<?xml version="1.0" encoding="utf-8"?>
<feed xmlns="http://www.w3.org/2005/Atom" xmlns:gd="http://schemas.google.com/g/2005" xmlns:opensearch="http://a9.com/-/spec/opensearch/1.1/" xmlns:xh="http://www.w3.org/1999/xhtml">
		
<title>Chemical blogspace - latest papers</title>
<link href='http://cb.openmolecules.net/'/>
<updated>2012-05-20T04:54:09Z</updated>
<author>
	<name>Republished content</name>
	<email>egon.willighagen@gmail.com</email>
	<uri>http://cb.openmolecules.net/</uri>
</author>
<link rel='alternate' type='text/html' href='http://cb.openmolecules.net/'/>
<link rel='self' type='application/atom+xml' href='http://cb.openmolecules.net/atom.php?type=latest_papers'/>
<id>http://cb.openmolecules.net/-2d26f75dac39b83e6f13d1440d943f4c</id>

	<entry>
		<title><![CDATA[Non-planar push-pull chromophores.]]></title>
		<author><name>Chem. Commun. (Camb.)</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3546"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3546</id>
		<updated>2012-05-18T13:48:25Z</updated>
		<summary><![CDATA[The development of a unique class of non-planar push-pull chromophores by means of [2 + 2] cycloaddition, followed by cycloreversion, of electron-deficient olefins, such as tetracyanoethene (TCNE), 7,7,8,8-tetracyanoquinodimethane (TCNQ) and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F(4)-TCNQ), as well as dicyanovinyl (DCV) and tricyanovinyl (TCV) derivatives, to donor-substituted alkynes is explored in this feature article. This high-yielding, &amp;quot;click-chemistry&amp;quot;-type transformation with acetylenic dendrimers affords dendritic electron sinks capable of multiple electron uptake within a narrow potential range. An [AB]-type oligomer with a dendralene backbone was synthesised by a one-pot, multi-component cascade reaction of polyyne oligomers with TCNE and tetrathiafulvalene (TTF). In most cases, the resulting chromophores feature intense intramolecular charge-transfer bands extending far into the near infrared region and some of them display high third-order optical nonlinearities. Despite substitution with strong donors, the electron-withdrawing moieties in the new chromophores remain potent acceptors and a number of them display positive first reduction potentials (vs. the ferrocenium/ferrocene (Fc(+)/Fc) couple in CH(2)Cl(2)), which rival those of parent TCNE, TCNQ and F(4)-TCNQ. The non-planarity of the chromophores strongly enhances their physical properties when compared to planar push-pull analogues. They feature high solubility, thermal stability and sublimability, which enables formation of amorphous, high-optical-quality thin films by vapour phase deposition and makes them interesting as advanced functional materials for novel opto-electronic devices.]]></summary>
		<contributor>
			<name>Chem. Commun. (Camb.)</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Chem. Commun. (Camb.)</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[A room-temperature molecular/organic-based magnet.]]></title>
		<author><name>Science</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3545"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3545</id>
		<updated>2012-05-18T13:48:24Z</updated>
		<summary><![CDATA[The reaction of bis(benzene)vanadium with tetracyanoethylene, TCNE, affords an insoluble amorphous black solid that exhibits field-dependent magnetization and hysteresis at room temperature. The critical temperature could not be estimated as it exceeds 350 kelvin, the thermal decomposition temperature of the sample. The empirical composition of the reported material is V(TCNE)x.Y(CH(2)Cl(2)) with x approximately 2 and Y approximately 1/2. On the basis of the available magnetic and infrared data, threedimensional antiferromagnetic exchange of the donor and acceptor spins resulting in ferrimagnetic behavior appears to be the mode of magnetic coupling.]]></summary>
		<contributor>
			<name>Science</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Science</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Stereoselectivities of histidine-catalyzed asymmetric aldol additions and contrasts with proline catalysis: a quantum mechanical analysis.]]></title>
		<author><name>J. Am. Chem. Soc.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3544"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3544</id>
		<updated>2012-05-16T07:46:47Z</updated>
		<summary><![CDATA[Quantum mechanical calculations reveal the origin of diastereo- and enantioselectivities of aldol reactions between aldehydes catalyzed by histidine, and differences between related reactions catalyzed by proline. A stereochemical model that explains both the sense and the high levels of the experimentally observed stereoselectivity is proposed. The computations suggest that both the imidazolium and the carboxylic acid functionalities of histidine are viable hydrogen-bond donors that can stabilize the cyclic aldolization transition state. The stereoselectivity is proposed to arise from minimization of gauche interactions around the forming C-C bond.]]></summary>
		<contributor>
			<name>J. Am. Chem. Soc.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Am. Chem. Soc.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[(S)-Proline-catalyzed nitro-Michael reactions: towards a better understanding of the catalytic mechanism and enantioselectivity.]]></title>
		<author><name>Org. Biomol. Chem.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3543"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3543</id>
		<updated>2012-05-16T07:46:44Z</updated>
		<summary><![CDATA[(S)-Proline-catalyzed nitro-Michael additions of aldehydes and ketones to ??-nitrostyrene were investigated computationally (MP2/6-311+G**//M06-2X/6-31G**). Contrary to what is usually assumed in organocatalysis, the lowest-energy transition states of proline-catalyzed nitro-Michael reactions do not necessarily involve the carboxylic acid group of the proline moiety directing the incoming nitroalkene to the same face through hydrogen bonding. For the aldehyde substrates examined, the TS leading to the major (R,S) product was found to involve the anti-enamine and nitroalkene approaching from the opposite face of the carboxyl group. In the case of ketone substrates, the lowest-energy TSs leading to both enantiomeric products are characterized by the absence of hydrogen bonds and s-cis conformation of the carboxyl group, which functions as an electron donor to stablize the developing iminium. When both hydrogen bonded and non-hydrogen bonded types of TSs are considered, the calculated enantioselectivities for Michael additions of aldehyde and ketone substrates are in good agreement with experimental findings.]]></summary>
		<contributor>
			<name>Org. Biomol. Chem.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Org. Biomol. Chem.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Unusual spectroscopic and ligand binding properties of the cytochrome P450-flavodoxin fusion enzyme XplA.]]></title>
		<author><name>The Journal of biological chemistry</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3541"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3541</id>
		<updated>2012-05-10T13:46:36Z</updated>
		<summary><![CDATA[The Rhodococcus rhodochrous strain 11Y XplA enzyme is an unusual cytochrome P450-flavodoxin fusion enzyme that catalyzes reductive denitration of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazene (RDX). We show by light scattering that XplA is a monomeric enzyme. XplA has high affinity for imidazole (Kd = 1.6 microM), explaining previous reports of a red-shifted XplA Soret band in pure enzyme. XplA's true Soret maximum is at 417 nm. Similarly, unusually weak XplA flavodoxin FMN binding (Kd = 1.09 microM) necessitates its purification in presence of the cofactor to produce hallmark flavin contributions absent in previously reported spectra. Structural and ligand-binding data reveal a constricted active site able to accommodate RDX and small inhibitory ligands (e.g. 4-phenylimidazole and morpholine) while discriminating against larger azole drugs. The crystal structure also identifies a high affinity imidazole binding site, consistent with its low Kd, and shows active site penetration by PEG, perhaps indicative of an evolutionary lipid metabolizing function for XplA. EPR studies indicate heterogeneity in binding mode for RDX and other ligands. The substrate analogue trinitrobenzene does not induce a substrate-like type I optical shift, but creates a unique low-spin EPR spectrum due to influence on structure around the distal water heme ligand. The substrate-free heme iron potential (-268 mV vs. NHE) is positive for a low-spin P450, and the elevated potential of the FMN semiquinone/hydroquinone couple (-172 mV) is also an adaptation that may reflect (along with absence of a key Thr/Ser residue conserved in oxygen activating P450s) XplA's evolution as a specialized RDX reductase catalyst.]]></summary>
