Amsterdam Density Functional Research Articles

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.

A DFT study of intrinsic point defects in monolayer MoSe2

This study is a computational investigation of the electronic structure of the eight most-frequently observed intrinsic point-defect configurations in monolayer Molybdenum diselenide (m-MoSe2); analyzed using the Amsterdam Density Functional (ADF) BAND package. Pristine m-MoSe2 is an intrinsic semiconductor with a direct band gap of 1.44 eV. MoSe2 is defect-sensitive due to the similar orbital character of the Valence Band Maximum (VBM) and Conduction Band Minimum (CBM), with deep states induced in the structure by the defects. These states can be attributed solely to the metal d and chalcogen p states, which spring enhanced photoluminescence, making MoSe2 a potential candidate for optoelectronic applications. Band-gap narrowing is proportional to the number of chalcogen vacancies. All defect configurations cause shifting of the Fermi-level, with metal vacancies shifting the semiconducting character of pristine m-MoSe2 to metallic. Only the antisite defect configuration of MoSe2 and Mo-vacancies at a large distance could introduce spin in the structure, with spin attributed to the metal d and chalcogen p states. These findings suggest the possible application of m-MoSe2 for fabricating DMS by defect engineering.

Computational investigation of the microstructural characteristics and physical properties of glycerol-based deep eutectic solvents

Recently, there has been significant interest in the possibility of using deep eutectic solvents (DESs) as novel green media and alternatives to conventional solvents and ionic liquids (ILs) in many applications. Due to their attractive properties, such as their biodegradability, low cost, easy preparation, and nontoxicity, DESs appear to be very promising solvents for use in the field of green chemistry. This computational study investigated six glycerol-based DESs: DES1 (glycerol:methyl triphenyl phosphonium bromide), DES2 (glycerol:benzyl triphenyl phosphonium chloride), DES3 (glycerol:allyl triphenyl phosphonium bromide), DES4 (glycerol:choline chloride), DES5 (glycerol:N,N-diethylethanolammonium chloride), and DES6 (glycerol:tetra-n-butylammonium bromide). The chemical structures and combination mechanisms as well as the sigma profiles and sigma potentials of the studied DESs were explored in detail. Moreover, density, viscosity, vapor pressure, and IR analytical data were predicted and compared with the corresponding experimental values reported in the literature for these DESs. To achieve these goals, the conductor-like screening model for realistic solvents (COSMO-RS) and the Amsterdam Density Functional (ADF) software package were used. The predicted results were found to be in good agreement with the corresponding experimental values reported in the literature. Further theoretical investigations are needed to confirm the experimental results-regarding both properties and applications-reported for these DESs.

Study of the structural and electronic properties of FeO at the LDA and GGA level

Due to its strongly correlated insulating nature, FeO is used in various catalytic applications. Structural and electronic properties of FeO are investigated by using density functional theory (DFT) with the BAND code in Amsterdam Density Functional (ADF) software at ambient conditions. The generalized gradient approximation (GGA) and local density approximation (LDA) without and with the Hubbard potential (U eV) are used to investigate the structural and electronic properties of FeO. Geometric optimization of FeO is carried out by using the LDA and GGA method. CAPZ (Ceperley–Alder–Perdew–Zunger) and PBE (Perdew–Burke–Ernzerhof) are used as exchange correlation potentials for the LDA and GGA, respectively. The Hubbard potential is optimized and U= 0.6eV is used to overcome the under-estimation of the band gap of FeO in both approximations. The band structure shows the metallic nature of FeO with the GGA and LDA while band gap of 2.34 and 2.08eV is observed by using GGA+U and LDA+U, respectively. Our calculated band gap value with the GGA+U is in good agreement with the reported experimental value, i.e. 2.4eV. The total and partial density of states are also plotted to show the band structure. To the best of our knowledge, no study has been reported yet at the U= 0.6eV value of the Hubbard potential.

Implementation of the SM12 Solvation Model into ADF and Comparison with COSMO.

In this article, an implementation of the newest iteration of the Minnesota solvation model, SM12, into the Amsterdam density functional (ADF) computational package is presented. ADF makes exclusive use of Slater-type orbitals (STO), which correctly represent the true atomic orbitals for atoms, whereas SM12 and the underlying charge model 5 (CM5) have previously only been tested on Gaussian-type orbitals (GTO). This new implementation is used to prove the basis set independence of both CM5 and SM12. A detailed comparison of the SM12 and COSMO solvation models, as implemented in ADF, is also presented. We show that this new implementation of SM12 has a mean unsigned error (MUE) of 0.68 kcal/mol for 272 molecules in water solvent, 4.10 kcal/mol MUE for 112 charged ions in water, and 0.92 kcal/mol MUE for 197 solvent calculations of various molecules. SM12 outperforms COSMO for all neutral molecules and performs as well as COSMO for cationic molecules, only falling short when anionic molecules are taken into consideration, likely due to CM5's use of Hirshfeld charges and their poor description of anionic molecules, though CM5 seems to improve upon this discrepancy.

