IJMS: Physical Chemistry, Theoretical and Computational Chemistry

IJMS, Vol. 11, Pages 1020-1047: A Review on Progress in QSPR Studies for Surfactants

Jiwei Hu — Mon, 08 Mar 2010 00:00:00 CET

This paper presents a review on recent progress in quantitative structure-property relationship (QSPR) studies of surfactants and applications of various molecular descriptors. QSPR studies on critical micelle concentration (cmc) and surface tension (γ) of surfactants are introduced. Studies on charge distribution in ionic surfactants by quantum chemical calculations and its effects on the structures and properties of the colloids of surfactants are also reviewed. The trends of QSPR studies on cloud point (for nonionic surfactants), biodegradation potential and some other properties of surfactants are evaluated .

IJMS, Vol. 11, Pages 927-942: Activated Carbon Modified with Copper for Adsorption of Propanethiol

Juan Carlos Moreno-Piraján — Thu, 04 Mar 2010 00:00:00 CET

Activated carbons were characterized texturally and chemically before and after treatment, using surface area determination in the BET model, Boehm titration, TPR, DRX and immersion calorimetry. The adsorption capacity and the kinetics of sulphur compound removal were determined by gas chromatography. It was established that the propanethiol retention capacity is dependent on the number of oxygenated groups generated on the activated carbon surface and that activated carbon modified with CuO at 0.25 M shows the highest retention of propanethiol. Additionally is proposed a mechanism of decomposition of propenothiol with carbon-copper system.

IJMS, Vol. 11, Pages 880-895: QSAR Studies on Andrographolide Derivatives as α-Glucosidase Inhibitors

Jun Xu — Tue, 02 Mar 2010 00:00:00 CET

Andrographolide derivatives were shown to inhibit α-glucosidase. To investigate the relationship between activities and structures of andrographolide derivatives, a training set was chosen from 25 andrographolide derivatives by the principal component analysis (PCA) method, and a quantitative structure-activity relationship (QSAR) was established by 2D and 3D QSAR methods. The cross-validation r2 (0.731) and standard error (0.225) illustrated that the 2D-QSAR model was able to identify the important molecular fragments and the cross-validation r2 (0.794) and standard error (0.127) demonstrated that the 3D-QSAR model was capable of exploring the spatial distribution of important fragments. The obtained results suggested that proposed combination of 2D and 3D QSAR models could be useful in predicting the α-glucosidase inhibiting activity of andrographolide derivatives.

IJMS, Vol. 11, Pages 507-520: Bacillus marcorestinctum sp. nov., a Novel Soil Acylhomoserine Lactone Quorum-Sensing Signal Quenching Bacterium

Yan Han — Wed, 03 Feb 2010 00:00:00 CET

A Gram-positive, facultatively anaerobic, endospore-forming and rod-shaped bacterium was isolated from soil samples and designated strain LQQ. This organism strongly quenches the acylhomoserine lactone quorum-sensing signal. The LQQ strain exhibits phenotypic characteristics consistent with its classification in the genus Bacillus. It is positive in catalase and no special growth factor is needed. It uses glucose as sole carbon source. The DNA G + C content is 39.8 mol %. The closest relatives based on the 16S rRNA gene sequence are Bacillus anthracis, Bacillus thuringiensis, and Brevibacillus brevis (syn. Bacillus brevis) with the similarity of 96.5%. The DNA–DNA hybridization data indicates a low level of genomic relatedness with the relative type strains of Bacillus thuringiensis (6.1%), Bacillus anthracis (10.5%) and Brevibacillus brevis (8.7%). On the basis of the phenotypic and phylogenetic data together with the genomic distinctiveness, the LQQ strain represents a novel species of the genus Bacillus, for which the name Bacillus marcorestinctum sp. nov. is proposed. The type strain is LQQT.

IJMS, Vol. 11, Pages 492-506: Effective Population Size, Gene Flow, and Species Status in a Narrow Endemic Sunflower, Helianthus neglectus, Compared to Its Widespread Sister Species, H. petiolaris

Andrew R. Raduski — Tue, 02 Feb 2010 00:00:00 CET

Species delimitation has long been a difficult and controversial process, and different operational criteria often lead to different results. In particular, investigators using phenotypic vs. molecular data to delineate species may recognize different boundaries, especially if morphologically or ecologically differentiated populations have only recently diverged. Here we examine the genetic relationship between the widespread sunflower species Helianthus petiolaris and its narrowly distributed sand dune endemic sister species H. neglectus using sequence data from nine nuclear loci. The two species were initially described as distinct based on a number of minor morphological differences, somewhat different ecological tolerances, and at least one chromosomal rearrangement distinguishing them; but detailed molecular data has not been available until now. We find that, consistent with previous work, H. petiolaris is exceptionally genetically diverse. Surprisingly, H. neglectus harbors very similar levels of genetic diversity (average diversity across loci is actually slightly higher in H. neglectus). It is extremely unlikely that such a geographically restricted species could maintain these levels of genetic variation in isolation. In addition, the two species show very little evidence of any genetic divergence, and estimates of interspecific gene flow are comparable to gene flow estimates among regions within H. petiolaris. These results indicate that H. petiolaris and H. neglectus likely do not represent two distinct, isolated gene pools; H. neglectus is probably more accurately thought of as a geographically restricted, morphologically and ecologically distinct subspecies of H. petiolaris rather than a separate species.

IJMS, Vol. 11, Pages 407-426: The Fibrillar Collagen Family

Jean-Yves Exposito — Thu, 28 Jan 2010 00:00:00 CET

Collagens, or more precisely collagen-based extracellular matrices, are often considered as a metazoan hallmark. Among the collagens, fibrillar collagens are present from sponges to humans, and are involved in the formation of the well-known striated fibrils. In this review we discuss the different steps in the evolution of this protein family, from the formation of an ancestral fibrillar collagen gene to the formation of different clades. Genomic data from the choanoflagellate (sister group of Metazoa) Monosiga brevicollis, and from diploblast animals, have suggested that the formation of an ancestral α chain occurred before the metazoan radiation. Phylogenetic studies have suggested an early emergence of the three clades that were first described in mammals. Hence the duplication events leading to the formation of the A, B and C clades occurred before the eumetazoan radiation. Another important event has been the two rounds of “whole genome duplication” leading to the amplification of fibrillar collagen gene numbers, and the importance of this diversification in developmental processes. We will also discuss some other aspects of fibrillar collagen evolution such as the development of the molecular mechanisms involved in the formation of procollagen molecules and of striated fibrils.