		<contributor>
			<name>The Journal of biological chemistry</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=The Journal of biological chemistry</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Enantioselective organocatalytic conjugate addition of aldehydes to nitrodienes.]]></title>
		<author><name>Org. Lett.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3542"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3542</id>
		<updated>2012-05-10T13:46:36Z</updated>
		<summary><![CDATA[The asymmetric organocatalyzed Michael addition of aldehydes to alpha,beta-gamma,delta-unsaturated nitro compounds has been accomplished using only 5 mol % of (S)-diphenylprolinol silyl ether and 2 equiv of aldehyde in a mixture of ethanol and water (5% v/v). The Michael adducts were obtained in good yields, diastereoselectivities up to 94/6, and ee's up to 99%. This process provides synthetically useful compounds which can easily lead to more complex molecules, as exemplified with substituted tetrahydropyran or cyclohexene.]]></summary>
		<contributor>
			<name>Org. Lett.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Org. Lett.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[The explosive-degrading cytochrome P450 XplA: biochemistry, structural features and prospects for bioremediation.]]></title>
		<author><name>Biochim. Biophys. Acta</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3540"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3540</id>
		<updated>2012-05-10T13:46:35Z</updated>
		<summary><![CDATA[XplA is a cytochrome P450 that mediates the microbial metabolism of the military explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). It has an unusual structural organisation comprising a heme domain that is fused to its flavodoxin redox partner. XplA along with its partnering reductase XplB are plasmid encoded and the gene xplA has now been found in divergent genera across the globe with near sequence identity. Importantly, it has only been detected at explosives contaminated sites suggesting rapid dissemination of this novel catabolic activity, possibly within the 50-year period since the introduction of RDX into the environment. The X-ray structure of XplA-heme has been solved, providing fundamental information on the heme binding site. Interestingly, oxygen is not required for the degradation of RDX, but its presence determines the final degradation products, demonstrating that the degradation chemistry is flexible with both anaerobic and aerobic pathways resulting in the release of nitrite from the substrate. Transgenic plants expressing xplA are able to remove saturating levels of RDX from soil leachate and may provide a low cost sustainable remediation strategy for contaminated military sites.]]></summary>
		<contributor>
			<name>Biochim. Biophys. Acta</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Biochim. Biophys. Acta</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Drugs of abuse in urban groundwater. A case study: Barcelona.]]></title>
		<author><name>Sci. Total Environ.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3539"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3539</id>
		<updated>2012-05-02T13:49:09Z</updated>
		<summary><![CDATA[This study is concerned with drugs of abuse (DAs) and their metabolites in urban groundwater at field scale in relation to (1) the spatial distribution of DAs in Barcelona's groundwater, (2) the depth of the groundwater samples, (3) the presence of DAs in recharge sources, and (4) the assessment of the fate of DAs in Barcelona aquifers. To this end, 37 urban groundwater samples were collected in the city of Barcelona and a total of 21 drugs were analyzed including cocainics, amphetamine-like compounds, opioids, lysergics and cannabinoids and the prescribed drugs benzodiazepines. Overall, the highest groundwater concentrations (around 200ng/L in SAP-4) and the largest number of detected DAs were found in zones basically recharged by a river that receives large amounts of effluents from waste water treatment plants (WWTPs). In contrast, the urbanized areas yielded not only lower concentrations but also a much smaller number of drugs, which suggests a local origin. In fact, cocaine and its metabolite were dominant in more prosperous neighborhoods, whereas the cheaper MDMA was the dominant DA in poorer districts. Measured concentrations were consistently smaller than those estimated from the waste water fraction in groundwater samples, suggesting that DAs undergo removal processes in both reducing and oxidizing conditions.]]></summary>
		<contributor>
			<name>Sci. Total Environ.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Sci. Total Environ.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Quantitative NMR-derived interproton distances combined with quantum mechanical calculations of 13C chemical shifts in the stereochemical determination of conicasterol F, a nuclear receptor ligand from Theonella swinhoei.]]></title>
		<author><name>J. Org. Chem.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3538"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3538</id>
		<updated>2012-05-01T07:52:45Z</updated>
		<summary><![CDATA[Here we report the first application of combined accurate ROE-distance analysis with DFT calculations of NMR chemical shifts to achieve the relative configuration assignment of a marine natural product, conicasterol F, a new polyhydroxylated steroid isolated from the marine sponge Theonella swinhoei. We demonstrate the substantial advantages of this combined approach as a tool for structural studies of natural products, providing a powerful alternative to, or information to underpin, total synthesis when more classical NMR data analysis fails to provide unequivocal results. In this paper, we also describe the isolation and structure elucidation of conicasterol F and its 24-ethyl derivative, theonellasterol I, and their pharmacological evaluation as human nuclear receptor modulators.]]></summary>
		<contributor>
			<name>J. Org. Chem.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Org. Chem.</uri>
		</contributor>
		<gd:rating value='2' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[A seed coat bedding assay shows that RGL2-dependent release of abscisic acid by the endosperm controls embryo growth in Arabidopsis dormant seeds.]]></title>
		<author><name>Proc. Natl. Acad. Sci. U.S.A.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3537"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3537</id>
		<updated>2012-04-30T07:49:54Z</updated>
		<summary><![CDATA[Seed dormancy is an ecologically important adaptive trait in plants whereby germination is repressed even under favorable germination conditions such as imbibition with water. In Arabidopsis and most plant species, dormancy absolutely requires an unidentified seed coat germination-repressive activity and constitutively higher abscisic acid (ABA) levels upon seed imbibition. The mechanisms underlying these processes and their possible relationship are incompletely understood. We developed a &amp;quot;seed coat bedding&amp;quot; assay monitoring the growth of dissected embryos cultured on a layer of seed coats, allowing combinatorial experiments using dormant, nondormant, and various genetically modified seed coat and embryonic materials. This assay, combined with direct ABA measurements, revealed that, upon imbibition, dormant coats, unlike nondormant coats, actively produce and release ABA to repress embryo germination, whatever the embryo origin, i.e., from dormant, nondormant, or never dormant aba seeds, unable to synthesize ABA. The persistent high ABA levels in imbibed dormant seeds requires the permanent expression of the DELLA gene RGL2, where it remains insensitive to gibberellins (GA) unlike in nondormant seeds. These findings present the seed coat as an organ actively controlling germination upon seed imbibition and provide a framework to investigate how environmental factors break seed dormancy.]]></summary>
		<contributor>
			<name>Proc. Natl. Acad. Sci. U.S.A.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Proc. Natl. Acad. Sci. U.S.A.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition.]]></title>
		<author><name>Genes Dev.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3536"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3536</id>
		<updated>2012-04-30T07:49:50Z</updated>
