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.

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

Recent theoretical studies are reviewed which show that the naked group 14 atoms E = C-Pb in the singlet (1)D state behave as bidentate Lewis acids that strongly bind two σ donor ligands L in the donor-acceptor complexes L→E←L. Tetrylones EL2 are divalent E(0) compounds which possess two lone pairs at E. The unique electronic structure of tetrylones (carbones, silylones, germylones, stannylones, plumbylones) clearly distinguishes them from tetrylenes ER2 (carbenes, silylenes, germylenes, stannylenes, plumbylenes) which have electron-sharing bonds R-E-R and only one lone pair at atom E. The different electronic structures of tetrylones and tetrylenes are revealed by charge- and energy decomposition analyses and they become obvious experimentally by a distinctively different chemical reactivity. The unusual structures and chemical behaviour of tetrylones EL2 can be understood in terms of the donor-acceptor interactions L→E←L. Tetrylones are potential donor ligands in main group compounds and transition metal complexes which are experimentally not yet known. The review also introduces theoretical studies of transition metal complexes [TM]-E which carry naked tetrele atoms E = C-Sn as ligands. The bonding analyses suggest that the group-14 atoms bind in the (3)P reference state to the transition metal in a combination of σ and π∥ electron-sharing bonds TM-E and π⊥ backdonation TM→E. The unique bonding situation of the tetrele complexes [TM]-E makes them suitable ligands in adducts with Lewis acids. Theoretical studies of [TM]-E→W(CO)5 predict that such species may becomes synthesized.

Hydrophilic interaction chromatography of nucleoside triphosphates with temperature as a separation parameter.

Eight deoxynucleoside triphosphates (dNTPs) and nucleoside triphosphates (NTPs): ATP, CTP, GTP, UTP, dATP, dCTP, dGTP and dTTP, were separated with two 15 cm ZIC-pHILIC columns coupled in series, using LC-UV instrumentation. The polymer-based ZIC-pHILIC column gave significantly better separations and peak shape than a silica-based ZIC-HILIC column. Better separations were obtained with isocratic elution as compared to gradient elution. The temperature markedly affected the selectivity and could be used to fine tune separation. The analysis time was also affected by temperature, as lower temperatures surprisingly reduced the retention of the nucleotides. dNTP/NTP standards could be separated in 35 min with a flow rate of 200 µL/min. In Escherichia coli cell culture samples dNTP/NTPs could be selectively separated in 7 0min using a flow rate of 100 µL/min.

Bonding analysis of metal-metal multiple bonds in R3M-M'R3 (M, M' = Cr, Mo, W; R = Cl, NMe2).

The bonding situation of homonuclear and heteronuclear metal-metal multiple bonds in R(3)M-M'R(3) (M, M' = Cr, Mo, W; R = Cl, NMe(2)) is investigated by density functional theory (DFT) calculations, with the help of energy decomposition analysis (EDA). The M-M' bond strength increases as M and M' become heavier. The strongest bond is predicted for the 5d-5d tungsten complexes (NMe(2))(3)W-W(NMe(2))(3) (D(e) = 103.6 kcal/mol) and Cl(3)W-WCl(3) (D(e) = 99.8 kcal/mol). Although the heteronuclear molecules with polar M-M' bonds are not known experimentally, the predicted bond dissociation energies of up to 94.1 kcal/mol for (NMe(2))(3)Mo-W(NMe(2))(3) indicate that they are stable enough to be isolated in the condensed phase. The results of the EDA show that the stronger R(3)M-M'R(3) bonds for heavier metal atoms can be ascribed to the larger electrostatic interaction caused by effective attraction between the expanding valence orbitals in one metal atom and the more positively charged nucleus in the other metal atom. The orbital interaction reveal that the covalency of the homonuclear and heteronuclear R(3)M-M'R(3) bonds is due to genuine triple bonds with one σ- and one degenerate π-symmetric component. The metal-metal bonds may be classified as triple bonds where π-bonding is much stronger than σ-bonding; however, the largest attraction comes from the quasiclassical contribution to the metal-metal bonding. The heterodimetallic species show only moderate polarity and their properties and stabilities are intermediate between the corresponding homodimetallic species, a fact which should allow for the experimental isolation of heterodinuclear species. CASPT2 calculations of Cl(3)M-MCl(3) (M = Cr, Mo, W) support the assignment of the molecules as triply bonded systems.