IJMS, Vol. 11, Pages 370-385: Phylogenetics Applied to Genotype/Phenotype Association and Selection Analyses with Sequence Data from Angptl4 in Humans

Taylor J. Maxwell — Mon, 25 Jan 2010 00:00:00 CET

Genotype/phenotype association analyses (Treescan) with plasma lipid levels and functional site prediction methods (TreeSAAP and PolyPhen) were performed using sequence data for ANGPTL4 from 3,551 patients in the Dallas Heart Study. Biological assays of rare variants in phenotypic tails and results from a Treescan analysis were used as “known” variants to assess the site prediction abilities of PolyPhen and TreeSAAP. The E40K variant in European Americans and the R278Q variant in African Americans were significantly associated with multiple lipid phenotypes. Combining TreeSAAP and PolyPhen performed well to predict “known” functional variants while reducing noise from false positives.

IJMS, Vol. 11, Pages 124-139: The Diverse Applications of Cladistic Analysis of Molecular Evolution, with Special Reference to Nested Clade Analysis

Alan R. Templeton — Fri, 08 Jan 2010 00:00:00 CET

The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This review demonstrates some of the many ways in which clades (branches) of haplotype trees have been applied in recent years, including the study of genotype/phenotype associations at candidate loci and in genome-wide association studies, the phylogeographic history of species, human evolution, the conservation of endangered species, and the identification of species.

IJMS, Vol. 10, Pages 5455-5470: Sharp Phylogeographic Breaks and Patterns of Genealogical Concordance in the Brine Shrimp Artemia franciscana

Stefania Maniatsi — Fri, 18 Dec 2009 00:00:00 CET

Genealogical concordance is a critical overlay of all phylogenetic analyses, irrespective of taxonomic level. To assess such patterns of congruence we have compiled and derived sequence data for two mitochondrial (16S rRNA, COI) and two nuclear (ITS1, p26) markers in 14 American populations of the hypersaline branchiopod Artemia franciscana. Cladistic analysis revealed three reciprocally monophyletic mitochondrial clades. For nuclear DNA, incomplete lineage sorting was evident presumably as a result of slower coalescence or male-mediated dispersal. Our findings capture the genealogical interval between gene splitting and population divergence. In this sense, strong indications are provided in favour of a superspecies status and ongoing speciation in A. franciscana.

IJMS, Vol. 10, Pages 5296-5325: On the Physical Meaning of the Isothermal Titration Calorimetry Measurements in Calorimeters with Full Cells

Jean-Pierre E. Grolier — Wed, 09 Dec 2009 00:00:00 CET

We have performed a detailed study of the thermodynamics of the titration Process in an isothermal titration calorimeter with full cells. We show that the relationship between the enthalpy and the heat measured is better described in terms of the equation ΔH = Winj + Q (where Winj is the work necessary to carry out the titration) than in terms of ΔH = Q. Moreover, we show that the heat of interaction between two components is related to the partial enthalpy of interaction at infinite dilution of the titrant component, as well as to its partial volume of interaction at infinite dilution.

IJMS, Vol. 10, Pages 5135-5216: A Review of Computational Methods in Materials Science: Examples from Shock-Wave and Polymer Physics

Martin O. Steinhauser — Tue, 01 Dec 2009 00:00:00 CET

This review discusses several computational methods used on different length and time scales for the simulation of material behavior. First, the importance of physical modeling and its relation to computer simulation on multiscales is discussed. Then, computational methods used on different scales are shortly reviewed, before we focus on the molecular dynamics (MD) method. Here we survey in a tutorial-like fashion some key issues including several MD optimization techniques. Thereafter, computational examples for the capabilities of numerical simulations in materials research are discussed. We focus on recent results of shock wave simulations of a solid which are based on two different modeling approaches and we discuss their respective assets and drawbacks with a view to their application on multiscales. Then, the prospects of computer simulations on the molecular length scale using coarse-grained MD methods are covered by means of examples pertaining to complex topological polymer structures including star-polymers, biomacromolecules such as polyelectrolytes and polymers with intrinsic stiffness. This review ends by highlighting new emerging interdisciplinary applications of computational methods in the field of medical engineering where the application of concepts of polymer physics and of shock waves to biological systems holds a lot of promise for improving medical applications such as extracorporeal shock wave lithotripsy or tumor treatment.

IJMS, Vol. 10, Pages 5104-5114: Formation Energies of Antiphase Boundaries in GaAs and GaP: An ab Initio Study

Oleg Rubel — Wed, 25 Nov 2009 00:00:00 CET

Electronic and structural properties of antiphase boundaries in group III-V semiconductor compounds have been receiving increased attention due to the potential to integration of optically-active III-V heterostructures on silicon or germanium substrates. The formation energies of {110}, {111}, {112}, and {113} antiphase boundaries in GaAs and GaP were studied theoretically using a full-potential linearized augmented plane-wave density-functional approach. Results of the study reveal that the stoichiometric {110} boundaries are the most energetically favorable in both compounds. The specific formation energy γ of the remaining antiphase boundaries increases in the order of γf113g ≈ γf112g < γf111g, which suggests {113} and {112} as possible planes for faceting and annihilation of antiphase boundaries in GaAs and GaP.