		<summary><![CDATA[The germination of Arabidopsis seeds is promoted by gibberellin (GA). Arabidopsis GAI, and RGA are genes encoding key GA signal-transduction components (GAI and RGA) that mediate GA regulation of stem elongation. The Arabidopsis genome contains two further genes, RGL1 and RGL2, that encode proteins (RGL1 and RGL2) that are closely related to GAI and RGA. Here, we show that RGL2 regulates seed germination in response to GA, and that RGL1, GAI, and RGA do not. In addition, we show that RGL2 transcript levels rise rapidly following seed imbibition, and then decline rapidly as germination proceeds. In situ GUS staining revealed that RGL2 expression in imbibed seeds is restricted to elongating regions of pre-emergent and recently emerged radicles. These observations indicate that RGL2 is a negative regulator of GA responses that acts specifically to control seed germination rather than stem elongation. Furthermore, as RGL2 expression is imbibition inducible, RGL2 may function as an integrator of environmental and endogenous cues to control seed germination.]]></summary>
		<contributor>
			<name>Genes Dev.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Genes Dev.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis.]]></title>
		<author><name>Nature</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3535"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3535</id>
		<updated>2012-04-25T01:46:43Z</updated>
		<summary><![CDATA[Polycyclic polyether natural products have fascinated chemists and biologists alike owing to their useful biological activity, highly complex structure and intriguing biosynthetic mechanisms. Following the original proposal for the polyepoxide origin of lasalocid and isolasalocid and the experimental determination of the origins of the oxygen and carbon atoms of both lasalocid and monensin, a unified stereochemical model for the biosynthesis of polyether ionophore antibiotics was proposed. The model was based on a cascade of nucleophilic ring closures of postulated polyepoxide substrates generated by stereospecific oxidation of all-trans polyene polyketide intermediates. Shortly thereafter, a related model was proposed for the biogenesis of marine ladder toxins, involving a series of nominally disfavoured anti-Baldwin, endo-tet epoxide-ring-opening reactions. Recently, we identified Lsd19 from the Streptomyces lasaliensis gene cluster as the epoxide hydrolase responsible for the epoxide-opening cyclization of bisepoxyprelasalocid A to form lasalocid A. Here we report the X-ray crystal structure of Lsd19 in complex with its substrate and product analogue to provide the first atomic structure-to our knowledge-of a natural enzyme capable of catalysing the disfavoured epoxide-opening cyclic ether formation. On the basis of our structural and computational studies, we propose a general mechanism for the enzymatic catalysis of polyether natural product biosynthesis.]]></summary>
		<contributor>
			<name>Nature</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Nature</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[An antidote for acute cocaine toxicity.]]></title>
		<author><name>Mol. Pharm.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3534"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3534</id>
		<updated>2012-04-18T07:48:07Z</updated>
		<summary><![CDATA[Not only has immunopharmacotherapy grown into a field that addresses the abuse of numerous illicit substances, but also the treatment methodologies within immunopharmacotherapy have expanded from traditional active vaccination to passive immunization with anti-drug monoclonal antibodies, optimized mAb formats, and catalytic drug-degrading antibodies. Many laboratories have focused on transitioning distinct immunopharmacotherapeutics to clinical evaluation, but with respect to the indication of cocaine abuse, only the active vaccine TA-CD, which is modeled after our original cocaine hapten GNC, (1) has been carried through to human clinical trials. (2) The successful application of murine mAb GNC92H2 to the reversal of cocaine overdose in a mouse model prompted investigations of human immunoglobulins with the clinical potential to serve as cocaine antidotes. We now report the therapeutic utility of a superior clone, human mAb GNCgzk (K(d) = 0.18 nM), which offers a 10-fold improvement in cocaine binding affinity. The GNCgzk manifold was engineered for rapid cocaine clearance, and administration of the F(ab')(2) and Fab formats even after the appearance of acute behavioral signs of cocaine toxicity granted nearly complete prevention of lethality. Thus, contrary to the immunopharmacotherapeutic treatment of drug self-administration, minimal antibody doses were shown to counteract the lethality of a molar excess of circulating cocaine. Passive vaccination with drug-specific antibodies represents a viable treatment strategy for the human condition of cocaine overdose.]]></summary>
		<contributor>
			<name>Mol. Pharm.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Mol. Pharm.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Steric crowding can stabilize a labile molecule: solving the hexaphenylethane riddle.]]></title>
		<author><name>Angew. Chem. Int. Ed. Engl.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3533"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3533</id>
		<updated>2012-04-16T13:47:23Z</updated>
		<summary><![CDATA[12 not so angry men: Hexaphenylethane is unstable, a phenomenon traditionally attributed to steric repulsion between the six phenyl rings. However, adding 12 bulky tert-butyl groups, one to each of the 12 meta positions, gives a stabile ethane derivative (see space-filling model and potential energy curve for the dissociation of the central C-C bond). This unexpected stabilization is shown to result from attractive dispersion interactions between the substituents.]]></summary>
		<contributor>
			<name>Angew. Chem. Int. Ed. Engl.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Angew. Chem. Int. Ed. Engl.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[The biology and future prospects of antivirulence therapies.]]></title>
		<author><name>Nat. Rev. Microbiol.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3532"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3532</id>
		<updated>2012-04-13T13:44:04Z</updated>
		<summary><![CDATA[The emergence and increasing prevalence of bacterial strains that are resistant to available antibiotics demand the discovery of new therapeutic approaches. Targeting bacterial virulence is an alternative approach to antimicrobial therapy that offers promising opportunities to inhibit pathogenesis and its consequences without placing immediate life-or-death pressure on the target bacterium. Certain virulence factors have been shown to be potential targets for drug design and therapeutic intervention, whereas new insights are crucial for exploiting others. Targeting virulence represents a new paradigm to empower the clinician to prevent and treat infectious diseases.]]></summary>
		<contributor>
			<name>Nat. Rev. Microbiol.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Nat. Rev. Microbiol.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Isotopic evidence for extraterrestrial non-racemic amino acids in the Murchison meteorite.]]></title>
		<author><name>Nature</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3530"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3530</id>
		<updated>2012-04-12T13:48:03Z</updated>
		<summary><![CDATA[Many amino acids contain an asymmetric centre, occurring as laevorotatory, L, or dextrorotatory, D, compounds. It is generally assumed that abiotic synthesis of amino acids on the early Earth resulted in racemic mixtures (L- and D-enantiomers in equal abundance). But the origin of life required, owing to conformational constraints, the almost exclusive selection of either L- or D-enantiomers, and the question of why living systems on the Earth consist of L-enantiomers rather than D-enantiomers is unresolved. A substantial fraction of the organic compounds on the early Earth may have been derived from comet and meteorite impacts. It has been reported previously that amino acids in the Murchison meteorite exhibit an excess of L-enantiomers, raising the possibility that a similar excess was present in the initial inventory of organic compounds on the Earth. The stable carbon isotope compositions of individual amino acids in Murchison support an extraterrestrial origin -- rather than a terrestrial overprint of biological amino acids-although reservations have persisted. Here we show that individual amino-acid enantiomers from Murchison are enriched in 15N relative to their terrestrial counterparts, so confirming an extraterrestrial source for an L-enantiomer excess in the Solar System that may predate the origin of life on the Earth.]]></summary>
		<contributor>
			<name>Nature</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Nature</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Evidence for the Likely Origin of Homochirality in Amino Acids, Sugars, and Nucleosides on Prebiotic Earth.]]></title>
		<author><name>Journal of the American Chemical Society</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3531"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3531</id>
		<updated>2012-04-12T13:48:03Z</updated>
