A chemical Hamiltonian approach study of the basis set superposition error changes on electron densities and one- and two-center energy components

A comparision of the local effects of the basis set superposition error (BSSE) on the electron densities and energy components of three representative H-bonded complexes was carried out. The electron densities were obtained with Hartee-Fock and density functional theory versions of the chemical Hamiltonian approach (CHA) methodology. It was shown that the effects of the BSSE were common for all complexes studied. The electron density difference maps and the chemical energy component analysis (CECA) analysis confirmed that the local effects of the BSSE were different when diffuse functions were present in the calculations

Effect of basis set superposition error on the electron density of molecular complexes

The effect of basis set superposition error (BSSE) on molecular complexes is analyzed. The BSSE causes artificial delocalizations which modify the first order electron density. The mechanism of this effect is assessed for the hydrogen fluoride dimer with several basis sets. The BSSE-corrected first-order electron density is obtained using the chemical Hamiltonian approach versions of the Roothaan and Kohn-Sham equations. The corrected densities are compared to uncorrected densities based on the charge density critical points. Contour difference maps between BSSE-corrected and uncorrected densities on the molecular plane are also plotted to gain insight into the effects of BSSE correction on the electron density

A quantum molecular similarity analysis of changes in molecular electron density caused by basis set flotation and electric field application

Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed

Basis set and electron correlation effects on initial convergence for vibrational nonlinear optical properties of conjugated organic molecules

The level of ab initio theory which is necessary to compute reliable values for the static and dynamic (hyper)polarizabilities of three medium size π-conjugated organic nonlinear optical (NLO) molecules is investigated. With the employment of field-induced coordinates in combination with a finite field procedure, the calculations were made possible. It is stated that to obtain reasonable values for the various individual contributions to the (hyper)polarizability, it is necessary to include electron correlation. Based on the results, the convergence of the usual perturbation treatment for vibrational anharmonicity was examined

Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31 G* and extended 6-31++ G* basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack

Endangered Species, Provincialism, and a Continental Approach to Bird Conservation

I examined lists of endangered species from northeastern and midwestern United States to assess the extent to which they were dominated by species considered rare due to their vulnerability to anthropogenic stressors or, instead, by species whose rarity might be explained otherwise. Northeastern states had longer species lists than midwestern states, and more species associated with locally rare prairie habitats. More species at the edge of their geographic range appeared on lists from the Northeast than the Midwest. About 70% of listed species overall have shown either no significant population trend, or increases, at the continental scale, but wetland and prairie species were frequently listed, consistent with the generally acknowledged, widespread loss of these habitats. Curiously, midwestern states tended to list fewer forest species, despite evidence that forest fragmentation there has had strongly deleterious effects on regional bird populations. Overall, species appear to be listed locally for a variety of reasons not necessarily related to their risk of extinction generally, potentially contributing to inefficient distributions of limited resources to deal effectively with species that legitimately require conservation attention. I advocate a continental perspective when listing species locally, and propose enhanced criteria for characterizing species as endangered at the local level.

Land Cover Sampling Biases Associated with Roadside Bird Surveys

Roadside surveys such as the Breeding Bird Survey (BBS) are widely used to assess the relative abundance of bird populations. The accuracy of roadside surveys depends on the extent to which surveys from roads represent the entire region under study. We quantified roadside land cover sampling bias in Tennessee, USA, by comparing land cover proportions near roads to proportions of the surrounding region. Roadside surveys gave a biased estimate of patterns across the region because some land cover types were over- or underrepresented near roads. These biases changed over time, introducing varying levels of distortion into the data. We constructed simulated population trends for five bird species of management interest based on these measured roadside sampling biases and on field data on bird abundance. These simulations indicated that roadside surveys may give overly negative assessments of the population trends of early successional birds and of synanthropic birds, but not of late-successional birds. Because roadside surveys are the primary source of avian population trend information in North America, we conclude that these surveys should be corrected for roadside land cover sampling bias. In addition, current recommendations about the need to create more early successional habitat for birds may need reassessment in the light of the undersampling of this habitat by roads.

Relationships between Duck and Grassland Bird Relative Abundance and Species Richness in Southern Saskatchewan

Digital map products that integrate long-term duck population and land-use data are currently being used to guide conservation program delivery on the Canadian Prairies. However, understanding the inter-relationships between ducks and other grassland bird species would greatly enhance program planning and delivery. We hypothesized that ducks, and Northern Pintail (Anas acuta) in particular, may function as an umbrella guild for the overall breeding habitat quality for other grassland bird species. We compared grassland bird species richness and relative abundance among areas of low, moderate, and high predicted waterfowl breeding densities (i.e., duck density strata) in the southern Missouri Coteau, Saskatchewan. We conducted roadside point counts and delineated habitats within a 400 m radius of each point. The duck high-density stratum supported greater avian species richness and abundance than did the duck low-density stratum. Overall, duck and other grassland bird species richness and abundance were moderately correlated, with all r between 0.37 and 0.69 (all P < 0.05). Although the habitat requirements of Northern Pintail may overlap with those of other grassland endemics, priority grassland bird species richness was only moderately correlated with total pintail abundance in both years, and the abundances of pintail and grassland songbirds listed by the Committee on the Status of Endangered Wildlife in Canada were not correlated. No differences in the mean number of priority grassland species were detected among the strata. Adequate critical habitat for several priority species may not be protected if conservation is focused only in areas of moderate to high wetland density because large tracts of contiguous, dry grassland habitat (e.g., pasture) occur infrequently in high-quality duck habitat.

