The edgewise interactions of anions with phenylalanine (Phe) aromatic rings in proteins, known as anion-quadrupole interactions, have been well studied. However, the anion-quadrupole interactions of the tyrosine (Tyr) and tryptophan (Trp) rings have been less well studied, probably because these have been considered weaker than interactions of anions hydrogen bonded to Trp/Tyr side chains. Distinguishing such hydrogen bonding interactions, we comprehensively surveyed the edgewise interactions of certain anions (aspartate, glutamate, and phosphate) with Trp, Tyr, and Phe rings in high-resolution, nonredundant protein single chains and interfaces (protein-protein, DNA/RNA-protein, and membrane-protein). Trp/Tyr anion-quadrupole interactions are common, with Trp showing the highest propensity and average interaction energy for this type of interaction. The energy of an anion-quadrupole interaction (-15.0 to 0.0 kcal/mol, based on quantum mechanical calculations) depends not only on the interaction geometry but also on the ring atom. The phosphate anions at DNA/RNA-protein interfaces interact with aromatic residues with energies comparable to that of aspartate/glutamate anion-quadrupole interactions. At DNA-protein interfaces, the frequency of aromatic ring participation in anion-quadrupole interactions is comparable to that of positive charge participation in salt bridges, suggesting an underappreciated role for anion-quadrupole interactions at DNA-protein (or membrane-protein) interfaces. Although less frequent than salt bridges in single-chain proteins, we observed highly conserved anion-quadrupole interactions in the structures of remote homologues, and evolutionary covariance-based residue contact score predictions suggest that conserved anion-quadrupole interacting pairs, like salt bridges, contribute to polypeptide folding, stability, and recognition.

Three 9,9-dihexyl-9H-fluorene (DHF) functionalized zinc porphyrin dyes (coded as ZZX-N3, ZZX-N4, and ZZX-N5) were designed and synthesized for dye-sensitized solar cells. Then, DHF and benzoic acid were conjugated to the porphyrin ring through triple bonds to act as a spacer to elongate the π-conjugation and as an acceptor for an efficient electron injection, respectively. A bis(9,9-dihexyl-9H-fluorene-7-yl)amine (BFA) and a bis(4-hexylphenyl)amine (BPA) were further linked to DHF to act as electron donors in ZZX-N3 and ZZX-N4, respectively. ZZX-N5 did not have any electron donor and served as a reference. Moreover, ZZX-N3- and ZZX-N4-sensitized cells exhibited broader sunlight absorption than ZZX-N5, and as a result, higher photon-to-electricity efficiency (PCE) (ZZX-N3, 3.83%; ZZX-N4, 4.2%; ZZX-N5, 3.70%) was observed. The results are consistent with well-separated HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) in ZZX-N3 and ZZX-N4 than in ZZX-N5. However, the overall conversion efficiency of ZZX-N3- and ZZX-N4-sensitized cells was low, which is due to significant dye aggregation induced by the extra long alkyl-chains on the donor groups. This was evidenced by blue and red shifts of the absorption spectra of dye-coated TiO2 films. In addition, the extra long-chains also did not offer better shielding to prevent electron recombination of injected electrons with I3− in electrolyte as revealed by electrochemical impedance spectroscopy. When a co-sensitizer (coded as PBS) was used, a new peak corresponding to the absorption of PBS at 560 nm was observed on the incident photon to charge carrier efficiency (IPCE) spectra; however, the overall photovoltaic performance was not improved due to the significant decrease of dye-loading density of porphyrin dyes, indicating a need to break off the trade-off between dye-loading and light-harvesting.

Plant proteins encoded by disease resistance genes (R-genes) are involved in detecting pathogen-attack and subsequently in activating defense mechanisms. Coiled coil Nucleotide binding site Leucine rich region (CNL) type of R-genes are present in all plant species. In this study, we aimed to identify Cis-acting Regulatory Elements (CREs) 2kb upstream of CNL disease resistance genes and elucidate their distribution and diversity across six plant species. Over 900 identified CNL genes from six plant species Oryza sativa, Glycine max, Populus trichocarpa, Medicago truncatula, Phaseolus vulgaris, and Arabidopsis thaliana were searched using 469 reference CREs available at the PLACE database. Using in-house Perl scripts, we parsed the sequence data to yield 327 of 469 CREs in the described region. Eight of the CREs were common to all genes, including the most-abundant DOFCOREZM, which appeared 27,619 times. Thirteen CREs had a frequency greater than 10 per gene. The only monocot included in this study, Oryza sativa, had a significantly lower number of CREs than dicot species. Previous studies have failed to identify a promoter that is universally present in all transcribed plant genes, but the present study identified eight CREs that appeared in the 2kb upstream region of all CNL genes sampled. Since the CREs are involved in initiating transcriptional processes, their identification would have future implication in developing durable resistance genes that are transcribed in predictable ways and that are maintained during the natural processes of reproduction of the plant, thus being useful in crop improvement.

Theoretical and compelling experimental evidence indicates that the interaction between an anion and an aromatic π system when the anion is directly above the ring face ("η(6)"-type anion-π), can be attractive. This may play an important role in the formation and recognition of biomolecular structures. We examined high-resolution structures of proteins and nucleic acids for the presence of "η(6)"-type anion-π. Though less frequent than its counterpart cation-π, "η(6)"-type anion-π is observed unambiguously, occurring in protein/nucleic acid loops and often involving conserved/coevolving sites in proteins, suggesting it plays an important role in macromolecular folding and function.

