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.

The bHLH protein PTF1-p48 is essential for the formation of the exocrine and the correct spatial organization of the endocrine pancreas

We have generated a mouse bearing a null allele of the gene encoding basic helix-loop-helix (bHLH) protein p48, the cell-specific DNA-binding subunit of hetero-oligomeric transcription factor PTF1 that directs the expression of genes in the exocrine pancreas. The null mutation, which establishes a lethal condition shortly after birth, leads to a complete absence of exocrine pancreatic tissue and its specific products, indicating that p48 is required for differentiation and/or proliferation of the exocrine cell lineage. p48 is so far the only developmental regulator known to be required exclusively for committing cells to an exocrine fate. The hormone secreting cells of all four endocrine lineages are present in the mesentery that normally harbors the pancreatic organ until day 16 of gestation. Toward the end of embryonic life, cells expressing endocrine functions are no longer detected at their original location but are now found to colonize the spleen, where they persist in a functional state until postnatal death of the organism occurs. These findings suggest that the presence of the exocrine pancreas is required for the correct spatial assembly of the endocrine pancreas and that, in its absence, endocrine cells are directed by default to the spleen, a site that, in some reptiles, harbors part of this particular cellular compartment.

Orbital overlap and chemical bonding

The chemical bonds in the diatomic molecules Li(2)-F(2) and Na(2)-Cl(2) at different bond lengths have been analyzed by the energy decomposition analysis (EDA) method using DFT calculations at the BP86/TZ2P level. The interatomic interactions are discussed in terms of quasiclassical electrostatic interactions DeltaE(elstat), Pauli repulsion DeltaE(Pauli) and attractive orbital interactions DeltaE(orb). The energy terms are compared with the orbital overlaps at different interatomic distances. The quasiclassical electrostatic interactions between two electrons occupying 1s, 2s, 2p(sigma), and 2p(pi) orbitals have been calculated and the results are analyzed and discussed. It is shown that the equilibrium distances of the covalent bonds are not determined by the maximum overlap of the sigma valence orbitals, which nearly always has its largest value at clearly shorter distances than the equilibrium bond length. The crucial interaction that prevents shorter bonds is not the loss of attractive interactions, but a sharp increase in the Pauli repulsion between electrons in valence orbitals. The attractive interactions of DeltaE(orb) and the repulsive interactions of DeltaE(Pauli) are both determined by the orbital overlap. The net effect of the two terms depends on the occupation of the valence orbitals, but the onset of attractive orbital interactions occurs at longer distances than Pauli repulsion, because overlap of occupied orbitals with vacant orbitals starts earlier than overlap between occupied orbitals. The contribution of DeltaE(elstat) in most nonpolar covalent bonds is strongly attractive. This comes from the deviation of quasiclassical electron-electron repulsion and nuclear-electron attraction from Coulomb's law for point charges. The actual strength of DeltaE(elstat) depends on the size and shape of the occupied valence orbitals. The attractive electrostatic contributions in the diatomic molecules Li(2)-F(2) come from the s and p(sigma) electrons, while the p(pi) electrons do not compensate for nuclear-nuclear repulsion. It is the interplay of the three terms DeltaE(orb), DeltaE(Pauli), and DeltaE(elstat) that determines the bond energies and equilibrium distances of covalently bonded molecules. Molecules like N(2) and O(2), which are usually considered as covalently bonded, would not be bonded without the quasiclassical attraction DeltaE(elstat).

New bonding modes of carbon and heavier group 14 atoms Si–Pb

Molecules which possess chemical bonds where a bare group-14 atom C–Pb is bonded to σ-donor ligands L or to a transition metal fragment [TM] through donor–acceptor interactions are discussed together with an analysis of the bonding situation with modern quantum chemical methods.

Unicorns in the world of chemical bonding models

The appearance and the significance of heuristically developed bonding models are compared with the phenomenon of unicorns in mythical saga. It is argued that classical bonding models played an essential role for the development of the chemical science providing the language which is spoken in the territory of chemistry. The advent and the further development of quantum chemistry demands some restrictions and boundary conditions for classical chemical bonding models, which will continue to be integral parts of chemistry.

Why Do the Heavy-Atom Analogues of Acetylene E2H2(E = Si−Pb) Exhibit Unusual Structures?