		<summary><![CDATA[Over the past century the origin of terrestrial prebiotic homochirality has been the subject of many speculations. For life to start on earth and elsewhere, it is critical that the building blocks of amino acids, sugars, and nucleosides be created in predominant homochiral form. Recent findings of a modest excess L chirality of ??-methylamino acids in some meteorites that landed on earth have furnished an important piece of evidence. We have shown how these meteoritic components can furnish normal L amino acids, and therefrom D sugars and nucleosides, in high chiral excess under sensible prebiotic conditions. Some important remaining goals are also described.]]></summary>
		<contributor>
			<name>Journal of the American Chemical Society</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Journal of the American Chemical Society</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Sorting through the cell biology of Alzheimer's disease: intracellular pathways to pathogenesis.]]></title>
		<author><name>Neuron</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3529"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3529</id>
		<updated>2012-04-12T13:47:59Z</updated>
		<summary><![CDATA[During the first 100 years of Alzheimer's disease research, this devastating and intractable disorder has been characterized at the clinical, histological, and molecular levels. Nevertheless, many key mechanistic questions remain unanswered. Here we will emphasize the importance of the cell biology of Alzheimer's disease, reviewing the relevant literature that has expanded our mechanistic understanding, with a particular focus on pathways regulating protein sorting. Accumulated evidence indicates that sorting pathways may be uniquely vulnerable to disease pathogenesis, and recent studies have begun to reveal disease-related defects in the regulation of protein sorting.]]></summary>
		<contributor>
			<name>Neuron</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Neuron</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Mining chemical information from open patents.]]></title>
		<author><name>J Cheminform</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3528"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3528</id>
		<updated>2012-04-11T07:48:38Z</updated>
		<summary><![CDATA[ABSTRACT: Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is a huge amount of information available in the published literature, the vast majority of which is not available in machine-understandable formats. PatentEye, a prototype system for the extraction and semantification of chemical reactions from the patent literature has been implemented and is discussed. A total of 4444 reactions were extracted from 667 patent documents that comprised 10 weeks' worth of publications from the European Patent Office (EPO), with a precision of 78% and recall of 64% with regards to determining the identity and amount of reactants employed and an accuracy of 92% with regards to product identification. NMR spectra reported as product characterisation data are additionally captured.]]></summary>
		<contributor>
			<name>J Cheminform</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J Cheminform</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[The Effect of the CO3^(2-) to Ca^(2+) Ion Activity Ratio on Calcite Precipitation Kinetics and Sr^(2+) partitioning.]]></title>
		<author><name>Geochemical transactions</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3527"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3527</id>
		<updated>2012-04-03T07:49:20Z</updated>
		<summary><![CDATA[ABSTRACT: BACKGROUND: A proposed strategy for immobilizing trace metals in the subsurface is to stimulate calcium carbonate precipitation and incorporate contaminants by co-precipitation. Such an approach will require injecting chemical amendments into the subsurface to generate supersaturated conditions that promote mineral precipitation. However, the formation of reactant mixing zones will create gradients in both the saturation state and ion activity ratios (i.e.,a_(CO_3^(2-) )a_(Ca^(2+) ) ). To better understand the effect of ion activity ratios on CaCO3 precipitation kinetics and Sr2+ co-precipitation, experiments were conducted under constant composition conditions where the supersaturation state (Omega) for calcite was held constant at 9.4, but the ion activity ratio (r= a_(CO_3^(2-) )a_(Ca^(2+) ) ) was varied between 0.0032 and 4.15. RESULTS: Calcite was the only phase observed, by XRD, at the end of the experiments. Precipitation rates increased from 41.3+/-3.4 mumol m-2 min-1 at r = 0.0315 to a maximum rate of 74.5+/-4.8 mumol m-2 min-1 at r = 0.306 followed by a decrease to 46.3+/-9.6 mumol m-2 min-1 at r = 1.822. The trend was simulated using a simple mass transfer model for solute uptake at the calcite surface. However, precipitation rates at fixed saturation states also evolved with time. Precipitation rates accelerated for low r values but slowed for high r values. These trends may be related to changes in effective reactive surface area. The a_(CO_3^(2-) )a_(Ca^(2+) ) ratios did not affect the distribution coefficient for Sr in calcite (DPSr2+), apart from the indirect effect associated with the established positive correlation between DPSr2+ and calcite precipitation rate. CONCLUSION: At a constant supersaturation state (Omega = 9.4), varying the ion activity ratio affects the calcite precipitation rate. This behavior is not predicted by affinity-based rate models. Furthermore, at the highest ion ratio tested, no precipitation was observed, while at the lowest ion ratio precipitation occurred immediately and valid rate measurements could not be made. The maximum measured precipitation rate was 2-fold greater than the minima, and occurred at a carbonate to calcium ion activity ratio of 0.306. These findings have implications for predicting the progress and cost of remediation operations involving enhanced calcite precipitation where mineral precipitation rates, and the spatial/temporal distribution of those rates, can have significant impacts on the mobility of contaminants.]]></summary>
		<contributor>
			<name>Geochemical transactions</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Geochemical transactions</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Improving integrative searching of systems chemical biology data using semantic annotation.]]></title>
		<author><name>Journal of cheminformatics</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3526"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3526</id>
		<updated>2012-04-03T07:49:17Z</updated>
		<summary><![CDATA[ABSTRACT: BACKGROUND: Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. RESULTS: We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. AVAILABILITY: Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.]]></summary>
		<contributor>
			<name>Journal of cheminformatics</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Journal of cheminformatics</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Ficaria verna Huds. extracts and their beta-cyclodextrin supramolecular systems.]]></title>
		<author><name>Chemistry Central journal</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3525"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3525</id>
		<updated>2012-04-03T07:49:13Z</updated>
		<summary><![CDATA[ABSTRACT: BACKGROUND: Obtaining new pharmaceutical materials with enhanced properties by using natural compounds and environment-friendly methods is a continuous goal for scientists. Ficaria verna Huds. is a widespread perennial plant with applications in the treat of haemorrhoids and to cure piles; it has also anti-inflammatory, astringent, and antibiotic properties. The goal of the present study is the obtaining and characterization of new F. verna extract/beta-cyclodextrin complexes by using only natural compounds, solvents, and environment-friendly methods in order to increase the quality and acceptability versus toxicity indicator. Thus, the flavonoid content (as quercetin) of Ficaria verna Huds. flowers and leaves from the West side of Romania was determined and correlated with their antioxidant activity. Further, the possibility of obtaining beta-cyclodextrin supramolecular systems was studied. RESULTS: F. verna flowers and leaves extracts were obtained by semi-continuous solid-liquid extraction. The raw concentrated extract was spectrophotometrically analyzed in order to quantify the flavonoids from plant parts and to evaluate the antioxidant activity of these extracts. The F. verna extracts were used for obtaining beta-cyclodextrin complexes; these were analyzed by scanning electron microscopy and Karl Fischer water titration; spectrophotometry was used in order to quantifying the flavonoids and evaluates the antioxidant activity. A higher concentration of flavonoids of 0.5% was determined in complexes obtained by crystallisation method, while only a half of this value was calculated for kneading method. The antioxidant activity of these complexes was correlated with the flavonoid content and this parameter reveals possible controlled release properties. CONCLUSIONS: The flavonoid content of F. verna Huds. from the West side of Romania (Banat county) is approximately the same in flowers and leaves, being situated at a medium value among other studies. beta-Cyclodextrin complexes of F. verna extracts are obtained with lower yields by crystallisation than kneading methods, but the flavonoids (as quercetin) are better encapsulated in the first case most probably due to the possibility to attain the host-guest equilibrium in the slower crystallisation process. F. verna extracts and their beta-cyclodextrin complexes have antioxidant activity even at very low concentrations and could be used in proper and valuable pharmaceutical formulations with enhanced bioactivity.]]></summary>
