J.A.N.F. Gomes

A comparison of Scopus and Web of Science for a typical university

For many years, the ISI Web of Knowledge from Thomson Reuters was the sole publication and citation database covering all areas of science thus becoming an invaluable tool in bibliometric analysis. In 2004, Elsevier introduced Scopus and this is rapidly becoming a good alternative. Several attempts have been made at comparing these two instruments from the point of view of journal coverage for research or for bibliometric assessment of research output.This paper attempts to answer the question that all researchers ask, i.e., what is to be gained by searching both databases? Or, if you are forced to opt for one of them, which should you prefer? To answer this question, a detailed paper by paper study is presented of the coverage achieved by ISI Web of Science and by Scopus of the output of a typical university. After considering the set of Portuguese universities, the detailed analysis is made for two of them for 2006, the two being chosen for their comprehensiveness typical of most European universities. The general conclusion is that about 2/3 of the documents referenced in any of the two databases may be found in both databases while a fringe of 1/3 are only referenced in one or the other. The citation impact of the documents in the core present in both databases is higher, but the impact of the fringe that are present only in one of the databases should not be disregarded as some high impact documents may be found among them.

Citations to scientific articles: Its distribution and dependence on the article features

The citation counts are increasingly used to assess the impact on the scientific community of publications produced by a researcher, an institution or a country. There are many institutions that use bibliometric indicators to steer research policy and for hiring or promotion decisions. Given the importance that counting citations has today, the aim of the work presented here is to show how citations are distributed within a scientific area and determine the dependence of the citation count on the article features. All articles referenced in the Web of Science in 2004 for Biology & Biochemistry, Chemistry, Mathematics and Physics were considered.

CONTRIBUTION OF UNUSUAL ARGININE-ARGININE SHORT-RANGE INTERACTIONS TO STABILIZATION AND RECOGNITION IN PROTEINS

Although the majority of the ion pairs found in proteins consists of two charges of opposite sign, the observation of some unusual arrangements of two arginines led us to a search of such occurrences in the Brookhaven Protein Data Bank. We have found 41 Arginine-Arginine interactions with a Cζ...Cζ distance less than 5 å. Computer graphics analysis of these structures shows that most of the Arg-Arg pairs are found in the vicinity of the surface of the proteins, in an easily hydrated region. In order to determine which factors could stabilize such arrangements of species of similar charge, we have carried out AM1 semi-empirical calculations on a model of two guanidinium ions surrounded by several water molecules. The results show the existence of stable clusters with six or more water molecules, with distances between Cζ atoms around 3 å. The bridging role of the water molecules is an important structural and energetic feature and we find bridges of two and three molecules between the guanidinium ions. These results are in good agreement with the structures found in our search of the experimental data. Enhancement of the electrostatic potential around these clusters, when compared to one of the guanidinium ions alone, is also demonstrated.

A theoretical study of the interaction of water molecules with the Cu(100), Ag(100) and Au(100) surfaces

The interaction of a water molecule with copper, silver and gold surfaces has been studied using a cluster model approximation. The B3LYP method has been used to introduce a correlation effect into this type of calculation. Since this is a relatively new technique, its performance in conjunction with different basis sets has been tested using the Cu-H2O system as a test case. These tests were performed to select the basis sets for water and metal atoms to be used in studies on the water—metal cluster interaction. Additionally, a set of B3LYP calculations for the Cun-H2O (n = 2, 4, 5, 9, 12) systems has been performed to investigate the influence of the metal cluster size on the results. Significant variations in the quantities computed have been found for the smaller clusters, while for the larger ones, a degree of convergence seems to be achieved. Thus, the Cu12, Ag12 and Au12 clusters have been used to mimic the (100) crystallographic plane of noble metals. The comparative results of the water—metal interaction for three different positions (on-top, bridge and hollow) are given; for each site the results for three different orientations of H2O molecule are shown. Two preferred conformations, bridge-perpendicular and top-tilted, have been found to be effectively indistinguishable in terms of adsorption energy; in both, water adsorbs via its oxygen end. For the on-top site, the tilt angle between the H2O molecular plane and the normal to the metal surface has been found to be in the range 50–65°, depending on the metal. The copper has been found to be the most hydrophilic metal (ΔEads = −31.8 kJ mol−1) when compared with less attractive gold (ΔEads = −29.7 kJ mol−1) and silver (ΔEads= −26.6 kJ mol−1). The results obtained from our calculations are compared with some earlier theoretical results and with the experimental data available.

