Quantum chemistry in parallel with PQS

This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux‐based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large—by ab initio standards—molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high‐level calculations (DFT, MP2, CI, and Coupled‐Cluster) can be performed on systems with up to several thousand basis functions on small (4‐32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post‐job visualization and display. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Polymer micelles from tadpole-shaped amphiphilic block-graft copolymers prepared by “Grafting-through” ATRP

A series of tadpole-shaped block-graft amphiphilic copolymers, i.e., block copolymers consisting of a cylindrical hydrophilic brush block and a coiled hydrophobic block were synthesized using “grafting-through” atom transfer radical polymerization. A tadpole-shaped block-graft copolymer from polystyrene bromide and a methacryloyl-terminated poly(tert-butyl acrylate) was prepared first. Then, hydrolysis of the poly(tert-butyl acrylate) side chains to polyacrylic acid side chains provided tadpole-shaped block-graft amphiphilic copolymers, which formed pH responsive micelles in water, the latter being confirmed by dynamic light scattering and atomic force microscopy.     

Synthesis,experimental and in silico studies of N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine,coupled with CSD data: a survey of interactions in the crystal structures of Fmoc–amino acids

Recently, fluorenylmethoxycarbonyl (Fmoc) amino acids (e.g. Fmoc–tyrosine or Fmoc–phenylalanine) have attracted growing interest in biomedical research and industry, with special emphasis directed towards the design and development of novel effective hydrogelators, biomaterials or therapeutics. With this in mind, a systematic knowledge of the structural and supramolecular features in recognition of those properties is essential. This work is the first comprehensive summary of noncovalent interactions combined with a library of supramolecular synthon patterns in all crystal structures of amino acids with the Fmoc moiety reported so far. Moreover, a new Fmoc‐protected amino acid, namely, 2‐{[(9H‐fluoren‐9‐ylmethoxy)carbonyl](methyl)amino}‐3‐{4‐[(2‐hydroxypropan‐2‐yl)oxy]phenyl}propanoic acid or N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine, Fmoc‐N‐Me‐Tyr(t‐Bu)‐OH, C₂₉H₃₁NO₅, was successfully synthesized and the structure of its unsolvated form was determined by single‐crystal X‐ray diffraction. The structural, conformational and energy landscape was investigated in detail by combined experimental and in silico approaches, and further compared to N‐Fmoc‐phenylalanine [Draper et al. (2015). CrystEngComm, 42 , 8047–8057]. Geometries were optimized by the density functional theory (DFT) method either in vacuo or in solutio. The polarizable conductor calculation model was exploited for the evaluation of the hydration effect. Hirshfeld surface analysis revealed that H…H, C…H/H…C and O…H/H…O interactions constitute the major contributions to the total Hirshfeld surface area in all the investigated systems. The molecular electrostatic potentials mapped over the surfaces identified the electrostatic complementarities in the crystal packing. The prediction of weak hydrogen‐bonded patterns via Full Interaction Maps was computed. Supramolecular motifs formed via C—H…O, C—H…π, (fluorenyl)C—H…Cl(I), C—Br…π(fluorenyl) and C—I…π(fluorenyl) interactions are observed. Basic synthons, in combination with the Long‐Range Synthon Aufbau Modules, further supported by energy‐framework calculations, are discussed. Furthermore, the relevance of Fmoc‐based supramolecular hydrogen‐bonding patterns in biocomplexes are emphasized, for the first time.     

Numerical analysis of the Gran methods. A comparative study

The paper concerns mainly the modified Gran methods, considered as extrapolative standard addition methods. Particularly, the approximation:

     

"Fatal adsorption" of brushlike macromolecules: high sensitivity of C-C bond cleavage rates to substrate surface energy

Adsorption-induced degradation of brushlike macromolecules was monitored through molecular imaging by atomic force microscopy. The rate constant for C-C bond cleavage was shown to be extremely sensitive to the substrate surface energy. A few percent increase in the surface energy from 69.2 to 71.2 mN/m led to an order of magnitude increase of the scission rate. The absolute values of the rupture forces ranging from 2.57 to 2.47 nN are in agreement with previously calculated and measured values for stretching surface-tethered molecules.     

Synthesis and structural studies of hydrazino-crown ethers and thermodynamic studies of their interaction with transition,and post-transition metal ions and methyl ammonium ion

Hydrazino-crown ethers have been synthesized in only 3 or 4 steps starting from 1,2-diacetylhydrazine. The X-ray crystal structure of protonated hydrazino-19-crown-7 (2) showed that one of the hydrazino nitrogen atoms was directed outside the ring cavity. A solvent methanol molecule is held in the cavity of the host ligand by three hydrogen bonds involving two hydrogen atoms bonded to nitrogens of the ligand and the alcohol hydrogen of the methanol. The logK values for the interaction of2 with CH₃NH ₊ ³ , Ag⁺, Pb²⁺, and Cd²⁺ were much less than those for the interaction of symmetrical triaza-l8-crown-6 (5) with the same cations. Hydrazino-crown2 reduced silver ions to silver metal when a solution of2 and silver ions in DMSO was allowed to stand for several days.     

Formation of poly(ethylene phosphates) in polycondensation of H3PO4 with ethylene glycol. Kinetic and mechanistic study

Conditions of synthesis of poly(ethylene phosphates) in reaction of H₃PO₄ with HOCH₂CH₂OH (EG), the actual path of polycondensation, and structure of the obtained polymers (mostly oligomers) and kinetics of reaction are described. Preliminary kinetic information, based on the comparison of the MALDI‐TOF‐ms and ³¹P{¹H} NMR spectra as a function of conversion is given as well. Because of the dealkylation process fragments derived from di‐ and triethylene glycols are also present in the repeating units. Structures of the end groups (? CH₂CH₂OH or ? OP(O)(OH)₂) depend on the starting ratio of [EG]₀/[H₃PO₄]₀, although even at the excess of EG the acidic end groups prevail because of the dealkylation process. In MALDI‐TOF‐ms products with P_n equal up to 21 have been observed. The average polymerization degrees (P_n) are lower and have been calculated from the proportion of the end groups. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 830–843, 2008     

Multielement determination of major elements in polymer additives by microwave induced plasma atomic emission spectrometry after microwave digestion

A method for multielement determination of major elements in polymer additives by microwave induced plasma atomic emission spectrometry (MIP-AES) has been elaborated. Microwave digestion with nitric acid was selected for sample preparation because of its speed and versatility. Sodium nitrate was added to the digestion mixture in order to reduce phosphorus losses. The precision obtained varied between 2 and 4.5% depending on the element determined. The accuracy of the method was studied by analyzing the Spex 5-element oil standard. The method was applied to a variety of commercial and in-house prepared compositions.     

4‐Benzoyl‐3,4‐dihydro‐2H‐1,4‐benzoxazine‐2‐carbonitrile: refinement using a multipolar atom model

The structural model for the title compound, C₁₆H₁₂N₂O₂, was refined using a multipolar atom model transferred from an experimental electron‐density database. The refinement showed some improvements of crystallographic statistical indices when compared with a conventional spherical neutral‐atom refinement. The title compound adopts a half‐chair conformation. The amide N atom lies almost in the plane defined by the three neighbouring C atoms. In the crystal structure, molecules are linked by weak intermolecular C—H...O and C—H...π hydrogen bonds.