		<contributor>
			<name>Chemistry Central journal</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Chemistry Central journal</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[CheS-Mapper - Chemical Space Mapping and Visualization in 3D.]]></title>
		<author><name>Journal of cheminformatics</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3524"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3524</id>
		<updated>2012-04-03T07:49:05Z</updated>
		<summary><![CDATA[ABSTRACT: Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis.]]></summary>
		<contributor>
			<name>Journal of cheminformatics</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Journal of cheminformatics</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Evidence of a ZnCr(2)Se(4) Spinel Inclusion at the Core of a Cr-Doped ZnSe Quantum Dot.]]></title>
		<author><name>J. Am. Chem. Soc.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3523"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3523</id>
		<updated>2012-04-03T01:44:19Z</updated>
		<summary><![CDATA[Herein we report doping of ZnSe by Cr ions leads to formation of small ZnCr(2)Se(4) spinel inclusions within the cubic sphalerite lattice of a 2.8 nm CrZnSe quantum dot (QD). The Cr ion incorporates as a pair of Cr(III) ions occupying edge-sharing tetragonal distorted octahedral sites generated by formation of three Zn ion vacancies in the sphalerite lattice in order to charge compensate the QD. The site is analogous to the formation of a subunit of the ZnCr(2)Se(4) spinel phase known to form as inclusions during peritectoid crystal growth in the ternary CrZnSe solid-state compound. The oxidation state and site symmetry of the Cr ion is confirmed by X-ray absorption near edge spectroscopy (XANES), crystal field absorption spectroscopy, and electron paramagnetic resonance (EPR). Incorporation as the Cr(III) oxidation state is consistent with the thermodynamic preference for Cr to occupy an octahedral site within a II-VI semiconductor lattice with a half-filled t(2g) d-level. The measured crystal field splitting energy for the CrZnSe QD is 2.08 eV (2.07 eV form XANES), consistent with a spinel inclusion. Further evidence of a spinel inclusion is provided by analysis of the magnetic data, where antiferromagnetic (AFM) exchange, a Curie-Weiss (C-W) temperature of ?? = -125 K, and a nearest-neighbor exchange coupling constant of J(NN) = -12.5 K are observed. The formation of stable spinel inclusions in a QD has not been previously reported.]]></summary>
		<contributor>
			<name>J. Am. Chem. Soc.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Am. Chem. Soc.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Exchange-enhanced reactivity in bond activation by metal-oxo enzymes and synthetic reagents.]]></title>
		<author><name>Nat Chem</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3522"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3522</id>
		<updated>2012-04-02T07:48:52Z</updated>
		<summary><![CDATA[Reactivity principles based on orbital overlap and bonding/antibonding interactions are well established to describe the reactivity of organic species, and atomic structures are typically predicted by Hund's rules to have maximum single-electron occupancy of degenerate orbitals in the ground state. Here, we extend the role of exchange to transition states and discuss how, for reactions and kinetics of bioinorganic species, the analogue of Hund's rules is exchange-controlled reactivity. Pathways that increase the number of unpaired and spin-identical electrons on a metal centre will be favoured by exchange stabilization. Such exchange-enhanced reactivity endows transition states with a stereochemistry different from that observed in cases that are not exchange-enhanced, and is in good agreement with the reactivity observed for iron-based enzymes and synthetic analogues. We discuss the interplay between orbital- and exchange-controlled principles, and how this depends on the identity of the transition metal, its oxidation number and its coordination sphere.]]></summary>
		<contributor>
			<name>Nat Chem</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Nat Chem</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[The Origins of Dramatic Axial Ligand Effects: Closed-Shell Mn(V) O Complexes Use Exchange-Enhanced Open-Shell States to Mediate Efficient H Abstraction Reactions.]]></title>
		<author><name>Angewandte Chemie (International ed. in English)</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3521"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3521</id>
		<updated>2012-04-02T07:48:48Z</updated>
		<summary><![CDATA[Spin-state effects: In [(Cz)Mn(V) O] complexes, even with singlet closed-shell ground states, the reactive state is the open-shell triplet B state (S(B) =1) that has a high oxyl radical character and a transition state (TS) stabilized by exchange-enhanced reactivity (EER; see picture). The dramatic axial ligand effect originates in the EER of this state.]]></summary>
		<contributor>
			<name>Angewandte Chemie (International ed. in English)</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Angewandte Chemie (International ed. in English)</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Sulfur-substituted tetrahedranes.]]></title>
		<author><name>J. Am. Chem. Soc.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3520"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3520</id>
		<updated>2012-04-01T13:46:15Z</updated>
		<summary><![CDATA[The stable sulfur-substituted tetrahedrane derivatives 2-4 were synthesized by the reaction of tris(trimethylsilyl)tetrahedranyllithium 1 with diphenyl disulfide, bis(4-nitrophenyl) disulfide, and bis(2,4-dinitrophenyl) disulfide, respectively, and characterized by both NMR spectroscopy and X-ray crystallography. Phenylsulfonyltetrahedrane 5 was prepared by the reaction of 2 and m-chloroperbenzoic acid. The UV-vis absorption spectra of 2-4 suggested an interaction of the ?? orbital of the tetrahedrane core and the lone-pair electrons on the sulfur atom, whereas no interaction for 5 was found. Thermal reactions of 2 and 5 are also reported; 2 underwent fragmentation into two acetylene molecules, whereas 5 gave the corresponding cyclobutadiene.]]></summary>
		<contributor>
			<name>J. Am. Chem. Soc.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Am. Chem. Soc.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Perfluoroaryltetrahedranes: tetrahedranes with extended sigma-pi conjugation.]]></title>
		<author><name>J. Am. Chem. Soc.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3519"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3519</id>
		<updated>2012-04-01T13:46:14Z</updated>
		<summary><![CDATA[The first stable aryl-substituted tetrahedrane derivatives 4-6 were synthesized by the reaction of tris(trimethylsilyl)tetrahedranyllithium with hexafluorobenzene or [(pentafluorophenyl)ethynyl]benzene in THF. Tetrahedranes having the fluoroaryl groups as electron-withdrawing substituents were found to be thermally stable up to 170 degrees C. X-ray analyses of 4 and 6 and UV-vis absorption spectra of 4-6 suggest sigma-pi conjugation between the strained tetrahedrane core and the benzene ring, which causes a considerable bathochromic shift.]]></summary>
		<contributor>
			<name>J. Am. Chem. Soc.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Am. Chem. Soc.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Tetrahedranyllithium: synthesis, characterization, and reactivity.]]></title>
		<author><name>J. Am. Chem. Soc.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3518"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3518</id>
		<updated>2012-04-01T13:46:13Z</updated>