DFT calculations at BP86/QZ4P have been carried out for different structures of E(2)H(2) (E = C, Si, Ge, Sn, Pb) with the goal to explain the unusual equilibrium geometries of the heavier group 14 homologues where E = Si-Pb. The global energy minima of the latter molecules have a nonplanar doubly bridged structure A followed by the singly bridged planar form B, the vinylidene-type structure C, and the trans-bent isomer D1. The energetically high-lying trans-bent structure D2 possessing an electron sextet at E and the linear form HEEH, which are not minima on the PES, have also been studied. The unusual structures of E(2)H(2) (E = Si-Pb) are explained with the interactions between the EH moieties in the (X(2)Pi) electronic ground state which differ from C(2)H(2), which is bound through interactions between CH in the a(4)Sigma(-) excited state. Bonding between two (X(2)Pi) fragments of the heavier EH hydrides is favored over the bonding in the a(4)Sigma(-) excited state because the X(2)Pi --> a(4)Sigma(-) excitation energy of EH (E = Si-Pb) is significantly higher than for CH. The doubly bridged structure A of E(2)H(2) has three bonding orbital contributions: one sigma bond and two E-H donor-acceptor bonds. The singly bridged isomer B also has three bonding orbital contributions: one pi bond, one E-H donor-acceptor bond, and one lone-pair donor-acceptor bond. The trans-bent form D1 has one pi bond and two lone-pair donor-acceptor bonds, while D2 has only one sigma bond. The strength of the stabilizing orbital contributions has been estimated with an energy decomposition analysis, which also gives the bonding contributions of the quasi-classical electrostatic interactions.

Is this a chemical bond? A theoretical study of Ng2@C60 (Ng=He, Ne, Ar, Kr, Xe)

Quantum-chemical calculations using DFT (BP86) and ab initio methods (MP2, SCS-MP2) have been carried out for the endohedral fullerenes Ng2@C60 (Ng=He-Xe). The nature of the interactions has been analyzed with charge- and energy-partitioning methods and with the topological analysis of the electron density (Atoms-in-Molecules (AIM)). The calculations predict that the equilibrium geometries of Ng2@C60 have D3d symmetry when Ng=Ne, Ar, Kr, while the energy-minimum structure of Xe2@C60 has D5d symmetry. The precession movement of He2 in He2@C60 has practically no barrier. The Ng--Ng distances in Ng2@C60 are much shorter than in free Ng2. All compounds Ng2@C60 are thermodynamically unstable towards loss of the noble gas atoms. The heavier species Ar2@C60, Kr2@C60, and Xe2@C60 are high energy compounds which are at the BSSE corrected SCS-MP2/TZVPP level in the range 96.7-305.5 kcal mol(-1) less stable than free C60+2 Ng. The AIM method reveals that there is always an Ng--Ng bond path in Ng2@C60. There are six Ng--C bond paths in (D3d) Ar2@C60, Kr2@C60, and Xe2@C60, whereas the lighter D3d homologues He2@C60 and Ne2@C60 have only three Ng--C2 paths. The calculated charge distribution and the orbital analysis clearly show that the bonding situation in Xe2@C60 significantly differs from those of the lighter homologues. The atomic partial charge of the [Xe2] moiety is +1.06, whereas the charges of the lighter dimers [Ng2] are close to zero. The a2u HOMO of (D3d) Xe2@C60 in the 1A1g state shows a large mixing of the highest lying occupied sigma* orbital of [Xe2] and the orbitals of the C60 cage. There is only a small gap between the a2u HOMO of Xe2@C60 and the eu LUMO and the a2u LUMO+1. The calculations show that there are several triplet states which are close in energy to each other and to the 1A1g state. The bonding analysis suggests that the interacting species in Xe2@C60 are the charged species Xe2q+ and C60q-, where 1<q<2. The calculated Xe--Xe distance in the endohedral fullerene (2.494 A) is even shorter than the calculated value for free Xe2(2+) (2.746 A). Thus, the Xe--C and Xe--Xe interactions in Xe2@C60 should be considered as genuine chemical bonds which are enforced by the compression energy. The Ng--Ng and Ng--C interactions in the lighter homologues Ar2@C60 and Kr2@C60 may also be considered as chemical bonds because the theoretically predicted properties of the endohedral fullerenes are significantly different from the free C60 and noble gas atoms. According to the bonding analysis, He2@C60 and Ne2@C60 are weakly bonded van der Waals complexes.

