An orbital localization criterion based on the topological analysis of the electron localization function at correlated level

This work describes a procedure for localizing orbitals based on the topological analysis of the electron localization function at correlated level. The decomposition of the overlap matrix according to the partitioning of the three dimensional physical space into basins provided by that function allows us to define a localization index to be maximized using isopycnic orbital transformations. The localization algorithm has been computationally implemented and its efficiency tested on selected molecular systems at equilibrium, stretched, and twisted geometries. We report results which allow to analyze the influence of the correlated and uncorrelated treatments on the orbital localization.     

An orbital localization criterion based on the topological analysis of the electron localization function

This work proposes a new molecular orbital localization procedure. The approach is based on the decomposition of the overlap matrix in accordance with the partitioning of the three‐dimensional physical space into basins with clear chemical meaning arising from the topological analysis of the electron localization function. The procedure is computationally inexpensive, provides a straightforward interpretation of the resulting orbitals in terms of their localization indices and basin occupancies, and preserves the σ/π‐separability in planar N‐electron systems. The localization algorithm is tested on selected molecular systems. © 2012 Wiley Periodicals, Inc.     

Development of a capillary electrophoresis method for the characterization of "palo azul" (Eysenhardtia polystachya)

The tree Eysenhardtia polystachya (Ortega) Sarg. has quite a wide popular use within the traditional Mexican medicine as herbal remedy. Popular practices constitute a relevant enough basis to design optimum analytical methods in order to determine basic principles of diverse medicinal plants. This has become one of the essentials needed to characterize such products, for which it is fundamentally important to develop an efficient and reliable separation method. This work presents the results concerning the development and optimization of a novel CE method for the separation of components from water/etanol (1:1) extracts of E. polystachya, using the following conditions, considered the best obtained: phosphate buffer 10 mM, 20 kV voltage, and pH 8.1 at 214 nm and 50 mM, 12.5 kV voltage with pH 8.1 at 426 nm. The optimization takes into account the parameters associated in the resulting electropherograms, such as number of peaks, migration times, and the Deltat(m) of the neighboring peaks. Under optimal conditions the separation intended was attained within 15 and 20 min for 214 and 426 nm, respectively. The characterization method developed was applied to the analysis of diverse extracts of E. polystachya.     

四（对叔丁基）硫杂杯[4]芳烃选择性包合四氟硼酸分子：晶体结构和理论研究

X－射线晶体衍射测定了4－(对叔丁基)硫杂杯[4]芳烃选择性地包合四氟硼酸分子。晶体学数据为：C₄₀H₄₉O₄S₄BF₄，M_r=808.88， 四方锥， 空间群 P4/nmm，a=1.5887(2), b=1.5887(2), c=0.8428(0) nm, V=2.127(2) nm³, Z=2, D_c=1.263 g·cm^-3, R₁=0.0405, _WR[I>2σ(I)]=0.1218. ¹⁹F NMR谱中，在-151.4 ppm处出现的峰，证实了四氟硼酸的存在。用Bader的分子中的原子理论方法计算了分子结构中的非共价键相互作用。结果显示，在四氟硼酸包合物中，除了F…H－C氢键作用和阳离子－阴离子的静电作用外，F^δ--C^δ+静电作用的存在也对4－(对叔丁基)硫杂杯[4]芳烃憎水空腔包合氟硼酸分子起到了稳定作用。     

Learning from "coffee rings": ordered structures enabled by controlled evaporative self-assembly

Research into the evaporation of solutions is not only aimed at a better understanding the physics of evaporation, but increasingly at capitalizing on the extremely simple method it offers to assemble diverse nonvolatile solutes into complex ordered structures on the submicron and longer length scales. This Review highlights recent advances in evaporative assembly of confined solutions, focusing especially on recently developed approaches that provide structures with unprecedented regularity composed of polymers, nanoparticles, and biomaterials, by controlled evaporation-driven, flow-aided self-assembly. A broad range of variables that can control the deposition are explored and the future directions of this rich field are presented.     

Re-shaping the coffee ring

Not your cup of tea? "Coffee rings" of spherical colloidal particles are left behind after water droplets resting on surfaces have dried out. This controlled evaporation of colloidal solutions can be exploited to deposit material in regular patterns. It is now shown that if spherical colloids are replaced by slightly elongated ones, the coffee ring is not formed and is replaced by an even more uniform deposition.     