		<summary><![CDATA[The first representative of stable tetrahedranyl anion, tris(trimethylsilyl)tetrahedranyllithium (3), has been synthesized by the reaction of tetrakis(trimethylsilyl)tetrahedrane (2) with methyllithium in tetrahydrofuran. The structural characterization of the tetrahedranyllithium has been achieved by X-ray crystallography, showing that the structure of 3.(TMEDA)1.5 represents a stretched tetrahedron. The endocyclic C(Li)-C(SiMe3) bond lengths range from 1.5408(15) to 1.5441(15) A (av 1.5425(15) A), and are longer than the endocyclic C(SiMe3)-C(SiMe3) bond lengths, which range from 1.4961(15) to 1.5009(15) A (av 1.4986(15) A). Methyl- and hydrogen-substituted tetrahedranes have also been prepared by the reaction of 3 with dimethyl sulfate and cyclopentadiene, respectively.]]></summary>
		<contributor>
			<name>J. Am. Chem. Soc.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Am. Chem. Soc.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Enabling the synthesis of perfluoroalkyl bicyclobutanes via 1,3 ??-silyl elimination.]]></title>
		<author><name>Org. Lett.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3517"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3517</id>
		<updated>2012-04-01T13:46:12Z</updated>
		<summary><![CDATA[Two new bicyclobutanes were prepared from cyclobutyl systems by a novel, solvolytic, carbocation-based methodology. An electron-withdrawing perfluoroalkyl group at the incipient cationic center enhances neighboring-group participation of the ??-silyl group, inducing facile, remarkably selective 1,3-elimination yielding only bicyclobutanes. The method unlocks potential access to a host of EWG-substituted strained rings and a potential new method for the synthesis of trifluoromethylcyclopropanes.]]></summary>
		<contributor>
			<name>Org. Lett.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Org. Lett.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Hexakis(trimethylsilyl)tetrahedranyltetrahedrane.]]></title>
		<author><name>Angew. Chem. Int. Ed. Engl.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3516"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3516</id>
		<updated>2012-04-01T13:46:05Z</updated>
		<summary><![CDATA[]]></summary>
		<contributor>
			<name>Angew. Chem. Int. Ed. Engl.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Angew. Chem. Int. Ed. Engl.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Metabolomics of sepsis-induced acute lung injury: a new approach for biomarkers.]]></title>
		<author><name>Am. J. Physiol. Lung Cell Mol. Physiol.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3515"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3515</id>
		<updated>2012-03-28T01:48:07Z</updated>
		<summary><![CDATA[]]></summary>
		<contributor>
			<name>Am. J. Physiol. Lung Cell Mol. Physiol.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Am. J. Physiol. Lung Cell Mol. Physiol.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Blogging on the sidelines.]]></title>
		<author><name>Nat Chem</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3514"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3514</id>
		<updated>2012-03-28T01:48:06Z</updated>
		<summary><![CDATA[]]></summary>
		<contributor>
			<name>Nat Chem</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Nat Chem</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Easy and accurate high-performance liquid chromatography retention prediction with different gradients, flow rates, and instruments by back-calculation of gradient and flow rate profiles.]]></title>
		<author><name>J Chromatogr A</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3513"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3513</id>
		<updated>2012-03-28T01:48:04Z</updated>
		<summary><![CDATA[Isocratic retention data should make a suitable foundation for an accurate, cross-instrument LC retention prediction system. Our previous work suggested that in order to accurately calculate (or &amp;quot;project&amp;quot;) gradient retention times on a wide range of HPLC systems using a single set of isocratic retention data, the precise shape of both the gradient and flow rate profiles produced by each instrument must be properly taken into account. However, accurate measurement of these system properties is difficult and time-consuming. In this work, we describe an approach that uses the measured gradient retention times of a set of standard solutes spiked into the sample along with their known isocratic retention vs. eluent composition relationships to determine the effective gradient and flow rate profiles by back-calculation. Retention &amp;quot;projections&amp;quot; of 20 other solutes using these back-calculated profiles, under various chromatographic conditions typical of metabolomics experiments, were remarkably accurate (as good as 0.23% of the gradient time, R2 up to 0.99996), being very near the level of retention reproducibility. Our calculations suggest that this level of accuracy will allow a quadrupole MS to identify 38-fold more compounds out of a simulated mixture of 7307; it would allow an FTICR-MS to improve its identification rate nearly two-fold with the same mixture. Moreover, very little effort is required of the user. This approach provides a simple way to correct for all instrument-related factors affecting retention, allowing dramatically streamlined and improved retention projection across gradients, flow rates, and HPLC instruments.]]></summary>
		<contributor>
			<name>J Chromatogr A</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J Chromatogr A</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Toward prediction of alkane/water partition coefficients.]]></title>
		<author><name>J. Med. Chem.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3512"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3512</id>
		<updated>2012-03-28T01:48:02Z</updated>
		<summary><![CDATA[Partition coefficients were measured for 47 compounds in the hexadecane/water ( P hxd) and 1-octanol/water ( P oct) systems. Some types of hydrogen bond acceptor presented by these compounds to the partitioning systems are not well represented in the literature of alkane/water partitioning. The difference, DeltalogP, between logP oct and logP hxd is a measure of the hydrogen bonding potential of a molecule and is identified as a target for predictive modeling. Minimized molecular electrostatic potential ( V min) was shown to be an effective predictor of the contribution of hydrogen bond acceptors to DeltalogP. Carbonyl oxygen atoms were found to be stronger hydrogen bond acceptors for their electrostatic potential than heteroaromatic nitrogen or oxygen bound to hypervalent sulfur or nitrogen. Values of V min calculated for hydrogen-bonded complexes were used to explore polarization effects. Predicted logP hxd and DeltalogP were shown to be more effective than logP oct for modeling brain penetration for a data set of 18 compounds.]]></summary>
		<contributor>
			<name>J. Med. Chem.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Med. Chem.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes.]]></title>
		<author><name>J. Med. Chem.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3511"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3511</id>
		<updated>2012-03-28T01:48:01Z</updated>
		<summary><![CDATA[Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble fragment libraries, and providers use them to select fragments for commercial offer. We question whether these rules are too stringent to compose fragment libraries with candidates exhibiting sufficient room for chemical subsequent growing and merging modifications as appropriate functional groups for chemical transformations are required. Usually these groups exhibit properties as hydrogen bond donors/acceptors and provide entry points for optimization chemistry. We therefore designed a fragment library (364 entries) without strictly applying the rule of 3. For initial screening for endothiapepsin binding, we performed a biochemical cleavage assay of a fluorogenic substrate at 1 mM. &amp;quot;Hits&amp;quot; were defined to inhibit the enzyme by at least 40%. Fifty-five hits were suggested and subsequently soaked into endothiapepsin crystals. Eleven crystal structures could be determined covering fragments with diverse binding modes: (i) direct binding to the catalytic dyad aspartates, (ii) water-mediated binding to the aspartates, (iii) no direct interaction with the dyad. They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes.]]></summary>
		<contributor>
			<name>J. Med. Chem.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Med. Chem.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis.]]></title>
		<author><name>Current bioinformatics</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3510"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3510</id>
		<updated>2012-03-28T01:48:00Z</updated>
