Comparison of CBS-QB3, CBS-APNO, G2, and G3 thermochemical predictions with experiment for formation of ionic clusters of hydronium and hydroxide ions complexed with water

The GAUSSIAN 2, GAUSSIAN 3, complete basis set-QB3, and complete basis set-APNO methods have been used to calculate ΔH∘ and ΔG∘ values for ionic clusters of hydronium and hydroxide ions complexed with water. Results for the clusters H3O+(H2O)n andOH−(H2O)n, where n=1–4 are reported in this paper, and compared against experimental values contained in the National Institutes of Standards and Technology (NIST) database. Agreement with experiment is excellent for the three ab initio methods for formation of these clusters. The high accuracy of these methods makes them reliable for calculating energetics for the formation of ionic clusters containing water. In addition this allows them to serve as a valuable check on the accuracy of experimental data reported in the NIST database, and makes them useful tools for addressing unresolved issues in atmospheric chemistry.

Broadband Fourier transform rotational spectroscopy for structure determination: The water heptamer

Over the recent years chirped-pulse, Fourier-transform microwave (CP-FTMW) spectrometers have chan- ged the scope of rotational spectroscopy. The broad frequency and large dynamic range make possible structural determinations in molecular systems of increasingly larger size from measurements of heavy atom (13C, 15N, 18O) isotopes recorded in natural abundance in the same spectrum as that of the parent isotopic species. The design of a broadband spectrometer operating in the 2–8 GHz frequency range with further improvements in sensitivity is presented. The current CP-FTMW spectrometer performance is benchmarked in the analyses of the rotational spectrum of the water heptamer, (H2O)7, in both 2– 8 GHz and 6–18 GHz frequency ranges. Two isomers of the water heptamer have been observed in a pulsed supersonic molecular expansion. High level ab initio structural searches were performed to pro- vide plausible low-energy candidates which were directly compared with accurate structures provided from broadband rotational spectra. The full substitution structure of the most stable species has been obtained through the analysis of all possible singly-substituted isotopologues (H218O and HDO), and a least-squares rm(1) geometry of the oxygen framework determined from 16 different isotopic species compares with the calculated O–O equilibrium distances at the 0.01 Å level.

Broadband Fourier transform rotational spectroscopy for structure determination: The water heptamer

Over the recent years chirped-pulse, Fourier-transform microwave (CP-FTMW) spectrometers have changed the scope of rotational spectroscopy. The broad frequency and large dynamic range make possible structural determinations in molecular systems of increasingly larger size from measurements of heavy atom (C-13, N-15, O-18) isotopes recorded in natural abundance in the same spectrum as that of the parent isotopic species. The design of a broadband spectrometer operating in the 2-8 GHz frequency range with further improvements in sensitivity is presented. The current CP-FTMW spectrometer performance is benchmarked in the analyses of the rotational spectrum of the water heptamer, (H2O)(7), in both 2-8 GHz and 6-18 GHz frequency ranges. Two isomers of the water heptamer have been observed in a pulsed supersonic molecular expansion. High level ab initio structural searches were performed to provide plausible low-energy candidates which were directly compared with accurate structures provided from broadband rotational spectra. The full substitution structure of the most stable species has been obtained through the analysis of all possible singly-substituted isotopologues ((H2O)-O-18 and HDO), and a least-squares r(m)((1)) geometry of the oxygen framework determined from 16 different isotopic species compares with the calculated O-O equilibrium distances at the 0.01 angstrom level. (C) 2013 Elsevier B.V. All rights reserved.

Photodissociation dynamics of tert-butylnitrite following excitation to the S(1) and S(2) states. A study by velocity-map ion-imaging and 3D-REMPI spectroscopy

