Integrated pharmacophore and docking‐based designing of dual inhibitors of aldose reductase (ALR2) and protein tyrosine phosphatase 1B (PTP1B) as novel therapeutics for insulin‐resistant diabetes and its complications

The dual inhibitors against aldose reductase (ALR2) and protein tyrosine phosphatase 1B (PTP1B) may present an anti‐diabetic potency in insulin resistance without risks of serious diabetic complications. Therefore, in the present study, we constructed two separate pharmacophore mapping‐based 3D quantitative structure–activity relationship models for ALR2 (AADRR.1109₃ with standard deviation 0.663, 0.719, F 22.3, root‐mean‐square error 0.705, 0.647, Pearson‐r 0.802) and PTP1B (AARR.15₅ with standard deviation 0.146, 0.945, F 82.70, root‐mean‐square error 0.351, 0.621, Pearson‐r 0.831) employing the dataset of 54 flavonoids as ALR2 inhibitors and 46 naphthoquinones as PTP1B inhibitors to identify structural features necessary for the inhibition of both enzymes. These models were subsequently used as 3D query search for hierarchical virtual screening‐based designing using the PHASE database of 1.5 million compounds. Designed dual inhibitors were further subjected to GLIDE XP docking analysis using high‐resolution 3D structures of ALR2 (1US0, at resolution of 0.66 Å) and PTP1B (2F71 at resolution of 1.55 Å) available in the Protein Data Bank to authenticate identified structural features with important binding interactions necessary for dual inhibition. Copyright © 2014 John Wiley & Sons, Ltd.     

Evaluation of two‐center,three‐ and four‐electron integrals over Slater‐type orbitals in elliptical coordinates

An algorithm for evaluation of two‐center, three‐electron integrals with the correlation factors of the type rr and rrr as well as four‐electron integrals with the correlation factors rrr and rrr in the Slater basis is presented. This problem has been solved here in elliptical coordinates, using the generalized and modified form of the Neumann expansion of the interelectronic distance function r for k ≥ ?1. Some numerical results are also included. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Ligand‐Enabled Enantioselective C –H Activation of Tetrahydroquinolines and Saturated Aza‐Heterocycles by RhI

The first rhodium(I)‐catalyzed enantioselective intermolecular C –H activation of various saturated aza‐heterocycles including tetrahydroquinolines, piperidines, piperazines, azetidines, pyrrolidines, and azepanes is presented. The combination of a rhodium(I) precatalyst and a chiral monodentate phosphonite ligand is shown to be a powerful catalytic system to access a variety of important enantio‐enriched heterocycles from simple starting materials. Notably, the C –H activation of tetrahydroquinolines is especially challenging due to the adjacent C −H bond. This redox‐neutral methodology provides a new synthetic route to α‐N‐arylated heterocycles with high chemoselectivity and enantioselectivity up to 97 % ee.     

Electron‐density delocalization in many‐electron atoms confined by penetrable walls: A Hartree–Fock study

The electronic structure of several many‐electron atoms, confined within a penetrable spherical box, was studied using the Hartree–Fock (HF) method, coupling the Roothaan's approach with a new basis set to solve the corresponding one‐electron equations. The resulting HF wave‐function was employed to evaluate the Shannon entropy, , in configuration space. Confinements imposed by impenetrable walls induce decrements on when the confinement radius, R_c, is reduced and the electron‐density is localized. For confinements commanded by penetrable walls, exhibits an entirely different behavior, because when an atom starts to be confined, delivers values less than those observed for the free system, in the same way that the results presented by impenetrable walls. However, from a confinement radius, shows increments, and precisely in these regions, the spatial restrictions spread to the electron density. Thus, from results presented in this work, the Shannon entropy can be used as a tool to measure the electron density delocalization for many‐electron atoms, as the hydrogen atom confined in similar conditions.     