		<summary><![CDATA[Biological systems are increasingly being studied in a holistic manner, using omics approaches, to provide quantitative and qualitative descriptions of the diverse collection of cellular components. Among the omics approaches, metabolomics, which deals with the quantitative global profiling of small molecules or metabolites, is being used extensively to explore the dynamic response of living systems, such as organelles, cells, tissues, organs and whole organisms, under diverse physiological and pathological conditions. This technology is now used routinely in a number of applications, including basic and clinical research, agriculture, microbiology, food science, nutrition, pharmaceutical research, environmental science and the development of biofuels. Of the multiple analytical platforms available to perform such analyses, nuclear magnetic resonance and mass spectrometry have come to dominate, owing to the high resolution and large datasets that can be generated with these techniques. The large multidimensional datasets that result from such studies must be processed and analyzed to render this data meaningful. Thus, bioinformatics tools are essential for the efficient processing of huge datasets, the characterization of the detected signals, and to align multiple datasets and their features. This paper provides a state-of-the-art overview of the data processing tools available, and reviews a collection of recent reports on the topic. Data conversion, pre-processing, alignment, normalization and statistical analysis are introduced, with their advantages and disadvantages, and comparisons are made to guide the reader.]]></summary>
		<contributor>
			<name>Current bioinformatics</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Current bioinformatics</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Believe it or not: how much can we rely on published data on potential drug targets?]]></title>
		<author><name>Nat Rev Drug Discov</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3509"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3509</id>
		<updated>2012-03-28T01:47:58Z</updated>
		<summary><![CDATA[]]></summary>
		<contributor>
			<name>Nat Rev Drug Discov</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Nat Rev Drug Discov</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Molecular shape and medicinal chemistry: a perspective.]]></title>
		<author><name>J. Med. Chem.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3508"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3508</id>
		<updated>2012-03-28T01:47:57Z</updated>
		<summary><![CDATA[The eight contributions here provide ample evidence that shape as a volume or as a surface is a vibrant and useful concept when applied to drug discovery. It provides a reliable scaffold for &amp;quot;decoration&amp;quot; with chemical intuition (or bias) for virtual screening and lead optimization but also has its unadorned uses, as in library design, ligand fitting, pose prediction, or active site description. Computing power has facilitated this evolution by allowing shape to be handled precisely without the need to reduce down to point descriptors or approximate metrics, and the diversity of resultant applications argues for this being an important step forward. Certainly, it is encouraging that as computation has enabled our intuition, molecular shape has consistently surprised us in its usefulness and adaptability. The first Aurelius question, &amp;quot;What is the essence of a thing?&amp;quot;, seems well answered, however, the third, &amp;quot;What do molecules do?&amp;quot;, only partly so. Are the topics covered here exhaustive, or is there more to come? To date, there has been little published on the use of the volumetric definition of shape described here as a QSAR variable, for instance, in the prediction or classification of activity, although other shape definitions have been successful applied, for instance, as embodied in the Compass program described above in &amp;quot;Shape from Surfaces&amp;quot;. Crystal packing is a phenomenon much desired to be understood. Although powerful models have been applied to the problem, to what degree is this dominated purely by the shape of a molecule? The shape comparison described here is typically of a global nature, and yet some importance must surely be placed on partial shape matching, just as the substructure matching of chemical graphs has proved useful. The approach of using surfaces, as described here, offers some flavor of this, as does the use of metrics that penalize volume mismatch less than the Tanimoto, e.g., Tversky measures. As yet, there is little to go on as to how useful a paradigm this will be because there is less software and fewer concrete results.Finally, the distance between molecular shapes, or between any shapes defined as volumes or surfaces, is a metric property in the mathematical sense of the word. As yet, there has been little, if any, application of this observation. We cannot know what new application to the design and discovery of pharmaceuticals may yet arise from the simple concept of molecular shape, but it is fair to say that the progress so far is impressive.]]></summary>
		<contributor>
			<name>J. Med. Chem.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Med. Chem.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Fragment-based screening using surface plasmon resonance technology.]]></title>
		<author><name>J Biomol Screen</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3507"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3507</id>
		<updated>2012-03-28T01:47:56Z</updated>
		<summary><![CDATA[Surface plasmon resonance (SPR) technology has emerged as a new and powerful technique to investigate the interaction between low-molecular-weight molecules and target proteins. In the present work, the authors assemble from a large compound collection a library of 2226 molecules (fragments having low molecular weights between 100 and 300 Da) to screen them for binding to chymase, a serine protease. Both the active chymase and a zymogen-like form of the protein were used in parallel to distinguish between specific and unspecific binding. The relative ligand-binding activity of the immobilized protein was periodically measured with a reference compound. The screening experiments were performed at 25 degrees C at a fragment concentration of 200 microM in the presence of 2% DMSO. Applying the filter cascade, affinity-selectivity-competition (competition with reference compounds and cross-competition with fragments), 80 compounds show up as positive screening hits. Competition experiments between fragments show that they bind to different parts of the active site. Of 36 fragments co-crystallized for X-ray studies, 12 could be located in the active site of the protein. These results validate the authors' library and demonstrate that the application of SPR technology as a filter in fragment screening can be achieved successfully.]]></summary>
		<contributor>
			<name>J Biomol Screen</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J Biomol Screen</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors.]]></title>
		<author><name>J. Med. Chem.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3506"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3506</id>
		<updated>2012-03-28T01:47:41Z</updated>
		<summary><![CDATA[Promiscuous binders achieve enzyme inhibition using a nonspecific aggregation-type binding mechanism to proteins. These compounds are a source of false-positive hits in biochemical inhibition assays and should be removed from screening hit lists because they are not good candidates to initiate medicinal chemistry programs. We introduce a robust approach to identify these molecules early in the lead generation process using real time surface plasmon resonance based biosensors to observe the behavior of the binding interactions between promiscuous compounds and proteins. Furthermore, the time resolution of the assay reveals a number of distinct mechanisms that promiscuous compounds employ to inhibit enzyme function and indicate that the type of mechanism can vary depending on the protein target. A classification scheme for these compounds is presented that can be used to rapidly characterize the hits from high-throughput screens and eliminate compounds with a nonspecific mechanism of inhibition.]]></summary>
		<contributor>
			<name>J. Med. Chem.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Med. Chem.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Experimental measures of amino acid hydrophobicity and the topology of transmembrane and globular proteins.]]></title>
		<author><name>J. Gen. Physiol.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3505"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3505</id>
		<updated>2012-03-28T01:47:40Z</updated>
		<summary><![CDATA[]]></summary>
		<contributor>
			<name>J. Gen. Physiol.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Gen. Physiol.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Synthesis and properties of [9]cyclo-1,4-naphthylene: a ??-extended carbon nanoring.]]></title>
		<author><name>J. Am. Chem. Soc.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3504"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3504</id>