Excitation of tert-butylnitrite into the first and second UV absorption bands leads to efficient dissociation into the fragment radicals NO and tert-butoxy in their electronic ground states (2)Π and (2)E, respectively. Velocity distributions and angular anisotropies for the NO fragment in several hundred rotational and vibrational quantum states were obtained by velocity-map imaging and the recently developed 3D-REMPI method. Excitation into the well resolved vibronic progression bands (k = 0, 1, 2) of the NO stretch mode in the S(1) ← S(0) transition produces NO fragments mostly in the vibrational state with v = k, with smaller fractions in v = k - 1 and v = k - 2. It is concluded that dissociation occurs on the purely repulsive PES of S(1) without barrier. All velocity distributions from photolysis via the S(1)(nπ*) state are monomodal and show high negative anisotropy (β ≈ -1). The rotational distributions peak near j = 30.5 irrespective of the vibronic state S(1)(k) excited and the vibrational state v of the NO fragment. On average 46% of the excess energy is converted to kinetic energy, 23% and 31% remain as internal energy in the NO fragment and the t-BuO radical, respectively. Photolysis via excitation into the S(2) ← S(0) transition at 227 nm yields NO fragments with about equal populations in v = 0 and v = 1. The rotational distributions have a single maximum near j = 59.5. The velocity distributions are monomodal with positive anisotropy β ≈ 0.8. The average fractions of the excess energy distributed into translation, internal energy of NO, and internal energy of t-BuO are 39%, 23%, and 38%, respectively. In all cases ∼8500 cm(-1) of energy remain in the internal degrees of freedom of the t-BuO fragment. This is mostly assigned to rotational energy. An ab initio calculation of the dynamic reaction path shows that not only the NO fragment but also the t-BuO fragment gain large angular momentum during dissociation on the purely repulsive potential energy surface of S(2).

Factor XIII activation peptide is released into plasma upon cleavage by thrombin and shows a different structure compared to its bound form

The first step of coagulation factor XIII (FXIII) activation involves cleavage of the FXIII activation peptide (FXIII-AP) by thrombin. However, it is not known whether the FXIII-AP is released into plasma upon cleavage or remains attached to activated FXIII. The aim of the present work was to study the structure of free FXIII-AP, develop an assay for FXIII-AP determination in human plasma, and to answer the question whether FXIII-AP is released into plasma. We used ab-initio modeling and molecular dynamics simulations to study the structure of free FXIII-AP. We raised monoclonal and polyclonal antibodies against FXIII-AP and developed a highly sensitive and specific ELISA method for direct detection of FXIII-AP in human plasma. Structural analysis showed a putative different conformation of the free FXIII-AP compared to FXIII-AP bound to the FXIII protein. We concluded that it might be feasible to develop specific antibodies against the free FXIII-AP. Using our new FXIII-AP ELISA, we found high levels of FXIII-AP in in-vitro activated plasma samples and serum. We showed for the first time that FXIIIAP is detached from activated FXIII and is released into plasma, where it can be directly measured. Our findings may be of major clinical interest in regard to a possible new marker in thrombotic disease.

Spin-strain coupling in a 3-D transition metal oxides

ab-initio Hartree Fock (HF), density functional theory (DFT) and hybrid potentials were employed to compute the optimized lattice parameters and elastic properties of perovskite 3-d transition metal oxides. The optimized lattice parameters and elastic properties are interdependent in these materials. An interaction is observed between the electronic charge, spin and lattice degrees of freedom in 3-d transition metal oxides. The coupling between the electronic charge, spin and lattice structures originates due to localization of d-atomic orbitals. The coupling between the electronic charge, spin and crystalline lattice also contributes in the ferroelectric and ferromagnetic properties in perovskites. The cubic and tetragonal crystalline structures of perovskite transition metal oxides of ABO3 are studied. The electronic structure and the physics of 3-d perovskite materials is complex and less well considered. Moreover, the novelty of the electronic structure and properties of these perovskites transition metal oxides exceeds the challenge offered by their complex crystalline structures. To achieve the objective of understanding the structure and property relationship of these materials the first-principle computational method is employed. CRYSTAL09 code is employed for computing crystalline structure, elastic, ferromagnetic and other electronic properties. Second-order elastic constants (SOEC) and bulk moduli (B) are computed in an automated process by employing ELASTCON (elastic constants) and EOS (equation of state) programs in CRYSTAL09 code. ELASTCON, EOS and other computational algorithms are utilized to determine the elastic properties of tetragonal BaTiO3, rutile TiO2, cubic and tetragonal BaFeO3 and the ferromagentic properties of 3-d transition metal oxides. Multiple methods are employed to crosscheck the consistency of our computational results. Computational results have motivated us to explore the ferromagnetic properties of 3-d transition metal oxides. Billyscript and CRYSTAL09 code are employed to compute the optimized geometry of the cubic and tetragonal crystalline structure of transition metal oxides of Sc to Cu. Cubic crystalline structure is initially chosen to determine the effect of lattice strains on ferromagnetism due to the spin angular momentum of an electron. The 3-d transition metals and their oxides are challenging as the basis functions and potentials are not fully developed to address the complex physics of the transition metals. Moreover, perovskite crystalline structures are extremely challenging with respect to the quality of computations as the latter requires the well established methods. Ferroelectric and ferromagnetic properties of bulk, surfaces and interfaces are explored by employing CRYSTAL09 code. In our computations done on cubic TMOs of Sc-Fe it is observed that there is a coupling between the crystalline structure and FM/AFM spin polarization. Strained crystalline structures of 3-d transition metal oxides are subjected to changes in the electromagnetic and electronic properties. The electronic structure and properties of bulk, composites, surfaces of 3-d transition metal oxides are computed successfully.