An efficient density-functional-theory force evaluation for large molecular systems.

An efficient, linear-scaling implementation of Kohn-Sham density-functional theory for the calculation of molecular forces for systems containing hundreds of atoms is presented. The density-fitted Coulomb force contribution is calculated in linear time by combining atomic integral screening with the continuous fast multipole method. For higher efficiency and greater simplicity, the near-field Coulomb force contribution is calculated by expanding the solid-harmonic Gaussian basis functions in Hermite rather than Cartesian Gaussians. The efficiency and linear complexity of the molecular-force evaluation is demonstrated by sample calculations and applied to the geometry optimization of a few selected large systems.

Hedgehog antagonists cyclopamine and dihydroveratramine can be mistaken for each other in Veratrum album.

A toxic plant, Veratrum album (ssp. viriscens), was found to have an inhibitory effect on Hedgehog (Hh), a developmental signaling pathway that has been shown to be active during development, in adult stem cells and in numerous human tumors. Based on earlier studies it was believed that the known Hh inhibitor cyclopamine was present in V. album (ssp. viriscens). Here we show that instead of cyclopamine, dihydroveratramine (DHV) was found in V. album (ssp. viriscens). These compounds are easily mistaken for each other, as both substances share the same molecular weight, and the same main MS/MS fragments. DHV was found to be a less potent Hh inhibitor compared to cyclopamine. This is the first reported occurrence of DVH in nature.

Mechanism for C-H bond activation in ethylene in the gas phase vs. in solution - vinylic or agostic? Revisiting the case of protonated Cp*Rh(C(2)H(4))(2).

When Cp*Rh(C(2)H(4))(2)H(+) (2) is exposed to C(2)H(4) in the gas phase, inside the cell of an FT-ICR mass spectrometer, the most notable feature is the lack of any bimolecular reactivity. Collisional activation of 2 leads to ethylene loss and formation of Cp*Rh(C(2)H(4)-mu-H)(+) (3). In contrast to the reactivity of 2 in solution, ethylene dimerisation is negligible in the gas phase. Coordinatively unsaturated 3, rather than 2, is the major species in which reactivity is observed to occur. Compound 3 reacts with ethylene in three parallel processes: (a) Slow addition of ethylene to give 2; (b) rapid, intermolecular hydrogen atom exchange (monitored in separate reactions with free C(2)D(4) to give 3-d(1-5)); (c) ligand substitution of ethylene in 3. DFT calculations reproduce these observations, showing low barriers for hydrogen scrambling, high barrier to ligand loss in 2, and even higher barriers to elimination of either H(2) or ethane. Mechanistic models for the elimination and scrambling processes are discussed.

Hedgehog antagonist cyclopamine isomerizes to less potent forms when acidified.

The effect of acid treatment of cyclopamine, a natural antagonist of the hedgehog (Hh) signaling pathway and a potential anti-cancer drug, has been studied. Previous reports have shown that under acidic conditions, as in the stomach, cyclopamine is less effective. Also, it has been stated that cyclopamine converts to veratramine, which has side effects such as hemolysis. In this study, we examined in detail the influence of acidification on structure and activity of cyclopamine. We found that of acidified cyclopamine converts to two previously unreported isomers, which we have called cyclopamine (S) and cyclopamine (X). These have likely gone undetected because cyclopamine is often analyzed with fast and hence lower resolving chromatographic methods. Compared to natural cyclopamine, these cyclopamine isomers have a significantly reduced effect on the ciliary transport of the Hh receptor smoothened, and reduced inhibition on the Hedgehog signaling pathway. The side effects of these isomers are unknown. Our findings can partly explain a reduced efficiency of cyclopamine in a gastric environment, and may help with the rational design of more pH independent cyclopamine analogues.

Influence of endohedral confinement on the electronic interaction between He atoms: a He2@C20H20 case study.

