Amsterdam Density Functional Program Research Articles

Calculating Molecular Polarizabilities Using Exact Frozen Density Embedding with External Orthogonality.

Frozen density embedding (FDE) with freeze-thaw cycles is a formally exact embedding scheme. In practice, this method is limited to systems with small density overlaps when approximate nonadditive kinetic energy functionals are used. It has been shown that the use of approximate nonadditive kinetic energy functionals can be avoided when external orthogonality (EO) is enforced, and FDE can then generate exact results even for strongly overlapping subsystems. In this work, we present an implementation of exact FDEc-EO (coupled FDE TDDFT with EO) for the calculation of polarizabilities in the Amsterdam density functional program package. EO is enforced using the level-shift projection operator method, which ensures that orbitals between fragments are orthogonal. For pure functionals, we show that only the symmetric EO contributions to the induced density matrix are needed. This leads to a simplified implementation for the calculation of polarizability that can exactly reproduce the supermolecular TDDFT results. We further discuss the limitation of exact FDEc-EO in interpreting subsystem polarizabilities due to the nonunique partitioning of the total density. We show that this limitation is due to the fact that subsystem polarizability partitioning is dependent on how the subsystems are initially polarized. As supermolecular virtual orbitals are exactly reproduced, this dependence is attributed to the description of the occupied orbitals. In contrast, for excitations of subsystems that are localized within one subsystem, we show that the excitation energies are stable with respect to the order of polarization. This observation shows that impacts from the nonunique nature of exact FDE on subsystem properties can be minimized by better fragmentation of the supermolecular systems if the property is localized. For global properties like polarizability, this is not the case, and nonuniqueness remains independent of the fragmentation used.

Computational Prediction of Graphdiyne-Supported Three-Atom Single-Cluster Catalysts

Computational Prediction of Graphdiyne-Supported Three-Atom Single-Cluster Catalysts

Evaluation of an Efficient 3D-RISM-SCF Implementation as a Tool for Computational Spectroscopy in Solution.

The 3D-RISM-SCF solvent-model implementation of Gusarov et al. [ J. Phys. Chem. A 2006, 110, 6083-6090] in the Amsterdam density functional program has been improved and extended. In particular, an accurate yet efficient representation of the solute electrostatic potential is provided. The Coulomb-potential fitting of many DFT codes can be used advantageously in this context. The extra effort compared to a point-charge representation is small for a given SCF cycle and compensated by faster SCF convergence. This allows applications to large solutes, as demonstrated by evaluation of the solvatochromism of Reichardt's dye. In general, TDDFT applications to excitation energies in solution stand out and are highlighted. Applications to the 17O NMR chemical shifts of N-methylformamide in different solvents also demonstrate the distinct advantages of 3D-RISM over continuum solvents. Limitations are observed in this case for water solvent, where the solvent shielding is overestimated. This shortcoming applies also to the 17O gas-to-liquid shift of water, where we used localized molecular orbital analyses for a deeper understanding. For such cases of extremely strong solute-solvent interactions, couplings between solute and solvent orbitals induced by the magnetic perturbation are relevant. These clearly require a quantum-mechanical treatment of the most closely bound solvent molecules. Except for such extreme cases, 3D-RISM-SCF is very well suited to treat solvent effects on NMR parameters. More serious limitations pertain to the treatment of vibrational spectra, where the absence of the coupling between solute and solvent vibrational modes limits the accuracy of applications of 3D-RISM-SCF. The reported extended, efficient, and numerically accurate 3D-RISM-SCF implementation should provide a useful tool to study chemical and spectroscopic properties of molecules of appreciable size in a realistic solvent environment.

Theoretical study on the aggregation of aluminium clusters on a silicone oil surface

By using Amsterdam Density Functional (ADF) program based on first-principles, we have in detail investigated the formation mechanism of the aluminium (Al) nanoparticles (NPs) on a silicone oil surface. Our investigation shows that two moving Al clusters on liquid substrate meet to form a random initial structure. Collisions and interactions may make it become a more compact, more stable structure. As the deposition density increases, a discshaped morphology would be formed because of isotropy on the silicone oil surfaces. The structures built on the Face-Centered Cubic (FCC) units are not stable. Both atomic displacement and adsorption can almost destroy them. It is difficult to form Al crystals on the silicone oil surfaces.