Functional ZnO nanostructures for electronic and energy applications

ZnO has proven to be a multifunctional material with important nanotechnological applications. ZnO nanostructures can be grown in various forms such as nanowires, nanorods, nanobelts, nanocombs etc. In this work, ZnO nanostructures are grown in a double quartz tube configuration thermal Chemical Vapor Deposition (CVD) system. We focus on functionalized ZnO Nanostructures by controlling their structures and tuning their properties for various applications. The following topics have been investigated: 1. We have fabricated various ZnO nanostructures using a thermal CVD technique. The growth parameters were optimized and studied for different nanostructures. 2. We have studied the application of ZnO nanowires (ZnONWs) for field effect transistors (FETs). Unintentional n-type conductivity was observed in our FETs based on as-grown ZnO NWs. We have then shown for the first time that controlled incorporation of hydrogen into ZnO NWs can introduce p-type characters to the nanowires. We further found that the n-type behaviors remained, leading to the ambipolar behaviors of hydrogen incorporated ZnO NWs. Importantly, the detected p- and n- type behaviors are stable for longer than two years when devices were kept in ambient conditions. All these can be explained by an ab initio model of Zn vacancy-Hydrogen complexes, which can serve as the donor, acceptors, or green photoluminescence quencher, depend on the number of hydrogen atoms involved. 3. Next ZnONWs were tested for electron field emission. We focus on reducing the threshold field (Eth) of field emission from non-aligned ZnO NWs. As encouraged by our results on enhancing the conductivity of ZnO NWs by hydrogen annealing described in Chapter 3, we have studied the effect of hydrogen annealing for improving field emission behavior of our ZnO NWs. We found that optimally annealed ZnO NWs offered much lower threshold electric field and improved emission stability. We also studied field emission from ZnO NWs at moderate vacuum levels. We found that there exists a minimum Eth as we scale the threshold field with pressure. This behavior is explained by referring to Paschen’s law. 4. We have studied the application of ZnO nanostructures for solar energy harvesting. First, as-grown and (CdSe) ZnS QDs decorated ZnO NBs and ZnONWs were tested for photocurrent generation. All these nanostructures offered fast response time to solar radiation. The decoration of QDs decreases the stable current level produced by ZnONWs but increases that generated by NBs. It is possible that NBs offer more stable surfaces for the attachment of QDs. In addition, our results suggests that performance degradation of solar cells made by growing ZnO NWs on ITO is due to the increase in resistance of ITO after the high temperature growth process. Hydrogen annealing also improve the efficiency of the solar cells by decreasing the resistance of ITO. Due to the issues on ITO, we use Ni foil as the growth substrates. Performance of solar cells made by growing ZnO NWs on Ni foils degraded after Hydrogen annealing at both low (300 °C) and high (600 °C) temperatures since annealing passivates native defects in ZnONWs and thus reduce the absorption of visible spectra from our solar simulator. Decoration of QDs improves the efficiency of such solar cells by increasing absorption of light in the visible region. Using a better electrolyte than phosphate buffer solution (PBS) such as KI also improves the solar cell efficiency. 5. Finally, we have attempted p-type doping of ZnO NWs using various growth precursors including phosphorus pentoxide, sodium fluoride, and zinc fluoride. We have also attempted to create p-type carriers via introducing interstitial fluorine by annealing ZnO nanostructures in diluted fluorine gas. In brief, we are unable to reproduce the growth of reported p-type ZnO nanostructures. However; we have identified the window of temperature and duration of post-growth annealing of ZnO NWs in dilute fluorine gas which leads to suppression of native defects. This is the first experimental effort on post-growth annealing of ZnO NWs in dilute fluorine gas although this has been suggested by a recent theory for creating p-type semiconductors. In our experiments the defect band peak due to native defects is found to decrease by annealing at 300 °C for 10 – 30 minutes. One of the major future works will be to determine the type of charge carriers in our annealed ZnONWs.