Energies for cyclic and acyclic aggregations of adamantane and diamantane units sharing vertices,edges, or six‐membered rings

Diamondoids are hydrocarbons having a carbon scaffold comprised from polymer‐like composites of adamantane cages. This article describes computed total energies and “SWB‐tension” energies (often referred to as “strain” energies) for species having n adamantane or diamantane units sharing pairwise: one carbon atom (spiro‐[n]adamantane or spiro‐[n]diamantane); one C? C bond (one‐bond‐sharing‐[n]adamantane or one‐bond‐sharing‐[n]diamantane); or one chair‐shaped hexagon of carbon atoms (1234‐helical‐cata‐[n]diamantanes). Each of the five investigated polymer‐like types is considered either as an acyclic or a cyclic chain of adamantane‐ or diamantane‐unit cages. With increasing n values, SWB‐tension energies for acyclic aggregates are found to increase linearly, while the net SWB‐tension energies of cyclic aggregates often go thru a minimum at a suitable value of . In all five cases, a limiting common energy per unit ( ) is found to be approached by both cyclic and acyclic chains as , as revealed from plots of versus 1/n for acyclic chains and of versus 1/n² for cyclic chains. © 2015 Wiley Periodicals, Inc.     

General build up of basis and matrix in the diagonalization approach. Determination of Kramers configuration state functions

Algorithms to build the basis and matrix representation to obtain the Kramers configuration space functions (KCSFs) via diagonalization will be formally generalized to an arbitrary number of unpaired (open shell) fermions. Effective build up of the matrix representation will be outlined (including threading and graphical processing unit parallelism) to subsequently obtain the KCSFs via calling external/numerical library routines for diagonalization. The effective build up of the matrix representation relays on a binary tree search algorithm to allow evaluation the action on a given basis vector. The binary tree search avoids the treatment of zero matrix elements which leads to an exponential acceleration. The implementation ( basis creation, matrix representation, and matrix diagonalization) will be done in an all in core and all at once manner, hence the available core memory sets the physical limits in practical applications. Memory limitations, sparsity of the matrix, general case of n fermions in m spinors, and the application of KCSFs will be put into further perspective.     

Ritz variational method for the high‐lying nonautoionizing doubly excited 1,3Fe states of two‐electron atoms

Energy eigenvalues of nonautoionizing doubly excited states originating from 2pnf ( ) configuration of two‐electron atoms have been calculated by expanding the basis set in explicitly correlated Hylleraas coordinates under the framework of Ritz variational method. A detailed discussion on the evaluation of correlated basis integrals is given. The energy eigenvalues of a number of these doubly excited states are being reported for the first time especially for the high lying states. The effective quantum numbers ( ) for the states mentioned above have been calculated by using the theory of quantum defect.     

Spin–orbit effects on magnetically induced current densities in the () clusters

This study reports the spin–orbit effects on the aromaticity of the , , , , , and anionic clusters via the magnetically induced current‐density method. All‐electron density functional theory (DFT) calculations were carried out using the four‐component Dirac‐Coulomb (DC) hamiltonian, including scalar and spin–orbit relativistic effects. The magnetic index of aromaticity was calculated by numerical integration over the current flow between two atoms in the pentagonal ring. These values were compared to the spin‐free values (spin–orbit coupling switched off), in order to assess the spin–orbit effect on aromaticity. It was found that in the heavy anions, and , there is a significant influence of the spin–orbit coupling. © 2018 Wiley Periodicals, Inc.     

Structure,stability, and nature of bonding in carbon monoxide bound complexes (E = group 14 element; X = H,F, Cl,Br, I)

A density functional theory study is performed to predict the structures and stability of carbon monoxide (CO) bound (E = C, Si, Ge, Sn, Pb; X = H, F, Cl, Br, I) complexes. The possibility of bonding through both C‐ and O‐sides of CO is considered. Thermochemical analysis reveals that all the dissociation processes producing CO and are endothermic in nature whereas most of the dissociation reactions are endergonic in nature at room temperature. The nature of bonding in E? C/O bonds is analyzed via Wiberg bond index, natural population analysis, electron density, and energy decomposition analyses in conjunction with natural orbitals for chemical valence scheme. In comparison to C? O stretching frequency ( ) in free CO, while a red shift is noted in O‐side binding, the C‐side binding results in a blue shift in . The relative change in values in CO bound complexes on changing either E or X is scrutinized and possible explanation is provided in terms of polarization in the σ‐ and π‐orbitals and the relative strength of C→E or O→E σ‐donation and E→C or E→O π‐back‐donation. © 2016 Wiley Periodicals, Inc.     

