Valence Basis Sets Research Articles

Europium-doped silicon clusters EuSi n (n = 3–11) and their anions: structures, thermochemistry, electron affinities, and magnetic moments

The structures, electron affinities, and dissociation energies of EuSi n (n = 3–11) and their anions have been examined by means of four hybrid and pure density functional theory (DFT) methods. Basis sets used in this work are of segmented (SEG) Gaussian valence basis sets and relativistic small-core effective core potentials (ECP) with additional diffuse 2pdfg functions, denoted aug-SEG/ECP for Eu atoms and aug-cc-pVTZ for Si atoms. The geometries are fully optimized with each DFT method independently. The ground-state structures for all of these species are found to be substitutional type, which can be regarded as being derived from the ground-state structure of Si n+1 (and/or Si +1 − ) by replacing a Si atom with a Eu atom. The theoretical adiabatic electron affinities (AEAs) of EuSi n predicted by the four DFT schemes are in excellent agreement with the experimental data, especially the AEAs of TPSSh and B2PLYP. The average absolute deviations from experiment are by 0.10, 0.06, 0.07, and 0.05 eV, and the largest deviations are 0.16, 0.12, 0.18, and 0.10 eV at the B3LYP, TPSSh, PBE, and B2PLYP levels, respectively. The AEA of EuSi n (n = 3–11) is less than that of Si n . With the increase in silicon cluster size, the AEA of EuSi n may be close to that of Si n , but cannot be larger than that of Si n . The Eu atom acts as an electron donor, and the bonding between Eu and silicon clusters is ionic in nature. The bond between Eu and silicon clusters of neutral EuSi n (n = 3–11) is stronger than that of the anions. The total magnetic moments of EuSi n /EuSi (n = 3–11) and the magnetic moments on the Eu atom do not quench, and the total magnetic moments are contributed by Eu atom. The dissociation energies of Eu atom from EuSi n and their anions have also been calculated to examine relative stabilities.

Effect of pressure on the lattice structure and dynamics of elpasolites Cs2NaRF6 (R = Y, Yb): ab initio calculation

The effect of hydrostatic compression on the lattice structure and dynamics of elpasolites Cs2NaYbF6 and Cs2NaYF6 (sp. gr. 225) has been investigated ab initio. The frequencies and types of fundamental oscillations are determined, and elastic constants are calculated. The computation is performed within the molecular orbitals-linear combinations of atomic orbitals (MO LCAO) approach using the density functional theory (DFT) method with hybrid functionals B3LYP and PBE0 in the CRYSTAL09 program. The rare-earth ion was described by representing the inner (in particular, 4f) orbitals in the form of a pseudopotential. The outer 5s and 5p orbitals, which determine chemical bonding, were described using valence basis sets.

Accurate Diels-Alder reaction energies from efficient density functional calculations.

We assess the performance of the semilocal PBE functional; its global hybrid variants; the highly parametrized empirical M06-2X and M08-SO; the range separated rCAM-B3LYP and MCY3; the atom-pairwise or nonlocal dispersion corrected semilocal PBE and TPSS; the dispersion corrected range-separated ωB97X-D; the dispersion corrected double hybrids such as PWPB95-D3; the direct random phase approximation, dRPA, with Hartree-Fock, Perdew-Burke-Ernzerhof, and Perdew-Burke-Ernzerhof hybrid reference orbitals and the RPAX2 method based on a Perdew-Burke-Ernzerhof exchange reference orbitals for the Diels-Alder, DARC; and self-interaction error sensitive, SIE11, reaction energy test sets with large, augmented correlation consistent valence basis sets. The dRPA energies for the DARC test set are extrapolated to the complete basis set limit. CCSD(T)/CBS energies were used as a reference. The standard global hybrid functionals show general improvements over the typical endothermic energy error of semilocal functionals, but despite the increased accuracy the precision of the methods increases only slightly, and thus all reaction energies are simply shifted into the exothermic direction. Dispersion corrections give mixed results for the DARC test set. Vydrov-Van Voorhis 10 correction to the reaction energies gives superior quality results compared to the too-small D3 correction. Functionals parametrized for energies of noncovalent interactions like M08-SO give reasonable results without any dispersion correction. The dRPA method that seamlessly and theoretically correctly includes noncovalent interaction energies gives excellent results with properly chosen reference orbitals. As the results for the SIE11 test set and H2(+) dissociation show that the dRPA methods suffer from delocalization error, good reaction energies for the DARC test set from a given method do not prove that the method is free from delocalization error. The RPAX2 method shows good performance for the DARC, the SIE11 test sets, and for the H2(+) and H2 potential energy curves showing no one-electron self-interaction error and reduced static correlation errors at the same time. We also suggest simplified DARC6 and SIE9 test sets for future benchmarking.

