“Chemical” domains of definition of mathematic relations in organic chemistry

The mathematic relations used in chemistry describe the processes with participation of various substances and the variations in the properties of chemical compounds. For the problems of the second type especially widely appearing in organic chemistry, introduction of concept of the chemical domains of definition of such relations, i.e. the scope of molecular structures in the domain for which application of these relations provides the maximum accuracy of obtained estimates, is expedient. By examples of some physical and chemical constants, including chromatography retention indices it, is shown that increase in the accuracy of the calculation equations can be reached not due to their complication, but by ascertaining definition of the chemical domains of their application. On the other hand, examples are demonstrated where the variation in the chemical domains of definition while the equations themselves remain unchanged open principally new opportunities of their application. Unlike mathematic domains of definition, their chemical equivalents cannot be revealed by the formal analysis of mathematic formulas. Solution of such problems, as a rule, requires computational checking of their applicability for compounds belonging to various groups.     

Recurrent approximation of densities and refractive indices of the homologs of different series

The mathematic relations used in chemistry describe the processes with participation of various substances and the variations in the properties of chemical compounds. For the problems of the second type especially widely appearing in organic chemistry, introduction of concept of the chemical domains of definition of such relations, i.e. the scope of molecular structures in the domain for which application of these relations provides the maximum accuracy of obtained estimates, is expedient. By examples of some physical and chemical constants, including chromatography retention indices it, is shown that increase in the accuracy of the calculation equations can be reached not due to their complication, but by ascertaining definition of the chemical domains of their application. On the other hand, examples are demonstrated where the variation in the chemical domains of definition while the equations themselves remain unchanged open principally new opportunities of their application. Unlike mathematic domains of definition, their chemical equivalents cannot be revealed by the formal analysis of mathematic formulas. Solution of such problems, as a rule, requires computational checking of their applicability for compounds belonging to various groups.     

Electron pairing and chemical bonds: pair localization in ELF domains from the analysis of domain averaged Fermi holes

This article reports the application of a recently proposed formalism of domain averaged Fermi holes to the problem of the localization of electron pairs in electron localization function (ELF) domains and its possible implications for the electron pair model of chemical bond. The main focus was on the systems, such as H2O or N2, in which the "unphysical" population of ELF domains makes the parallel between these domains and chemical bond questionable. On the basis of the results of the Fermi-hole analysis, we propose that the above problems could be due to the fact that in some cases the boundaries of the ELF domains need not be determined precisely enough.     

EGF‐like and Other Disulfide‐rich Microdomains as Therapeutic Scaffolds

Disulfide bonds typically introduce conformational constraints into peptides and proteins, conferring improved biopharmaceutical properties and greater therapeutic potential. In our opinion, disulfide‐rich microdomains from proteins are potentially a rich and under‐explored source of drug leads. A survey of the UniProt protein database shows that these domains are widely distributed throughout the plant and animal kingdoms, with the EGF‐like domain being the most abundant of these domains. EGF‐like domains exhibit large diversity in their disulfide bond topologies and calcium binding modes, which we classify in detail here. We found that many EGF‐like domains are associated with disease phenotypes, and the interactions they mediate are potential therapeutic targets. Indeed, EGF‐based therapeutic leads have been identified, and we further propose that these domains can be optimized to expand their therapeutic potential using chemical design strategies. This Review highlights the potential of disulfide‐rich microdomains as future peptide therapeutics.     

DARC系统——计算机化学的一个缩影

本文从化学结构的 DARC 码表述方法,结构-性质相关研究的 DARC-PELCO 方法,化学数据库和计算机辅助有机合成四个方面介绍了著名的法国计算机化学研究系统,即 DARC 系统。由于这四个方面包括了计算机化学最主要的研究领域,因此本文也就概要地介绍了计算机化学。     

Probing the local structure and mechanical response of nanostructures using force modulation and nanofabrication

Nanostructures of self-assembled monolayers (SAMs) are designed and produced using coadsorption and nanografting techniques. Because the structures of these artificially engineered domains are predesigned and well-characterized, a systematic investigation is possible to study the mechanical responses to force modulation under atomic force microscope tips. Force modulation imaging reveals characteristic contrast sensitivity to changes in molecular-level packing, molecule chain lengths, domain boundaries, and surface chemical functionalities in SAMs. By means of actively tuning the driving frequency, the resonances at the tip-surface contact are selectively activated. Therefore, specific surface features, such as the edges of the domains and nanostructures or desired chemical functionalities, can be selectively enhanced in the amplitude images. These observations provide a new and active approach in materials characterization and the study of nanotribology using atomic force microscopy.     

