Ligand‐based design,virtual screening,and ADME/T‐based profiling on a dataset of 1,3,5‐triazine‐substituted benzene sulfonamides as carbonic anhydrase inhibitors

A quantitative structure–activity relationship (QSAR) analysis was performed on a dataset of 62 (1,3,5‐triazine‐substituted) benzene sulfonamides as carbonic anhydrase II and IX inhibitors using simulated annealing‐based multiple linear regression analysis. The selected QSAR model for carbonic anhydrase II inhibition (cross‐validated Q² = 0.689, , ) showed that aromaticity, lipophilicity, electronegativity, and molecular projection in the XZ plane influence the activity, whereas that for carbonic anhydrase IX inhibition (cross‐validated Q² = 0.767, , ) showed that activity was influenced by hydrophilicity, linker between the aromatic rings, electronegativity, and molecular weight. The QSAR model selected was internally and externally validated to define its predictability. Activity prediction of an external dataset containing nine compounds (within the same sphere of applicability) was performed to prove the models' specificity, selectivity, and sensitivity. The hypothesis in the form of the QSAR model was used for ligand‐based virtual screening on the ZINC database to obtain some potential hits. Similarly, docking studies on screened hits showed that the molecules interact and orient at the catalytic site in a way similar to acetazolamide. Additionally, an absorption, distribution, metabolism, excretion, and toxicity screening was also performed, and results showed that most of the compounds that can be possible drug candidates obey the Lipinski rule of five and Jorgensen rule of three. Copyright © 2013 John Wiley & Sons, Ltd.     

(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.     

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.     

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.     

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.     

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.     

Theoretical prediction of the optical rotation of chiral molecules in ordered media: A computational study of (Ra)‐1,3‐dimethylallene, (2R)‐2‐methyloxirane,and (2R)‐N‐methyloxaziridine

A theoretical procedure has been developed and implemented to calculate the optical rotation of chiral molecules in ordered phase via origin‐independent diagonal components , of the optical activity tensor and origin‐independent components , for , of the mixed electric dipole‐electric quadrupole polarizability. Origin independence was achieved by referring these tensors to the principal axis system of the electric dipole dynamic polarizability at the same laser frequency ω. The approach has been applied, allowing for alternative quantum mechanical methods based on different gauges, to estimate near Hartree–Fock values for three chiral molecules, (2R)‐N‐methyloxaziridine C₂NOH₅, (2R)‐2‐methyloxirane (also referred to as propylene oxide) C₃OH₆, and ( )‐1,3‐dimethylallene C₅H₈, at two frequencies. The theoretical predictions can be useful for an attempt at measuring correspondent experimental values in crystal phase. © 2015 Wiley Periodicals, Inc.     

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.     

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.     

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.     

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.     

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.     

Universality in Branching Frequencies and Molecular Dimensions during Hyperbranched Polymer Formation: Step Polymerization of AB2 Type Monomer with Equal Reactivity

Hyperbranched polymer formation during step polymerization of AB₂ type monomer with equal reactivity of two B's is investigated theoretically, focusing the attention to the degree of branching (DB) and the mean square radius of gyration for the unperturbed chains, . It is found that the DB‐value at large degree of polymerization (P) limit, = 0.5 is unchanged during the whole course of polymerization. The average value of having the same P is invariant throughout the polymerization. The universal curve between and P agrees perfectly with that for the self‐condensing vinyl polymerization (SCVP), another method to synthesize hyperbranched polymers, when the reactivity ratio for SCVP, r_SCVP, is 2.589 that gives = 0.5. The power law, is found for large values of P.

     

Ruthenium(II) complexes bearing pyridine‐based tridentate and bidentate ligands: catalytic activity for transfer hydrogenation of aryl ketones

