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.     

Amidines. Part 37. Comparison of substituent effects in cis and trans formamidines by ab initio 3-21G optimization of molecular structures of fluoro derivatives and their protonation products

The influence of the configuration at the CN double bond and of substitution at each site of an amidino group on the effect of substituents at the other two sites has been studied by ab initio 3-21G optimization for eight derivatives of formamidine (all in the cis configuration at the CN double bond) with up to three fluorine substituents in different combinations, and the corresponding formamidinium cations (protonated at the imino nitrogen). The results were compared with those obtained previously for an identical set of compounds but in the trans configuration. The differences between the influence of substitution at various sites in cis and trans isomers of amidines on basicity, tautomerization, and the geometry of the molecules are discussed.     

Structure/Enthalpy of Formation Relationships for Hydrocarbons Containing Benzene Rings

Simple protocols to convert molecular mechanics (MMX/PCMODEL), semiempirical PM3, and HF ab initio energies to accurate heats of formation for hydrocarbons with benzene rings are described. The data set consists of every hydrocarbon benzene derivative with an experimentally determined ΔH_f^o (g), and the ΔH_f^o (g)'s cover a range of -140 to +410 kJ/mol. The molecular structures are comprised of numerous structural types. Hierarchical sets of molecular structure parameters are defined to describe these molecules. The independent variables include atom types (level 1), group and ring terms (level 2), nonbonded atom interactions (level 3), and the calculated MMX, PM3 or ab initio HF energies, which contribute a final level 4 parameter for rectification of the ΔH_f^o (g) data. The additivity, level 1-3 parameters give an excellent correlation of the experimental ΔH_f^o (g)'s, average error = 3.4 kJ, and maximum error = 12.1 kJ. However, the correlations are further enhanced by addition of any level 4 parameter, with maximum improvement coming at the 6-31G*//STO-3G HF level of calculation.     

Sm‐Doped LaSi3N5: Synthesis,Computed Electronic Structure,and Band Gaps

LaSi₃N₅‐based phosphor doped with Sm was prepared by the nitridation of LaSi‐Si‐Si₃N₄‐Sm₂O₃ powder mixture. The emission spectrum shows two main bands with maxima at 595 nm in the orange region and at ~650 nm in the red region. The excitation spectrum of Sm‐doped LaSi₃N₅ shows a maxima at 585, 570, and 405 nm. First‐principles density‐functional theory calculations were performed using Vienna ab initio simulation package to enhance the understanding of the electronic structure of the stoichiometric LaSi₃N₅ and Sm‐doped LaSi₃N₅. The electronic structure and band gaps were calculated in 2 × 1 × 2 supercell with 144 atoms using the more precise screened Coulomb hybrid functional HSE06. Both La³⁺/Sm³⁺ and La³⁺/Sm²⁺ substitutions were calculated. The calculated band gap of Sm(III)‐doped LaSi₃N₅ is 2.01 eV, in reasonable agreement with the experimental value of 2.12 eV, but corresponds to the unrealistic transition between the N, Si p states, and unoccupied Sm 4f states. The band gap of 1.43 eV calculated for Sm(II)‐doped LaSi₃N₅ is smaller than the available experimental value, but corresponds to the correct transition between nonbonding Sm 4f states and empty La 5d states. Optical properties are found to be governed by f electrons of the Sm(II) dopant.     

Protection of copper corrosion by carbazole and N-vinylcarbazole self-assembled films in NaCl solution

Self-assembled films of carbazole (CZ) and N-vinylcarbazole (NVC) were prepared on copper surfaces. The corrosion protection abilities of the films were evaluated in an air-saturated 0.5 mol dm^–3 NaCl solution using electrochemical impedance spectroscopy (EIS), polarization and cyclic voltammetry. The results indicate that CZ and NVC form dense protective films on copper. Fourier transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS) were used to characterize the film. It was found that the NVC molecules are tilted at an angle to the copper surface. The theoretical ab initio calculations support the experimental results.     

Some crystallographic considerations on the novel orthorhombic ZrO2 stabilized with Ta doping

Some crystallographic considerations on the novel orthorhombic ZrO₂ (o-ZrO₂) stabilized at ambient conditions by Ta substitutional doping are presented. Specifically, how the Ta-doped o-ZrO₂ was observed for the first time by conventional X-ray diffractometry (XRD) is reported, after which the ab initio and non-ab initio procedures used to resolve its crystal structure are detailed. The crystal structure is then explicitly reported (i.e., space group and cell parameters, as well as atomic positions of the asymmetric unit). It is also shown that this novel Ta-doped o-ZrO₂ has a crystal structure similar, but not identical, to the high-pressure o-ZrO₂. Additionally, given that the crystal structure of the Ta-doped o-ZrO₂ is identified as being a symmetry-breaking distortion of the typical tetragonal ZrO₂ (t-ZrO₂) stabilized with the commonest dopants, a complete analysis is also made of the structural distortions relating both the Ta-doped o-ZrO₂ and the high-pressure o-ZrO₂ to the t-ZrO₂. Finally, a justification for the apparent greater immunity of the Ta-doped o-ZrO₂ to aging is provided.     