Description of functional groups by means of domain-restricted reduced density matrices

This report constitutes an application of our previous theoretical works on partitionings of the first-order reduced density matrix according to the atomic domains defined in the theory of atoms in molecules. The numerical determinations obtained reveal that the domain-restricted reduced density matrices, which are the tools resulting from the former treatments, are suitable devices to describe chemical features of molecular fragments. We have focused attention on a study of functional groups in several series of organic compounds confirming the usefulness of these tools.     

Spectroscopic and thermal studies of silicate-phosphate glass

The structure of silicate-phosphate glass containing the different amounts of phosphorus, magnesium and calcium cations, acting as macroelements was examined by FTIR, XRD and thermal (DTA/DSC) methods. It has been found that in the structure of silicate-phosphate glass modified by an addition of Mg²⁺ and Ca²⁺ there are formed domains characterized by certain degree of ordering of the units present in their composition, while the structure of the newly formed domains is similar to the structure of the crystal compounds formed during crystallization of these glasses. The changing character of domains structure may be the reason of different chemical activity of glass acting as glassy fertilizers.     

Preparation and methodology for chemical mapping of sol–gel thin films containing lysozyme

Sol–gels are seeing widespread interest as suitable materials for the immobilization of biomolecules in applications ranging from optical coatings to specialty biocatalysts. Although there are numerous studies that have characterized these materials in terms of their macroscopic properties, few studies have examined and correlated these properties at the microscopic level. This study describes a spin-coating technique for the preparation of aluminum-supported sol–gel thin films containing immobilized lysozyme [E.C. 3.2.1.17] that are suitable for chemical mapping using FTIR microscopy operating in reflectance mode. This type of information can then be used to understand a variety of aspects of these materials which can be used for optimal engineering of these materials, as well as insightful design and modeling. A data analysis method was developed to extract information on chemical speciation and domain information on the materials from FTIR data matrices. Results from these studies indicated that, contrary to what might be expected, these sol–gels are not homogeneous on the microscopic level. Instead, they are heterogeneous in both the distribution of lysozyme and hydrophobic monomers at the scale investigated (20 μm resolution). The method described here has promise in terms of providing a non-invasive approach of chemically mapping concentrations of proteinaceous and related substances as well as chemical domains in situ in sol–gel thin films.     

Explorations of catalytic domains in non-ribosomal peptide synthetase enzymology

Covering up to the end of 2011Many pharmaceuticals on the market today belong to a large class of natural products called nonribosomal peptides (NRPs). Originating from bacteria and fungi, these peptide-based natural products consist not only of the 20 canonical l-amino acids, but also non-proteinogenic amino acids, heterocyclic rings, sugars, and fatty acids, generating tremendous chemical diversity. As a result, these secondary metabolites exhibit a broad array of bioactivity, ranging from antimicrobial to anticancer. The biosynthesis of these complex compounds is carried out by large multimodular megaenzymes called nonribosomal peptide synthetases (NRPSs). Each module is responsible for incorporation of a monomeric unit into the natural product peptide and is composed of individual domains that perform different catalytic reactions. Biochemical and bioinformatic investigations of these enzymes have uncovered the key principles of NRP synthesis, expanding the pharmaceutical potential of their enzymatic processes. Progress has been made in the manipulation of this biosynthetic machinery to develop new chemoenzymatic approaches for synthesizing novel pharmaceutical agents with increased potency. This review focuses on the recent discoveries and breakthroughs in the structural elucidation, molecular mechanism, and chemical biology underlying the discrete domains within NRPSs.     

Role of dipolar interaction in the mesoscopic domains of phospholipid monolayers: dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylethanolamine

The role of dipolar interactions in determining the lipid domain shapes at the air-water interface with a change in the chemical structure of the head groups of lipids is theoretically studied. The phospholipids considered are dipalmitoylphosphatidylcholine (D,L-DPPC) and dipalmitoylphosphatidylethanolamine (DPPE). Despite closely similar chemical structures, the domains of the two lipids are strikingly different. The DPPC domains exhibit elongated arms, while the DPPE domains are nearly round-shaped. To compare the dipolar repulsions in the domains of the two phospholipids, different energy-minimized conformers of DPPC and DPPE are studied using the semiempirical quantum chemical method (PM3). It is found that the dipole moment of DPPC is significantly larger than that of DPPE. The in-plane and out-of-plane components of the dipole moments are calculated using grazing incidence X-ray diffraction data at different surface pressure values, as used in the experiment. The result indicates that the magnitude of the dipolar interaction is significantly larger in DPPC than that in DPPE over the surface pressure range considered. The enhanced dipolar repulsion corroborates well with the difference in the domain shapes in the two phospholipid monolayers. The larger dipolar repulsion in DPPC leads to development of elongated domain arms, while relatively less dipolar repulsion allows a closed shape of the condensed-phase DPPE domains.     