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.

Effect Of Non-metal Elements (C, N, S) As Anionic Dopants On Electronic Structure Of Tio2-Anatase By Density-Functional Theory Approach

This article is a theoritical approach to calculate the electronic structure of undoped- and non-metal anions doped-TiO2-anatase. The objective of the research is to calculate abinitio the band structure and the density of states (DOS) of undoped-, C-, N-, and S-doped TiO2-anatase. Kohn-Sham equations are performed with the density functional theory (DFT) using the local density approximation (LDA) for exchange-correlation functional. The first-principle calculations were done using supercell (2x2x1) methods as implemented within Amsterdam Density Functional (ADF)-BAND version 2014.10. The ab-initio calculation of the band structures show that all samples are direct- and indirect-gap type semiconductor. The band gap of TiO2-anatase with DFT using LDA is 2.43 eV. The addition of C atom at 0.943% in 48 atoms produces width intermediate band about 0.76 eV, which is 0.38 eV above the valence band (VB) and 1.38 eV below the conduction band (CB). The addition of N atom at 1.103% and S atom at 2.478% in the lattice structure of TiO2-anatase resulted in the addition of the VB width to 0.47 eV and 0.11 eV, while the resulting gap between the VB and the CB to 1.97 eV and 2.33 eV, respectively.

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.

A DFT study of the effects of Sc doping on electronic and optical properties of CdS nanoparticles

AbstractIn the present work a systematic study was carried out to understand the influence of Sc doping on electronic and optical properties of CdS nanoparticles. The geometry optimization and symmetry computation for CdS and Sc doped CdS nanoparticles using Density Functional Theory (DFT) on B3LYP level with the QZ4P for Cd and DZ2P for sulphur and Sc were performed by Amsterdam Density Functional (ADF). The results show that HOMO-LUMO gap as well as electronic and optical properties of CdS clusters vary with Sc doping. The HOMO-LUMO gap is affected by the dopant and its value decreases to 0.6 eV. Through considering the numerical integration scheme in the ADF package, we investigated different vibrational modes and our calculated Raman and IR spectra are consistent with the reported result. The calculated IR and Raman peaks of CdS and Sc doped CdS clusters were in the range of 100 to 289 cm−1, 60 cm−1 to 350 cm−1 and 99 cm−1 to 282 cm−1, 60 cm−1 to 350 cm−1, respectively, which was also confirmed by experiment as well as a blue shift occurrence. Subsequently, for deeper research of pure and doped CdS clusters, their absorption spectra were calculated using time-dependent DFT method.

Ferrocene Orientation Determined Intramolecular Interactions Using Energy Decomposition Analysis.

Two very different quantum mechanically based energy decomposition analyses (EDA) schemes are employed to study the dominant energy differences between the eclipsed and staggered ferrocene conformers. One is the extended transition state (ETS) based on the Amsterdam Density Functional (ADF) package and the other is natural EDA (NEDA) based in the General Atomic and Molecular Electronic Structure System (GAMESS) package. It reveals that in addition to the model (theory and basis set), the fragmentation channels more significantly affect the interaction energy terms (ΔE) between the conformers. It is discovered that such an interaction energy can be absorbed into the pre-partitioned fragment channels so that to affect the interaction energies in a particular conformer of Fc. To avoid this, the present study employs a complete fragment channel—the fragments of ferrocene are individual neutral atoms. It therefore discovers that the major difference between the ferrocene conformers is due to the quantum mechanical Pauli repulsive energy and orbital attractive energy, leading to the eclipsed ferrocene the energy preferred structure. The NEDA scheme further indicates that the sum of attractive (negative) polarization (POL) and charge transfer (CL) energies prefers the eclipsed ferrocene. The repulsive (positive) deformation (DEF) energy, which is dominated by the cyclopentadienyle (Cp) rings, prefers the staggered ferrocene. Again, the cancellation results in a small energy residue in favour of the eclipsed ferrocene, in agreement with the ETS scheme. Further Natural Bond Orbital (NBO) analysis indicates that all NBO energies, total Lewis (no Fe) and lone pair (LP) deletion all prefer the eclipsed Fc conformer. The most significant energy preferring the eclipsed ferrocene without cancellation is the interactions between the donor lone pairs (LP) of the Fe atom and the acceptor antibond (BD*) NBOs of all C–C and C–H bonds in the ligand, LP(Fe)-BD*(C–C & C–H), which strongly stabilizes the eclipsed (D5h) conformation by −457.6 kcal·mol−1.