To the limit of gas-phase electron diffraction: Molecular structure of magnesium octa(m-trifluoromethylphenyl)porphyrazine

The gas-phase molecular structure of the magnesium octa(m-trifluoromethylphenyl)porphyrazine (MgC72H32N8F24) has been studied by a synchronous gas-phase electron diffraction and mass spectrometric experiment at T=667(10) K in combination with DFT calculations using B3LYP hybrid method and triple-ζ valence basis sets. The molecule has an equilibrium structure of D4 symmetry. The following values of selected internuclear distances have been determined: rh1, Å: r(Mg–N)=1.979(5), r(N–C)=1.363(3), r(Nmezo–C)=1.334(4), r(Cpyr–CPh)=1.469(3), r(CPh–CF3)=1.510(5), r(C–F)=1.349(3), r(Cα–Cβ)=1.466(3), r(Cβ–Cβ)=1.380(7). A slight (less than 1 to 2 degrees) twisting deformation of the macrocycle from planarity, caused by the presence of the eight bulky PhCF3 substituents, planes of which are turned by 132.6(9) degrees relative to the adjacent pyrrole rings, has been found. The deviation of phenyl ring planes from 90 degrees orientation is caused by stabilizing donor–acceptor interactions between π-natural orbitals of pyrrole and phenyl moieties. Substitution effects and coordination bonding in magnesium porphyrazine complexes, MgPz, MgPzPh8 and MgPz(CF3Ph)8, are discussed. Sensitivity of GED data to long range interatomic distances of large molecules has been shown.

On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer.

We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for De = - 16.1 ± 0.1 kcal/mol and for D0 = - 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of -14.22 ± 0.12 kcal/mol.

Short-range stabilizing potential for computing energies and lifetimes of temporary anions with extrapolation methods.

The energy of a temporary anion can be computed by adding a stabilizing potential to the molecular Hamiltonian, increasing the stabilization until the temporary state is turned into a bound state, and then further increasing the stabilization until enough bound state energies have been collected so that these can be extrapolated back to vanishing stabilization. The lifetime can be obtained from the same data, but only if the extrapolation is done through analytic continuation of the momentum as a function of the square root of a shifted stabilizing parameter. This method is known as analytic continuation of the coupling constant, and it requires--at least in principle--that the bound-state input data are computed with a short-range stabilizing potential. In the context of molecules and ab initio packages, long-range Coulomb stabilizing potentials are, however, far more convenient and have been used in the past with some success, although the error introduced by the long-rang nature of the stabilizing potential remains unknown. Here, we introduce a soft-Voronoi box potential that can serve as a short-range stabilizing potential. The difference between a Coulomb and the new stabilization is analyzed in detail for a one-dimensional model system as well as for the (2)Πu resonance of CO2(-), and in both cases, the extrapolation results are compared to independently computed resonance parameters, from complex scaling for the model, and from complex absorbing potential calculations for CO2(-). It is important to emphasize that for both the model and for CO2(-), all three sets of results have, respectively, been obtained with the same electronic structure method and basis set so that the theoretical description of the continuum can be directly compared. The new soft-Voronoi-box-based extrapolation is then used to study the influence of the size of diffuse and the valence basis sets on the computed resonance parameters.