Interaction of halide ions with copper: the DFT approach

Abstract The applicability of density functional theory to the adsorbate-adsorbent interaction has been tested with the final goal of defining an appropriate combination of the DFT method with basis sets for metal cluster-halide ions studies. The Cu-X− (X = F, Cl, Br, I) systems have been taken as tests cases to probe the different DFT methods (SVWN, BP86 and B3LYP) together with different combinations of basis sets for systems of this type. For comparison, the standard HF and its MP2 and MP4 corrections have also been calculated. Additionally, the results of a test for the Cu5I− cluster are presented. The good quality of the DFT methods is recorded as they give results comparable to the MP2 and, for some cases, even to the MP4 level of standard calculations. The B3LYP method combined with a fairly inexpensive description of the metal atoms is proposed as an appropriate option for studies of the adsorption of halide ions at noble metal surfaces.

A computational analysis of the insertion of carbon nanotubes into cellular membranes

Carbon nanotubes have been proposed to serve as nano-vehicles to deliver genetic or therapeutic material into the interior of cells because of their capacity to cross the cell membrane. A detailed picture of the molecular mode of action of such a delivery is, however, difficult to obtain because of the concealing effects of the cell membrane. Here we report a systematic computational study of membrane insertion of individual carbon nanotubes and carbon nanotube bundles using two entirely different and unrelated techniques. First a static scan of the environmental free energy is carried out based on a membrane mimicry approach and different insertion geometries are assessed. Then the dynamics is investigated with a coarse-grained approach that was previously used in the study of the integration dynamics of nanoparticles into the bilayer. The results of both models point, for unfunctionalized carbon nanotubes, at a preference for the horizontal orientation inside the internal hydrophobic layer of the cell membrane. Finally, the energetics of the formation of bundles of carbon nanotubes is studied. The cellular membrane promotes aggregation of carbon nanotubes in its hydrophobic core and modifies the structural stability of the bundles.

The adsorption of ethylene on the (100) surfaces of platinum, palladium and nickel: a DFT study

The density functional theory and the cluster model approach have been used to study the adsorption of the ethylene molecule on the (100) surfaces of platinum, palladium and nickel. For each metal surface, two adsorption sites have been considered: the atop site (π) and the bridge site (di-σ). For each case, optimized geometries, adsorption energies and vibrational wavenumbers have been calculated. The results show that ethylene adsorbs strongly on the three metal surfaces. Upon adsorption, the degree of distortion of the ethylene molecule (relative to its gas phase geometry), as well as the binding strength to the metal surface increases in the order Pd<Ni<Pt. On the three metal surfaces the di-σ adsorption mode is the preferred one. There is a good general agreement between the calculated results and the available experimental data.

Topological elements of the magnetically induced orbital current densities

A detailed topological analysis is given, both for the standard orbital current density and for the complete orbital current density. The concepts developed here provide a very useful instrument for the description of the vector field of the magnetically induced currents and should be very helpful for the understanding of the contributions that different regions of a molecule give to its magnetic properties. The ingredients for this topological analysis are (1) the symmetry properties of the electronic Hamiltonian in the presence of the magnetic field and (2) the nature of certain singular points. Two categories of singular points are considered: (i) Nodal vortices which have associated a circulation around a nodal line and may be of the axial or toroidal types as previously considered by Hirschfelder; (ii) Stagnation points where the current vanishes without the vanishing of the charge density. There is a considerable variety of stagnation points and, under certain conditions basically on the magnetic fi...

Ring magnetic susceptibilities in conjugated hydrocarbons

In the context of an SCF π-electron theory an exact expression is derived which yields xπ ⊥, the total π-electron contribution to the magnetic susceptibility perpendicular to the plane of a polycyclic conjugated hydrocarbon. Once given the first-order correction to the bond-order matrix of the molecule in question (which, in the present calculation, is obtained via a coupled Hartree-Fock procedure), this expression makes no further appeal to the London integral approximation. The terms which occur in the expression for xπ ⊥ due to the ‘integrated current densities’ correspond to those which would have arisen if the London approximation had been invoked, the remaining terms being, in general, non-zero if this approximation is not made. The relative ‘integrated current densities’ associated with the various constituent rings in 12 molecules agree well with the corresponding ‘ring current’ intensities estimated via the London-Pople-McWeeny method. It is shown that for polycyclic conjugated systems which are ...

Theoretical study of arginine-carboxylate interactions

The importance of the guanidinium‐carboxylate interactions has sprung from the observed salt bridges often present in biological systems involving the arginine‐glutamate or arginine‐aspartate side chains. The strength of these interactions has been explained on the basis of a great coulombic energy gain, due to the closeness of two charges of opposite sign and the occurrence of H-bond interactions. However, in some environments proton transfer, from guanidinium to carboxylate, can occur with the consequent annihilation of charge. In this work, both ab-initio (6-31G** and MP2/6-31G**) and semi-empirical (AM1) calculations were performed in vacuo on appropriate models, methylguanidinium ‐acetate and methylguanidine‐acetic acid to simulate the zwitterionic and the neutral forms, respectively. The results obtained indicate that, in solvent-free hydrophobic environments, the neutral form should be more stable than the zwitterionic one. q 1999 Elsevier Science B.V. All rights reserved.