The behavior of the catanionic system of dioctadecyldimethylammonium bromide (DODAB) and sodium dodecyl sulfate (SDS) was investigated at 23 +/- 1 degrees C at the air-water interface using a Langmuir trough. The surface pressure as a function of surface area was measured while monitoring domain structures using epifluorescence microscopy. At high surface densities, the monolayer exhibits collapse through reversible folding at about 47 mN m(-1). This corresponds to the DODAB collapse surface pressure. The number of folds increases with the rate of compression speed and is history-dependent.

We have investigated the liquid state of atomic clusters interacting through a classical pair-wise Lennard–Jones 6–12 potential, using constant energy molecular dynamics simulations. For larger clusters (N ≳ 500–600 atoms) desorption events are frequent and a cluster in the liquid state eventually always converts to a solid state. To study the cluster as it cools, one must isolate the central cluster from the desorbed atoms. In this paper, we investigate using the atomic potential energy as a very simple criterion for removing desorbed atoms from the simulation, and examine the spatial profile of atomic potential energy in various size liquid and solid clusters.

A rare-gas atomic cluster in the size range of 10-200 atoms can be prepared in either a liquid or solid state, an effect clearly seen in computer simulations and also to some extent in experiments. Larger clusters have not been studied in detail, especially the liquid state. Larger clusters prepared computationally initially in a liquid state seem to show a spontaneous, sharp transition to the solid. To study this effect in detail, one must be able to efficiently simulate the dynamics of clusters with thousands or tens of thousands of atoms. In order to meet these demands, high performance computing solutions and methods of improving and parallelizing the molecular dynamics program were investigated. A rack-mounted four node dual-processor cluster running the Clustermatic software package (developed at Los Alamos Labs) was designed to meet the high processing demands. This cluster has achieved a performance of 21.5 Gi gaFLOPS during initial testing using HPL, a benchmark based on matrix calculations. The molecular dynamics program was parallelized using MPI (message passing interface). We have run clusters up to 10,000 atoms, seeing a roughly 7.7 factor speed increase, with results confirming the presence of the spontaneous transition from liquid to solid, which now appears to be ubiquitous for large clusters.

The plotting program Gnuplot is freely available, general purpose, easy to use, and available on a variety of platforms. Complex three-dimensional surfaces, including the familiar angular parts of the hydrogen atom orbitals, are easily represented using Gnuplot. Contour plots allow viewing the radial and angular variation of the probability density in an orbital. Examples are given of how Gnuplot is used in an undergraduate physical chemistry class to view familiar atomic orbitals in new ways or to generate views of orbital functions that the student may have not seen before. Gnuplot may also be easily integrated into the environment of a Web page; an example of this is discussed (and is available at http://onsager.bd.psu.edu/~moore/orbitals_gnuplot). The plotting commands are entered with a form and a CGI script is used to run Gnuplot and display the result back to the browser.

We have performed computer simulations of atomic clusters with the goal of studying the structure of the liquid phase. Classical constant energy molecular dynamics was used, with the atoms interacting via a Lennard-Jones 6-12 potential. Liquid clusters were formed by evaporation from a lattice with a relatively large lattice constant; for comparison, solid clusters were formed by a 10–15% scaling of the coordinates of the minimum-energy configurations. The liquid clusters formed ranged in size from approximately 50 to 1000 atoms. The liquid radial distribution functions [g(r)] show a split second peak (which is sometimes attributed to “glassy” behavior) which becomes much less pronounced as the size increases. A common neighbour analysis shows a high degree of local polytetrahedral ordering in the liquid and only a very small amount of local octahedral order, in contrast to the solid g(r). Radial density profiles [ρ(r)] of the liquid clusters show a very clear radial layering; the layer separation is approximately the repulsive hard core diameter. For the larger clusters, the layering is progressively less pronounced, and nearly absent for the largest cluster studied (1085 particles). In two cases, the cluster began in a liquid state which persisted long enough for structural quantities to be taken [g(r) and ρ(r)] but then showed evidence of the onset of solid structure. Mean squared displacements resolved into interior/exterior of the cluster show that there is a strong spatial dependence of the diffusion in the smaller liquid clusters.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTeaching Theoretical Physical Chemistry: Density Functional Theory and the Taylor Expansion of the van der Waals Free EnergyBrian G. Moore and John D. Mize View Author Information Penn State Erie, Division of Science, The Behrend College, Station Road, Erie, PA 16563-0203Cite this: J. Chem. Educ. 1998, 75, 7, 858Publication Date (Web):July 1, 1998Publication History Received3 August 2009Published online1 July 1998Published inissue 1 July 1998https://pubs.acs.org/doi/10.1021/ed075p858https://doi.org/10.1021/ed075p858research-articleACS PublicationsRequest reuse permissionsArticle Views589Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Density functional theory,Free energy,Physical chemistry,Teaching and learning methods,Undergraduates Get e-Alerts

The dynamics and structural properties of clusters composed of two chemical species are investigated. The demixing process starting from the unstable fully-mixed state in the clusters possesses some features that are similar to domain formation and growth following a critical quench in a binary fluid. The structural properties of the phase separated clusters differ from those of the bulk fluid and are studied as a function of the temperature, concentration and interaction strength.