Ru(II) complexes of the general formula [RuCl₂(′′)(L)] (1: ′N = N_b, L = MeOH; 2: ′N = N_b, L = CH₃CN; 3: ′N = N_d, L = CH₃CN; 4: ′N = N_p, L = CH₃CN), [Ru(p‐cymene)(_a–b)Cl]Cl (5a: N N_a = 2,2′‐bipyridine; 5b: N N_b = 4,4′‐dimethyl–2,2′‐bipyridine), [Ru(′′)(_a–b)Cl]Cl (6a: ′N = N_b, _a = 2,2′‐bipyridine; 6b: ′N = N_b, _b = 4,4′‐dimethyl‐2,2′‐bipyridine; 7a: ′N = N_d, _a = 2,2′‐bipyridine; 7b: ′N = N_d, _b = 4,4′‐dimethyl‐2,2′‐bipyridine; 8a: ′N = N_p, _a = 2,2′‐bipyridine; 8b: ′N = N_p, _b = 4,4′‐dimethyl‐2,2′‐bipyridine) and [Ru(′′)(_a)Cl]BF₄ (9a: ′N = N_b; _a = 2,2′‐bipyridine) were synthesized from the corresponding [RuCl₂(p‐cymene)]₂ dimer, ′′ and _a–b ligands. The compounds were characterized by elemental analysis, IR and NMR. Complex 9a was studied by X‐ray diffraction, confirming its cationic‐mononuclear [RuCl(_bb)(_a)]⁺ nature. The synthesized Ru(II) complexes (1–8) were employed as catalysts for the transfer hydrogenation of ketones to secondary alcohols in the presence of KOH using 2‐propanol as a hydrogen source at 82°C. The rates of the transfer hydrogenation reactions strongly depended on the type of and ancillary ligands. Copyright © 2012 John Wiley & Sons, Ltd.     

An Efficient N‐Heterocyclic Carbene‐Ruthenium Complex: Application Towards the Synthesis of Polyesters and Polyamides

The ruthenium benzimidazolylidene‐based N‐heterocyclic carbene (NHC) complex 4 catalyzes the direct dehydrogenative condensation of primary alcohols into esters and primary alcohols in the presence of amines to the corresponding amides in high yields. This efficient new catalytic system shows a high selectivity towards the conversion of diols to polyesters and of a mixture of diols and diamines to polyamides. The only side product formed in this reaction is molecular hydrogen. Remarkable is the conversion of hydroxytelechelic polytetrahydrofuran ( = 1000 g mol⁻¹)—a polydispers starting material—into a hydrolytically degradable polyether with ester linkages ( = 32 600 g mol⁻¹) and, in the presence of aliphatic diamines, into a polyether with amide linkages in the back bone ( = 16 000 g mol⁻¹).

     

Full–dimensional quantum molecular dynamics calculations of the rovibrationally mediated X → 2 transition of nitrous oxide

A full dimensional time‐dependent quantum wavepacket approach is used to study the photodissociation dynamics of nitrous oxide for the X → 2 bound–bound transition based on new highly accurate potential energy and transition dipole moment surfaces. The computed 2 absorption spectra at room temperature are characterized by sharp vibrational structures that contribute slightly to the diffuse vibrational structures around the maximum peak at 180 nm of the first ultraviolet absorption band (from the contribution of 2 , 1 , and 2 states) of N₂O. Transitions from different initial rovibrational states reveal that the sharp structures arise mainly from N₂? O bending vibrations, whereas, at higher temperatures, the N₂? O and N? NO stretching vibrations are responsible for enhancing the intensity of the structures. At absorption wavelengths 166 nm and 179 nm, vibrational quantum state distributions of N₂ product fragments decrease monotonically with increasing vibrational quantum number v = 0, 1, 2. At 166 nm, rotational quantum state distributions of N₂ at fixed v = 0 and v = 1 display multimodal profiles with maximum peaks at j = 77 and j = 75, respectively, whereas, the distributions at the 179 nm absorption wavelength display bimodal profiles with maximum peaks at j = 73 and j = 71, respectively. Accordingly, the presence of rotationally hot N₂ from previous experimental and theoretical works in the first band strongly implies a significant influence of the 2 state in determining the final dissociation pathway of N₂ + O. © 2016 Wiley Periodicals, Inc.     

Carbon–sulfur chains: A high‐resolution infrared and quantum‐chemical study of C3S and SC7S

In the course of a 5 μm high‐resolution infrared study of laser ablation products from carbon–sulfur targets, the ν₁ vibrational mode region of linear C₃S has been studied continuously from 2046 to 2065 cm^?1. Besides the prominent vibrational fundamental, the region was found to feature the , and even hot bands, the latter two of which were observed for the first time. Owing to the high signal‐to‐noise ratio obtained, the ν₁ mode of S could also be observed in natural abundance for the first time at high spectral resolution in the infrared. At 2061 cm^?1, hidden inside the branch of the C₃S ν₁ fundamental mode, a weak new band is observed which exhibits very tight line spacing and stems from a heavy both carbon and sulfur containing carrier. On the basis of high‐level quantum‐chemical calculations of selected carbon–sulfur chains and other carbon‐rich cumulenes, this feature is attributed to the ν₅ vibrational fundamental of linear SC₇S, which stands for the first gas‐phase spectroscopic detection of this long cumulenic chain.