The solvent effect on two competing reaction mechanisms involving hypervalent iodine reagents (λ3‐iodanes): Facing the limit of the stationary quantum chemical approach

Trifluoromethylation of acetonitrile with 3,3‐dimethyl‐1‐(trifluoromethyl)?1λ³,2‐ benziodoxol is assumed to occur via reductive elimination (RE) of the electrophilic CF₃‐ligand and MeCN bound to the hypervalent iodine. Computations in gas phase showed that the reaction might also occur via an S_N2 mechanism. There is a substantial solvent effect present for both reaction mechanisms, and their energies of activation are very sensitive toward the solvent model used (implicit, microsolvation, and cluster‐continuum). With polarizable continuum model‐based methods, the S_N2 mechanism becomes less favorable. Applying the cluster‐continuum model, using a shell of solvent molecules derived from ab initio molecular dynamics (AIMD) simulations, the gap between the two activation barriers ( ) is lowered to a few kcal mol^?1 and also shows that the activation entropies ( ) and volumes ( ) for the two mechanisms differ substantially. A quantitative assessment of will therefore only be possible using AIMD. A natural bond orbital‐analysis gives further insight into the activation of the CF₃‐reagent by protonation. © 2014 Wiley Periodicals, Inc.     

The Trifluoromethyl Anion: Evidence for [K(crypt‐222)]+

[K(crypt‐222)]⁺ ( 1 ) and [K(crypt‐222)]⁺ ( 3 ) are isostructural, displaying nearly identical unit cell parameters. The two structures are similar to the extent that the previously reported [K(crypt‐222)]⁺ model can be refined against the new data for [K(crypt‐222)]⁺ , with extra electron density being observed from the fourth fluorine atom of the . In agreement with experimental observations, theoretical calculations suggest that deprotonated [K(crypt‐222)]⁺ is highly unstable even at as low as 195 K. The previously considered 1:1 CHF ₃ clathrate of deprotonated [K(crypt‐222)]⁺ (crystallographically indistinguishable from 1 ) is ruled out on the basis of all available data.     

Geometric and electronic structures of silicon fluorides (N = 4 – 6) and potential energy surfaces for dissociation reactions → SiF4 + F– and → + F–

The geometric and electronic structures of a series of silicon fluorides (n = 4 ? 6) were computationally studied with the aid of density functional theory (DFT) method with B3LYP and M06‐2X functionals and coupled cluster (CCSD and CCSD(T)) methods with 6‐311++G(d,p) basis set. The nature of the Si‐F bonds in these compounds was analyzed in the framework of the natural bond orbital theory and natural resonance theory. Energy characteristics (heats of reactions and energy barriers) of the dissociation reactions → SiF₄ + F^– and → + F^– were calculated using the DFT and CCSD methods. The potential energy surface of elimination of a fluoride anion from has a specific topology with valley‐ridge inflection points corresponding to bifurcations of the minimal energy reaction path. © 2016 Wiley Periodicals, Inc.     

(Rg = He ∼ Rn,n = 1–4): In quest of the potential trapping ability of the aromatic ring

A new series of divalent boron‐rare gas cations (Rg = He ∼ Rn, n = 1–4) have been predicted theoretically at the B3LYP, MP2, and CCSD(T) levels to present the structures, stability, charge distributions, bond natures, and aromaticity. The Rg B bond energies are quite large for heavy rare gases and increase with the size of the Rg atom. Because of steric hindrance new Rg atoms introduced to the B₄ ring will weaken the Rg B bond. Thus in the Rg B bond has the largest binding energy 90–100 kcal/mol. p‐ has a slightly shorter Rg B bond length and a larger bond energy than o‐ . NBO and AIM analyses indicate that for the heavy Rg atoms Ar ∼ Rn the B Rg bonds have character of typical covalent bonds. The energy decomposition analysis shows that the σ‐donation from rare gases to the boron ring is the major contribution to the Rg B bonding. Adaptive natural density partitioning and nuclear‐independent chemical shift analyses suggest that both and have obvious aromaticity.     