Phases of many flavors QCD: Lattice results

This note is based on our recent results on QCD with varying number of flavors of fundamental fermions. Topics include unusual, strong dynamics in the preconformal, confining phase, the physics of the conformal window and the role of ab-initio lattice simulations in establishing our current knowledge of the phases of many flavor QCD.

Peptide nucleic acids: Mechanism of tight binding and application in artificial nuclease

Peptide nucleic acids (PNA) are mimics of nucleic acids with a peptidic backbone. Duplexes and triplexes formed between PNA and DNA or RNA possess remarkable thermal stability, they are resistant to nuclease cleavage and can better discriminate mismatches. Understanding the mechanism for the tight binding between PNA and oligonucleotides is important for the design and development of better PNA-based drugs.^ We have performed molecular dynamics (MD) simulations of 8-mer PNA/DNA duplex and two analogous duplexes with chiral modification of PNA strand (D- or L-Alanine modification). MD simulations were performed with explicit water and Na$\sp{+}$ counter ions. The 1.5-ns simulations were carried out with AMBER using periodic boundary and particle mesh Ewald summation. The point charges for PNA monomers were derived from fitting electrostatic potentials, obtained from ab initio calculation, to atomic centers using RESP. Derived charges reveal significantly altered charge distribution on the PNA bases and predict the Watson-Crick H-bonds involving PNA to be stronger. Results from NMR studies investigating H-bond interactions between DNA-DNA and DNA-PNA base pairs in non-polar environment are consistent with this prediction. MD simulations demonstrated that the PNA strand is more flexible than the DNA strand in the same duplex. That this flexibility might be important for the duplex stability is tested by introducing modification into the PNA backbones. Results from MD simulation revealed dramatically altered structures for the modified PNA-DNA duplexes. Consistent with previous NMR results, we also found no intrachain hydrogen bonds between O7$\sp\prime$ and N1$\sp\prime$ of the neighboring residues in our MD study. Our study reveals that in addition to the lack of charge repulsion, stronger Watson-Crick hydrogen bonds together with flexible backbone are important factors for the enhanced stability of the PNA-DNA duplex.^ In a related study, we have developed an application of Gly-Gly-His-(Gly)$\sb3$-PNA conjugate as an artificial nuclease. We were able to demonstrate cleavage of single stranded DNA at a single site upon Ni(II) binding to Gly-Gly-His tripeptide and activation of nuclease with monoperoxyphthalic acid. ^

Quantum chemical investigation on iodine oxides and their role in the formation of atmospheric aerosols

En esta contribución se presenta un estudio teórico de diferentes reacciones químicas entre óxidos de iodo y agua que pueden contribuir a la formación de partículas en la atmósfera. Mediante el uso de cálculos quimicocuánticos ab initio con tratamiento de la correlación electrónica se han obtenido propiedades termodinámicas para caracterizar esas reacciones

Simulación atomística de metales líquidos y aleaciones para reactores de fusión nuclear = Atomistic simulation of liquid metals and alloys for nuclear fusion reactors