Quantum Mechanics Calculations on PASH: Attempts to Correlate Thermodynamic Properties to Chromatographic Behaviour and/or Relative Abundance or Presence in Petroleum Samples

Polycyclic Aromatic Compounds containing one sulfur atom i.e. Polycyclic Aromatic Sulfur Heterocycles (PASH) form a very diversified subclass of compounds and the number of compounds increases with alkylation. Nonsubstituted as well as mono- and dimethylated PASH are found in crude oils. Identification and analysis of these compounds is a difficult challenge that can be facilitated by theoretical calculations up-side.

The purpose of this study was to use quantum mechanics calculations to generate properties such as molecular shape or thermodynamic stability that could be related to chromatographic indices. Tricyclic (dibenzothiophene, naphthothiophenes) and tetracyclic (phenanthrothiophenes, anthrathiophenes and benzonaphthothiophenes) parent molecules and mono- and di-methylated analogues have been studied. A special attention has been paid to compounds with a crowded bay region that results in a twisted molecular geometry.

The results from semi-empirical methods (AMPAC 6.51-MNDO, AM1) and ab initio Hartree-Fock methods (RHF/6-31G) have been compared to X-ray determined geometries when available and attempts have been made to correlate enthalpies of formation and chromatographic behaviour and/or relative abundance or presence in petroleum samples.     

Organometallic molecular modelling – the computational chemistry of metallocenes: a review

The application of ab initio, density functional theory and molecular mechanical methods to the modelling of metallocenes, particularly ferrocene, is reviewed. Approaches to the representation of the metal‐ring π‐bonding in molecular mechanics and the quality of computed results from ab initio and density functional theory serve to illustrate the utility of modelling studies in organometallic chemistry. © 1999 Society of Chemical Industry     

Crystal and Molecular Structures of Triasterane Derivatives

The geometries of trimethylenetriasterane 1 , triasteranetrione 2 , and trispirocyclopropanetriasterane 3 have been determined by X-ray crystal structure analyses. All three compounds have D_3h symmetry and contain two skeletal cyclopropane rings which are symmetrically cis-trisubstituted. The vinyl and the carbonyl substituents in 1 and 2 apparently exert about the same acceptor effect on the central cyclopropane rings and cause a small but significant lengthening of the endocyclic C-C bonds (1.517 Å in 1 and in 2 ) in comparison to an average normal bond length in cyclopropanes of 1.508 Å, while in 3 no effect of the spirocyclopropane groups on the bond length in the central rings (1.506 Å) is evident The vinylcyclopropane and bicyclopropyl subunits in 1 and 3 respectively are ideally antiperiplanar and almost undistorted with respect to the parent hydrocarbons as evidenced by the bond angles and ¹³C-¹³C coupling constants (¹J_CC).     

Base-induced reactions of isothiazolium salts with active 5-methyl or 5-methylene groups

It is shown that N-phenyl-substituted isothiazolium salts 2/3a–e with active 5-methyl or 5-methylene groups can easily be obtained by reaction of β-thiocyanatovinylaldehydes 1 and substituted anilines. Based on a wide variety of isothiazolium salts accessible in that way, a study of their various reaction products, e.g. 1,6-diphenyl-substituted thiadiazapentalenes 4a–d , 5a–j and special spiro compounds 6 , and the influence of donor and acceptor substituents becomes possible. The structure of the basic skeleton of the thiadiazapentalenes was confirmed by X-ray analysis and ab initio MO calculations. Some mechanistic aspects are supported by the MO results.     

Structural optimization and vibrational analysis of an antidiabetic drug: tolbutamide

The purpose of this study is to investigate the vibrational spectrum of tolbutamide by ab initio techniques in combination with experimental studies. The Fourier transform infrared spectra (400–4000?cm^?1) and Laser-Raman spectra (100–4000?cm^?1) of tolbutamide have been obtained in the solid phase. Assignments have been found by the combination of the vibrational frequencies and the contribution of the potential energy distributions. Assignments have been compared with the theoretical and experimental results of similar structures as reported in the literature. Structural parameters such as bond lengths and angles, frequencies and infrared intensities and Raman activities of tolbutamide have been computed by density functional theory and Hartree–Fock methods using 6–311G++(d,p) and 6–31G(d) basis sets. The computed vibrational frequencies and optimized structural parameters are consistent with the corresponding experimental results. In addition, the images of tolbutamide frontier molecular orbitals (highest occupied and lowest unoccupied) and its energy gaps have been interpreted with the assistance of quantum chemical calculations.     

