Correlation of Quantitative Structure and Inhibition Phytotoxicity for Aromatic Compounds Using Ab Initio Method

1 INTRODUCTION Quantitative structure-activity relationship (QSAR) is one of the necessary methods to evaluate the ha- zards of organic chemicals. QSAR equation could be employed to forecast the biological activity of un- known compounds, which is significant for initial screening and evaluation of toxic compounds[1]. Aro- matic compounds are toxic organic compounds with relatively low water solubility, and their structure- activity relationship has been investigated with AM1 method[2]…     

Tuning the π-Accepting Properties of Mesoionic Carbenes: A Combined Computational and Experimental Study

Mesoionic imidazolylidenes are recognized as excellent electron-donating ligands in organometallic and main group chemistry. However, these carbene ligands typically show poor π-accepting properties. A computational analysis of 71 mesoionic imidazolylidenes that bear different aryl or heteroaryl substituents in C2 position was performed. The study has revealed that a diphenyltriazinyl (Dpt) substituent renders the corresponding carbene particularly π-acidic. The computational results could be corroborated experimentally. A mesoionic imidazolylidene with a Dpt substituent was found to be a better σ-donor and a better π-acceptor compared to an Arduengo-type N-heterocyclic carbene. To demonstrate the utility of the new carbene, the ligand was used to stabilize a low-valent paramagnetic tin compound.     

One-Dimensional Intercalation Compound 2 HgS⋅SnBr2: Ab Initio Electronic Structure Calculations and Molecular Dynamics Simulations

The one-dimensional intercalation compound 2 HgS⋅SnBr₂ (figure; white: Hg, light gray: S, dark grey: Sn, and black: Br) is an example of the ability of weak host–guest interactions to induce structural modifications in the HgS host. The stability and dynamic behavior of the intercalation compound and its precursors HgS and SnBr₂ have been analyzed by means of DFT/plane wave calculations. The molecular dynamics simulations facilitate the understanding of the structural rearrangements during the intercalation process.     

Ab Initio Chemical Kinetics for the Thermal Decomposition of SiH4 + Ion and Related Reverse Ion–Molecule Reactions of Interest to PECVD of a-Si:H Films

Plasma Chemistry and Plasma Processing - The thermal unimolecular decomposition of SiH4 + ion and its related reverse reactions, SiH3 + + H and SiH2 + + H2, have...     

Palladium-Catalyzed C8-Arylation of Naphthalenes through C−H Activation: A Combined Experimental and Computational Study

Herein, a direct C8-arylation reaction of 1-amidonaphthalenes is described. By using diaryliodonium salts as arylating agents, the palladium-catalyzed C−H activation reaction showed perfect C8 regioselectivity and a wide functional group tolerance. In most cases, the desired polyaromatic compounds were isolated in good to excellent yields. To explain the observed regioselectivity, DFT calculations were performed and highlighted the crucial role of the amide directing group. Finally, the utility of this method is showcased by the synthesis of benzanthrone derivatives.     

Lewis Acid Assisted Brønsted Acid Catalysed Decarbonylation of Isocyanates: A Combined DFT and Experimental Study

An efficient and mild reaction protocol for the decarbonylation of isocyanates has been developed using catalytic amounts of Lewis acidic boranes. The electronic nature (electron withdrawing, electron neutral, and electron donating) and the position of the substituents (ortho/meta/para) bound to isocyanate controls the chain length and composition of the products formed in the reaction. Detailed DFT studies were undertaken to account for the formation of the mono/di-carboxamidation products and benzoxazolone compounds.     

Stereospecificity of Diels–Alder Reactions Validated Using Ab Initio Calculations: Synthesis of Novel Coumarin and Phenanthridine Derivatives

A new series of coumarin derivatives (2–5) was synthesized by reaction of phenylsulfonylacetonitrile (1) with 2-hydroxy-1-naphthaldehyde and/or salicyaldehyde. Compounds 3 and 5 were converted to the corresponding phenanthridine analogs 6 and 7, respectively. Compound 9a was treated with different dienophiles to furnish the endo adducts of compounds (11a–d) rather than the exo adducts. Ab initio calculations at the Hartree-Fock (HF) level using the basis set 6-31 G (d,p) was used to study and validate the stereospecificity of compounds 11a–d and showed clearly that the endo adducts were thermodynamically favorable. PM3 parameters also showed that the endo adducts are thermodynamically and kinetically favorable. Tetrahydrobenzochromenone (11) was synthesized and allowed to react with different aromatic diazonium salts to give the corresponding 4-arylazo derivatives (13), which were converted to the corresponding diazaindenophenanthrene derivatives (14) by reaction with o-diamines.     

