Derivatives of molecular surface area and volume: simple and exact analytical formulas

The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library.     

Characterization of cyanide-trapped methylated metabonates formed during reactive drug metabolite screening in vitro

Reactive metabolites are estimated to be one of the main reasons behind unexpected drug-induced toxicity, by binding covalently to cell proteins or DNA. Due to their high reactivity and short lifespan, reactive metabolites are analyzed after chemical trapping with nucleophilic agents such as glutathione or cyanide. Recently, unexplained and uncharacterized methylated reaction products were reported in a human liver microsome based reactive metabolite trapping assay utilizing potassium cyanide as a trapping agent. Here, a similar assay was utilized to produce mono- or dimethylated and further cyanide-trapped reaction products from propranolol, amlodipine and ciprofloxacin, followed by ultra-performance liquid chromatography/time-of-flight mass spectrometry (UPLC/TOF-MS) and ultra-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) experiments for their more detailed structural elucidation. Formation of all observed cyanide-trapped products was clearly NADPH-dependent and thus metabolism-mediated. The suggested reaction pathways included N-methylation leading to iminium formation in primary and/or secondary amines preceded by cytochrome P450 (CYP)-mediated reactions. As the methylation reaction was suggested to be involved in formation of the actual reactive iminium ion, the observed cyanide-trapped products were experimental artifacts rather than trapped reactive metabolites. The results stress that to avoid overestimating the formation of reactive metabolites in vitro, this methylation phenomenon should be taken into account when interpreting the results of cyanide-utilizing reactive metabolite trapping assays. This in turn emphasizes the importance of identification of the observed cyano conjugates during such studies. Yet, metabolite identification has a high importance to avoid overestimation of in vitro metabolic clearance in the cases where this kind of metabonate formation has a high impact in the disappearance rate of the compound.     

Selective dispersion of single-walled carbon nanotubes with specific chiral indices by poly(N-decyl-2,7-carbazole)

Physico-chemical methods to sort single-walled carbon nanotubes (SWNTs) by chiral index are presently lacking but are required for in-depth experimental analysis and also for potential future applications of specific species. Here we report the unexpected selectivity of poly(N-decyl-2,7-carbazole) to almost exclusively disperse semiconducting SWNTs with differences of their chiral indices (n - m) ≥ 2 in toluene. The observed selectivity complements perfectly the dispersing features of the fluorene analogue poly(9,9-dialkyl-2,7-fluorene), which disperses semiconducting SWNTs with (n - m) ≤ 2 in toluene. The dispersed samples are further purified by density gradient centrifugation and analyzed by photoluminescence excitation spectroscopy. All-atom molecular modeling with decamer model compounds of the polymers and (10,2) and (7,6) SWNTs suggests differences in the π-π stacking interaction as origin of the selectivity. We observe energetically favored complexes between the (10,2) SWNT and the carbazole decamer and between the (7,6) SWNT and the fluorene decamer, respectively. These findings demonstrate that subtle structural changes of polymers lead to selective solvation of different families of carbon nanotubes. Furthermore, chemical screening of closely related polymers may pave the way toward simple, low-cost, and index-specific isolation of SWNTs.     

Mixed phosphine and group-13 metal ligator complexes [(PR3)(a)M(ECp*)b] (M = Mo, Ni; E = Ga, Al; R = C6H5, cyclo-C6H11, CH3)

Treatment of [Mo(N(2))(PMe(3))(5)] with two equivalents GaCp* (Cp* = η(5)-C(5)(CH(3))(5)) leads to the formation of cis-[Mo(GaCp*)(2)(PMe(3))(4)] (1), while AlCp* did not react with this precursor. In addition, [Ni(GaCp*)(2)(PPh(3))(2)] (2a), [Ni(AlCp*)(2)(PPh(3))(2)] (2b), [Ni(GaCp*)(2)(PCy(3))(2)] (3a), [Ni(GaCp*)(2)(PMe(3))(2)] (3b), [Ni(GaCp*)(3)(PCy(3))] (4) and [Ni(GaCp*)(PMe(3))(3)] (5) have been prepared in high yields by a direct synthesis from [Ni(COD)(2)] and stoichiometric amounts of the ligands PR(3) and ECp* (E = Al, Ga), respectively. All compounds have been fully characterized by (1)H, (13)C, and (31)P NMR spectroscopy, elemental analysis and single crystal X-ray diffraction studies.     