Pharmaceutical microcalorimetry: recent advances in the study of solid state materials

This paper discusses the theory and experimental application of microcalorimetry to the study of solid state reactions of pharmaceutical importance. The practical example selected is that of formulated products containing benzoyl peroxide – a treatment for acne and athlete’s foot. A newly developed procedure for data analysis is outlined and preliminary results from chemometric-based analysis of complex solid state reaction schemes is presented. Finally, the microcalorimetric requirements for such stability studies are contrasted with the newly emerging multi-channel “chip calorimeters” that operate in the nano range (watts, material, concentration) with high throughput potential.     

A comparative post-Hartree–Fock and density functional theory study of monochalcogenide diatomic molecules

HOMO and LUMO (FMOs) play important role in the optical properties of meridianal isomer of tris(8-hydroxyquinolino)aluminum (mer-Alq3) and its derivatives. The frontier molecular orbitals (FMOs) also play a vital role in the process of charge transport. It is urgent to find the reason of FMO distribution pattern among the ligands. The structures of mer-Alq3 and its “CH”/N substituted derivatives have been optimized at the B3LYP/6-31G^* level. Energy decomposition analysis has been performed at the B3LYP/DZP level. The results of energy-partitioning analysis of ground states are discussed. It has been explained that HOMOs are on A-ligands due to weaker electrostatic interaction energy between L_a-AlL_bL_c fragments while LUMOs are on B-ligands due to weaker orbital interaction energy between L_b-AlL_aL_c fragments.     

Second-order atomic Fukui indices from the electron-pair density in the framework of the atoms in molecules theory

Atomic Fukui indices, which are obtained from the electron density, have been previously shown to be useful in predicting which atoms in a molecule are most likely to suffer nucleophilic, electrophilic, or radicalary attacks. Here, we present a second-order generalization of these indices based on the electron pair density. We show how second-order atomic Fukui indices can be used to analyze the effects of electron loss or gain in several molecules from an electron pair point of view. Further, these indices also highlight which atoms or pairs of atoms are more likely to suffer nucleophilic, electrophilic, or radical attacks. In conclusion, second-order indices can complement first-order ones by affording relevant information on molecular reactivity from an electron pair perspective.     

"Quasi flexible" automatic docking processing for studying stereoselective recognition mechanisms, part 2: Prediction of DeltaDeltaG of complexation and 1H-NMR NOE correlation

The purpose of this work is to apply the global molecular interaction evaluation ("Glob-MolInE") computational protocol to the study of two molecular complexes characterized by a chiral selector and a couple of enantiomeric selectands experimentally known to give large difference in the free energy of complexation much higher than the experimental error normally associated to the molecular mechanic calculations. We have considered the well known diastereomeric complexes between the selector (S)-N-(3,5-dinitrobenzoyl)-leucine-n-propylamide (S)-1 and the selectands (R) or (S)-N-(2-naphthyl)-alanine methyl ester 2, widely studied by enantioselective HPLC, NMR and X-ray. The experimental difference of free energy of complexation between [(S)-1*(R)-2] and [(S)-1*(S)-2] (-1.34 kcal/mol) was reproduced by the new computational protocol with an excellent confidence error. Detailed results about the conformational search, the "quasi-flexible" docking and the thermodynamic estimation are presented in this work. A remarkable correlation between the theoretical results and experimental data (NOE measurements, X-ray crystallographic structure of the [(S)-1*(S)-2] complex and the free energy of complexation) supports the validity of the computational approach and underline the importance of the conformational multiplicity in the definition of the macroscopic properties of the complex in solution.     

Principal components of phenolics to characterize red Vinho Verde grapes: Anthocyanins or non-coloured compounds?

Phenolic profile of 10 different varieties of red “Vinho Verde” grapes (Azal Tinto, Borraçal, Brancelho, Doçal, Espadeiro, Padeiro de Basto, Pedral, Rabo de ovelha, Verdelho and Vinhão), from Minho (Portugal) were studied. Nine Flavonols, four phenolic acids, three flavan-3-ols, one stilben and eight anthocyanins were determined. Malvidin-3-O-glucoside was the most abundant anthocyanin while the main non-coloured compound was much more heterogeneous: catechin, epicatechin, myricetin-3-O-glucoside, quercetin-3-O-glucoside or syringetin-3-O-glucoside. Anthocyanin contents ranged from 42 to 97%. Principal component analysis (PCA) was applied to analyse the date and study the relations between the samples and their phenolic profiles. Anthocyanin profile proved to be a good marker to characterize the varieties even considering different origin and harvest. “Vinhão” grapes showed anthocyanins levels until twenty four times higher than the rest of the samples, with 97% of these compounds.     