Laser ablation of AgSbS2 and cluster analysis by time‐of‐flight mass spectrometry

Thin films of AgSbS₂ are important for phase‐change memory applications. This solid is deposited by various techniques, such as metal organic chemical vapour deposition or laser ablation deposition, and the structure of AgSbS₂(s), as either amorphous or crystalline, is already well characterized. The pulsed laser ablation deposition (PLD) of solid AgSbS₂ is also used as a manufacturing process. However, the processes in plasma have not been well studied. We have studied the laser ablation of synthesized AgSbS₂(s) using a nitrogen laser of 337 nm and the clusters formed in the laser plume were identified. The ablation leads to the formation of various single charged ternary Ag_pSb_qS_r clusters. Negatively charged AgSbS, AgSb₂S, AgSb₂S, AgSb₂S and positively charged ternary AgSbS⁺, AgSb₂S⁺, AgSb₂S, AgSb₂S clusters were identified. The formation of several singly charged Ag⁺, Ag, Ag, Sb, Sb, S ions and binary Ag_pS_r clusters such as AgSb, Ag₃S^?, SbS (r = 1–5), Sb₂S^?, Sb₂S, Sb₃S (r = 1–4) and AgS, SbS⁺, SbS, Sb₂S⁺, Sb₂S, Sb₃S (r = 1–4), AgSb was also observed. The stoichiometry of the clusters was determined via isotopic envelope analysis and computer modeling. The relation of the composition of the clusters to the crystal structure of AgSbS₂ is discussed. Copyright © 2009 John Wiley & Sons, Ltd.     

A chiral polymer‐based turn‐on fluorescent sensor for specific recognition of hydrogen sulfate

A new kind of polymeric chemosensor containing chiral naphthaldimine moiety in the side chain was synthesized by the reversible addition‐fragmentation chain transfer polymerization of N‐{[2‐(4‐vinylbenzyloxy)‐1‐naphthyl]‐methylene}‐(S)‐2‐phenylglycinol (VNP). The resulting polymers (PVNP) showed high selectivity for hydrogen sulfate relative to other anions including F^?, Cl^?, Br^?, H₂PO, CH₃CO, and NO in tetrahydrofuran (THF) solution as judged from UV?vis, fluorescence, and circular dichroism spectrophotometric titrations. Compared with its monomer, the polymer has proven to be more attractive for detection of HSO in terms of sensitivity and reproducibility. Upon addition of the anion it gives remarkable spectral responses concomitant with detectable color change from colorless to pale yellow. Furthermore, the HSO‐induced CD or fluorescence signal can be totally reversed with addition of base and eventually recovered the initial state, leading to a reproducible molecular switch with two distinguished “on” and “off” states. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

A Fluorescence Ratiometric Protein Assay Using Light‐Harvesting Conjugated Polymers

Summary: A highly selective protein assay was created which combines the fluorescent ratiometric technique based on FRET with the light‐harvesting properties of conjugated polymers. The cationic poly[(9,9‐bis(6′‐N,N,N‐trimethylammonium)‐hexyl)‐fluorene phenylene] bromide (PFP‐NMe) and the negatively charged biotinylated fluorescein probe (Fl‐B) were used to detect the target protein streptavidin optically. The strong electrostatic interactions between PFP‐NMe and fluorescein result in efficient FRET from PFP‐NMe to fluorescein. In the presence of streptavidin, however, the biotin moiety of Fl‐B specifically associates with streptavidin and the fluorescein molecule is buried deeply in the adjacent vacant binding sites. This separates the fluorescein spatially from the PFP‐NMe moiety, resulting in inefficient FRET from PFP‐NMe to fluorescein. Although a nonspecific protein, such as BSA, shows nonspecific interactions with PFP‐NMe, it does not affect the fluorescent ratio value of PFP‐NMe to fluorescein. Hence, the charged neutral complex of two oppositely charged conjugated polymers can eliminate the nonspecific interactions, and thus optimize their application in protein assays.

A schematic representation of the protein assay operation.