The electronic interaction between confined pairs of He atoms in the C(20)H(20) dodecahedrane cage is analyzed. The He-He distance is only 1.265 A, a separation that is less than half the He-He distance in the free He dimer. The energy difference between the possible isomers is negligible (less than 0.15 kcal mol(-1)), illustrating that there is a nearly free precession movement of the He(2) fragment around its midpoint in the cage. We consider that a study of inclusion complexes, such as the case we have selected and other systems that involve artificially compressed molecular fragments, are useful reference points in testing and extending our understanding of the bonding capabilities of otherwise unreactive or unstable species. A key observation about bonding that emerges uniquely from endohedral (confinement) complexes is that a short internuclear separation does not necessarily imply the existence of a chemical bond.

Carbon complexes as electronically and sterically tunable analogues of carbon monoxide in coordination chemistry.

Quantum chemical calculations at DFT (BP86) and ab initio levels (CCSD(T)) have been carried out for transition metal carbon complexes [MX2(PR3)2(C)] with various combinations of M = Fe, Ru, Os, X = F, Cl, Br, I, and R = H, Me, Ph, Cyc. Calculations have also been performed for [RuCl2(PMe3)(NHC)(C)] and [RuCl2(NHC)2(C)] where NHC = N-heterocyclic carbene and for [M(Por)(C)] (M = Fe, Ru, Os; Por = porphyrin). The properties of the carbon complexes as donor ligands were studied by calculating the geometries and bond dissociation energies of the Lewis acid-base adducts with the Lewis acids M(CO)5 (M = Cr, Mo, W), PdCl2SMe2, BH3, BCl3, and Fe2(CO)8. The latter species are compared to the analogous CO complexes. The nature of the donor-acceptor interactions between the Lewis acids LA and carbon complexes [TM]C-LA is compared to the bonding in OC-LA. The bonding analysis was carried out with charge- and energy-partitioning methods. The bond strength and the donor-acceptor properties of metal carbon complexes closely resemble those of CO, and thus carbon complexes may be considered as electronically tuneable analogues of carbon monoxide. Similar properties are also calculated for the porphyrin carbon complexes 10MC, which bind more strongly and are slightly stronger pi acceptors than the [(X2(R)2M(C)] species. The carbon complexes [(X2(R)2M(C)] are slightly weaker pi acceptors than CO, and thus they tend to have slightly weaker bonds than CO in group-6 donor-acceptor complexes. The calculations suggest that bond energies of carbon complexes as ligands with d10 transition metals are larger than those of CO. The theoretical results let it seem possible that adducts with more than one carbon complex as ligands may be synthesized and that even homoleptic complexes may be prepared.

Variational and robust density fitting of four-center two-electron integrals in local metrics.

Density fitting is an important method for speeding up quantum-chemical calculations. Linear-scaling developments in Hartree-Fock and density-functional theories have highlighted the need for linear-scaling density-fitting schemes. In this paper, we present a robust variational density-fitting scheme that allows for solving the fitting equations in local metrics instead of the traditional Coulomb metric, as required for linear scaling. Results of fitting four-center two-electron integrals in the overlap and the attenuated Gaussian damped Coulomb metric are presented, and we conclude that density fitting can be performed in local metrics at little loss of chemical accuracy. We further propose to use this theory in linear-scaling density-fitting developments.

Two complementary molecular energy decomposition schemes: the Mayer and Ziegler-Rauk methods in comparison.

In the present paper we discuss and compare two different energy decomposition schemes: Mayer's Hartree-Fock energy decomposition into diatomic and monoatomic contributions [Chem. Phys. Lett. 382, 265 (2003)], and the Ziegler-Rauk dissociation energy decomposition [Inorg. Chem. 18, 1558 (1979)]. The Ziegler-Rauk scheme is based on a separation of a molecule into fragments, while Mayer's scheme can be used in the cases where a fragmentation of the system in clearly separable parts is not possible. In the Mayer scheme, the density of a free atom is deformed to give the one-atom Mulliken density that subsequently interacts to give rise to the diatomic interaction energy. We give a detailed analysis of the diatomic energy contributions in the Mayer scheme and a close look onto the one-atom Mulliken densities. The Mulliken density rho(A) has a single large maximum around the nuclear position of the atom A, but exhibits slightly negative values in the vicinity of neighboring atoms. The main connecting point between both analysis schemes is the electrostatic energy. Both decomposition schemes utilize the same electrostatic energy expression, but differ in how fragment densities are defined. In the Mayer scheme, the electrostatic component originates from the interaction of the Mulliken densities, while in the Ziegler-Rauk scheme, the undisturbed fragment densities interact. The values of the electrostatic energy resulting from the two schemes differ significantly but typically have the same order of magnitude. Both methods are useful and complementary since Mayer's decomposition focuses on the energy of the finally formed molecule, whereas the Ziegler-Rauk scheme describes the bond formation starting from undeformed fragment densities.