Determination of the Absolute Configuration of Super-Carbon-Chain Compounds by a Combined Chemical,Spectroscopic, and Computational Approach: Gibbosols A and B

Marine dinoflagellates produce remarkable organic molecules, particularly those with polyoxygenated long-carbon-chain backbones, namely super-carbon-chain compounds (SCCCs), characterized by the presence of numerous stereogenic carbon centers on acyclic polyol carbon chains. Even today, it is a challenge to determine the absolute configurations of these compounds. In this work, the planar structures and absolute configurations of two highly flexible SCCCs, featuring either a C₆₉- or C₇₁-linear carbon backbone, gibbosols A and B, respectively, each containing thirty-seven stereogenic carbon centers, were unambiguously established by a combined chemical, spectroscopic, and computational approach. The discovery of gibbosols A and B with two hydrophilic acyclic polyol chains represents an unprecedented class of SCCCs. A reasonable convergent strategy for the biosynthesis of these SCCCs was proposed.     

Ab Initio Studies on the Structure and Binding Interaction of M~ CO_2(M=Sc,Ti…Zn)

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Ab Initio Chemical Kinetics for the Thermal Decomposition of SiH2+ and SiH3+ Ions and Related Reverse Ion–Molecule Reactions of Interest to PECVD of α-Si:H Films

Plasma Chemistry and Plasma Processing - The mechanisms and kinetics for the thermal decomposition of SiH2+ and SiH3+ ions, and related reverse reactions involving their ion fragments have been...     

Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex

The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable ¹⁹F chemical-shift predictions to deduce ligand-binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the ¹⁹F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of ¹⁹F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.     

Thickness, Morphology and Structure of Sol-Gel Hybrid Films: II—The Role of the Solvent

The influence of the solvent on the thickness, morphology and structure of silica-polytetrahydrofuran hybrid films, prepared by spin coating, has been analysed. The inorganic precursor, tetraethylorthosilicate, was hydrolysed under acid catalysis, the hydrolysis molar ratio being 4. Polymers of average molecular weight (M _n) 650 and 2900 were incorporated in the initial colloidal solutions, in a low concentration (organic/inorganic molar ratio 0.01). Two solvents were compared: ethanol, protic, and tetrahydrofuran, aprotic and a little less polar. The thickness and surface texture parameters of the films were determined by profilometry, their morphology characterized by SEM and their structure studied by FTIR. It is shown that the solvent has no effect on the molecular structure of the films, but strongly influences the surface texture and the morphology of both pure silica and hybrid films. The solutions prepared in tetrahydrofuran present shorter gelation times (t _G) and allow the deposition of good quality films almost up to the gelation point (to a reduced time, t/t _G, of 0.9). The films are thinner than those prepared from corresponding ethanolic solutions at the same reduced ageing times. For pure silica films, tetrahydrofuran is the best choice, since it reduces the fractured region on the edge of the substrate. For hybrid films, this effect is achieved by the polymer and tetrahydrofuran is responsible for a higher arithmetical mean roughness. Therefore, ethanol becomes the preferable solvent.     

Hydration of DNA Bases and Compounds Containing Small Rings—A Model for Interactions of the Ricin Toxin A-Chain. A Theoretical Ab Initio Study

Ab initio quantum chemical calculations were performed for four neutral gas phase adenine and four pterin tautomers along with guanine and formycin bases. The water complexes of the lowest energy tautomers of these bases have been studied to mimic their interaction with the ricin toxin A chain (RTA). The water molecules create a full first hydration shell around the bases. Full geometry optimizations without any constraints on the planarity of these hydrated complexes were carried out at the HF/6-31G(d,p) level. Single point calculations were also performed at the correlated MP2/6-31G(d,p)//HF/6-31G(d,p) level of theory. Hydration energies were corrected for the basis set superposition error. Hydration energies of adenine and formycin are predicted to be lower (in magnitude) than those for the pterin and guanine. Due to these properties, two pterin tautomers can be considered as potentially useful inhibitors of RTA.     

Structure, Electronic Properties and Interaction of MRn n + (n?=?1–3, M?=?Cu, Ag and Au) Clusters: Ab Initio Calculations

The structures and stabilities of MRn _n ⁺ (n?=?1–3, M?=?Cu, Ag and Au) series at the CCSD(T) theoretical level are performed. The n?=?2 systems are more stable than its neighbours. The role of the interaction is investigated using the natural bond orbital analysis, Laplacian, electron localization function and reduced density gradient analysis. The results show the intermediate character in the M–Rn interaction.     

