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Find video protocols related to scientific articles indexed in Pubmed.
The Dalton quantum chemistry program system.
Wiley Interdiscip Rev Comput Mol Sci
PUBLISHED: 10-14-2014
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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.
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New bonding modes of carbon and heavier group 14 atoms Si-Pb.
Chem Soc Rev
PUBLISHED: 06-11-2014
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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 ? 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 ? and ?? electron-sharing bonds TM-E and ?? 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.
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Hydrophilic interaction chromatography of nucleoside triphosphates with temperature as a separation parameter.
J Chromatogr A
PUBLISHED: 01-18-2011
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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 ?L/min. In Escherichia coli cell culture samples dNTP/NTPs could be selectively separated in 7 0min using a flow rate of 100 ?L/min.
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Bonding analysis of metal-metal multiple bonds in R3M-MR3 (M, M = Cr, Mo, W; R = Cl, NMe2).
Inorg Chem
PUBLISHED: 01-06-2011
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The bonding situation of homonuclear and heteronuclear metal-metal multiple bonds in R(3)M-MR(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-MR(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-MR(3) bonds is due to genuine triple bonds with one ?- and one degenerate ?-symmetric component. The metal-metal bonds may be classified as triple bonds where ?-bonding is much stronger than ?-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.
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An efficient density-functional-theory force evaluation for large molecular systems.
J Chem Phys
PUBLISHED: 08-07-2010
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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.
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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).
Dalton Trans
PUBLISHED: 06-04-2010
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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.
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Hedgehog antagonists cyclopamine and dihydroveratramine can be mistaken for each other in Veratrum album.
J Pharm Biomed Anal
PUBLISHED: 03-16-2010
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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.
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Hedgehog antagonist cyclopamine isomerizes to less potent forms when acidified.
J Pharm Biomed Anal
PUBLISHED: 02-08-2010
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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.
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Influence of endohedral confinement on the electronic interaction between He atoms: a He2@C20H20 case study.
Chemistry
PUBLISHED: 02-20-2009
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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.
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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.