Zinc-rich compounds of iron and cobalt: formation of [Fe2Zn(n)] (n = 2-4) and [Co2Zn3] cores

The reactions of heteroleptic GaCp*/CO containing transition metal complexes of iron and cobalt, namely [(CO)(3)M(μ(2)-GaCp*)(m)M(CO)(3)] (Cp* = pentamethylcyclopentadienyl; M = Fe, m = 3; M = Co, m = 2) and [Fe(CO)(4)(GaCp*)], with ZnMe(2) in toluene and the presence of a coordinating co-solvent were investigated. The reaction of the iron complex [Fe(CO)(4)(GaCp*)] with ZnMe(2) in presence of tetrahydrofurane (thf) leads to the dimeric compound [(CO)(4)Fe{μ(2)-Zn(thf)(2)}(2)Fe(CO)(4)] (1). Reaction of [(CO)(3)Fe(μ(2)-GaCp*(3))Fe(CO)(3)] with ZnMe(2) and stoichiometric amounts of thf leads to the formation of [(CO)(3)Fe{μ(2)-Zn(thf)(2)}(2)(μ(2)-ZnMe)(2)Fe(CO)(3)] (2) containing {Zn(thf)(2)} as well as ZnMe ligands. Using pyridine (py) instead of thf leads to [(CO)(3)Fe{μ(2)-Zn(py)(2)}(3)Fe(CO)(3)] (3) via replacement of all GaCp* ligands by three{Zn(py)(2)} groups. In contrast, reaction of [(CO)(3)Co(μ(2)-GaCp*)(2)Co(CO)(3)] with ZnMe(2) in the presence of py or thf leads in both cases to the formation of [(CO)(3)Co{μ(2)-ZnL(2)}(μ(2)-ZnCp*)(2)Co(CO)(3)] (L = py (4), thf (5)) via replacement of GaCp* with {Zn(L)(2)} units as well as Cp* transfer from the gallium to the zinc centre. All compounds were characterised by NMR spectroscopy, IR spectroscopy, single crystal X-ray diffraction and elemental analysis.     

Highly efficient one-pot access to functionalized arylboronic acids via noncryogenic bromine/magnesium exchanges

A general and convenient protocol for the electrophilic borylation of aryl Grignard reagents prepared from arylbromides by direct insertion of magnesium in the presence of LiCl or by Mg/Br exchange with (i)PrMgCl·LiCl has been developed. Various aryl boronic acids were synthesized in a straightforward manner in excellent yields at 0 °C.     

The rich chemistry of [Zn2Cp*2]: trapping three different types of zinc ligands in the PdZn7 complex [Pd(ZnCp*)4(ZnMe)2{Zn(tmeda)}

The synthesis, structural characterization, and bonding situation analysis of a novel, all-zinc, hepta-coordinated palladium complex [Pd(ZnCp*)(4)(ZnMe)(2){Zn(tmeda)}] (1) is reported. The reaction of the substitution labile d(10) metal starting complex [Pd(CH(3))(2)(tmeda)] (tmeda = N,N,N',N'-tetramethyl-ethane-1,2-diamine) with stoichiometric amounts of [Zn(2)Cp*(2)] (Cp* = pentamethylcyclopentadienyl) results in the formation of [Pd(ZnCp*)(4)(ZnMe)(2){Zn(tmeda)}] (1) in 35% yield. Compound 1 has been fully characterized by single-crystal X-ray diffraction, (1)H and (13)C NMR spectroscopy, IR spectroscopy, and liquid injection field desorption ionization mass spectrometry. It consists of an unusual [PdZn(7)] metal core and exhibits a terminal {Zn(tmeda)} unit. The bonding situation of 1 with respect to the properties of the three different types of Zn ligands Zn(R,L) (R = CH(3), Cp*; L = tmeda) bonded to the Pd center was studied by density functional theory quantum chemical calculations. The results of energy decomposition and atoms in molecules analysis clearly point out significant differences according to R vs L. While Zn(CH(3)) and ZnCp* can be viewed as 1e donor Zn(I) ligands, {Zn(tmeda)} is best described as a strong 2e Zn(0) donor ligand. Thus, the 18 valence electron complex 1 nicely fits to the family of metal-rich molecules of the general formula [M(ZnR)(a)(GaR)(b)] (a + 2b = n ≥ 8; M = Mo, Ru, Rh; Ni, Pd, Pt; R = Me, Et, Cp*).     

Two- and four-component relativistic generalized-active-space coupled cluster method: implementation and application to BiH

A string-based coupled-cluster method of general excitation rank and with optimal scaling which accounts for special relativity within the four-component framework is presented. The method opens the way for the treatment of multi-reference problems through an active-space inspired single-reference based state-selective expansion of the model space. The evaluation of the coupled-cluster vector function is implemented by considering contractions of elementary second-quantized operators without setting up the amplitude equations explicitly. The capabilities of the new method are demonstrated in application to the electronic ground state of the bismuth monohydride molecule. In these calculations simulated multi-reference expansions with both doubles and triples excitations into the external space as well as the regular coupled-cluster hierarchy up to full quadruples excitations are compared. The importance of atomic outer core-correlation for obtaining accurate results is shown. Comparison to the non-relativistic framework is performed throughout to illustrate the additional work of the transition to the four-component relativistic framework both in implementation and application. Furthermore, an evaluation of the highest order scaling for general-order expansions is presented.     

Versatile wet-chemical synthesis of non-agglomerated CaCO3 vaterite nanoparticles

Calcium carbonate (vaterite) nanoparticles of 20-60 nm size were obtained without stabilizing tensides by heating a dispersion of calcium bicarbonate (CaHCO(3)) in ethylene glycol for 30 minutes at 40 to 100 °C.