La presente tesis comprende un estudio de metales líquidos, Li, Pb y eutéctico Li17Pb en el ámbito de la tecnología de fusión nuclear. Uno de los problemas fundamentales en futuros reactores de fusión es la producción y extracción de tritio en la denominada envoltura regeneradora (blanket en inglés). Dicho blanket tendrá dos propósitos, la extracción del calor generado por las reacciones de fusión para su posterior conversión en energía eléctrica así como la producción de tritio para realimentar el proceso. Dicha producción se realizará mediante el “splitting” del Li con los neutrones provenientes de la fusión. Esta reacción produce tritio y helio por lo que la interacción del T y el He con el metal líquido, con los materiales estructurales así como con el He es un problema fundamental aun no bien entendido y de gran importancia para futuros diseños. Los capítulos 1 2 y 3 presentan una introducción a dichos problemas. El capítulo 1 introduce al lector en la tecnología de fusión nuclear. El segundo capítulo explica en mayor detalle el uso de metales líquidos en reactores de fusión, no solo en blankets sino también como primera pared, divertor etc, lo que se denomina en general “plasma facing materials”. Por último se ofrece una breve introducción a las técnicas de dinámica molecular clásica (CMD) y un breve resumen de los potenciales más usados. El estudio se ha llevado a cabo utilizando simulación atomística mediante potenciales semi-empíricos del tipo átomo embebido (EAM). La Tesis consta de 4 partes bien definidas. En primer lugar se verificó la idoneidad de los potenciales tipo EAM para simular las propiedades de los metales Li y Pb en fase líquida. Dicho estudio se detalla en el Capítulo 4 y en su extensión, el Apéndice 1, en el que se estudia los límites de validez de esta aproximación. Los resultados de dicho estudio han sido publicados y presentados en diversos congresos internacionales. Un resumen de la metodología seguida fue publicado como capítulo de libro en Technofusión 2011. Los resultados se presentaron en diversos congresos internacionales, entre ellos ICENES 2011, (Artículo en ICENES Proceedings) ICOPS-SOFE 2011, en una presentación oral etc. El trabajo ha sido aceptado recientemente en Journal of Nuclear Materiales (Fraile et al 2012). La segunda parte y más importante comprende el desarrollo de un potencial para el estudio de la mezcla de ambos metales. Éste es el trabajo más novedoso e importante dado que no existía en la literatura un potencial semejante. Se estudiaron dos aproximaciones distintas al problema, un potencial tipo EAM/cd y un potencial EAM/alloy. Ambos potenciales dan resultados satisfactorios para la simulación del eutéctico (y concentraciones de Li menores que el 17%). Sin embargo el sistema LiPb en todas las concentraciones es un sistema que se aparta enormemente de una solución ideal y dicho potencial no daba buenos resultados para mezclas PbLi con concentraciones de Li grandes. Este problema fue solventado mediante el desarrollo de un segundo potencial, esta vez tipo EAM/alloy (segunda parte del Capítulo 5). Dicho trabajo será enviado a Physical Review Letters o a Phys. Rev. B, y una extensión junto con un estudio detallado de las propiedades del eutéctico de acuerdo con nuestras simulaciones se enviará a continuación a Phys. Rev. B. En tercer lugar se estudió el problema de la difusividad del H en metales líquidos aprovechando distintos potenciales existentes en la literatura. El problema del H en metales líquidos es importante en metalurgia. En dicho capítulo se estudió la difusividad del H en Pd, Ni y Al con potenciales tipo EAM, y también con un potencial más sofisticado que tiene en cuenta la dependencia angular de las interacciones (ADP por sus siglas en inglés). De este modo disponemos de un estudio detallado del problema con diferentes modelos y diferentes metales. La conclusión apunta a que si se compara con los resultados experimentales (muy escasos) los resultados obtenidos mediante CMD dan valores bajos de la difusividad del H. Las razones de dicho desacuerdo entre simulación y experimentos se detallan en el Capítulo 6. Este trabajo ha sido presentado en una presentación oral en el reciente congreso internacional “Trends on Nanothecnology” TNT 2012 celebrado en Madrid. El trabajo será publicado en un futuro próximo. Por último, como se dijo anteriormente, el estudio del He, la formación de burbujas en metales líquidos, su difusión nucleación y cavitación es otro problema deseable de ser estudiado mediante técnicas atomísticas. Para ello es necesario el desarrollo de diversos potenciales, He-Li, He-Pb y un potencial ternario Pb-Li-He. Para ello se han realizado simulación ab initio de los sistemas Pb+He y Li+He. Dicho estudio pretende calcular las fuerzas entre los átomos del metal (Pb o Li) con intersticiales de He. De este modo aplicaremos el “force matching method” (FMM) para el desarrollo de dichos potenciales. En el Capítulo 7 se detallan los resultados obtenidos referidos a las posiciones más favorables de las impurezas de He dentro de redes cristalinas de Pb y Li así como el efecto de tener en cuenta el acoplo spin-orbita (SOC en inglés). El análisis de los resultados en términos de transferencia de carga y análisis de las densidades electrónicas, así como la creación de los potenciales mencionados está en progreso. En conjunto la tesis presenta un estudio de los diversos problemas relacionados con el uso de metales líquidos en reactores de fusión y representa un primer paso en la determinación de parámetros de gran importancia para el diseño de blankets y sistemas de primera pared. Con la simulación MD de dichos problemas mediante, importante, potenciales realistas, valores de difusión, solubilidad etc de especies ligeras, H (o sus isotopos) y He en metales líquidos podrá ser calculada complementando así la base de datos que presenta enormes incertidumbres.