Effects of poly (ethylene glycol) chains conformational transition on the properties of mixed DMPC/DMPE-PEG thin liquid films and monolayers

Foam thin liquid films (TLF) and monolayers at the air–water interface formed by DMPC mixed with DMPE-bonded poly (ethylene glycol)s (DMPE-PEG₅₅₀, DMPE-PEG₂₀₀₀ and DMPE-PEG₅₀₀₀) were obtained. The influence of both (i) PEG chain size (evaluated in terms of Mw) and mushroom-to-brush conformational transition and (ii) of the liposome/micelle ratio in the film-forming dispersions, on the interfacial properties of mixed DMPC/DMPE-PEG films was compared.

Foam film studies demonstrated that DMPE-PEG addition to foam TLFs caused (i) delayed kinetics of film thinning and black spot expansion and (ii) film stabilization. At the mushroom-to-brush transition, due to steric repulsion increased DMPE-PEG films thickness reached 25 nm while pure DMPC films were only 8 nm thick Newton black films. It was possible to differentiate DMPE-PEG_2000/5000 from DMPE-PEG₅₅₀ by the ability to change foam TLF formation mechanism, which could be of great importance for “stealth” liposome design.

Monolayer studies showed improved formation kinetics and equilibrium surface tension decrease for DMPE-PEG monolayers compared with DMPC pure films.

SEM observations revealed “smoothing” and “sealing” of the defects in the solid-supported layer surface by DMPE-PEGs adsorption, which could explain DMPE-PEGs ability to stabilize TLFs and to decrease monolayer surface tension.

All effects in monolayers, foam TLFs and solid-supported layers increased with the increase of PEG Mw and DMPE-PEG concentration. However, at the critical DMPE-PEG concentration (where mushroom-to-brush conformational transition occurred) maximal magnitude of the effects was reached, which only slightly changed at further DMPE-PEG content and micelle/liposome ratio increase.     

New insights on the bridge carbon-carbon bond in propellanes: a theoretical study based on the analysis of the electron localization function

The nature of the bonding between bridgehead carbon atoms (Ca, Ca') as well as the ring strain in a family of 10 propellanes formed by three-, four-, or five-member rings: [1.1.1] (I), [2.1.1] (II), [3.1.1] (III), [2.2.1] (IV), [3.2.1] (V), [2.2.2] (VI), [3.3.1] (VII), [3.2.2] (VIII), [3.3.2] (IX), and [3.3.3] (X) are studied by means of the electron localization function (ELF) at the DFT level (B3LYP/cc-pVTZ). The ELF analysis of smaller propellanes (I, II, and III) reveals the coexistence of two resonance forms: one with a nonbonding electron pair partially delocalized between Ca and Ca' atoms outside the cage (ionic) and the other with a bridge bond between the same atoms (covalent). The weights of each form are calculated according to the ELF-basin populations, yielding 94, 88, and 53% for the ionic structure of I, II, and III, respectively, while larger propellanes (IV-X) present only the covalent form. The question of the s-character of the bridge bond is addressed by dissecting the bridge-bond ELF basin into the molecular orbital contributions. Finally, sigma-aromaticity associated to surface electron delocalization has been analyzed by means of nucleus-independent chemical shift (NICS) calculations. The results point out that the stability of the fused ring structure of propellanes I, II, and III, can be assigned to the remarkable sigma-aromaticity of the involved three-member rings.     

Synthesis and properties of novel aromatic polyamides based on “multi-ring” flexible dicarboxylic acids

The five benzene rings-containing (hereafter referred to as “five-ring”) dicarboxylic acids α,α′-bis[4-(4-carboxyphenoxy)phenyl]-1,4-diisopropylbenzene (p- III ) and α,α′-bis[4-(4-carboxyphenoxy)phenyl]-1,3-diisopropylbenzene (m- III ) were prepared by the fluoro-displacement of α,α′-bis(4-hydroxyphenyl)-1,4-diisopropylbenzene and α,α′-bis(4-hydroxyphenyl)-1,3-diisopropylbenzene with p-fluorobenzonitrile, and subsequent alkaline hydrolysis of the intermediate dinitriles. A number of high-molecular-weight polyamides based on these two “five-ring” dicarboxylic acids (p- III and m- III ) and various aromatic diamines were directly synthesized in N-methyl-2-pyrrolidone (NMP) containing lithium chloride (LiCl) or calcium chloride (CaCl₂) using triphenyl phosphite and pyridine as condensing agents. These polyamides were obtained with inherent viscosities above 0.51 and up to 0.91 dL/g. The weight-average molecular weight were in the range of 51,000–211,000. Most of these polyamides were amorphous and readily soluble in polar solvents such as NMP, N,N-dimethylacetamide (DMAc), N,N-dimethylformamide (DMF), and dimethyl sulfoxide (DMSO), and afforded tough, flexible, and transparent films by solution-casting. The films had tensile strength of 50–83 MPa, elongation to break of 4–8%, and tensile modulus of 1.3–2.0 GPa. Most polyamides showed distinct glass transitions on the differential scanning calorimetry (DSC) curves ranging from 147 to 177°C. In nitrogen or air, all the polymers showed no significant weight loss up to 490°C, as indicated by thermogravimetric analysis (TG). © 1996 John Wiley & Sons, Inc.     