Computational study of the structures and photoelectron spectra of gas-phase nitrosamines: Dimethylnitrosamine, N-nitrosopyrrolidine and 1-nitrosoaziridine

The structures of three nitrosamines in gas phase are optimized with various levels of theory available in the Gaussian program. For dimethylnitrosamine and N-nitrosopyrrolidine, the reported rotational constants from microwave spectra let us select the best optimized geometry. For 1-nitrosoaziridine, however, we decide to choose the geometry optimized by CCSD/cc-pVTZ method. At these geometries, the photoelectron spectra are calculated with established methods using the Amsterdam Density Functional program. The calculated ionization energies of valence electrons agree well with available experimental data and provide values for the missing photoelectron data. On the other hand, the computed core-electron binding energies of dimethylnitrosamine agree well with the values from 1975 X-ray solid-state photoelectron spectra after adding the work function. The predicted values for N-nitrosopyrrolidine and 1-nitrosoaziridine must wait for experiments for confirmation.

Computational study of polarizability anisotropies

The dipole polarizabilities (α) and polarizability anisotropies (Δα) of over 20 molecules are calculated to search for negative Δα. The geometry of each molecule is first optimized at the level of CCSD(T)/cc-pVQZ. Then, the α tensors are computed both with CCSD(T)/daug-cc-pVTZ in Gaussian 09 and with the exchange-correlation potential Vxc known as SAOP in the Amsterdam density functional theory program called ADF and a large basis set called QZ3P-3DIFFUSE. In addition to the popular formula of the ΔαRaman connected with Raman spectroscopy, we also present values of an alternative definition of the polarizability anisotropy ΔαKerr connected with Kerr spectroscopy, recently proposed by Kampfrath and colleagues (2018. Chem. Phys. Lett. 692: 319). On one hand, the signs of many ΔαRaman are undetermined; on the other hand, we obtain negative ΔαKerr for more than one-half of the small molecules studied. Of the 24 molecules studied, 18 have negative ΔαKerr.

Geometry Optimizations in a Subsystem Density Functional Theory Formalism: A Benchmark Study.

We present a benchmark study on equilibrium structures optimized with subsystem density functional theory (sDFT) employing a new analytical gradient implementation in the program SERENITY. Geometry optimizations are performed on all complexes of the S22 [Jurečka et al. Phys. Chem. Chem. Phys. 2006, 8, 1985-1993] and A24 [Řezáč and Hobza. J. Chem. Theory Comput. 2013, 9, 2151-2155] test sets. While some combinations of approximate exchange-correlation (XC) and nonadditive kinetic-energy functionals (e.g., LDA/Thomas-Fermi or PW91/PW91k) more or less successfully mimic the effect of medium-range dispersion in these complexes, we also include the combination of BP86/LLP91. This functional reproduces the dispersion problem of the corresponding BP86 Kohn-Sham (KS-)DFT calculations and can hence successfully be corrected by empirical dispersion corrections developed for KS-DFT. We propose this as a robust and accurate strategy for sDFT geometry optimizations, which appears to be preferable over the previously used strategy relying on error cancellation between XC and nonadditive kinetic-energy functionals. In fact, the best results in our benchmark are obtained from BP86/LLP91 together with a D3-type dispersion correction. We also discuss the difference between our Gaussian-type orbital implementation in SERENITY and a Slater-type orbital based implementation in the Amsterdam density functional (ADF) program but only find small differences in most cases.

Study on the Mixed ZnO Clusters and Ring-Like ZnO Ions

The pure Znm (m = 2–10), mixed ZnmOm (m = 1–10), ZnmO10− m (m = 1–9) clusters and the univalent and divalent ring-like ZnmOm (m = 2–10) cluster ions are systematically investigated by using Amsterdam density functional (ADF) program with Triple-zeta with two polarization functions basis set in conjunction with self-consistent field. Our calculated results show that the Zn4 and Zn7 clusters are the magic clusters. The structures of the ZnmOm (m = 1–10) clusters evolve from two-dimension to three-dimension after m = 8. For the ZnmO10− m (m = 1–9) clusters, the Zn-rich structures evolve gradually from three-dimension to plane with an increase in the O ratios. The Zn5O5 cluster with equal ratio has a two dimensional structure. In the O-rich clusters, the O dimers can be easily detached from them. The O and Zn atoms partly adopt sp2 and sp hybridization, respectively, in the ring-like ZnmOm (m = 2–10) clusters and their ions. Gain and loss charge would affect the degree of hybridization and change their geometries. Their structural changes can be explained by valence bond theory.