Effects of Spruce Budworm (Choristoneura fumiferana (Clem.)) Outbreaks on Boreal Mixed-Wood Bird Communities

This study examined the influence of a spruce budworm (Choristoneura fumiferana (Clem.)) outbreak on a boreal mixed-wood bird community in forest stands ranging in age from 0 to 223 yr. We asked if (1) patterns of species response were consistent with the existence of spruce budworm specialists, i.e., species that respond in a stronger quantitative or qualitative way than other species; (2) the superabundance of food made it possible for species to expand their habitat use in age classes that were normally less used; and (3) the response to budworm was limited to specialists or was it more widespread. Results here indicated that three species, specifically the Bay-breasted Warbler (Dendroica castanea), Tennessee Warbler (Vermivora peregrina), and Cape May Warbler (Dendroica tigrina), had a larger numerical response to the budworm outbreak. They responded with increases in density of up to tenfold over 4 or 5 yr. No other species responded with more than a twofold increase in the same time period. These species also showed a functional response by breeding more frequently in young stands aged 1–21 yr and intermediate stands aged 22–36 yr as budworm numbers increased. Our data also suggested that many species profited to a lesser extent from budworm outbreaks, but that this effect may be too subtle to detect in most studies. We found evidence of a positive numerical effect in at least 18 additional species in one or two stand-age categories but never in all three for any one species. Given the numerical response in many species and the potential influence of budworm on bird populations because of the vast extent of outbreaks, we believe that the population cycle of spruce budworm should be considered in any evaluation of population trends in eastern boreal birds.

Population Change in a Marine Bird Colony is Driven By Changes in Recruitment

The population dynamics of long-lived birds are thought to be very sensitive to changes in adult survival. However, where natal philopatry is low, recruitment from the larger metapopulation may have the strongest effect on population growth rate even in long-lived species. Here, we illustrate such a situation where changes in a seabird colony size appeared to be the consequence of changes in recruitment. We studied the population dynamics of a declining colony of Ancient Murrelets (Synthliboramphus antiquus) at East Limestone Island, British Columbia. During 1990-2010, Ancient Murrelet chicks were trapped at East Limestone Island while departing to sea, using a standard trapping method carried on throughout the departure period. Adult murrelets were trapped while departing from the colony during 1990-2003. Numbers of chicks trapped declined during 1990-1995, probably because of raccoon predation, increased slightly from 1995-2000 and subsequently declined again. Reproductive success was 30% lower during 2000-2003 than in earlier years, mainly because of an increase in desertions. The proportion of nonbreeders among adult birds trapped at night also declined over the study period. Mortality of adult birds, thought to be mainly prebreeders, from predators more than doubled over the same period. Apparent adult survival of breeders remained constant during 1991-2002 once the first year after banding was excluded, but the apparent survival rates in the first year after banding fell and the survival of birds banded as chicks to age three halved over the same period. A matrix model of population dynamics suggested that even during the early part of the study immigration from other breeding areas must have been substantial, supporting earlier observations that natal philopatry in this species is low. The general colony decline after 2000 probably was related to diminished recruitment, as evidenced by the lower proportion of nonbreeders in the trapped sample. Hence the trend is determined by the recruitment decisions of externally reared birds, rather than demographic factors operating on the local breeding population, an unusual situation for a colonial marine bird. Because of the contraction in the colony it may now be subject to a level of predation pressure from which recovery will be impossible without some form of intervention.

Estimated Mortality of Selected Migratory Bird Species from Mowing and Other Mechanical Operations in Canadian Agriculture

Mechanical operations such as mowing, tilling, seeding, and harvesting are well-known sources of direct avian mortality in agricultural fields. However, there are currently no mortality rate estimates available for any species group or larger jurisdiction. Even reviews of sources of mortality in birds have failed to address mechanical disturbance in farm fields. To overcome this information gap we provide estimates of total mortality rates by mechanical operations for five selected species across Canada. In our step-by-step modeling approach we (i) quantified the amount of various types of agricultural land in each Bird Conservation Region (BCR) in Canada, (ii) estimated population densities by region and agricultural habitat type for each selected species, (iii) estimated the average timing of mechanical agricultural activities, egg laying, and fledging, (iv) and used these values and additional demographical parameters to derive estimates of total mortality by species within each BCR. Based on our calculations the total annual estimated incidental take of young ranged from ~138,000 for Horned Lark (Eremophila alpestris) to as much as ~941,000 for Savannah Sparrow (Passerculus sandwichensis). Net losses to the fall flight of birds, i.e., those birds that would have fledged successfully in the absence of mechanical disturbance, were, for example ~321,000 for Bobolink (Dolichonyx oryzivorus) and ~483,000 for Savannah Sparrow. Although our estimates are subject to an unknown degree of uncertainty, this assessment is a very important first step because it provides a broad estimate of incidental take for a set of species that may be particularly vulnerable to mechanical operations and a starting point for future refinements of model parameters if and when they become available.