Torgeir A. Ruden

The Dalton quantum chemistry program system

Dalton is a powerful general‐purpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational self‐consistent‐field, Møller–Plesset, configuration‐interaction, and coupled‐cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic‐structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge‐origin‐invariant manner. Frequency‐dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one‐, two‐, and three‐photon processes. Environmental effects may be included using various dielectric‐medium and quantum‐mechanics/molecular‐mechanics models. Large molecules may be studied using linear‐scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.

AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

BackgroundLarge multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites.ResultsHere we present a batch-oriented web-based program package, named AIR that allows 1) transformation of several single genes to one multigene alignment, 2) identification of evolutionary rates in multigene alignments and 3) removal of fast evolving sites. These three processes can be done with the programs AIR-A ppender, AIR-I dentifier, and AIR-R emover (AIR), which can be used independently or in a semi-automated pipeline. AIR produces user-friendly output files with filtered and non-filtered alignments where residues are colored according to their evolutionary rates. Other bioinformatics applications linked to the AIR package are available at the Bioportal http://www.bioportal.uio.no, University of Oslo; together these greatly improve the flexibility, efficiency and quality of phylogenomic analyses.ConclusionThe AIR program package allows for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes.

Multigene Phylogeny of Choanozoa and the Origin of Animals

Animals are evolutionarily related to fungi and to the predominantly unicellular protozoan phylum Choanozoa, together known as opisthokonts. To establish the sequence of events when animals evolved from unicellular ancestors, and understand those key evolutionary transitions, we need to establish which choanozoans are most closely related to animals and also the evolutionary position of each choanozoan group within the opisthokont phylogenetic tree. Here we focus on Ministeria vibrans, a minute bacteria-eating cell with slender radiating tentacles. Single-gene trees suggested that it is either the closest unicellular relative of animals or else sister to choanoflagellates, traditionally considered likely animal ancestors. Sequencing thousands of Ministeria protein genes now reveals about 14 with domains of key significance for animal cell biology, including several previously unknown from deeply diverging Choanozoa, e.g. domains involved in hedgehog, Notch and tyrosine kinase signaling or cell adhesion (cadherin). Phylogenetic trees using 78 proteins show that Ministeria is not sister to animals or choanoflagellates (themselves sisters to animals), but to Capsaspora, another protozoan with thread-like (filose) tentacles. The Ministeria/Capsaspora clade (new class Filasterea) is sister to animals and choanoflagellates, these three groups forming a novel clade (filozoa) whose ancestor presumably evolved filose tentacles well before they aggregated as a periciliary collar in the choanoflagellate/sponge common ancestor. Our trees show ichthyosporean choanozoans as sisters to filozoa; a fusion between ubiquitin and ribosomal small subunit S30 protein genes unifies all holozoa (filozoa plus Ichthyosporea), being absent in earlier branching eukaryotes. Thus, several successive evolutionary innovations occurred among their unicellular closest relatives prior to the origin of the multicellular body-plan of animals.

Vibrational corrections to indirect nuclear spin-spin coupling constants calculated by density-functional theory

At the present level of electronic-structure theory, the differences between calculated and experimental indirect nuclear spin–spin coupling constants are typically as large as the vibrational contributions to these constants. For a meaningful comparison with experiment, it is therefore necessary to include vibrational corrections in the calculated spin–spin coupling constants. In the present paper, such corrections have been calculated for a number of small molecular systems by using hybrid density-functional theory (DFT), yielding results in good agreement with previous wave-function calculations. A set of empirical equilibrium spin–spin coupling constants has been compiled from the experimentally observed constants and the calculated vibrational corrections. A comparison of these empirical constants with calculations suggests that the restricted-active-space self-consistent field method is the best approach for calculating the indirect spin–spin coupling constants of small molecules, and that the secon...