From Zinc Clusters to One-Dimensional Crystals on Quasi-Free Sustained Substrates

By using the Amsterdam density functional (ADF) program based on first-principles, we have in detail investigated the Zn n (n = 2–20) clusters, several series of stacked structures, and the growth mechanism of zinc nanorods on silicone oil surfaces, which are isotropic, and can be generally considered as quasi-free sustained substrates. For the Zn n (n = 2–20) clusters, some new ground-state structures are found. The additional boundary atoms can enhance the stability of the stacked structures containing unit cells. The structures from the transverse array of the unit cells on (002) crystal plane are more stable than those stacked along the [002] direction as atomic number increases. The transverse arrayed structures can grow along the [002] direction. However, there is an atomic dislocation between the (002) crystal planes. In fact, the dislocation forms its one side surface of (101). By means of a single point SCF calculation in the ADF program, the adsorption energies per atom on the (101) and (002) crystal planes are calculated. According to the Boltzmann distribution probability law, the adsorption probability on the (101) plane is larger than that on the (002) plane, and the ratio between them is about 24–900. This shows that the Zn nanorods grow preferentially along the [110] direction on the (101) planes. These are in good agreement with our experimental findings.

Excited-states of a rhenium carbonyl diimine complex: solvation models, spin-orbit coupling, and vibrational sampling effects.

We present a quantum-chemical investigation of the excited states of the complex [Re(CO)3(Im)(Phen)]+ (Im = imidazole; Phen = 1,10-phenanthroline) in solution including spin-orbit couplings and vibrational sampling. To this aim, we implemented electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) in the Amsterdam Density Functional program suite, suitable for time-dependent density functional calculations including spin-orbit couplings. The new implementation is employed to simulate the absorption spectrum of the complex, which is compared to the results of implicit continuum solvation and frozen-density embedding. Molecular dynamics simulations are used to sample the ground state conformations in solution. The results demonstrate that any study of the excited states of [Re(CO)3(Im)(Phen)]+ in solution and their dynamics should include extensive sampling of vibrational motion and spin-orbit couplings.

A new time‐dependent density‐functional method for molecular plasmonics: Formalism, implementation, and the Au144(SH)60 case study

We describe the implementation and application of a recently developed time‐dependent density‐functional theory (TDDFT) algorithm based on the complex dynamical polarizability to calculate the photoabsorption spectrum of large metal clusters, with specific attention to the field of molecular plasmonics. The linear response TDDFT equations are solved in the space of the density fitting functions, so the problem is recast as an inhomogeneous system of linear equations whose resolution needs a numerical effort comparable to that of a SCF procedure. The construction of the matrix representation of the dielectric susceptibility is very efficient and is based on the discretization of the excitation energy, so such matrix is easily obtained at each photon energy value as a linear combination of constant matrix and energy‐dependent coefficients. The code is interfaced to the Amsterdam Density Functional (ADF) program and is fully parallelized with standard message passing interface. Finally, an illustrative application of the method to the photoabsorption of the Au144(SH)60 cluster is presented. © 2016 Wiley Periodicals, Inc.