Estructura electrónica de fotocatalizadores compuestos ZnO-TiO2

Recientes publicaciones han mostrado propiedades fotocatalíticas interesantes en sistemas basados en TiO2 y ZnO. En unos casos hay presentes fases de ambos óxidos binarios en íntimo contacto [1] y en otros se tienen óxidos mixtos (titanatos de Zn) de distintas estequiometrías [2]; estos últimos, además, se han podido dopar con nitrógeno para obtener actividad con luz visible [3]. Las características electrónicas relevantes de estos sistemas (posición relativa de los niveles de ambas fases en el primero, estructura de bandas para los titanatos con o sin N) se conocen muy poco. Aquí se realiza un estudio teórico cuántico de estos materiales, usando para mayor exactitud funcionales híbridos (pues es sabido que la DFT estándar predice mal los bandgaps). Además se tienen en cuenta desarrollos teóricos recientes que permiten determinar ab initio, para semiconductores de gap alto, el coeficiente más adecuado de mezcla de intercambio HF [4, 5], y formular reglas para obtener con más exactitud el alineamiento de bandas que se establece a través de una interfaz [5, 6].

Conformation of coenzyme pyrroloquinoline quinone and role of Ca2+ in the catalytic mechanism of quinoprotein methanol dehydrogenase

The ab initio structures of 2,7,9-tricarboxypyrroloquinoline quinone (PQQ), semiquinone (PQQH), and dihydroquinone (PQQH2) have been determined and compared with ab initio structures of the (PQQ)Ca2+, (PQQH)Ca2+, and (PQQH2)Ca2+ complexes as well as the x-ray structure of (PQQ)Ca2+ bound at the active site of the methanol dehydrogenase (MDH) of methyltropic bacteria. Plausible mechanisms for the MDH oxidation of methanol involving the (PQQ)Ca2+ complex are explored via ab initio computations and discussed. Considering the reaction of methanol with PQQ in the absence of Ca2+, nucleophilic addition of methanol to the PQQ C-5 carbonyl followed by a retro-ene elimination is deemed unlikely due to large energy barrier. A much more favorable disposition of the methanol C-5 adduct to provide formaldehyde involves proton ionization of the intermediate followed by elimination of methoxide concerted with hydride transfer to the oxygen of the C-4 carbonyl. Much the same transition state is reached if one searches for the transition state beginning with Asp-303–CO2−general-base removal of the methanol proton of the (PQQ)Ca2+O(H)CH3 complex concerted with hydride transfer to the oxygen at C-4. For such a mechanism the role of the Ca2+ moiety would be to (i) contribute to the formation of the ES complex (ii) provide a modest decrease in the pKa of methanol substrate,; and (iii) polarize the oxygen at C-5.

Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution

Understanding the detailed mechanism of protein folding requires dynamic, site-specific stereochemical information. The short time response of vibrational spectroscopies allows evaluation of the distribution of populations in rapid equilibrium as the peptide unfolds. Spectral shifts associated with isotopic labels along with local stereochemical sensitivity of vibrational circular dichroism (VCD) allow determination of the segment sequence of unfolding. For a series of alanine-rich peptides that form α-helices in aqueous solution, we used isotopic labeling and VCD to demonstrate that the α-helix noncooperatively unwinds from the ends with increasing temperature. For these blocked peptides, the C-terminal is frayed at 5°C. Ab initio level theoretical simulations of the IR and VCD band shapes are used to analyze the spectra and to confirm the conformation of the labeled components. The VCD signals associated with the labeled residues are amplified by coupling to the nonlabeled parts of the molecule. Thus small labeled segments are detectable and stereochemically defined in moderately large peptides in this report of site-specific peptide VCD conformational analysis.

RefSeq and LocusLink: NCBI gene-centered resources

Thousands of genes have been painstakingly identified and characterized a few genes at a time. Many thousands more are being predicted by large scale cDNA and genomic sequencing projects, with levels of evidence ranging from supporting mRNA sequence and comparative genomics to computing ab initio models. This, coupled with the burgeoning scientific literature, makes it critical to have a comprehensive directory for genes and reference sequences for key genomes. The NCBI provides two resources, LocusLink and RefSeq, to meet these needs. LocusLink organizes information around genes to generate a central hub for accessing gene-specific information for fruit fly, human, mouse, rat and zebrafish. RefSeq provides reference sequence standards for genomes, transcripts and proteins; human, mouse and rat mRNA RefSeqs, and their corresponding proteins, are discussed here. Together, RefSeq and LocusLink provide a non-redundant view of genes and other loci to support research on genes and gene families, variation, gene expression and genome annotation. Additional information about LocusLink and RefSeq is available at http://www.ncbi.nlm.nih.gov/LocusLink/.