Coupled-cluster connected quadruples and quintuples corrections to the harmonic vibrational frequencies and equilibrium bond distances of HF, N 2 ,F 2 , and CO

Using the coupled-cluster method, we have examined the contributions from the connected quadruple and quintuple virtual excitations to the harmonic vibrational frequencies and equilibrium bond distances of HF, N(2), F(2), and CO. Whereas the largest quadruples contributions are -18.8 cm(-1) to the harmonic frequency of N(2) and 0.43 pm to the bond distance of F(2), the largest quintuples contributions are -3.9 cm(-1) to the harmonic frequency of N(2) and 0.03 pm to the bond distances of N(2) and F(2). As we improve the description by going from the coupled-cluster singles-and-doubles model with a perturbative triples correction [CCSD(T)] to the coupled-cluster singles-doubles-triples-and-quadruples model, the mean and maximum absolute errors in the calculated frequencies relative to experiment are reduced from 11.3 and 15.8 cm(-1), respectively, to 3.2 and 4.7 cm(-1); for the bond distances, the mean and maximum absolute errors are reduced from 0.16 and 0.47 pm, respectively, to 0.04 and 0.13 pm. The calculations presented here confirm previous observations that, to some extent, the relatively small errors in the CCSD(T) equilibrium bond distances and harmonic frequencies arise from a cancellation of errors in the approximate (perturbative) treatment of the connected triples and the neglect of higher-order connected excitations. Further inclusion of quintuples contributions, relativistic corrections, and adiabatic corrections reduces the mean and maximum absolute errors to 1.1 and 2.3 cm(-1), respectively, for the harmonic frequencies and to 0.02 and 0.05 pm, respectively, for the bond distances.

Automated calculation of fundamental frequencies: Application to AlH3 using the coupled-cluster singles-and-doubles with perturbative triples method

An automated scheme for calculating numerical derivatives of functions is presented and applied to the Taylor expansion of potential energy surfaces. The computational cost is reduced by invoking the symmetry properties of noncubic groups. The scheme is applied to the quartic force field of isotopomers of AlH3 by numerical differentiation of the CCSD~T! energy, using the cc-pCVQZ basis for the harmonic part of the potential and the cc-pCVTZ basis for the anharmonic part. From this force field, zero-order vibrational corrections to the geometry and the fundamental frequencies are calculated by second-order perturbation theory. The results are compared with experiment and previous calculations.

Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource

BackgroundTo identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences (ESTs or full length sequences) and attempt to predict function. Such libraries allow identification of a large number of different transcripts and can provide valuable information on genes expressed in a particular tissue at a specific developmental stage. This data is important in constructing a microarray chip, identifying SNPs in coding regions, and for future identification of genes in the whole genome sequence. An important factor that determines the usefulness of generated data for biologists is efficient data access. Public searchable databases play a crucial role in providing such service.DescriptionTwenty-three Atlantic salmon cDNA libraries were constructed from 15 tissues, yielding nearly 155,000 clones. From these libraries 58,109 ESTs were generated, of which 57,212 were used for contig assembly. Following deletion of mitochondrial sequences 55,118 EST sequences were submitted to GenBank. In all, 20,019 unique sequences, consisting of 6,424 contigs and 13,595 singlets, were generated. The Norwegian Salmon Genome Project Database has been constructed and annotation performed by the annotation transfer approach. Annotation was successful for 50.3% (10,075) of the sequences and 6,113 sequences (30.5%) were annotated with Gene Ontology terms for molecular function, biological process and cellular component.ConclusionWe describe the construction of cDNA libraries from juvenile/pre-smolt Atlantic salmon (Salmo salar), EST sequencing, clustering, and annotation by assigning putative function to the transcripts. These sequences represents 97% of all sequences submitted to GenBank from the pre-smoltification stage. The data has been grouped into datasets according to its source and type of annotation. Various data query options are offered including searches on function assignments and Gene Ontology terms. Data delivery options include summaries for the datasets and their annotations, detailed self-explanatory annotations, and access to the original BLAST results and Gene Ontology annotation trees. Potential presence of a relatively high number of immune-related genes in the dataset was shown by annotation searches.