IJMS, Vol. 10, Pages 5054-5089: Combined Molecular Algorithms for the Generation, Equilibration and Topological Analysis of Entangled Polymers: Methodology and Performance

Nikos Ch. Karayiannis — Mon, 23 Nov 2009 00:00:00 CET

We review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the implementation of both, the Monte Carlo (MC) procedure for the system generation and equilibration, and a postprocessing step, where we identify the underlying topological structure of the simulated systems in the form of primitive paths. In order to demonstrate our arguments, we study how molecular length and packing density (volume fraction) affect the performance of the MC scheme built around chain-connectivity altering moves. In parallel, we quantify the effect of finite system size, of polydispersity, and of the definition of the number of entanglements (and related entanglement molecular weight) on the results about the primitive path network. Along these lines we approve main concepts which had been previously proposed in the literature.

IJMS, Vol. 10, Pages 4816-4940: Path Integrals for Electronic Densities, Reactivity Indices, and Localization Functions in Quantum Systems

Mihai V. Putz — Tue, 10 Nov 2009 00:00:00 CET

The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr’s quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions – all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems.

IJMS, Vol. 10, Pages 4723-4741: The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework

Daniel P. Faith — Tue, 03 Nov 2009 00:00:00 CET

The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional specieslevel ecological indices to the features level. The “phylogenetic beta diversity” framework developed by microbial ecologists calculates PD-dissimilarities between community localities. Interpretation of these PD-dissimilarities at the feature level explains the framework’s success in producing ordinations revealing environmental gradients. An example gradients space using PD-dissimilarities illustrates how evolutionary features form unimodal response patterns to gradients. This features model supports new application of existing species-level methods that are robust to unimodal responses, plus novel applications relating to climate change, commercial products discovery, and community assembly.

IJMS, Vol. 10, Pages 4474-4497: Köln-Timişoara Molecular Activity Combined Models toward Interspecies Toxicity Assessment

Sergiu A. Chicu — Thu, 22 Oct 2009 00:00:00 CEST

Aiming to provide a unified picture of computed activity – quantitative structure activity relationships, the so called Köln (ESIP-ElementSpecificInfluenceParameter) model for activity and Timisoara (Spectral-SAR) formulation of QSAR were pooled in order to assess the toxicity modeling and inter-toxicity correlation maps for aquatic organisms against paradigmatic organic compounds. The Köln ESIP model for estimation of a compound toxicity is based on the experimental measurement expressing the direct action of chemicals on the organism Hydractinia echinata so that the structural influence parameters are reflected by the metamorphosis degree itself. As such, the calculation of the structural parameters is absolutely necessary for correct evaluation and interpretation of the evolution of M(easured) and the C(computed) values. On the other hand, the Timişoara Spectral-SAR analysis offers correlation models and paths for H.e. species as well as for four other different organisms with which the toxicity may be inter-changed by means of the same mechanism of action induced by certain common chemicals.

IJMS, Vol. 10, Pages 4342-4351: First-Principles Molecular Dynamics Calculations of the Equation of State for Tantalum

Shigeaki Ono — Fri, 09 Oct 2009 00:00:00 CEST

The equation of state of tantalum (Ta) has been investigated to 100 GPa and 3,000 K using the first-principles molecular dynamics method. A large volume dependence of the thermal pressure of Ta was revealed from the analysis of our data. A significant temperature dependence of the calculated effective Grüneisen parameters was confirmed at high pressures. This indicates that the conventional approach to analyze thermal properties using the Mie-Grüneisen approximation is likely to have a significant uncertainty in determining the equation of state for Ta, and that an intrinsic anharmonicity should be considered to analyze the equation of state.

IJMS, Vol. 10, Pages 4310-4329: Modelling Catalyst Surfaces Using DFT Cluster Calculations

Izabela Czekaj — Wed, 30 Sep 2009 00:00:00 CEST

We review our recent theoretical DFT cluster studies of a variety of industrially relevant catalysts such as TiO2, γ-Al2O3, V2O5-WO3-TiO2 and Ni/Al2O3. Aspects of the metal oxide surface structure and the stability and structure of metal clusters on the support are discussed as well as the reactivity of surfaces, including their behaviour upon poisoning. It is exemplarily demonstrated how such theoretical considerations can be combined with DRIFT and XPS results from experimental studies.

IJMS, Vol. 10, Pages 4284-4289: Theoretical Study on Reactions of Triplet Excited State Thioxanthone with Indole

Liang Shen — Wed, 30 Sep 2009 00:00:00 CEST

In the present work, a theoretical study on the deactivation of triplet excited (T1) state thioxanthone (TX) by indole (INH) was performed, based on density functional theory calculations. Three feasible pathways, namely direct electron transfer from INH to T1 state TX, electron transfer followed by proton transfer from INH·+ to TX·– , and H-atom transfer from nitrogen of INH to keto oxygen of T1 state TX, were proposed theoretically to be involved in T1 state TX deactivation by INH.

IJMS, Vol. 10, Pages 4137-4156: Binding and Docking Interactions of NO, CO and O2 in Heme Proteins as Probed by Density Functional Theory

Vangelis Daskalakis — Tue, 22 Sep 2009 00:00:00 CEST

Dynamics and reactivity in heme proteins include direct and indirect interactions of the ligands/substrates like CO, NO and O2 with the environment. Direct electrostatic interactions result from amino acid side chains in the inner cavities and/or metal coordination in the active site, whereas indirect interactions result by ligands in the same coordination sphere. Interactions play a crucial role in stabilizing transition states in catalysis or altering ligation chemistry. We have probed, by Density Functional Theory (DFT), the perturbation degree in the stretching vibrational frequencies of CO, NO and O2 molecules in the presence of electrostatic interactions or hydrogen bonds, under conditions simulating the inner cavities. Moreover, we have studied the vibrational characteristics of the heme bound form of the CO and NO ligands by altering the chemistry of the proximal to the heme ligand. CO, NO and O2 molecules are highly polarizable exerting vibrational shifts up to 80, 200 and 120 cm-1, respectively, compared to the non-interacting ligand. The importance of Density Functional Theory (DFT) methodology in the investigation of the heme-ligand-protein interactions is also addressed.