Chemical Approaches for Studying the Biology and Pharmacology of Membrane Transporters: The Histidine/Large Amino Acid Transporter SLC7A5 as a Benchmark

The localization of membrane transporters at the forefront of natural barriers makes these proteins very interesting due to their involvement in the absorption and distribution of nutrients and xenobiotics, including drugs. Over the years, structure/function relationship studies have been performed employing several strategies, including chemical modification of exposed amino acid residues. These approaches are very meaningful when applied to membrane transporters, given that these proteins are characterized by both hydrophobic and hydrophilic domains with a different degree of accessibility to employed chemicals. Besides basic features, the chemical targeting approaches can disclose information useful for pharmacological applications as well. An eminent example of this picture is the histidine/large amino acid transporter SLC7A5, known as LAT1 (Large Amino Acid Transporter 1). This protein is crucial in cell life because it is responsible for mediating the absorption and distribution of essential amino acids in peculiar body districts, such as the blood brain barrier and placenta. Furthermore, LAT1 can recognize a large variety of molecules of pharmacological interest and is also considered a hot target for drugs due to its over-expression in virtually all human cancers. Therefore, it is not surprising that the chemical targeting approach, coupled with bioinformatics, site-directed mutagenesis and transport assays, proved fundamental in describing features of LAT1 such as the substrate binding site, regulatory domains and interactions with drugs that will be discussed in this review. The results on LAT1 can be considered to have general applicability to other transporters linked with human diseases.     

Mechanism and kinetics of ordering in diblock copolymer thin films on chemically nanopatterned substrates

Lamellae forming diblock copolymer domains can be directed to assemble without defects and in registration with chemically nanopatterned substrates. Initially, thin films of the lamellar poly(styrene-b-methyl methacrylate) block copolymer form hexagonally close-packed styrene domains when annealed on chemical nanopatterned striped surfaces. These styrene domains then coalesce to form linear styrene domains that are not fully registered with the underlying chemical surface pattern. Defects coarsen, until defect-free directed assembly is obtained, by breaking linear styrene domains and reforming new structures until registered lamellae have been formed. At all stages in the process, two factors play an important role in the observed degree of registration of the block copolymer domains as a function of annealing time: the interfacial energy between the blocks of the copolymer and the chemically nanopatterned substrate and the commensurability of the bulk repeat period of the block copolymer and the substrate pattern period. Insight into the time-dependent three-dimensional behavior of the block copolymer structures is gained from single chain in mean field simulations. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 3444–3459, 2005     

Reactive domains of energy hypersurfaces and the stability of minimum energy reaction paths

Special properties of the Riemannian metric for energy hypersurfaces, defined within the framework of the Born-Oppenheimer approximation, are utilized in devising a partitioning scheme for domains of nuclear coordinates. The chemically important coordinate domains are distinguished from domains of lesser importance by their curvature properties. Conditions are derived for the stability of minimum energy reaction paths, and the effects of instability regions are investigated. Instability domains along minimum energy paths may allow small vibrational perturbations to alter the outcome of the chemical reaction.     

New improved convergence analysis for Newton-like methods with applications

We present a new semilocal convergence analysis for Newton-like methods using restricted convergence domains in a Banach space setting. The main goal of this study is to expand the applicability of these methods in cases not covered in earlier studies. The advantages of our approach include, under the same computational cost as previous studies, a more precise convergence analysis under the same computational cost on the Lipschitz constants involved. Numerical studies including a chemical application are also provided in this study.     

Parallel Chemical Protein Synthesis on a Surface Enables the Rapid Analysis of the Phosphoregulation of SH3 Domains

Analysis of postranslationally modified protein domains is complicated by an availability problem, as recombinant methods rarely allow site‐specificity at will. Although total synthesis enables full control over posttranslational and other modifications, chemical approaches are limited to shorter peptides. To solve this problem, we herein describe a method that combines a) immobilization of N‐terminally thiolated peptide hydrazides by hydrazone ligation, b) on‐surface native chemical ligation with self‐purified peptide thioesters, c) radical‐induced desulfurization, and d) a surface‐based fluorescence binding assay for functional characterization. We used the method to rapidly investigate 20 SH3 domains, with a focus on their phosphoregulation. The analysis suggests that tyrosine phosphorylation of SH3 domains found in Abl kinases act as a switch that can induce both the loss and, unexpectedly, gain of affinity for proline‐rich ligands.     

