A new density functional (DF) of the generalized gradient approximation (GGA) type for general chemistry applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C(6) x R(-6). A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common density functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on standard thermochemical benchmark sets, for 40 noncovalently bound complexes, including large stacked aromatic molecules and group II element clusters, and for the computation of molecular geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for standard functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean absolute deviation of only 3.8 kcal mol(-1). The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the average CCSD(T) accuracy. The basic strategy in the development to restrict the density functional description to shorter electron correlation lengths scales and to describe situations with medium to large interatomic distances by damped C(6) x R(-6) terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chemical method for large systems where dispersion forces are of general importance.

Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

We present two new hybrid meta exchange- correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals.The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree–Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree–Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions.

/pdf/the-m06-suite-of-density-functionals-for-main-group-1748swzp1l.pdf

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

We present an analysis of the performances of a parameter free density functional model (PBE0) obtained combining the so called PBE generalized gradient functional with a predefined amount of exact exchange. The results obtained for structural, thermodynamic, kinetic and spectroscopic (magnetic, infrared and electronic) properties are satisfactory and not far from those delivered by the most reliable functionals including heavy parameterization. The way in which the functional is derived and the lack of empirical parameters fitted to specific properties make the PBE0 model a widely applicable method for both quantum chemistry and condensed matter physics.

Toward reliable density functional methods without adjustable parameters: The PBE0 model

We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functional [J.-D. Chai and M. Head-Gordon, J. Chem. Phys., 2008, 128, 084106] to include empirical atom–atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, ωB97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.

/pdf/long-range-corrected-hybrid-density-functionals-with-damped-44ti6za9f3.pdf

Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections

I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

Principles of Neural Science

A new direct difference method for the computation of molecular interactions has been based on a bivariational transcorrelated treatment, together with special methods for the balancing of other errors. It appears that these new features can give a strong reduction in the error of the interaction energy, and they seem to be particularly suitable for computations in the important region near the minimum energy. It has been generally accepted that this problem is dominated by unresolved difficulties and the relation of the new methods to these apparent difficulties is analysed here.

The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors

https://digilander.libero.it/lyrgus/FIcetola%20De%20Bernardi%202004%20amphibians%20human%20dominated%20landscape.pdf

Amphibians in a human-dominated landscape: the community structure is related to habitat features and isolation

Studies on riparian buffers have usually focused on the amount of land needed as habitat for the terrestriallifestagesofsemiaquaticspecies.Nevertheless,thelandscapesurroundingwetlandsisalsoimportant for other key processes, such as dispersal and the dynamics of metapopulations. Multiple elements that influence these processes should therefore be considered in the delineation of buffers. We analyzed landscape elements (forest cover, density of roads, and hydrographic network) in concentric buffers to evaluate the scale at which they influence stream amphibians in 77 distinct landscapes. To evaluate whether our results could be generalized to other contexts, we determined whether they were consistent across the study areas. Amphibians required buffers of 100-400 m of suitable terrestrial habitat, but interspecific differences in the amount of habitat were large. The presence of amphibians was related to roads and the hydrographic network at larger spatial scales (300-1500 m), which suggests that wider buffers are needed with these elements. This pattern probablyarosebecausetheseelementsinfluencedispersalandmetapopulationpersistence,processesthatoccur at large spatial scales. Furthermore, in some cases, analyses performed on different sets of landscapes provided different results, which suggests caution should be used when conservation recommendations are applied to disparate areas. Establishment of riparian buffers should not be focused only on riparian habitat, but should take a landscape perspective because semiaquatic species use multiple elements for different functions. This approach can be complex because different landscape elements require different spatial extents. Nevertheless, a shift of attention toward the management of different elements at multiple spatial scales is necessary for the long-term persistence of populations.

/pdf/influence-of-landscape-elements-in-riparian-buffers-on-the-12dupkks3x.pdf

Influence of landscape elements in riparian buffers on the conservation of semiaquatic amphibians.

Development rate early in the ontogeny is believed to correlate positively with fitness. Geographic variation in intrinsic development rate suggests the existence of trade-offs between development rate and other fitness related traits. We investigated whether these trade-offs exist between intrinsic larval development rate and post-metamorphic traits in an organism with a complex life cycle. In laboratory, we measured if the tadpoles of the frog Rana latastei with fast intrinsic development rate have a suboptimal post-metamorphic morphology, by comparing froglets from five populations. Then, we evaluated the relationship between age at metamorphosis, hindlimb length and jumping performance for frogs grown in nature in two populations. Under laboratory conditions, froglets with fast intrinsic development had shorter absolute and shorter size-adjusted tibiofibulas. We observed a strong, positive relationship between tibiofibula length and jumping performance. In nature, froglets from the last metamorphosing population had longer absolute and size-adjusted tibiofibulas, and were able to jump further. The cost of fast development could be the shorter legs of early metamorphosing frogs, and their poor jumping performance. Thus, a fast intrinsic development rate may not always be positively related to lifetime fitness, since delayed effects of larval development persist also across life history stages.

/pdf/trade-off-between-larval-development-rate-and-post-56pn2weg1c.pdf

Trade-off between larval development rate and post-metamorphic traits in the frog Rana latastei

Aim Early assessment of the impact of invasive alien species is crucial to set up timely management, but often the impact is evident when it is too late for action. We evaluated relationships between the alien crayfish, Procambarus clarkii, the distribution of native amphibians, and the abundance of their larvae. We assessed whether considering measures of reproductive success provide a more prompt measure of impact than considering just species distribution.



Location  One hundred and twenty-five wetlands in Northern Italy, in an area recently invaded by P. clarkii.



Methods  We surveyed wetlands to assess the presence of breeding activity of amphibians and the distribution of P. clarkii. We measured the abundance of amphibian larvae before metamorphosis through pipe sampling. We built models analysing the relationships between amphibian and crayfish distribution, while taking into account spatial autocorrelation and environmental features. Analyses were performed at both the species level (generalized linear models and spatial eigenvector mapping) and community level (constrained redundancy analysis).



Results  In terms of breeding site distribution, only two amphibians (Lissotriton vulgaris and Hyla intermedia) were negatively associated with P. clarkii, while the relationships between other the species and P. clarkii were positive or not significant. However, larval abundance for all amphibian species was negatively associated with the alien crayfish. Analyses performed at community and single species levels yielded consistent results.



Main conclusions Procambarus clarkii impacts amphibians through different processes. Newts probably avoid invaded wetlands for breeding. Other species attempt breeding in wetlands with crayfish, but suffer very low success. Considering distribution data alone would not provide a correct picture of the impact of this alien species; measures of reproductive success may allow a more accurate assessment of the impact.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1472-4642.2011.00797.x

Fiorenza De Bernardi

Papers

The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors

Amphibians in a human-dominated landscape: the community structure is related to habitat features and isolation

Influence of landscape elements in riparian buffers on the conservation of semiaquatic amphibians.

Trade-off between larval development rate and post-metamorphic traits in the frog Rana latastei

Early assessment of the impact of alien species: differential consequences of an invasive crayfish on adult and larval amphibians