Nonpolar dihydrogen bonds--on a gliding scale from weak dihydrogen interaction to covalent H-H in symmetric radical cations [HnE-H-H-EHn]+.

The electronic structures and bonding patterns for a new class of radical cations, [HnE-H-H-EHn]+ (EHn=element hydride, E=element of Groups 15-18), have been investigated by applying quantum-chemical methods. All structures investigated give rise to symmetric potential energy minimum structures. We envisage clear periodic trends. The H--H bond length is shorter for elements toward the bottom of the periodic table of elements, and a short H--H bond corresponds to accumulation of electron density in the central H--H region. All [HnE-H-H-EHn]+ of Groups 15-17 are thermodynamically unstable towards loss of either H2 or H. The barriers for these dissociations are rather low. The Group 18 congeners, except E=Xe, appear to be global minima of the respective potential energy surfaces. The findings are discussed in terms of H2 bond activation, and a general mechanistic scheme for the standard reduction process 2H+ + 2e(-) --> H2 is given. Finally, it is proposed that some of the symmetric radical cations are likely to be observed in mass spectrometric or matrix isolation experiments.

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

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.

A new look at the ylidic bond in phosphorus ylides and related compounds: energy decomposition analysis combined with a domain-averaged fermi hole analysis.

Geometries and bond dissociation energies of the ylide compounds H2CPH3, H2CPMe3, H2CPF3, (BH2)2CPH3, H2CNH3, H2CAsH3, H2SiPH3, and (BH2)2SiPH3 have been calculated using ab initio (MP2, CBS-QB3) and DFT (B3LYP, BP86) methods. The nature of the ylidic bond R2E1-E2X3 was investigated with an energy decomposition analysis and with the domain-averaged Fermi hole (DAFH) analysis. The results of the latter method indicate that the peculiar features of the ylidic bond can be understood in terms of donor-acceptor interactions between closed-shell R2E1 and E2X3 fragments. The DAFH analysis clearly shows that there are two bonding contributions to the ylidic bond. The strength of the donor and acceptor contributions to the attractive orbital interactions can be estimated from the energy decomposition analysis (EDA) calculations, which give also the contributions of the electrostatic attraction and the Pauli repulsion of the chemical bonding. The EDA and DAFH results clearly show that the orbital interactions take place through the singlet ground state of the R2E1 fragment where the donor orbital of E1 yields pi-type back-donation while the E2X3 lone-pair orbital yields sigma-type bonding. Both bonds are polarized toward E2X3 when E2 = P, while the sigma-type bonding remains more polarized at E2X3 when E2 = N, As. This shows that the phosphorus ylides exhibit a particular bonding situation which is clearly different from that of the nitrogen and arsenic homologues. With ylides built around a P-C linkage, the pi-acceptor strength of phosphorus and the sigma-acceptor strength at carbon contribute to a double bond which is enhanced by electrostatic contributions. The strength of the sigma and pi components and the electrostatic attraction are then fine-tuned by the substituents at C and P, which yields a peculiar type of carbon-phosphorus bonding. The EDA data reveal that the relative strength of the ylidic bond may be determined not only by the R2E1 --> E2X3 pi back-donation, but also by the electrostatic contribution to the bonding. The calculations of the R2E1-E2X3 bond dissociation energy using ab initio methods predict that the order of the bond strength is H2C-PMe3 > H2C-PF3 > H2C-PH3 > (BH2)2C-PH3 > H2C-AsH3 > H2C-NH3 approximately H2Si-PH3 approximately (BH2)2Si-PH3. The DFT methods predict a similar trend, but they underestimate the bond strength of (BH2)2CPH3.

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.