IJMS, Vol. 10, Pages 3951-3970: Host Defense Peptides as Effector Molecules of the Innate Immune Response: A Sledgehammer for Drug Resistance?

Lars Steinstraesser — Wed, 09 Sep 2009 00:00:00 CEST

Host defense peptides can modulate the innate immune response and boost infection-resolving immunity, while dampening potentially harmful pro-inflammatory (septic) responses. Both antimicrobial and/or immunomodulatory activities are an integral part of the process of innate immunity, which itself has many of the hallmarks of successful anti-infective therapies, namely rapid action and broad-spectrum antimicrobial activities. This gives these peptides the potential to become an entirely new therapeutic approach against bacterial infections. This review details the role and activities of these peptides, and examines their applicability as development candidates for use against bacterial infections.

IJMS, Vol. 10, Pages 3918-3930: A Proline-Based Neuraminidase Inhibitor: DFT Studies on the Zwitterion Conformation, Stability and Formation

Zhi-Wei Yang — Mon, 07 Sep 2009 00:00:00 CEST

The designs of potent neuraminidase (NA) inhibitors are an efficient way to deal with the recent “2009 H1N1” influenza epidemic. In this work, density functional calculations were employed to study the conformation, stability and formation of the zwitterions of 5-[(1R,2S)-1-(acetylamino)-2-methoxy-2-methylpentyl]-4-[(1Z)-1-propenyl]-(4S,5R)-D-proline (BL), a proline-based NA inhibitor. Compared to proline, the zwitterion stability of BL is enhanced by 1.76 kcal mol-1 due to the introduction of functional groups. However, the zwitterion of BL will not represent a local minimum on the potential energy surface until the number of water molecules increases up to two (n = 2). With the addition of two and three water molecules, the energy differences between the zwitterions and corresponding canonical isomers were calculated at 3.13 and -1.54 kcal mol-1, respectively. The zwitterions of BL are mainly stabilized by the H-bonds with the water molecules, especially in the case of three water molecules where the carboxyl-O atoms are largely coordination-saturated by three H-bonds of medium strengths, causing the zwitterion stability even superior to the canonical isomer. With the presence of two and three water molecules, the energy barriers for the conversion processes from the canonical isomers to the zwitterions are equal to 4.96 and 3.13 kcal mol-1, respectively. It indicated that the zwitterion formation is facile to take place with addition of two molecules and further facilitated by more water molecules. Besides, the zwitterion formation of BL is finished in a single step, different from other NA inhibitors. Owing to the above advantages, BL is a good NA inhibitor candidate and more attention should be paid to explorations of BL-based drugs.

IJMS, Vol. 10, Pages 3836-3860: Reticulate Evolution and Marine Organisms: The Final Frontier?

Michael L. Arnold — Thu, 03 Sep 2009 00:00:00 CEST

The role that reticulate evolution (i.e., via lateral transfer, viral recombination and/or introgressive hybridization) has played in the origin and adaptation of individual taxa and even entire clades continues to be tested for all domains of life. Though falsified for some groups, the hypothesis of divergence in the face of gene flow is becoming accepted as a major facilitator of evolutionary change for many microorganisms, plants and animals. Yet, the effect of reticulate evolutionary change in certain assemblages has been doubted, either due to an actual dearth of genetic exchange among the lineages belonging to these clades or because of a lack of appropriate data to test alternative hypotheses. Marine organisms represent such an assemblage. In the past half-century, some evolutionary biologists interested in the origin and trajectory of marine organisms, particularly animals, have posited that horizontal transfer, introgression and hybrid speciation have been rare. In this review, we provide examples of such genetic exchange that have come to light largely as a result of analyses of molecular markers. Comparisons among these markers and between these loci and morphological characters have provided numerous examples of marine microorganisms, plants and animals that possess the signature of mosaic genomes.

IJMS, Vol. 10, Pages 3743-3754: Theoretical Investigation of the NO3 Radical Addition to Double Bonds of Limonene

Lei Jiang — Thu, 27 Aug 2009 00:00:00 CEST

The addition reactions of NO3 to limonene have been investigated using ab initio methods. Six different possibilities for NO3 addition to the double bonds, which correspond to the two C–C double bonds (endocyclic or exocyclic) have been considered. The negative activation energies for the addition of NO3 to limonene are calculated and the energies of NO3-limonene radical adducts are found to be 14.55 to 20.17 kcal mol-1 more stable than the separated NO3 and limonene at the CCSD(T)/6-31G(d) + CF level. The results also indicate that the endocyclic addition reaction is more energetically favorable than the exocyclic one.

IJMS, Vol. 10, Pages 3671-3712: Chemical Interactions and Their Role in the Microphase Separation of Block Copolymer Thin Films

Richard A. Farrell — Tue, 25 Aug 2009 00:00:00 CEST

The thermodynamics of self-assembling systems are discussed in terms of the chemical interactions and the intermolecular forces between species. It is clear that there are both theoretical and practical limitations on the dimensions and the structural regularity of these systems. These considerations are made with reference to the microphase separation that occurs in block copolymer (BCP) systems. BCP systems self-assemble via a thermodynamic driven process where chemical dis-affinity between the blocks driving them part is balanced by a restorative force deriving from the chemical bond between the blocks. These systems are attracting much interest because of their possible role in nanoelectronic fabrication. This form of self-assembly can obtain highly regular nanopatterns in certain circumstances where the orientation and alignment of chemically distinct blocks can be guided through molecular interactions between the polymer and the surrounding interfaces. However, for this to be possible, great care must be taken to properly engineer the interactions between the surfaces and the polymer blocks. The optimum methods of structure directing are chemical pre-patterning (defining regions on the substrate of different chemistry) and graphoepitaxy (topographical alignment) but both centre on generating alignment through favourable chemical interactions. As in all self-assembling systems, the problems of defect formation must be considered and the origin of defects in these systems is explored. It is argued that in these nanostructures equilibrium defects are relatively few and largely originate from kinetic effects arising during film growth. Many defects also arise from the confinement of the systems when they are ‘directed’ by topography. The potential applications of these materials in electronics are discussed.