Estimating the Impact of an All-Electron Basis Set and Scalar Relativistic Effects on the Structure, Stability, and Reactivity of Small Copper Clusters

Basis sets of valence double and quadruple zeta qualities and the Douglas-Kroll-Hess (DKH) approximation are used to estimate the impact of an all-electron basis set and scalar relativistic effects on the structure, stability, and electronic properties of small neutral copper clusters (Cun, n ≤ 8). At the Becke three-parameter for exchange and Perdew-Wang 91 for correlation (B3PW91) non-relativistic and relativistic levels of theory, the bond length, binding energy, ionization potential, electron affinity, chemical potential, chemical hardness, and electrophilicity index are calculated. The results show that the agreement with experiment improves significantly when the DKH Hamiltonian combined with an all-electron relativistic basis set is used. Polarizabilities and hyperpolarizability are also reported. At the B3PW91 level, all-electron basis sets are shown to be more reliable than effective core potential valence basis sets in the determination of the second hyperpolarizability of copper clusters.

Structure and potential energy function of PuNO molecules

Density functional (B3LPY) method has been utilized to optimize the possible structures of PuN, PuO, NO and PuNO molecules using the contracted valence basis set (LANL2 DZ) for Pu atom, and the AUG-cc-pVTZ basis set for N and O atoms. It is shown that the ground state of the PuNO molecules has Cv (Pu-N-O) symmetry and the ground electronic state is 6-. The equilibrium nuclear distances for Pu-N and N-O bonds in the PuNO molecules are RPuN=0.22951 nm and RNO=0.12257 nm, and the dissociation energy is De=8.10537 eV. Furthermore, the other two metastable states of the PuNO molecules are also obtained, and the electronic states of the two configurations are 6- and A with Cv (Pu-O-N) and Cs (O-Pu-N) symmetry, respectively. Then the Murrell-Sorbie potential energy functions of the PuN, PuO and NO molecules have been simulated and the analytical potential energy function of the PuNO molecules has been derived using the many-body expansion theory. The contours of the potential energy functions reproduce exactly the most stable equilibrium structures, the two metastable state structures as well as the dissociation energy of the PuNO molecules. The molecular static reaction pathway, based on the potential energy function, is also discussed.

Rhodium-catalyzed hydroformylation of ketal-masked β-isophorone: computational explanation for the unexpected reaction evolution of the tertiary Rh-alkyl via an exocyclic β-elimination derivative.

Ketal-masked β-isophorone (7,9,9-trimethyl-1,4-dioxaspiro[4.5]dec-7-ene) is an interesting case study of Rh-catalyzed hydroformylations not only for the competition between secondary and tertiary rhodium alkyls but also for the unexpected isomerization of the tertiary Rh-alkyl to the exocyclic olefin which undergoes hydroformylation, yielding the acetaldehyde derivative (2) of 7,9,9-trimethyl-1,4-dioxaspiro[4.5]decane. Although experimental results at 100 °C pointed to reaction reversibility, the reason for this kind of behavior was however obscure. A thorough density functional theory (DFT) computational investigation of the various transition states (TS) and intermediates along the reaction pathways making use of B3P86 hybrid functionals and the 6-31G* basis set, coupled to effective core potentials for Rh in the LanL2DZ valence basis set, has been carried out to shed some light on the reaction mechanism. The TS barrier heights, based on alkyl-Rh TS free energies, computed under the hypothesis of nonreversibility were in favor of a normal hydroformylation reaction (III:II = 70:30). While the endocyclic olefins produced skew or twisted arrangements of the six-membered ring similarly to the CO insertion TS that can be even higher than the alkyl-Rh ones, grid-point calculations during the potential energy surface (PES) scan produced the much more stable chair conformation for the exocyclic olefin complex. The relevant TS were found to be very favorable as well, thus explaining the preference for the exocyclic arrangement of the tertiary intermediate, for which the reaction is therefore entirely reversible and invariably proceeds to the acetaldehyde derivative (2). Conversely for the secondary isomers, the reaction is only partially reversible, thus enriching the tertiary fraction and producing the secondary aldehyde (3) in a very limited amount.