		<updated>2012-03-27T19:46:27Z</updated>
		<summary><![CDATA[The first synthesis of a ??-extended carbon nanoring, [9]cyclo-1,4-naphthylene ([9]CN), has been achieved. Careful structure-property analyses uncovered a number of unique features of [9]CN that are quite different from those of [9]CPP, a simple carbon nanoring.]]></summary>
		<contributor>
			<name>J. Am. Chem. Soc.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Am. Chem. Soc.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[One-pot multistep Bohlmann-Rahtz heteroannulation reactions: synthesis of dimethyl sulfomycinamate.]]></title>
		<author><name>J. Org. Chem.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3503"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3503</id>
		<updated>2012-03-26T19:51:39Z</updated>
		<summary><![CDATA[[reaction: see text] The synthesis of dimethyl sulfomycinamate, the acidic methanolysis product of the sulfomycin family of thiopeptide antibiotics, from methyl 2-oxo-4-(trimethylsilyl)but-3-ynoate is achieved in a 2,3,6-trisubstituted pyridine synthesis that proceeds with total regiocontrol in 13 steps by the Bohlmann-Rahtz heteroannulation of a 1-(oxazol-4-yl)enamine or in 12 steps and 9% yield by three-component cyclocondensation with N-[3-oxo-3-(oxazol-4-yl)propanoyl]serine and ammonia in ethanol.]]></summary>
		<contributor>
			<name>J. Org. Chem.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Org. Chem.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Synthesis of vinyl-functionalized oxazoles by olefin cross-metathesis.]]></title>
		<author><name>J. Org. Chem.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3502"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3502</id>
		<updated>2012-03-26T19:51:38Z</updated>
		<summary><![CDATA[A ruthenium-based catalyzed olefin cross-methathesis reaction involving 2- and 4-vinyl-functionalized oxazoles was developed. A wide range of olefinic partners was coupled in good to excellent yields and high stereoselectivities under mild conditions. This methodology offers new opportunities for the synthesis of a plethora of biologically active natural products.]]></summary>
		<contributor>
			<name>J. Org. Chem.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Org. Chem.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[One-pot Crabb?? homologation-radical cascade cyclisation with memory of chirality.]]></title>
		<author><name>Chem. Commun. (Camb.)</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3501"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3501</id>
		<updated>2012-03-25T19:49:45Z</updated>
		<summary><![CDATA[The tandem Crabb?? homologation-radical rearrangement of terminal enediynes leads, in a one-pot procedure, to the enantioselective synthesis of six- and seven-membered ring ??-aminoesters bearing a quaternary stereocenter based on the phenomenon of memory of chirality.]]></summary>
		<contributor>
			<name>Chem. Commun. (Camb.)</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Chem. Commun. (Camb.)</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[OSCAR4: a flexible architecture for chemical text-mining.]]></title>
		<author><name>J Cheminform</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3500"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3500</id>
		<updated>2012-03-21T19:43:56Z</updated>
		<summary><![CDATA[ABSTRACT: The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the separation of the core OSCAR functionality and its release as the OSCAR4 library. This library features a modular API (based on reduction of surface coupling) that permits client programmers to easily incorporate it into external applications. OSCAR4 offers a domain-independent architecture upon which chemistry specific text-mining tools can be built, and its development and usage are discussed.]]></summary>
		<contributor>
			<name>J Cheminform</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J Cheminform</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[Effects of ethynyl substitution on cyclobutadiene.]]></title>
		<author><name>J Phys Chem A</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3499"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3499</id>
		<updated>2012-03-20T13:45:15Z</updated>
		<summary><![CDATA[The effects of ethynyl substitution on cyclobutadiene are explored via density functional theory and coupled-cluster calculations. The computed singlet-triplet gaps indicate a monotonic dependence on the degree of ethynyl substitution, which differentially stabilizes the triplet relative to the singlet ground state and reduces the gap. A series of isodesmic, homodesmotic, and hyperhomodesmotic equations are employed to quantify the stabilization upon ethynyl substitution. Analyses that rely on a simple isodesmic equation and/or B3LYP/6-31G(d) values are found to be problematic. Analyses that rely on homodesmotic or hyperhomodesmotic equations, in conjunction with CCSD/cc-pVDZ values, are more robust. Using a hyperhomodesmotic equation to assess the stabilization enthalpies of tetra-substituted singlet cyclobutadienes, our analysis predicts tetramethylcyclobutadiene (??H(0)(rxn) = -17.3 kcal/mol) to be more stable than tetraethynylcyclobutadiene (??H(0)(rxn) = -11.7 kcal/mol), which, in turn, is substantially more stable than tetracyanocyclobutadiene (??H(0)(rxn) = +12.7 kcal/mol).]]></summary>
		<contributor>
			<name>J Phys Chem A</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J Phys Chem A</uri>
		</contributor>
		<gd:rating value='2' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[The immigration delay disease: adermatoglyphia-inherited absence of epidermal ridges.]]></title>
		<author><name>J. Am. Acad. Dermatol.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3498"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3498</id>
		<updated>2012-03-16T19:47:17Z</updated>
		<summary><![CDATA[In the digital age, personal identification by fingerprints (epidermal ridges) has become more frequent and is often required for biometric passports. The more fingerprints are analyzed, the more variants in their formation are documented. Individuals completely missing fingerprints as an isolated finding are extremely rare. Only 4 kindreds have been described to date, with additional clinical features in most cases. We describe a female patient with missing epidermal ridges on the fingers, palms, toes, and soles as an isolated feature. Absent fingerprints, or adermatoglyphia, were inherited over 4 generations of her family in an autosomal dominant fashion. We present the clinical features of the index patient, and compare the case with previous reports in the literature. Because of problems in personal identification, this embryologic malformation caused the patient significant difficulties when traveling to other countries, which is why we name it the immigration delay disease.]]></summary>
		<contributor>
			<name>J. Am. Acad. Dermatol.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=J. Am. Acad. Dermatol.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	
	<entry>
		<title><![CDATA[A mutation in a skin-specific isoform of SMARCAD1 causes autosomal-dominant adermatoglyphia.]]></title>
		<author><name>Am. J. Hum. Genet.</name></author>
		<link rel='alternate' href="http://cb.openmolecules.net/paper.php?paper_id=3497"/>
		<id>http://cb.openmolecules.net/paper.php?paper_id=3497</id>
		<updated>2012-03-16T19:47:16Z</updated>
		<summary><![CDATA[Monogenic disorders offer unique opportunities for researchers to shed light upon fundamental physiological processes in humans. We investigated a large family affected with autosomal-dominant adermatoglyphia (absence of fingerprints) also known as the &amp;quot;immigration delay disease.&amp;quot; Using linkage and haplotype analyses, we mapped the disease phenotype to 4q22. One of the genes located in this interval is SMARCAD1, a member of the SNF subfamily of the helicase protein superfamily. We demonstrated the existence of a short isoform of SMARCAD1 exclusively expressed in the skin. Sequencing of all SMARCAD1 coding and noncoding exons revealed a heterozygous transversion predicted to disrupt a conserved donor splice site adjacent to the 3' end of a noncoding exon uniquely present in the skin-specific short isoform of the gene. This mutation segregated with the disease phenotype throughout the entire family. Using a minigene system, we found that this mutation causes aberrant splicing, resulting in decreased stability of the short RNA isoform as predicted by computational analysis and shown by RT-PCR. Taken together, the present findings implicate a skin-specific isoform of SMARCAD1 in the regulation of dermatoglyph development.]]></summary>
		<contributor>
			<name>Am. J. Hum. Genet.</name>
			<uri>http://cb.openmolecules.net/journal_search.php?journal_id=Am. J. Hum. Genet.</uri>
		</contributor>
		<gd:rating value='1' min='0' max='100'/>
	</entry>
	</feed>