Crystallographic study of two monoazo disperse dyes with a D–π–A system

Two azo disperse dyes, 2,6‐dichoro‐4‐nitro‐4′,4′‐N‐cyanoethyl‐N‐benzyl‐azobenzene ( D1 ) and 3‐(3‐methyl‐4‐N‐ethyl‐N‐benzyl‐phenyldiazenyl)‐5‐nitro‐2,1‐benzisothiazole ( D2 ), were synthesised and characterised. The crystal morphologies and single crystal structures were measured. The various packing and supramolecular interactions were described. D1 formed stellate crystals. The two benzene rings bilateral to the azo unit were not coplanar. Their dihedral angle was 75.72°. They were linked by the azo unit and were twisted. The coupling‐component N‐substituted benzyl and benzene rings were not coplanar. The chemical structure was not the typical azo structure. A dimeric packing mode was formed between adjacent molecules in a head‐to‐head and tail‐to‐tail manner. One molecule was inserted between two dimeric molecules in a head‐to‐tail manner. D2 formed globe crystals. The isothiazole and benzene rings of the azo unit were coplanar, with the typical π–π conjugated structure. The benzene rings of the azo unit and the coupling‐component N‐substituted benzyl were vertical. Their torsion angle was 179.9°.     

Local Fracture Toughness of Si3N4 Ceramics Measured using Single‐Edge Notched Microcantilever Beam Specimens

Local fracture toughness gives us useful and important information to understand and improve mechanical properties of bulk ceramics. In this study, the local fracture toughness of silicon nitride (Si₃N₄) ceramics was directly measured using single‐edge notched microcantilever beam specimens prepared by the focused ion beam technique. The measured fracture toughness of grain boundary of the Si₃N₄ ceramics is higher than the fracture toughness of SiAlON glass, which exists in the grain boundaries of Si₃N₄ ceramics. It is also shown that the fracture toughness of grain boundary depends on the rare earth oxide added as a sintering aid, which is expected in terms of the difference in the grain‐boundary structure. The fracture toughness of a single β‐Si₃N₄ grains is higher than the grain‐boundary fracture toughness. It was also higher than the value estimated from ab initio calculations and surface energy, which means that any dissipative energy should be included in the fracture toughness of a grain in spite of the brittle fracture in Si₃N₄. The fracture toughness of polycrystals of Si₃N₄ ceramics measured using single‐edge notched microcantilever beam specimens is intermediate between those of grains and grain boundaries, and it agrees with the estimated initial value of the Rcurve, K_I0, in Si₃N₄ ceramics.     

On the Reaction of Nitrilium Salts with Tropones

Tropone 2a and tropolone methyl ether 2b react with nitrilium salts ( 1a-j ) to give the bicyclic oxazolium salts 3, 5 . Cleavage of the N–C3a bond of 3, 5 followed by y Chapman rearrangement afford the stable N-acyliminium salts 4, 8 . A crystal structure analysis for 3a is reported. AM1 calculations are in accord with the proposed mechanisms for the formation of 3, 5 and 4, 8 .     

Amines vs. N‐Oxides as Organocatalysts for Acylation,Sulfonylation and Silylation of Alcohols: 1‐Methylimidazole N‐Oxide as an Efficient Catalyst for Silylation of Tertiary Alcohols

A comparison of the relative catalytic efficiencies of Lewis‐basic amines vs. N‐oxides for the acylation, sulfonylation and silylation of primary, secondary and tertiary alcohols is reported. Whilst the amines are generally superior to the N‐oxides for acylation, the N‐oxides are superior for sulfonylation and silylation. In particular, 1‐methylimidazole N‐oxide (NMI‐O) is found to be a highly efficient catalyst for sulfonylation and silylation reactions. To the best of our knowledge, NMI‐O is the first amine or N‐oxide Lewis basic organocatalyst capable of promoting the efficient silylation of tert‐alcohols in high yield with low catalyst loading under mild reaction conditions.