Pathways for the cyclotetramerization of dibenz[c,e][1,2]azaborine, a BN‐phenanthryne

The BN‐phenanthryne dibenz[c,e][1,2]azaborine (9) was previously inferred as a reactive intermediate in the solution phase thermolysis of 9‐azido‐9‐borafluorene by isolation of its cyclic tetramer. The mechanism of the cyclotetramerization of BN‐phenanthryne (9) is investigated using a meta‐generalized gradient approximation density functional (TPSS‐D3) in conjunction with a polarized split valence basis set and single energy points using a double‐hybrid functional (B2PYLP‐D3) with a polarized triple‐zeta basis set. The most favorable mechanism involves the dimerization of 9 to diazadiboretidine derivative 10, followed by dimerization of 10 for which two different pathways were identified computationally. The more favorable one involves a B4N4 bicyclo[4.2.0]octa‐2,4,7‐triene intermediate. An alternative mechanism, slightly higher in energy, proceeds through a B4N4 cube isomer that lies in an unexpectedly deep potential energy minimum. The low barriers of dimerization of 10 make it a short lived reactive intermediate that likely is too reactive to be trapped by the still more reactive cyclic iminoborane 9. Copyright © 2014 John Wiley & Sons, Ltd.

A new accurate ground-state potential energy surface of ethylene and predictions for rotational and vibrational energy levels.

In this paper we report a new ground state potential energy surface for ethylene (ethene) C2H4 obtained from extended ab initio calculations. The coupled-cluster approach with the perturbative inclusion of the connected triple excitations CCSD(T) and correlation consistent polarized valence basis set cc-pVQZ was employed for computations of electronic ground state energies. The fit of the surface included 82,542 nuclear configurations using sixth order expansion in curvilinear symmetry-adapted coordinates involving 2236 parameters. A good convergence for variationally computed vibrational levels of the C2H4 molecule was obtained with a RMS(Obs.-Calc.) deviation of 2.7 cm(-1) for fundamental bands centers and 5.9 cm(-1) for vibrational bands up to 7800 cm(-1). Large scale vibrational and rotational calculations for (12)C2H4, (13)C2H4, and (12)C2D4 isotopologues were performed using this new surface. Energy levels for J = 20 up to 6000 cm(-1) are in a good agreement with observations. This represents a considerable improvement with respect to available global predictions of vibrational levels of (13)C2H4 and (12)C2D4 and rovibrational levels of (12)C2H4.

Geometries, stabilities, and electronic properties of small GanTi(0, ±1) (n = 1–10) clusters studied by density functional theory

The Geometries, relative stabilities, and electronic properties of the most stable host Gan+1 and doped GanTi(0,±1) (n=1–10) clusters are studied using density functional theory (DFT) with valence basis set LANL2DZ. We determine the equilibrium geometries of host Gan+1 and doped GanTi(0,±1) (n=1–10) clusters by optimizing the bond length and bond angle of various structural isomers. With increasing cluster size, the GanTi(0,±1) clusters tend to adopt compact structures, and the ground state structures of GanTi±1 keep the similar geometric structure as the GanTi clusters. When the number of Ga atom is even, the natural population analysis of GanTi− clusters possess high charges transfer. In order to study the stability of cluster, the average binding energies per atom (Eb/atom), fragmentation energies (Ef), second-order differences of total energies (Δ2E) of host Gan+1 and doped GanTi(0,±1) (n=1–10) clusters are studied. The calculation results of fragmentation energies of Gan+1 clusters present a leaping odd–even oscillatory behavior from n=1 to n=10. Furthermore, the calculated HOMO–LUMO gaps of GanTi clusters are distinctly higher than those of Gan+1 clusters, except for Ga3Ti clusters. The size dependence of cluster’s vertical electron detachment energies (VDE), adiabatic electron affinities (AEA), and adiabatic ionization potentials (AIP), vertical ionization potentials (VIP) are discussed.