IJMS, Vol. 10, Pages 3658-3670: Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome

Huai-Kuang Tsai — Fri, 21 Aug 2009 00:00:00 CEST

Neighboring genes in the eukaryotic genome have a tendency to express concurrently, and the proximity of two adjacent genes is often considered a possible explanation for their co-expression behavior. However, the actual contribution of the physical distance between two genes to their co-expression behavior has yet to be defined. To further investigate this issue, we studied the co-expression of neighboring genes in zebrafish, which has a compact genome and has experienced a whole genome duplication event. Our analysis shows that the proportion of highly co-expressed neighboring pairs (Pearson’s correlation coefficient R>0.7) is low (0.24% ~ 0.67%); however, it is still significantly higher than that of random pairs. In particular, the statistical result implies that the co-expression tendency of neighboring pairs is negatively correlated with their physical distance. Our findings therefore suggest that physical distance may play an important role in the co-expression of neighboring genes. Possible mechanisms related to the neighboring genes’ co-expression are also discussed.

IJMS, Vol. 10, Pages 3531-3546: The Role of Probiotics in the Poultry Industry

S. M. Lutful Kabir — Wed, 12 Aug 2009 00:00:00 CEST

The increase of productivity in the poultry industry has been accompanied by various impacts, including emergence of a large variety of pathogens and bacterial resistance. These impacts are in part due to the indiscriminate use of chemotherapeutic agents as a result of management practices in rearing cycles. This review provides a summary of the use of probiotics for prevention of bacterial diseases in poultry, as well as demonstrating the potential role of probiotics in the growth performance and immune response of poultry, safety and wholesomeness of dressed poultry meat evidencing consumer’s protection, with a critical evaluation of results obtained to date.

IJMS, Vol. 10, Pages 3502-3516: Theoretical Study for High-Energy-Density Compounds Derived from Cyclophosphazene. IV. DFT Studies on 1,1-Diamino-3,3,5,5,7,7-hexaazidocyclotetraphosphazene and Its Isomers

Jianguo Zhang — Thu, 06 Aug 2009 00:00:00 CEST

In the present study, a theoretical study of 1,1-diaminohexaazidocyclo-tetraphophazene (DAHA) and its isomers has been performed, using quantum computational density functional theory (B3LYP and B3PW91 methods) with 6-31G* and 6-31G** basis sets implemented in Gaussian 03 program suite. Molecular structure and bonding, vibrational frequencies, Milliken population analysis, and natural bond orbit (NBO) have been studied. The heats of formation from atomization energies have also been calculated based on the optimized geometry. The obtained heats of formation data are compared with their homologous cyclophosphazene in order to demonstrate the accuracy of the methods, which indicate that the studied compounds might be potentially used as high energetic materials. In addition, the relative stability of five isomers have been deduced based on the total energy and the gap of frontier orbital energies.

IJMS, Vol. 10, Pages 3488-3501: Conformational Analysis of Thioether Musks Using Density Functional Theory

William N. Setzer — Tue, 04 Aug 2009 00:00:00 CEST

A conformational analysis of nine macrocyclic thioether musks has been carried out using molecular mechanics (MMFF), density functional theory (DFT) using both B3LYP and M06 functionals, as well as Hartree-Fock and post-Hartree-Fock (MP2) ab initio methods. 6-Thia-, 10-thia- and 4-methyl-5-thia-14-tetradecananolide, 4-thia-, 7-thia-, 11-thia- and 12-thia-15-pentadecanolide and 6-thia- and 12-thia-16-hexadecanolide were modeled. Unfortunately, there was little agreement between the computational methods at the levels of theory used in this study.

IJMS, Vol. 10, Pages 3478-3487: Accurate Analysis of Tumor Margins Using a Fluorescent pH Low Insertion Peptide (pHLIP)

James Segala — Tue, 04 Aug 2009 00:00:00 CEST

The recurrence of certain cancers remains quite high due to either incomplete surgical removal of the primary tumor or the presence of small metastases that are invisible to the surgeon. Near infrared (NIR) fluorescence imaging might improve surgical outcomes by providing sensitive, specific, and real-time visualization of normal and diseased tissues if agents can be found that discriminate between normal and diseased tissue and define tumor margins. We have developed a new approach for revealing tumor borders by using NIR fluorescently labeled pH Low Insertion Peptide (pHLIP) and have created a computational program for the quantitative assessment of tumor boundaries. The approach is tested in vivo by co-localization of GFP-tumors and NIR emission from the fluorescently labeled pHLIP, and it is found that boundaries are accurately reported and that sub-millimeter masses can be detected.

IJMS, Vol. 10, Pages 3457-3477: Analysis of Cooperativity by Isothermal Titration Calorimetry

Alan Brown — Tue, 04 Aug 2009 00:00:00 CEST

Cooperative binding pervades Nature. This review discusses the use of isothermal titration calorimetry (ITC) in the identification and characterisation of cooperativity in biological interactions. ITC has broad scope in the analysis of cooperativity as it determines binding stiochiometries, affinities and thermodynamic parameters, including enthalpy and entropy in a single experiment. Examples from the literature are used to demonstrate the applicability of ITC in the characterisation of cooperative systems.

IJMS, Vol. 10, Pages 3420-3441: RNA Relics and Origin of Life

Jacques Demongeot — Fri, 31 Jul 2009 00:00:00 CEST

A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells.

IJMS, Vol. 10, Pages 3400-3419: Plant Antimicrobial Agents and Their Effects on Plant and Human Pathogens

Rocío González-Lamothe — Fri, 31 Jul 2009 00:00:00 CEST

To protect themselves, plants accumulate an armoury of antimicrobial secondary metabolites. Some metabolites represent constitutive chemical barriers to microbial attack (phytoanticipins) and others inducible antimicrobials (phytoalexins). They are extensively studied as promising plant and human disease-controlling agents. This review discusses the bioactivity of several phytoalexins and phytoanticipins defending plants against fungal and bacterial aggressors and those with antibacterial activities against pathogens affecting humans such as Pseudomonas aeruginosa and Staphylococcus aureus involved in respiratory infections of cystic fibrosis patients. The utility of plant products as “antibiotic potentiators” and “virulence attenuators” is also described as well as some biotechnological applications in phytoprotection.