Onset of Amorphous Structure in CaCO3: Geometric and Electronic Structures of (CaCO3) n (n?=?2–7) Clusters by Ab Initio Calculations

Electronic structures, vibrational analyses, stabilization energies and amorphicity were analyzed for the most stable configurations of the neutral gas phase clusters of calcium carbonate (CaCO₃) _n (n?=?2?C7). Minimum-energy structures were generated through simulated annealing using a mix of molecular dynamics/semiempirical optimization and then full optimization at the ab initio level (RHF/6-31G*). HF-level results are calibrated versus MP2/6-31G* results. Though many clusters are symmetric, the structural arrangements are not crystalline and resemble neither calcite nor aragonite. In general, greater symmetry means a lower stabilization energy. The BSSE- and zero point energy-corrected stabilization energies appear to plateau at about ?113?kcal/mol when n?=?7. Amorphous clusters start appearing when n?=?4 and the lowest-energy minima for n????5 are of C₁ symmetry. No solvent effect is necessary to induce amorphism.     

Influence of the Flexibility of Nickel PCP-Pincer Complexes on C−H and P−C Bond Activation and Ethylene Reactivity: A Combined Experimental and Theoretical Investigation

Using a pincer platform based on a bridgehead NHC donor with functional side arms, the combined effect of increased flexibility in six-membered pyrimidine-type heterocycles compared to the more often studied five-membered imidazole, and rigidity of phosphane side arms was examined. The unique features observed include: 1) the reaction of the azolium C_sp2−H bond with [Ni(cod)₂] affording a carbanionic ligand in [NiCl(PC_sp3^HP)] ( 8 ) rather than a carbene; 2) its transformation into the NHC, hydrido complex [NiH(PC^NHCP)]PF₆ ( 9 ) upon halide abstraction; 3) ethylene insertion into the Ni−H bond of the latter and ethyl migration to the N−C−N carbon atom of the heterocycle in [Ni(PC^EtP)]PF₆ ( 10 ); and 4) an unprecedented C−P bond activation transforming the P−C^NHC−P pincer ligand of 8 in a C−C^NHC−P pincer and a terminal phosphanido ligand in [Ni(PPh₂)(CC^NHCP)] ( 15 ). The data are supported by nine crystal structure determinations and theoretical calculations provided insights into the mechanisms of these transformations, which are relevant to stoichiometric and catalytic steps of general interest.     

Structure Based Library Approach to Photosynthesis Inhibitors:The Solid Phase Synthesis of Hydro-Uracils and Thiouracils

Combinatorialchemistryhasemergedasanefficienttoolforchedriststosynthesize"comPoundslibraries"fortheraPididentificationandoPtforizationofnewleads-lSolidphaseorganicsynthesisprovidesaraPidmeansforpreparationofcomPoundslibraries,andhasbeenusedfortheconstrUctionofoligomericcomPounds,'andsmallorganicmoleculessuchasbenzodiazepine,'9-lactams,'andquinolones.'ThemajortargetfortheinhibitionofphotosystemII(PSII)istheDlprotein,apolyPePtidewithamolecularweightof32kDa.'Wehavedevelopedmodelsoftheher-b…     

Chemical Mimics of Aspartate-Directed Proteases: Predictive and Strictly Specific Hydrolysis of a Globular Protein at Asp−X Sequence Promoted by Polyoxometalate Complexes Rationalized by a Combined Experimental and Theoretical Approach

Creating efficient and residue-directed artificial proteases is a challenging task due to the extreme inertness of the peptide bond, combined with the difficulty of achieving specific interactions between the catalysts and the protein side chains. Herein we report strictly site-selective hydrolysis of a multi-subunit globular protein, hemoglobin (Hb) from bovine blood, by a range of Zr^IV-substituted polyoxometalates (Zr-POMs) in mildly acidic and physiological pH solutions. Among 570 peptide bonds in Hb, selective cleavage was observed at only eleven sites, each occurring at Asp−X peptide bonds located in the positive patches on the protein surface. The molecular origins of the observed Asp−X selectivity were rationalized by means of molecular docking, DFT-based binding, and mechanistic studies on model peptides. The proposed mechanism of hydrolysis involves coordination of the amide oxygen to Zr^IV followed by a direct nucleophilic attack of the side chain carboxylate group on the C-terminal amide carbon atom with formation of a cyclic anhydride, which is further hydrolyzed to give the reaction products. The activation energy for the cleavage of the structurally related Glu−X sequence compared to Asp−X was calculated to be higher by 1.4 kcal mol⁻¹, which corresponds to a difference of about one order of magnitude in the rates of hydrolysis. The higher activation energy is attributed to the higher strain present in the six-membered ring of glutaric anhydride (Glu−X), as compared to the five-membered ring of the succinic anhydride (Asp−X) intermediate. Similarly, the cleavage at X−Asp and X−Glu bonds are predicted to be kinetically less likely as the corresponding activation energies were 6 kcal mol⁻¹ higher_, explaining the experimentally observed selectivity. The synergy between the negatively charged polyoxometalate cluster, which binds at positive patches on protein surfaces, and selective activation of Asp−X peptide bonds located in these regions by Zr^IV ions, results in a novel class of artificial proteases with aspartate-directed reactivity, which is very rare among naturally occurring proteases.