Experimental and computational studies of 4H-cyclopenta[2,1-b:3,4-b′]dithiophen-4-one (CPDTO)-oligomers

4H-Cyclopenta[2,1-b:3,4-b′]dithiophen-4-one (CPDTO), CPDTO ketal (CPDTO-k) and their oligomers have been synthesized and their optical absorption, fluorescent, electrochemical properties are characterized. Structure optimization and time-dependent energy calculation have been carried out for (CPDTO-k)1,2,3,6 and (CPDTO)1,2,3,6 using the B3LYP functional and standard split valence plus polarization basis set 6-31G(d,p) in the DFT formalism. The pi conjugation between carbonyl oxygen and thiophene, which is orthogonal to the backbone conjugation, is evident from the DFT calculation and analysis, and is responsible for the observed slower narrowing of bandgaps (Eg) of CPDTO oligomers with increasing number of repeat units. The orthogonal conjugation also leads to different distribution of LUMO from that of HOMO and makes CPDTO oligomers weak in the lowest energy absorption. Enhanced intensity and red-shifted peak wavelength of the lowest energy UV–vis absorption of CPDTO film suggest the presence of strong intermolecular interactions among CPDTO molecules in the solid state, which may explain why the bandgap (1.1–1.2 eV) reported for the electrochemically deposited CPDTO homopolymer film is significantly lower than the bandgap (1.5–1.7 eV) estimated in this study for PCPDTO chloroform solution from the Egs of CPDTO oligomers.

Benchmark theoretical study of the π-π binding energy in the benzene dimer.

We establish a new estimate for the binding energy between two benzene molecules in the parallel-displaced (PD) conformation by systematically converging (i) the intra- and intermolecular geometry at the minimum, (ii) the expansion of the orbital basis set, and (iii) the level of electron correlation. The calculations were performed at the second-order Møller-Plesset perturbation (MP2) and the coupled cluster including singles, doubles, and a perturbative estimate of triples replacement [CCSD(T)] levels of electronic structure theory. At both levels of theory, by including results corrected for basis set superposition error (BSSE), we have estimated the complete basis set (CBS) limit by employing the family of Dunning's correlation-consistent polarized valence basis sets. The largest MP2 calculation was performed with the cc-pV6Z basis set (2772 basis functions), whereas the largest CCSD(T) calculation was with the cc-pV5Z basis set (1752 basis functions). The cluster geometries were optimized with basis sets up to quadruple-ζ quality, observing that both its intra- and intermolecular parts have practically converged with the triple-ζ quality sets. The use of converged geometries was found to play an important role for obtaining accurate estimates for the CBS limits. Our results demonstrate that the binding energies with the families of the plain (cc-pVnZ) and augmented (aug-cc-pVnZ) sets converge [within <0.01 kcal/mol for MP2 and <0.15 kcal/mol for CCSD(T)] to the same CBS limit. In addition, the average of the uncorrected and BSSE-corrected binding energies was found to converge to the same CBS limit much faster than either of the two constituents (uncorrected or BSSE-corrected binding energies). Due to the fact that the family of augmented basis sets (especially for the larger sets) causes serious linear dependency problems, the plain basis sets (for which no linear dependencies were found) are deemed as a more efficient and straightforward path for obtaining an accurate CBS limit. We considered extrapolations of the uncorrected (ΔE) and BSSE-corrected (ΔEcp) binding energies, their average value (ΔEave), as well as the average of the latter over the plain and augmented sets (ΔẼave) with the cardinal number of the basis set n. Our best estimate of the CCSD(T)/CBS limit for the π-π binding energy in the PD benzene dimer is De = -2.65 ± 0.02 kcal/mol. The best CCSD(T)/cc-pV5Z calculated value is -2.62 kcal/mol, just 0.03 kcal/mol away from the CBS limit. For comparison, the MP2/CBS limit estimate is -5.00 ± 0.01 kcal/mol, demonstrating a 90% overbinding with respect to CCSD(T). The spin-component-scaled (SCS) MP2 variant was found to closely reproduce the CCSD(T) results for each basis set, while scaled opposite spin (SOS) MP2 yielded results that are too low when compared to CCSD(T).