Large-scale supramolecular structure in solutions of low molar mass compounds and mixtures of liquids: I. Light scattering characterization

Static and dynamic laser light scattering were used to bring evidence of large-scale supramolecular structure in solutions of low molar mass electrolytes, nonelectrolytes, and mixtures of liquids. It was shown that solutes are distributed inhomogeneously on large length scales. Regions of higher and lower solute concentration exist in solution and give sufficient scattering contrast for experimental observation. A detailed light scattering study showed that these regions can be characterized as close-to-spherical discrete domains of higher solute density in a less dense rest of solution. These domains do contain solvent inside and can be therefore characterized as loose associates (giant clusters, aggregates). Their size distributions are significantly broad, ranging up to several hundreds of nanometers. Characteristic sizes of these inhomogenities thus exceed angstrom dimensions of individual molecules by several orders of magnitude. The number of solute molecules per domain varies approximately in the range 10(3)-10(8). Phenomena described were observed in a very broad range of solutes and solvents. Among others, selected data on most common substances of great chemical and biological importance such as sodium chloride, citric acid, glucose, urea, acetic acid, and ethanol are presented.     

Surface derivatization strategy for combinatorial analysis of cell response to mixtures of protein domains

We report a robust strategy for conjugating mixtures of two or more protein domains to nonfouling polyurethane surfaces. In our strategy, the carbamate groups of polyurethane are reacted with zirconium alkoxide from the vapor phase to give a surface-bound oxide that serves as a chemical layer that can be used to bond organics to the polymer substrate. A hydroxyalkylphosphonate monolayer was synthesized on this layer, which was then used to covalently bind primary amine groups in protein domains using chloroformate-derived cross-linking. The effectiveness of this synthesis strategy was gauged by using an ELISA to measure competitive, covalent bonding of cell-binding (III(9-10)) and fibronectin-binding (III(1-2)) domains of the cell adhesion protein fibronectin. Cell adhesion, spreading, and fibronectin matrix assembly were examined on surfaces conjugated with single domains, a 1:1 surface mixture of III(1-2) and III(9-10), and a recombinant protein "duplex" containing both domains in one fusion protein. The mixture performed as well as or better than the other surfaces in these assays. Our surface activation strategy is amenable to a wide range of polymer substrates and free amino group-containing protein fragments. As such, this technique may be used to create biologically specific materials through the immobilization of specific protein groups or mixtures thereof on a substrate surface.     

Design and properties of functional hybrid organic-inorganic membranes for fuel cells

This critical review presents a discussion on the major advances in the field of organic-inorganic hybrid membranes for fuel cells application. The hybrid organic-inorganic approach, when the organic part is not conductive, reproduces to some extent the behavior of Nafion where discrete hydrophilic and hydrophilic domains are homogeneously distributed. A large variety of proton conducting or non conducting polymers can be combined with various functionalized, inorganic mesostructured particles or an inorganic network in order to achieve high proton conductivity, and good mechanical and chemical properties. The tuning of the interface between these two components and the control over chemical and processing conditions are the key parameters in fabricating these hybrid organic-inorganic membranes with a high degree of reproducibility. This dynamic coupling between chemistry and processing requires the extensive use and development of complementary ex situ measurements with in situ characterization techniques, following in real time the molecular precursor solutions to the formation of the final hybrid organic-inorganic membranes. These membranes combine the intrinsic physical and chemical properties of both the inorganic and organic components. The development of the sol-gel chemistry allows a fine tuning of the inorganic network, which exhibits acid-based functionalized pores (-SO(3)H, -PO(3)H(2), -COOH), tunable pore size and connectivity, high surface area and accessibility. As such, these hybrid membranes containing inorganic materials are a promising family for controlling conductivity, mechanical and chemical properties (349 references).     

Electron pairing and chemical bonds. Electron fluctuation and pair localization in ELF domains

This article reports the numerical comparison of the quantities characterizing the extent of electron fluctuation and pair localization in the domains determined by the direct minimization of electron fluctuation with the domains resulting from the partitioning of the molecules based on the topological analysis of the so-called electron localization function (ELF). Such a comparison demonstrates that the ELF partitioning can be regarded as a feasible alternative to computationally much more demanding direct optimization of minimum fluctuation domains. This opened the possibility of the systematic scrutiny of the electron pair model of the chemical bond, and as it was demonstrated, the previous pessimistic claims about the applicability of this model are not completely justified.