IJMS, Vol. 10, Pages 3358-3370: Computational Study on the Conformation and Vibration Frequencies of β-Sheet of ε-Polylysine in Vacuum

Shiru Jia — Wed, 29 Jul 2009 00:00:00 CEST

Two oligomers, each containing 3 L-lysine residues, were used as model molecules for the simulation of the β-sheet conformation of ε-polylysine (ε-PLL) chains. Their C terminals were capped with ethylamine and N terminals were capped with α-L-aminobutanoic acid, respectively. The calculations were carried out with the hybrid two-level ONOIM (B3LYP/6-31G:PM3) computational chemistry method. The optimized conformation was obtained and IR frequencies were compared with experimental data. The result indicated that the two chains were winded around each other to form a distinct cyclohepta structure through bifurcated hydrogen bonds. The groups of amide and α-amidocyanogen coming from one chain and the carbonyl group from the other chain were involved in the cyclohepta structure. The bond angle of the bifurcated hydrogen bonds was 66.6°. The frequency analysis at ONIOM [B3LYP/6-31G (d):PM3] level showed the IR absorbances of the main groups, such as the amide and amidocyanogen groups, were in accordance with the experimental data.

IJMS, Vol. 10, Pages 3316-3337: Classification of 5-HT1A Receptor Ligands on the Basis of Their Binding Affinities by Using PSO-Adaboost-SVM

Zhengjun Cheng — Wed, 29 Jul 2009 00:00:00 CEST

In the present work, the support vector machine (SVM) and Adaboost-SVM have been used to develop a classification model as a potential screening mechanism for a novel series of 5-HT1A selective ligands. Each compound is represented by calculated structural descriptors that encode topological features. The particle swarm optimization (PSO) and the stepwise multiple linear regression (Stepwise-MLR) methods have been used to search descriptor space and select the descriptors which are responsible for the inhibitory activity of these compounds. The model containing seven descriptors found by Adaboost-SVM, has showed better predictive capability than the other models. The total accuracy in prediction for the training and test set is 100.0% and 95.0% for PSO-Adaboost-SVM, 99.1% and 92.5% for PSO-SVM, 99.1% and 82.5% for Stepwise-MLR-Adaboost-SVM, 99.1% and 77.5% for Stepwise-MLR-SVM, respectively. The results indicate that Adaboost-SVM can be used as a useful modeling tool for QSAR studies.

IJMS, Vol. 10, Pages 3283-3315: Isothermal Microcalorimetry to Investigate Non Specific Interactions in Biophysical Chemistry

Vincent Ball — Tue, 28 Jul 2009 00:00:00 CEST

Isothermal titration microcalorimetry (ITC) is mostly used to investigate the thermodynamics of “specific” host-guest interactions in biology as well as in supramolecular chemistry. The aim of this review is to demonstrate that ITC can also provide useful information about non-specific interactions, like electrostatic or hydrophobic interactions. More attention will be given in the use of ITC to investigate polyelectrolyte-polyelectrolyte (in particular DNA-polycation), polyelectrolyte-protein as well as protein-lipid interactions. We will emphasize that in most cases these “non specific” interactions, as their definition will indicate, are favoured or even driven by an increase in the entropy of the system. The origin of this entropy increase will be discussed for some particular systems. We will also show that in many cases entropy-enthalpy compensation phenomena occur.

IJMS, Vol. 10, Pages 3237-3254: Prediction of Skin Sensitization with a Particle Swarm Optimized Support Vector Machine

Hua Yuan — Fri, 17 Jul 2009 00:00:00 CEST

Skin sensitization is the most commonly reported occupational illness, causing much suffering to a wide range of people. Identification and labeling of environmental allergens is urgently required to protect people from skin sensitization. The guinea pig maximization test (GPMT) and murine local lymph node assay (LLNA) are the two most important in vivo models for identification of skin sensitizers. In order to reduce the number of animal tests, quantitative structure-activity relationships (QSARs) are strongly encouraged in the assessment of skin sensitization of chemicals. This paper has investigated the skin sensitization potential of 162 compounds with LLNA results and 92 compounds with GPMT results using a support vector machine. A particle swarm optimization algorithm was implemented for feature selection from a large number of molecular descriptors calculated by Dragon. For the LLNA data set, the classification accuracies are 95.37% and 88.89% for the training and the test sets, respectively. For the GPMT data set, the classification accuracies are 91.80% and 90.32% for the training and the test sets, respectively. The classification performances were greatly improved compared to those reported in the literature, indicating that the support vector machine optimized by particle swarm in this paper is competent for the identification of skin sensitizers.

IJMS, Vol. 10, Pages 3186-3193: A TD-DFT Study on the Photo-Physicochemical Properties of Chrysophanol from Rheum

Xue Zhao — Mon, 13 Jul 2009 00:00:00 CEST

As a naturally occurring anthraquinone pigment, chrysophanol (MHAQ) has attracted considerable attention in recent years owing to its efficient photosensitivity under the solar spectrum. Considering the successful use of time-dependent density functional theory (TD-DFT) in investigating the photo-physicochemical behaviors of dyes and pigments, we performed a study by means of TD-DFT calculations, which provided us with various excited state properties of chrysophanol, including absorption spectrum, lowest triplet excited-state energy, vertical electron affinity and vertical ionization potential. On the basis of the calculated results, the photosensitive mechanisms of chrysophanol were discussed and some deeper insights were gained. First, we indicated that the experimentally observed chrysophanol’s photo-damage to DNA in oxygen-free media is more likely to arise from MHAQ •+ rather than from T1 state chrysophanol. Second, we revealed that it is the MHAQ •− that is responsible for the O2•− generation in solvents. Based on the photosensitive activities, chrysophanol may be potentially used as the photodynamic medicine for clinical therapy of the diseases occurring on the shallow surface and vascular capillary diseases.

