor. The nanoscalar supramolecular metallacycles were capable of efficiently reducing cell proliferation of different cancer lines (A549, HepG2, HeLa). The anticancer activity of the larger of the two macrocycles was higher even at lower concentrations and IC50 values are comparable with that of cisplatin. TUNEL assay suggested that macrocycles induces apoptotic cell death. These results suggest that the nanoscalar supramolecular metallacycles could find potential biomedical applications as therapeutic agents.

Photoresponsive Chirality-Tunable Supramolecular Metallacycles.

Chirality-tunable supramolecular metallacycles containing two light-responsive dithienylethene units and two chiral 1,1'-bi-2-naphthol (BINOL) units have been successfully constructed via coordination-driven self-assembly. These new metallacycles are well-characterized with 1D multinuclear NMR (1 H and 31 P NMR), 2D 1 H-1 H COSY and DOSY, ESI-TOF-MS, and PM6 semiempirical molecular orbital methods. Interestingly, upon irradiation with ultraviolet and visible light, the conformation of these metallacycles can undergo reversible transformation between ring-open and ring-closed forms accompanied with the obvious change of CD signals. Further investigation reveals that the photoisomerization of the dithienylethene moieties induces the change in the dihedral angle of the binaphthyl rings, thus leading to the chiral modulation of supramolecular metallacycles. Thus, this study provides very few examples of the light-induced chirality-tunable metallosupramolecular assemblies, which may find potential application in mimicking the function of natural systems in the future.

Synthesis, spectroscopic, thermal, fluorescence properties and molecular modeling of novel Pt(II) complex with schiff base containing NS donor atoms

New transition metal complex of Pt(II) of the Schiff base ligand with (E)-2-((1-(thiophen-2-yl)ethylidene)amino)phenol HL have been synthesized using the ultrasonic irradiation and characterized by physicochemical and spectroscopic methods. The IR spectrum of Pt(II) complex showed that the coordination in metal ions via the imine N and S atoms. Magnetic and UV–Vis spectra showed that the geometrical structure of Pt(II) complex is square planar. The molar conductance data revealed that Pt(II) complex is non-electrolyte. The thermodynamic parameters for thermal decomposition of Pt(II) complex was calculated from analysis of the TG-DTG curves using Hörowitz–Metzger method. The fluorescence of the ligand HL and its Pt(II) complex in different solvents and pH conditions have also been studied in detail. The quenching of the fluorescence intensity of the ligand can be noted obviously, in the presence of Pt(II) ion. Geometry optimization of the compounds was calculated by semiempirical molecular orbital theory PM3 method using Hyperchem 7.52 program.

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.

Self-Assembly of [2+2] Platina Macrocycles Using a Flexible Organometallic Clip

Synthesis of a new pyrazine-based “flexible” and ditopic platinum(II) organometallic clip (3) is being reported. Flexibility is incorporated by ether functional groups that bridge the rigid core (pyrazine) and periphery (PtIIcenters). Its self-assembly with various dicarboxylates in a 1:1 stoichiometric ratio yields [2 + 2] dimeric neutral metallacycles (4–6). Formation of macrocycles was supported by multinuclear NMR, ESI-MS and elemental analyses. Crystal structure of one of the macrocycles confirmed its rectangular shape. The geometry of each supramolecular structure was optimized by using PM6 semiempirical molecular orbital method.

Quantitative structure–property relationship modelling for photoreduction‐fast azo dyes on a nylon substrate: a methodology for thermochemical analysis of the photocleavage of azo dyes using theRM1 semi‐empirical molecular orbital method

The rates of fading of 18 reactive azo dyes on polyamide fabrics and films upon exposure to a carbon arc in air have been determined from the initial slopes. The rates have been thermochemically analysed by calculating the heats of formation of the reactants, intermediates, and products by chemical equations describing (1) the second-order disproportionation (redox reaction) between the photoinduced hydrazinyl radicals and (2) the intramolecular H-transfer (self-decomposition) of the radicals, using the RM1 semi-empirical molecular orbital method. The rates of azo cleavage (or reductive fading) were studied to correlate the molecular structures with three molecular descriptors: (a) the heats of reaction for two reaction pathways, (b) the thermodynamic stability of the photoinduced hydrazinyl radicals, and (c) the quantum yields of generation. The possibility of structure optimisation of the examined azo dyes is discussed from the perspectives of (a) and (b). The light fastness of several previously reported substituted phenylazophenol (model) dyes on a polyamide substrate has been analysed by the same procedure. Two of the latter dyes exhibit typical photoreduction-fast properties, which determine the threshold ΔrH°(gas) value of the N11-hydrazinyl dye radical for (1), indicating that the chemical structures of azo dyes may, in principle, be modified to include reduction-fast azo groups. The current state of reactive azo dyes is considerably below the level required to achieve reduction-fast dye. The chemical structures of current reactive azo dyes appear not to have been optimised on the basis of the molecular descriptors (a) and (b), and only insufficiently on the basis of (c).