C5H4?BR2 Bending in Ferrocenylboranes: A Delocalized Through-Space Interaction Between Iron and Boron

A comparison of the molecular structures of mono-, di- and tetraborylated ferrocenes [Fc{B(R(1))(R(2))}] (R(1)/R(2)=Br/Br, Br/Fc, Br/Me, Me/Me, Me/OH, OMe/OMe), 1,1'-[fc{B(R(1))(R(2))}(2)] (R(1)/R(2)=Br/Br, Br/Me, OMe/OMe), and 1,1',3,3'-[Fe{C(5)H(3)(BMe(2))(2)}(2)] revealed the boryl substituent(s) to be bent out of the Cp ring plane towards the iron center. The corresponding dip angle alpha* decreases with decreasing Lewis acidity of the boron atom and with increasing degree of borylation at the ferrocene core. This trend is well reproduced by DFT calculations (including [FcBH(2)], not yet accessible experimentally). A Bader analysis of the electron density topology of [FcBH(2)] (alpha*=26.5 degrees ; BP86/TZVP) clearly showed that there is no direct iron-boron bonding in this compound. Instead, strongly delocalized orbital interactions have been identified that involve the boron p orbital, C(ipso) of the adjacent Cp ring, d orbitals at iron, and a through-space interaction with the second Cp ring. A second important factor is attractive electrostatic interactions, which are enhanced upon ligand bending. Cyclic voltammetric measurements on the series [FcBMe(2)], 1,1'-[fc(BMe(2))(2)], and 1,1',3,3'-[Fe{C(5)H(3)(BMe(2))(2)}(2)] indicate a substantial anodic shift in the oxidation potential of the central iron atom upon introduction of BMe(2) substituents. Addition of 4-dimethylaminopyridine (DMAP) does not just counterbalance this effect, but leads to a cathodic shift of the Fe(II)/Fe(III) redox transition far beyond the half-wave potential of parent ferrocene. In the Mossbauer spectra, a continuous decrease in the quadrupole splitting (QS) is observed upon going from parent ferrocene to [FcBMe(2)], to 1,1'-[fc(BMe(2))(2)], and to 1,1',3,3'-[Fe{C(5)H(3)(BMe(2))(2)}(2)]. In contrast, no significant differences are found between the QS values of ferrocene, [Fc(BMe(2)-DMAP)], and 1,1'-[fc(BMe(2)-DMAP)(2)].

Transition Metal−Carbon Complexes. A Theoretical Study

The equilibrium geometries and bond dissociation energies of 16VE and 18VE complexes of ruthenium and iron with a naked carbon ligand are reported using density functional theory at the BP86/TZ2P level. Bond energies were also calculated at CCSD(T) using TZ2P quality basis sets. The calculations of [Cl2(PMe3)2Ru(C)] (1Ru), [Cl2(PMe3)2Fe(C)] (1Fe), [(CO)2(PMe3)2Ru(C)] (2Ru), [(CO)2(PMe3)2Fe(C)] (2Fe), [(CO)4Ru(C)] (3Ru), and [(CO)4Fe(C)] (3Fe) show that 1Ru has a very strong Ru-C bond which is stronger than the Fe-C bond in 1Fe. The metal-carbon bonds in the 18VE complexes 2Ru-3Fe are weaker than those in the 16VE species. Calculations of the related carbonyl complexes [(PMe3)2Cl2Ru(CO)] (4Ru), [(PMe3)2Cl2Fe(CO)] (4Fe), [(PMe3)2Ru(CO)3] (5Ru), [(PMe3)2Fe(CO)3] (5Fe), [Ru(CO)5] (6Ru), and [Fe(CO)5] (6Fe) show that the metal-CO bonds are much weaker than the metal-C bonds. The 18VE iron complexes have a larger BDE than the 18VE ruthenium complexes, while the opposite trend is calculated for the 16VE compounds. Charge and energy decomposition analyses (EDA) have been carried out for the calculated compounds. The Ru-C and Fe-C bonds in 1Ru and 1Fe are best described in terms of two electron-sharing bonds with sigma and pi symmetry and one donor-acceptor pi bond. The bonding situation in the 18 VE complexes 2Ru-3Fe is better described in terms of closed shell donor-acceptor interactions in accordance with the Dewar-Chatt-Duncanson model. The bonding analysis clearly shows that the 16VE carbon complexes 1Ru and 1Fe are much more strongly stabilized by metal-C sigma interactions than the 18VE complexes which is probably the reason why the substituted homologue of 1Ru could become isolated. The EDA calculations show that the nature of the TM-C and TM-CO binding interactions resembles each other. The absolute values for the energy terms which contribute to Delta(Eint) are much larger for the carbon complexes than for the carbonyl complexes, but the relative strengths of the energy terms are not very different from each other. The pi bonding contribution to the orbital interactions in the carbon complexes is always stronger than sigma bonding. There is no particular bonding component which is responsible for the reversal of the relative bond dissociation energies of the Ru and Fe complexes when one goes from the 16VE complexes to the 18VE species. That the 18 VE compounds have longer and weaker TM-C and TM-CO bonds than the respective 16 VE compounds holds for all complexes. This is because the LUMO in the 16 VE species is a sigma-antibonding orbital which becomes occupied in the 18 VE species.