IJMS, Vol. 10, Pages 3128-3148: Density Functional Study of Structures and Electron Affinities of BrO4F/BrO4F-

Liangfa Gong — Wed, 08 Jul 2009 00:00:00 CEST

The structures, electron affinities and bond dissociation energies of BrO4F/BrO4F− species have been investigated with five density functional theory (DFT) methods with DZP++ basis sets. The planar F-Br…O2…O2 complexes possess 3A' electronic state for neutral molecule and 4A' state for the corresponding anion. Three types of the neutral-anion energy separations are the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). The EAad value predicted by B3LYP method is 4.52 eV. The bond dissociation energies De (BrO4F → BrO4-mF + Om) (m = 1-4) and De- (BrO4F- → BrO4-mF- + Om and BrO4F- → BrO4-mF + Om-) are predicted. The adiabatic electron affinities (EAad) were predicted to be 4.52 eV for F-Br…O2…O2 (3A'← 4A') (B3LYP method).

IJMS, Vol. 10, Pages 3106-3127: Additive SMILES-Based Carcinogenicity Models: Probabilistic Principles in the Search for Robust Predictions

Andrey A. Toropov — Wed, 08 Jul 2009 00:00:00 CEST

Optimal descriptors calculated with the simplified molecular input line entry system (SMILES) have been utilized in modeling of carcinogenicity as continuous values (logTD50). These descriptors can be calculated using correlation weights of SMILES attributes calculated by the Monte Carlo method. A considerable subset of these attributes includes rare attributes. The use of these rare attributes can lead to overtraining. One can avoid the influence of the rare attributes if their correlation weights are fixed to zero. A function, limS, has been defined to identify rare attributes. The limS defines the minimum number of occurrences in the set of structures of the training (subtraining) set, to accept attributes as usable. If an attribute is present less than limS, it is considered “rare”, and thus not used. Two systems of building up models were examined: 1. classic training-test system; 2. balance of correlations for the subtraining and calibration sets (together, they are the original training set: the function of the calibration set is imitation of a preliminary test set). Three random splits into subtraining, calibration, and test sets were analysed. Comparison of abovementioned systems has shown that balance of correlations gives more robust prediction of the carcinogenicity for all three splits (split 1: rtest2=0.7514, stest=0.684; split 2: rtest2=0.7998, stest=0.600; split 3: rtest2=0.7192, stest=0.728).

IJMS, Vol. 10, Pages 3044-3064: Chirality Emergence in Thin Solid Films of Amino Acids by Polarized Light from Synchrotron Radiation and Free Electron Laser

Jun-ichi Takahashi — Tue, 07 Jul 2009 00:00:00 CEST

One of the most attractive hypothesis for the origin of homochirality in terrestrial bioorganic compounds is that a kind of “chiral impulse” as an asymmetric excitation source induced asymmetric reactions on the surfaces of such materials such as meteorites or interstellar dusts prior to the existence of terrestrial life (Cosmic Scenario). To experimentally introduce chiral structure into racemic films of amino acids (alanine, phenylalanine, isovaline, etc.), we irradiated them with linearly polarized light (LPL) from synchrotron radiation and circularly polarized light (CPL) from a free electron laser. After the irradiation, we evaluated optical anisotropy by measuring the circular dichroism (CD) spectra and verified that new Cotton peaks appeared at almost the same peak position as those of the corresponding non-racemic amino acid films. With LPL irradiation, two-dimensional anisotropic structure expressed as linear dichroism and/or linear birefringence was introduced into the racemic films. With CPL irradiation, the signs of the Cotton peaks exhibit symmetrical structure corresponding to the direction of CPL rotation. This indicates that some kinds of chiral structure were introduced into the racemic film. The CD spectra after CPL irradiation suggest the chiral structure should be derived from not only preferential photolysis but also from photolysis-induced molecular structural change. These results suggest that circularly polarized light sources in space could be associated with the origin of terrestrial homochirality; that is, they would be effective asymmetric exciting sources introducing chiral structures into bio-organic molecules or complex organic compounds.

IJMS, Vol. 10, Pages 2986-2998: Organic Analysis of Peridotite Rocks from the Ashadze and Logatchev Hydrothermal Sites

Marie-Paule Bassez — Fri, 03 Jul 2009 00:00:00 CEST

This article presents an experimental analysis of the organic content of two serpentinized peridotite rocks of the terrestrial upper mantle. The samples have been dredged on the floor of the Ashadze and Logatchev hydrothermal sites on the Mid-Atlantic Ridge. In this preliminary analysis, amino acids and long chain n-alkanes are identified. They are most probably of biological/microbial origin. Some peaks remain unidentified.

IJMS, Vol. 10, Pages 2935-2957: Applications of Isothermal Titration Calorimetry in Biophysical Studies of G-quadruplexes

Bruno Pagano — Thu, 02 Jul 2009 00:00:00 CEST

G-quadruplexes are higher-order nucleic acids structures formed by G-rich sequences that are stabilized by tetrads of hydrogen-bonded guanine bases. Recently, there has been growing interest in the study of G-quadruplexes because of their possible involvement in many biological processes. Isothermal titration calorimetry (ITC) has been proven to be a useful tool to study the energetic aspects of G-quadruplex interactions. Particularly, ITC has been applied many times to determine the thermodynamic properties of drug-quadruplex interactions to screening among various drugs and to address drug design. In the present review, we will focus on the ITC studies of G-quadruplex structures and their interaction with proteins and drugs and the most significant results will be discussed.