     

The Structure and Dynamics of BmR1 Protein from Brugia malayi: In Silico Approaches

Brugia malayi is a filarial nematode, which causes lymphatic filariasis in humans. In 1995, the disease has been identified by the World Health Organization (WHO) as one of the second leading causes of permanent and long-term disability and thus it is targeted for elimination by year 2020. Therefore, accurate filariasis diagnosis is important for management and elimination programs. A recombinant antigen (BmR1) from the Bm17DIII gene product was used for antibody-based filariasis diagnosis in “Brugia Rapid”. However, the structure and dynamics of BmR1 protein is yet to be elucidated. Here we study the three dimensional structure and dynamics of BmR1 protein using comparative modeling, threading and ab initio protein structure prediction. The best predicted structure obtained via an ab initio method (Rosetta) was further refined and minimized. A total of 5 ns molecular dynamics simulation were performed to investigate the packing of the protein. Here we also identified three epitopes as potential antibody binding sites from the molecular dynamics average structure. The structure and epitopes obtained from this study can be used to design a binder specific against BmR1, thus aiding future development of antigen-based filariasis diagnostics to complement the current diagnostics.     

Effects and Mechanism of Combinational Chemical Agents on Solution‐Derived K0.5Na0.5NbO3 Piezoelectric Thin Films

Sodium potassium niobate (KNN) piezoelectric ceramic thin films were prepared by a chemical solution deposition method, in which the introduction of appropriately combinational organic stabilizing agents, including monoethanolamine (MEA), diethanolamine (DEA), and ethylenediaminetetraacetic acid (EDTA), dramatically suppressed the volatile loss of the alkali ions, improved the crystallinity, and promoted crystal orientation of the perovskite phase in the resulting KNN thin films. Theoretical analyses including ab initio calculation based on molecular model indicated that stronger binding structure could form comprising the alkali ions and the combinational EDTA‐(DEA‐MEA) chemical agents than the cases of using individual binding agents separately. Outstandingly large effective piezoelectric strain coefficient d₃₃ under the substrate clamping condition was achieved. The theoretical and experimental results provide the insight on the underlying interaction mechanism between the multiple stabilizing chemical agents and metal ions, and the guidance for establishing the methodology for producing high quality oxide thin films from chemical solutions with dedicatedly designed combinational stabilizing agents.     

Material and Elastic Properties of Al‐Tobermorite in Ancient Roman Seawater Concrete

The material characteristics and elastic properties of aluminum‐substituted 11 Å tobermorite in the relict lime clasts of 2000‐year‐old Roman seawater harbor concrete are described with TG‐DSC and ²⁹Si MAS NMR studies, along with nanoscale tomography, X‐ray microdiffraction, and high‐pressure X‐ray diffraction synchrotron radiation applications. The crystals have aluminum substitution for silicon in tetrahedral bridging and branching sites and 11.49(3) Å interlayer (002) spacing. With prolonged heating to 350°C, the crystals exhibit normal behavior. The experimentally measured isothermal bulk modulus at zero pressure, K₀, 55 ±5 GPa, is less than ab initio and molecular dynamics models for ideal tobermorite with a double‐silicate chain structure. Even so, K₀, is substantially higher than calcium‐aluminum‐silicate‐hydrate binder (C–A–S–H) in slag concrete. Based on nanoscale tomographic study, the crystal clusters form a well connected solid, despite having about 52% porosity. In the pumiceous cementitious matrix, Al‐tobermorite with 11.27 Å interlayer spacing is locally associated with phillipsite, similar to geologic occurrences in basaltic tephra. The ancient concretes provide a sustainable prototype for producing Al‐tobermorite in high‐performance concretes with natural volcanic pozzolans.     

A theoretical investigation on the properties of the new poly(N‐vinylcarbazole)‐3‐methylthiophene (PVK‐3MeT) synthesized graft copolymer

In this article, we present quantum chemical calculations, based on density functional theory (DFT), performed to investigate the geometries and the opto‐electronic properties of a new synthesized graft copolymer based on poly(N‐vinylcarbazole) (PVK) and poly(3‐methylthiophene) (PMeT) named PVK‐3MeT. First, we have theoretically computed and compared the structural, optical, and vibrational parameters of both neutral and doped states. In addition, the excited state was theoretically obtained by the ab initio RCIS/STO‐3G method. To assign the absorption and emission peaks observed experimentally, we computed the energies of the lowest singlet excited state with the time‐dependent density functional theory (TD‐DFT) method. Electronic parameters such as the HOMO‐LUMO band gap, the ionization potential (IP), and electron affinity (EA) are extracted. Calculations show that the PVK‐3MeT copolymer is nonplanar in its ground neutral state. Meanwhile, upon doping or photoexcitation, an enhancement of the planarity is observed, resulting on a decrease of the inter‐ring torsion angle between 3‐methylthiophene units. Such modifications in the geometric parameters induce a dramatic change on the HOMO and LUMO orbitals in the doped or excited states. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011.