Electronic structure of CO—An exercise in modern chemical bonding theory

This paper discusses recent progress that has been made in the understanding of the electronic structure and bonding situation of carbon monoxide which was analyzed using modern quantum chemical methods. The new results are compared with standard models of chemical bonding. The electronic charge distribution and the dipole moment, the nature of the HOMO and the bond dissociation energy are discussed in detail.

S. pombe cdc11p, together with sid4p, provides an anchor for septation initiation network proteins on the spindle pole body

BACKGROUND

The signal for the onset of septum formation in the fission yeast Schizosaccharomyces pombe is transduced by the septation initiation network (SIN). Many of the components of the SIN are located on the spindle pole body during mitosis, from where it is presumed that the signal for septum formation is delivered. Cdc11 mutants are defective in SIN signaling, but the role of cdc11 in the pathway has remained enigmatic.

RESULTS

We have cloned the cdc11 gene by a combination of chromosome walking and transfection of cosmids into a cdc11 mutant. Cdc11p most closely resembles Saccharomyces cerevisiae Nud1p and is essential for septum formation. Cdc11p is a phosphoprotein, which becomes hyperphosphorylated during anaphase. It localizes to the spindle pole body at all stages of the cell cycle, in a sid4p-dependent manner, and cdc11p is required for the localization of all the known SIN components, except sid4p, to the SPB. Cdc11p and sid4p can be coimmunoprecipitated from cell extracts. Finally, like its S. cerevisiae ortholog Nud1p, cdc11p is involved in the proper organization of astral microtubules during mitosis.

CONCLUSIONS

We propose that cdc11p acts as a bridge between sid4p and the other SIN proteins, mediating their association with the spindle pole body.

Growth of tobacco in short-day conditions leads to high starch, low sugars, altered diurnal changes in the Nia transcript and low nitrate reductase activity, and inhibition of amino acid synthesis

Diurnal changes in carbohydrates and nitrate reductase (NR) activity were compared in tobacco (Nicotiana tabacum. L.cv. Gatersleben) plants growing in a long (18 h light/6 h dark) and a short (6 h light/18 h dark) day growth regime, or after short-term changes in the light regime. In long-day-grown plants, source leaves contained high levels of sugars throughout the light and dark periods. In short-day-grown plants, levels of sucrose and reducing sugars were very low at the end of the night and, although they rose during the light period, remained much lower than in long days and declined to very low levels again by the middle of the night. Starch accumulated more rapidly in short-day-than long-day-grown plants. Starch was completely remobilised during the night in short days, but not in long days. A single short day/long night cycle sufficed to stimulate starch accumulation during the following light period. In long-day-grown plants, the Nia transcript level was high at the end of the night, decreased during the day, and recovered gradually during the night. In short-day-grown plants, the Nia transcript level was relatively low at the end of the night, decreased to very low levels at the end of the light period, increased to a marked maximum in the middle of the night, and decreased during the last 5 h of the dark period. In long-day-grown plants, NR activity in source leaves rose by 2- to 3-fold in the first part of the light period and decreased in the second part of the light period. In short-day-grown plants, NR activity was low at the end of the night, and only increased slightly after illumination. Dark inactivation of source-leaf NR was partially reversed in long-day-grown plants, but not in short day-grown plants. In both growth regimes, mutants with one instead of four functional copies of the Nia gene had a 60% reduction in maximum NR activity in the source leaves, compared to wild-type plants. The diurnal changes in NR activity were almost completely suppressed in the mutants in long days, whereas the mutants showed similar or slightly larger diurnal changes than wild-type plants in short days. When short-day-grown plants were transferred to long-day conditions for 3 d, NR activity and the diurnal changes in NR activity resembled those in long-day-grown plants. Phloem export from source leaves of short-day-grown plants was partially inhibited by applying a cold-girdle for one light and dark cycle. The resulting increase in leaf sugar was accompanied by an marked increase in the Nia transcript level and a 2-fold increase in NR activity at the end of the dark period. When wild-type plants were subjected to a single short day/long night cycle of increasing severity, NR activity in source leaves at the end of the night decreased when the endogenous sugars declined below about 3 mumol hexose (g FW)-1. In sink leaves in short-day conditions, sugars were higher and the light-induced rise in NR activity was much larger than in source leaves on the same plants. The source leaves of wild-type plants in short-day conditions contained very high levels of nitrate, very low levels of glutamine, low levels of total amino acids, and lower protein and chlorophyll, compared to long-day-grown plants. Plants grown in short days had relatively high levels of glutamate and aspartate, and extremely low levels of most of the minor amino acids in their source leaves at the end of the night. Illumination led to a decrease in glutamate and an increase in the minor amino acids. A single short day/long night cycle led to an increase in glutamate, and a large decrease in the minor acids at the end of the dark period, and reillumination led to a decrease in glutamate and an increase in the minor amino acids. It is proposed that sugar-mediated control of Nia expression and NR activity overrides regulation by nitrogenous compounds when sugars are in short supply, resulting in a severe inhibition of nitrate assimilation. It is also proposed that su