NEW PHOSPHORUS COMPOUNDS K[PCL3(X)] (X= SCN, CN): PREPARATION AND DFT AND SPECTROSCOPIC STUDIES

Two new phosphorus complexes, potassium trichlorothiocyanophosphate (III) (PTCTCP; K[PCl 3 (SCN)]) and potassium trichlorocyanophosphate (III) (PTCCP; K[PCl 3 (CN)]) were synthesized from the reaction of KSCN and KCN, respectively, with PCl 3 . The chemical formulas and compositions of these compounds were determined by elemental analysis and spectroscopic methods, such as phosphorus-31 nuclear magnetic resonance (NMR) spectroscopy ( 31 P-NMR), Fourier transform infrared (FTIR) spectroscopy, ultraviolet-visible (UV-Vis) spectroscopy and mass spectrophotometry. All of the theoretical calculations and determinations of the properties of these compounds were performed as part of the Amsterdam Density Functional (ADF) program. Excitation energies were assessed using time-dependent perturbation density functional theory (TD-DFT). In addition, the molecular geometry was optimized and the frequencies and excitation energies were calculated using standard Slater-type orbital (STO) basis sets with triple-zeta quality double plus polarization functions (TZ2P) for all of the atoms. The assignment of the principal transitions and total densities of state (TDOS) for orbital analysis were performed using the GaussSum 2.2 program.

Stabilities of AlnCu (n = 1–19) Clusters and Magnetic Properties of Three Cu-Doped Al Clusters

By using the Amsterdam Density Functional program, we have studied the geometric features, stabilities and magnetic properties of AlnCu (n = 1–19) clusters. The magnetic structures of Al17Cu2 and Al19Cu clusters are found. Although the high spin ground state of Al12Cu cluster is in accordance with the Hund’s rule under spherical Jellium model (SJM), it is difficult to explain why the Al17Cu2 and Al19Cu clusters exhibit larger magnetic moments by the model. A superatom model under equivalent charge distribution is proposed. The magnetic properties of the Cu-doped Al clusters can be explained well by combination of the superatom model with SJM.

A Local Variant of the Conductor-Like Screening Model for Fragment-Based Electronic-Structure Methods.

Due to steadily rising computational power and sophisticated modeling approaches, increasingly larger molecular systems can be modeled with ab initio methods. An especially promising approach is subsystem methods, where the total system is broken down into smaller subunits that can be treated individually. If an implicit solvent environment such as the conductor-like screening model (COSMO) is included in the description, then additional environmental effects can be incorporated at relatively low cost. For very large systems described with subsystem methods, however, the solution of the COSMO equations can actually become the bottleneck of the calculation. A prominent example in this area is biomolecular systems such as proteins, which can, for instance, be described with frozen density embedding (FDE), especially the related 3-FDE approach. In this article, we present an alternative COSMO variant, which exploits the subsystem nature of the underlying electronic description and has been implemented in a development version of the Amsterdam Density Functional program suite (Adf). We show that the computational cost for the solvent model can be reduced dramatically while retaining the accuracy of the regular description. We compare several schemes for density and surface charge updates and assess the effect of the single tuning parameter.

Frozen Density Embedding with External Orthogonality in Delocalized Covalent Systems.

Frozen density embedding (FDE) has become a popular subsystem density functional theory (DFT) method for systems with weakly overlapping charge densities. The failure of this method for strongly interacting and covalent systems is due to the approximate kinetic energy density functional (KEDF), although the need for approximate KEDFs may be eliminated if each subsystem's Kohn-Sham (KS) orbitals are orthogonal to the other, termed external orthogonality (EO). We present an implementation of EO into the FDE framework within the Amsterdam density functional program package, using the level-shift projection operator method. We generalize this method to remove the need for orbital localization schemes and to include multiple subsystems, and we show that the exact KS-DFT energies and densities may be reproduced through iterative freeze-and-thaw cycles for a number of systems, including a charge delocalized benzene molecule starting from atomic subsystems. Finally, we examine the possibility of a truncated basis for systems with and without charge delocalization, and found that subsystems require a basis that allows them to correctly describe the supermolecular delocalized orbitals.

First principle study on SimNm and SimNm±1 (m = 2–10) clusters

The mixed SimNm and SimNm±1 (m=2–10) clusters are investigated systematically using Amsterdam Density Functional (ADF) program with TZ2P basis set in conjunction with self-consistent field (SCF). The total binding energy, dipole moments, energy gap between the HOMO (highest-occupied molecular orbital)–LUMO (lowest-unoccupied molecular orbital) and constant volume heat capacity of these clusters are computed. Calculation results show the structures of these clusters evolve from linear to planar and three dimensions as the atom number increases. The N dimer can easily form and escape from N-rich clusters, whose physical properties are dominated by the remaining parts. Mulliken population analyses indicate partial charge transfer from silicon to nitrogen atoms.