Relativistic Small-Core Pseudopotentials for Actinium, Thorium, and Protactinium

Small-core pseudopotentials for actinium, thorium, and protactinium have been energy-adjusted to multiconfiguration Dirac-Hartree-Fock reference data based on the Dirac-Coulomb-Breit Hamiltonian and the Fermi nucleus model. Corresponding optimized valence basis sets of polarized valence quadruple-ζ quality are presented. Atomic test calculations for the first four ionization potentials show satisfactory results at both the Hartree-Fock and the multireference averaged coupled-pair functional level. Highly correlated Fock-space coupled cluster calculations demonstrate that the new pseudopotentials yield ionization potentials, which are in excellent agreement with corresponding all-electron results and experimental data. The pseudopotentials and basis sets supplement a similar set previously published for uranium.

Thermodynamical Criteria of the Higher Selectivity of Zirconium Oxycations over Hafnium Oxycations towards Organophosphorus Ligands: Density Functional Theoretical Investigation

AbstractDensity Functional theory (DFT) has been used to optimize the structures of Cyanex925 [bis(2,4,4‐trimethylpentyl)octylphosphine oxide], tributyl phosphate (TBP), and their complexes with Hf and Zr oxycations by employing the triple‐zeta valence plus polarization (TZVP) basis set. The effect of noncovalent interactions was examined by using the TPSSH and M06‐2X density functionals. The free energy of extraction ΔGext from the aqueous to organic phase was calculated by using the standard thermodynamic procedure in conjunction with the conductor‐like screening model (COSMO). The calculated ΔGext, either with an implicit or explicit solvation model, fails to capture the experimentally reported preferential selectivity of ZrO2+ ions over HfO2+ ions in the absence of nitrate anions towards Cyanex925 over TBP. The presence of nitrate anions along with the second solvation shell (n = 6 + 1 water molecules) around the oxycation shows consistent results with the calculated ΔGext for the selectivity as reported in solvent extraction experiments [the calculated ΔΔΔGext value (–4.72 kcal/mol) is in qualitative agreement with the experimental ΔΔΔGext (–0.82 kcal/mol) results; separation factor (SF) ≈ exp(–ΔΔΔGex/RT)]. Different bonding analyses indicate the electrostatic nature of the interactions between the metal oxycations and the organophosphorus ligands. The present study will further assist in the design of new ligand/solvent systems for the preferential extraction of ZrO2+ ions over HfO2+ ions in solvent extraction experiments.

High-level ab initio calculation of the stability of mercury–thiolate complexes

The reliability of ab initio methods to predict accurate thermodynamic properties and coordination geometries of mercury–thiolate complexes was examined with calculations at various levels of theory. The second-order Moller–Plesset perturbation theory (MP2) method in connection with the Stuttgart–Dresden–Bonn relativistic effective core potentials and the related correlation consistent valence basis set gives optimized Hg(RS) n model structures in good agreement with experimental data. Differences in thermodynamic stability among various models can be estimated with chemical precision using single-point energy calculation at the CCSD(T) level of theory performed on the MP2-optimized structures. This computational scheme was applied next to calculate the stability of aqueous linear (two coordinated), trigonal, and tetrahedral mercury–thiolate complexes. In alkaline solutions, the difference in complexation Gibbs free energy between the most stable (trigonal) and the less stable (tetrahedral) model complexes formed with free ligands is only −4.7 kcal mol−1. At neutral pH, the linear coordination is most stable. When the thiol ligands are structurally associated, as in biological systems, the trigonal coordination is most stable from pH 4.8 to 10.6. The relative stabilities of the three Hg–(RS) n bonding configurations reported herein can be further modified in biological environment by Hg-induced folding of proteins.