A quantitative measure of bond polarity from the electron localization function and the theory of atoms in molecules

 A quantitative measure of the polarity of a bond can be obtained through combining the two complementary topological partitionings of the electron density obtained from the atoms in molecules theory, on the one hand, and the electron localization function, on the other. This requires an integration of the electron density in the atomic subbasins of a common bond electron localization basin. We present the first numerical application of the resulting topological definition of bond polarity to a set of small linear systems consisting of the FCN, HF, HCl, HBr, and NaCl molecules and the NeAr van der Waals dimer. It is shown that the findings are essentially in line with common expectation for these simple molecules, thus confirming the potential value of the novel bond polarity index for the analysis of controversial bonding situations. Additional insight is provided through the detailed investigation of fluctuations in the basin populations. Received: 10 January 2001 / Accepted 12 February 2001 / Published online: 22 May 2001     

Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide

An analysis of the water molecules in the first solvation shell obtained from the molecular dynamics simulation of the amyloid beta(10-35)NH2 peptide and the amyloid beta(10-35)NH2E22Q "Dutch" mutant peptide is presented. The structure, energetics, and dynamics of water in the hydration shell have been investigated using a variety of measures, including the hydrogen bond network, the water residence times for all the peptide residues, the diffusion constant, experimentally determined HN amide proton exchange, and the transition probabilities for water to move from one residue to another or into the bulk. The results of the study indicate that: (1) the water molecules at the peptide-solvent interface are organized in an ordered structure similar for the two peptide systems but different from that of the bulk, (2) the peptide structure inhibits diffusion perpendicular to the peptide surface by a factor of 3 to 5 relative to diffusion parallel to the peptide surface, which is comparable to diffusion of bulk water, (3) water in the first solvation shell shows dynamical relaxation on fast (1-2 ps) and slow (10-40 ps) time scales, (4) a novel solvent relaxation master equation is shown to capture the details of the fast relaxation of water in the peptide's first solvation shell, (5) the interaction between the peptide and the solvent is stronger in the wild type than in the E22Q mutant peptide, in agreement with earlier results obtained from computer simulations [Massi, F.; Straub, J. E. Biophys J 2001, 81, 697] correlated with the observed enhanced activity of the E22Q mutant peptide.     

A two-step supercritical fluid extraction of polycyclic aromatic hydrocarbons from roadside soil samples

A two-step procedure for the supercritical fluid extraction (SFE) of polycyclic aromatic hydrocarbons from soil samples was developed. The procedure consists of a static supercritical fluid treatment in a closed extraction cell at a high temperature (T=250 or 340degreesC for 20 min) and an SFE with a solvent trapping. During the static phase, the sample is exposed to a supercritical organic solvent (methanol, toluene, dichloromethane, ACN, acetone, and hexane). The solvent penetrates particles of the matrix to substitute strongly bonded molecules and dissolves the analytes in the supercritical phase. At ambient temperature, supercritical fluids became liquid and lost their solvation abilities. Most of the analytes condense on the surface of the particles or on the extraction cell walls without forming strong bonds or penetrating deep into the matrix. Thus, the pretreatment liberates the analytes and they behave similar to those in freshly spiked samples. The common SFE with toluene-modified CO2 as an extraction fluid follows the static phase. With the use of the most suitable extraction phases (toluene, ACN), the extraction efficiency of the combined procedure is much higher (approximately100%). The results of the combined procedure are compared to the SFE procedure of the same untreated sample (difference less than 5%) and to the Soxhlet extraction. The extracts were analyzed using a GC with the flame ionization detection.     

Ab initio crystal orbital studies on linear chains of H atoms

Anab initio crystal orbital method is used to calculate the energies of an infinite chain of H atoms and of linear arrangements of H₂ molecules with different interatomic distances. The H₂ arrangements are not stable in respect to isolated molecules. The cohesive energy of an optimized arrangement of H atoms chain is 0.0354 a.u.