IJMS, Vol. 10, Pages 2921-2934: The Dimeric Proto-Ribosome: Structural Details and Possible Implications on the Origin of Life

Ilana Agmon — Tue, 30 Jun 2009 00:00:00 CEST

A symmetric pocket-like entity, composed of two L-shaped RNA units, encircles the peptide synthesis site within the contemporary ribosome. This entity was suggested to be the vestige of a dimeric proto-ribosome, which could have formed spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and elongation. This structural element, beyond offering the initial step in the evolution of translation, is hypothesized here to be linked to the origin of life. By catalyzing the production of random peptide chains, the proto-ribosome could have enabled the formation of primary enzymes, launching a process of co-evolution of the translation apparatus and the proteins, thus presenting an alternative to the RNA world hypothesis.

IJMS, Vol. 10, Pages 2911-2920: Heats of Mixing Using an Isothermal Titration Calorimeter: Associated Thermal Effects

Manuel Rodríguez de Rivera — Mon, 29 Jun 2009 00:00:00 CEST

The correct determination of the energy generated or absorbed in the sample cell of an Isothermal Titration Calorimeter (ITC) requires a thorough analysis of the calorimetric signal. This means the identification and quantification of any thermal effect inherent to the working method. In this work, it is carried out a review on several thermal effects, studied by us in previous work, and which appear when an ITC is used for measuring the heats of mixing of liquids in a continuous mode. These effects are due to: (i) the difference between the temperature of the injected liquid and the temperature of the mixture during the mixing process, (ii) the increase of the liquid volume located in the mixing cell and (iii) the stirring velocity. Besides, methods for the identification and quantification of the mentioned effects are suggested.

IJMS, Vol. 10, Pages 2873-2895: Thermodynamics of Surfactants, Block Copolymers and Their Mixtures in Water: The Role of the Isothermal Calorimetry

Rosario De Lisi — Mon, 29 Jun 2009 00:00:00 CEST

The thermodynamics of conventional surfactants, block copolymers and their mixtures in water was described to the light of the enthalpy function. The two methodologies, i.e. the van’t Hoff approach and the isothermal calorimetry, used to determine the enthalpy of micellization of pure surfactants and block copolymers were described. The van’t Hoff method was critically discussed. The aqueous copolymer+surfactant mixtures were analyzed by means of the isothermal titration calorimetry and the enthalpy of transfer of the copolymer from the water to the aqueous surfactant solutions. Thermodynamic models were presented to show the procedure to extract straightforward molecular insights from the bulk properties.

IJMS, Vol. 10, Pages 2860-2872: Protease Inhibitors from Plants with Antimicrobial Activity

Jin-Young Kim — Tue, 23 Jun 2009 00:00:00 CEST

Antimicrobial proteins (peptides) are known to play important roles in the innate host defense mechanisms of most living organisms, including plants, insects, amphibians and mammals. They are also known to possess potent antibiotic activity against bacteria, fungi, and even certain viruses. Recently, the rapid emergence of microbial pathogens that are resistant to currently available antibiotics has triggered considerable interest in the isolation and investigation of the mode of action of antimicrobial proteins (peptides). Plants produce a variety of proteins (peptides) that are involved in the defense against pathogens and invading organisms, including ribosome-inactivating proteins, lectins, protease inhibitors and antifungal peptides (proteins). Specially, the protease inhibitors can inhibit aspartic, serine and cysteine proteinases. Increased levels of trypsin and chymotrypsin inhibitors correlated with the plants resistance to the pathogen. Usually, the purification of antimicrobial proteins (peptides) with protease inhibitor activity was accomplished by salt-extraction, ultrafiltration and C18 reverse phase chromatography, successfully. We discuss the relation between antimicrobial and anti-protease activity in this review. Protease inhibitors from plants potently inhibited the growth of a variety of pathogenic bacterial and fungal strains and are therefore excellent candidates for use as the lead compounds for the development of novel antimicrobial agents.

IJMS, Vol. 10, Pages 2809-2837: Calculation of the Aqueous Thermodynamic Properties of Citric Acid Cycle Intermediates and Precursors and the Estimation of High Temperature and Pressure Equation of State Parameters

Peter Dalla-Betta — Mon, 22 Jun 2009 00:00:00 CEST

The citric acid cycle (CAC) is the central pathway of energy transfer for many organisms, and understanding the origin of this pathway may provide insight into the origins of metabolism. In order to assess the thermodynamics of this key pathway for microorganisms that inhabit a wide variety of environments, especially those found in high temperature environments, we have calculated the properties and parameters for the revised Helgeson-Kirkham-Flowers equation of state for the major components of the CAC. While a significant amount of data is not available for many of the constituents of this fundamental pathway, methods exist that allow estimation of these missing data.

IJMS, Vol. 10, Pages 2752-2762: Titration Calorimetry Standards and the Precision of Isothermal Titration Calorimetry Data

Lina Baranauskienė — Thu, 18 Jun 2009 00:00:00 CEST

Current Isothermal Titration Calorimetry (ITC) data in the literature have relatively high errors in the measured enthalpies of protein-ligand binding reactions. There is a need for universal validation standards for titration calorimeters. Several inorganic salt co-precipitation and buffer protonation reactions have been suggested as possible enthalpy standards. The performances of several commercial calorimeters, including the VP-ITC, ITC200, and Nano ITC-III, were validated using these suggested standard reactions.

IJMS, Vol. 10, Pages 2722-2732: Amino Acid Synthesis in a Supercritical Carbon Dioxide - Water System

Kouki Fujioka — Mon, 15 Jun 2009 00:00:00 CEST

Mars is a CO2-abundant planet, whereas early Earth is thought to be also CO2-abundant. In addition, water was also discovered on Mars in 2008. From the facts and theory, we assumed that soda fountains were present on both planets, and this affected amino acid synthesis. Here, using a supercritical CO2/liquid H2O (10:1) system which mimicked crust soda fountains, we demonstrate production of amino acids from hydroxylamine (nitrogen source) and keto acids (oxylic acid sources). In this research, several amino acids were detected with an amino acid analyzer. Moreover, alanine polymers were detected with LC-MS. Our research lights up a new pathway in the study of life’s origin.