On the perfect MgH2(–Nb,–Zr) systems and the influence of vacancy-like defects on their structural properties. A self-consistent first principle calculations study of the electron and positron parameters

The electronic and structural properties of MgH2 systems containing vacancies and Zr or Nb as dopants were studied using self-consistent calculations. The density of states were computed using the Vienna Ab initio Simulation Package (VASP) and the orbital overlap population weighted DOS with the Amsterdam Density Functional program. The metal–metal and metal–hydrogen bonds in the perfect hydride and this material containing a neutral Mg or H vacancies or a neutral mixed Mg–H vacancy complex were analyzed. The same calculations were also performed in the magnesium hydride with a Nb or a Zr atom as a substitutional impurity and on these systems containing the above mentioned vacancies. Simultaneously, the influence of vacancies in the hydride was studied through the calculation of the positron lifetimes and the positron–electron momentum distributions in the previously referred materials. Secondly, information on the influence of vacancies on the electron momentum density of the MgH2(–Nb,–Zr) systems was additionally obtained through the calculation of the positron–electron momentum distributions. The results obtained indicate that in the pure hydride the presence of vacancies and impurities notable diminishes the force in the atomic bonds. The stability decrease of the bonds was correlated with changes in the positron wave function in the same sites of the structures. Moreover, it was found that these changes in the positron wave function are in good agreement with the decrease of the positron lifetimes.

Experimental (IR) and theoretical (LDA) studies of the structure and vibrational-reorientational dynamics of ferroelastic 1-aminopyridinium iodide

Calculations of the molecular structure and normal vibration frequencies have been performed using ADF (Amsterdam Density Functional) program package for initial structural data of 1-aminopyridinium iodide, (1-NH2C5H5N)+I−, low temperature phase (110K). Cambridge Structural Database survey has been carried out in order to explore hydrogen bond patterns of 1-aminopyridinium ring and to analyze the strength of intermolecular N–H⋯I− interactions. Infrared spectra of powdered (1-NH2C5H5N)+I− in a frequency range 4000–400cm−1 in a wide temperature region (from 300 to 413K), covering ferroelastic-paraelastic phase transition at 384/383K (heating/cooling), are presented and analyzed. The mechanism of the phase transition is discussed.

First-principles study on mixed SimNn (m + n = 2–9) clusters

The structures and stabilities of the mixed SimNn (m+n=2–9) clusters have been investigated systematically by using Amsterdam Density Functional (ADF) program with TZ2P basis set in conjunction with self-consistent field (SCF). In the silicon–nitrogen binary cluster system, their structures transfer gradually from the three-dimensional structures of Si-rich clusters into the like-planar or like-linear structures of N-rich clusters. Near m=n stoichiometry, the lowest energy structures have higher stability. They usually feature a strong alternation of Si and N atoms. In addition, some N dimers and one small isomer can be observed in N-rich clusters. The binding energy between the N dimers and the small isomer is less than 0.02eV. The most stable structures for pure Nn clusters with odd atom number also contain one N trimer besides some N dimers. A series of meta-stable like-zigzag linear structures in the pure Nn clusters have been also studied. The investigation on magnetism for the mixed clusters indicates that only SiN2 cluster presents the magnetic moment of 2.0μB.

Interaction of gibbsite with oleic acid: Surface energetics and modelling

We examined the surface interaction energetics of gibbsite with oleic acid by employing both experimental techniques and quantum chemical calculations. The infrared frequencies computed for the pure oleic acid as well as for the sodium–oleate complex using the Amsterdam Density Functional program show a shift to lower wavenumbers associated with the formation of a metal-carboxylate fragment. Our MSINDO calculations indicate that the oleic acid-surface complex may form and influence the growth of gibbsite at a pH range of 5 to 9 as compared to more alkaline pH, however adsorption is most favoured at defect and dopant sites. Comparison of the theoretical results with experimental findings imply the possible role of intermediate species such as sodium–oleate at high pH. The morphological importance of the [110] prismatic face is shown by the more favourable adsorption energies for oleic acid (−201kJ/mol) and sodium–oleate (−173kJ/mol) evaluated for this face.