PCR-identification of a Nicotiana plumbaginifolia cDNA homologous to the high-affinity nitrate transporters of the crnA family

A family of high-affinity nitrate transporters has been identified in Aspergillus nidulans and Chlamydomonas reinhardtii, and recently homologues of this family have been cloned from a higher plant (barley). Based on six of the peptide sequences most strongly conserved between the barley and C. reinhardtii polypeptides, a set of degenerate primers was designed to permit amplification of the corresponding genes from other plant species. The utility of these primers was demonstrated by RT-PCR with cDNA made from poly(A)+ RNA from barley, C. reinhardtii and Nicotiana plumbaginifolia. A PCR fragment amplified from N. plumbaginifolia was used as probe to isolate a full-length cDNA clone which encodes a protein, NRT2;1Np, that is closely related to the previously isolated crnA homologue from barley. Genomic Southern blots indicated that there are only 1 or 2 members of the Nrt2 gene family in N. plumbaginifolia. Northern blotting showed that the Nrt2 transcripts are most strongly expressed in roots. The effects of external treatments with different N sources showed that the regulation of the Nrt2 gene(s) is very similar to that reported for nitrate reductase and nitrite reductase genes: their expression was strongly induced by nitrate but was repressed when reduced forms of N were supplied to the roots.

Ribulose-1,5-bisphosphate carboxylase-oxygenase, other Calvin-cycle enzymes, and chlorophyll decrease when glucose is supplied to mature spinach leaves via the transpiration stream

The inhibition of photosynthesis after supplying glucose to detached leaves of spinach (Spinacia oleracea L.) was used as a model system to search for mechanisms which potentially contribute to the "sink" regulation of photosynthesis. Detached leaves were supplied with 50 mM glucose or water for 7 d through the transpiration stream, holding the leaves in low irradiance (16 μmol photons · m(-2) · s(-1)) and a cycle of 9 h light/15 h darkness to prevent any endogenous accumulation of carbohydrate. Leaves supplied with water only showed marginal changes of photosynthesis, respiration, enzyme levels or metabolites. When leaves were supplied with 50 mM glucose, photosynthesis was gradually inhibited over several days. The inhibition was most marked when photosynthesis was measured in saturating irradiance and ambient CO2, less marked in saturating irradiance and saturating CO2, and least marked in limiting irradiance. There was a gradual loss of ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) protein, fructose-1,6-bisphosphatase, NADP-glyceraldehyde-3-phosphate dehydrogenase and chlorophyll. The inhibition of photosynthesis was accompanied by a large decrease of glycerate-3-phosphate, an increase of triose-phosphates and fructose-1,6-bisphospate, and a small decrease of ribulose-1,5-bisphosphate. The stromal NADPH/NADP ratio increased (as indicated by increased activation of NADP-malate dehydrogenase), and the ATP/ADP ratio increased. Chlorophyll-fluorescence analysis indicated that thylakoid energisation was increased, and that the acceptor side of photosystem II was more reduced. Similar results were obtained when glucose was supplied by floating leaf discs in low irradiance on glucose solution, and when detached spinach leaves were held in high light to produce an endogenous accumulation of carbohydrate. Feeding glucose also led to an increased rate of respiration. This was not accompanied by any changes of pyruvate kinase, phosphofructokinase, or pyrophosphate: fructose-6-phosphate phosphotransferase activity. There was a decrease of phosphoenolpyruvate, glycerate-3-phosphate and glycerate-2-phosphate, an increase of pyruvate and triose-phosphates, and an increased ATP/ADP ratio. These results show (i) that accumulation of carbohydrate can inhibit photosynthesis via a long-term mechanism involving a decrease of Rubisco and other Calvin-cycle enzymes and (ii) that respiration is stimulated due to an unknown mechanism, which increases the utilisation of phosphoenolpyruvate.