Ab-initio and Conformational Analysis of a Potent VEGFR-2 Inhibitor: A Case Study on Motesanib.

Vascular endothelial growth factor receptor-2 (VEGFR-2); a cell surface receptor for vascular endothelial growth factors, is a key pharmacological target involved in the cell proliferation/angiogenesis. It has been revealed that VEGFR-2 induces proliferation through activation of the extracellular signal-regulated kinases pathway. In this regard, targeting the VEGFR-2 has been considered as an efficient route to develop anti-tumor agents. Motesanib is a small-molecule antagonist of VEGFR-1, 2, and 3 (IC50s; 2 nM, 3 nM, 6 nM, respectively). It is an experimental drug candidate undergoing clinical trials against some types of cancer. In the present study, Motesanib (AMG 706) was evaluated in terms of its binding energies with individual amino acids of VEGFR-2 active site (amino acid decomposition analysis). For this purpose, functional B3LYP associated with split valence basis set using polarization functions (Def2-SVP) was used. Comparative conformational analysis of the ligand in optimized and crystallographic states revealed that Motesanib does not necessarily bind to the VEGFR-2 active site in its minimum energy conformer.

Structures and Stabilities of the Metal Doped Gold Nano-Clusters: M@Au10 (M = W, Mo, Ru, Co)

The structures and stabilities of a series of endohedral gold clusters containing ten gold atoms M@Au10 (M = W, Mo, Ru, Co) have been determined using density functional theory. The gradient-corrected functional BP86, the Tao-Perdew-Staroverov-Scuseria TPSS meta-GGA functional, and the hybrid density functionals B3LYP and PBE1PBE were employed to calculate the structures, binding energies, adiabatic ionization potentials, and adiabatic electron affinities for these clusters. The LanL2DZ effective core potentials and the corresponding valence basis sets were employed. The M@Au10 (M = W, Mo, Ru, Co) clusters have higher binding energies than an empty Au10 cluster. In addition, the large HOMO-LUMO gaps suggest that the M@Au10 (M = W, Mo, Ru, Co) clusters are all likely to be stable chemically. The ionization potentials and electron affinities for these clusters are very high, and the W@Au10 and Mo@Au10 clusters have electron affinities similar to the super-halogen Al13.

Density functional theoretical study on the preferential selectivity of macrocyclic dicyclohexano-18-crown-6 for Sr+2 ion over Th+4 ion during extraction from an aqueous phase to organic phases with different dielectric constants

The preferential selectivity of dicyclohexano-18-crown-6 (DCH18C6) for bivalent Sr(+2) ion over tetravalent Th(+4) ion was investigated using generalized gradient approximated (GGA) BP86 and the hybrid B3LYP density functional, employing split valence plus polarization (SV(P)) and triple-zeta valence plus polarization (TZVP) basis sets in conjunction with the COSMO (conductor-like screening model) solvation approach. The calculated theoretical selectivity of DCH18C6 for Sr(+2) ion over Th(+4) ion was found to be in accord with the selectivity for Sr(+2) ion over Th(+4) ion observed when performing liquid-liquid extraction experiments in different organic solvents. While 1:1(M:L) stoichiometric complexation reactions can be used to predict the preferential selectivity of Sr(2+) ion over Th(4+) ion, the results obtained are not consistent with the experimental results observed upon increasing the dielectric constant of the solvent. The calculated theoretical gas-phase data for the free energy of complexation, ∆G, fail to explain the selectivity for Sr(+2) ion over Th(+4) ion. However, when 1:2 (M:L) stoichiometric complexation reactions (reported in previous X-ray crystallography studies) are considered, correct and consistent results for the selectivity for Sr(+2) ion over a wide range of dielectric constants are predicted. The distribution constant for Sr(2+) and Th(4+) ions was found to gradually increase with increasing dielectric constant of the organic solvent, and was found to be highest in nitrobenzene. The selectivity data calculated from ∆∆G ext are in excellent agreement with the results obtained from solvent extraction experiments.