First-principles study on stability and magnetism of MAln (n = 2–12; M = Cr, Mn, Fe, Co, Ni, Cu, Zn) clusters

By using the Amsterdam Density Functional (ADF) with TZ2P basis set in conjunction with self-consistent-field (SCF), we have studied the geometric features, stabilities and magnetic properties of MAln (M=Cr, Mn, Fe, Co, Ni, Cu, Zn; n=2–12) clusters. All the calculations have been made in the framework of the generalized gradient approximation (GGA) by means of the Becke–Perdew functional. The pronounced stabilities and magnetism of some 3d metal atom doped Al clusters can be explained by the spherical jellium model (SJM). From atom Mn to Zn, only the MAln (M=Cr, Mn, Fe; n=2–12) clusters exhibit the large magnetic moments, especially for the MnAln (n=2–12) clusters. And for the other MAln (M=Co, Ni, Cu, Zn; n=2–12) clusters, only a few clusters has a total magnetic moment of less than or equal to 3μB.

Quantum Chemical Investigation and Detonation Characterization of DNAZ·HCl

3,3-Dinitroazetidinium hydrochloride (DNAZ·HCl) is a novel insensitive high energy explosive. The density functional theory (DFT) method of the Amsterdam density functional (ADF) was used to calculate the geometry and frequencies. The detonation velocity (D) and detonation pressure (P) of DNAZ·HCl were estimated using the nitrogen equivalent equation according to the experimental density. Results showed that the initial decomposition step of DNAZ·HCl is the loss of NO2from C2 and Cl is the point of molecular reactivity.DandPare 6881.40 m·s-1and 20.85GPa, respectively.

Theoretical Chemical Investigation and Detonation Characterization of AAOF and ACOF

3-Amino-4-aminoximidofurazan (AAOF) and 3-Amino-4-chloroximidofurazan (ACOF) are important precursor of synthesizing new furazanon (furoxano) energetic compounds. The density functional theory (DFT) method of the Amsterdam density functional (ADF) was used to calculate the geometry and frequency of AAOF and ACOF. The detonation velocity (D) and pressure (P) of the two compounds were estimated using the nitrogen equivalent equation according to the experimental density. Results showed that the initial decomposition step of AAOF and ACOF is the loss of OH from N4, the changed in group have some effect on HOMO, but this have little effect on HOMO, AAOF has better thermal stability and detonation performance than ACOF.

Comparative Study of Stability and Detonation Characterization of AMF and ACF

3-Amino-4-aminoximidofurazan (AMF) and 3-Amino-4-cyanofurazan (ACF) are important precursor of synthesizing new furazanon (furoxano) energetic compounds. The density functional theory (DFT) method of the Amsterdam density functional (ADF) was used to calculate the geometry and frequency of AMF and ACF. The detonation velocity (D) and pressure (P) of the two compounds were estimated using the nitrogen equivalent equation according to the experimental density. Results showed that the initial decomposition step of AMF and ACF is the loss of NH2 from C2, N3 is the point of molecular reactivity of AMF and ACF, the changed in group have little effect on HOMO and LUMO. AMF has better thermal stability than ACF, but the detonation performance of ACF is finer than AMF.

Density Functional Theory Investigation and Detonation Characterization of DNPDNAZ

N-2’,4’-dinitrophenyl-3,3-dinitroazetidine (DNPDNAZ) is an important derivative of 3,3-dinitroazetidine (DNAZ). The density functional theory (DFT) method of the Amsterdam density functional (ADF) was used to calculate the geometry and frequencies. The detonation velocity (D) and detonation pressure (P) of DNPDNAZ were estimated using the nitrogen equivalent equation according to the experimental density. Results showed that the initial decomposition step of DNPDNAZ is the loss of NO2from C2 and N1 is the point of molecular reactivity,DandPare 7364.42 m·s-1and 23.75 GPa, respectively.

Detonation Characterization and Density Functional Theory Investigation of BDNAZ

N-benzoyl-3,3-dinitroazetidine (BDNAZ) is a insensitive high energy explosive. The detonation velocity (D) and pressure (P) of BDNAZ were estimated using the nitrogen equivalent equation according to the experimental density. The density functional theory (DFT) method of the Amsterdam density functional (ADF) was used to calculate the geometry and frequencies. Results showed thatDandPare 5568.08 m·s-1and 12.34 GPa, respectively, the initial decomposition step of BDNAZ is the loss of NO2from C2 and O5 is the point of molecular reactivity,

Topological Model on the Inductive Effect in Alkyl Halides Using Local Quantum Similarity and Reactivity Descriptors in the Density Functional Theory

We present a topological analysis to the inductive effect through steric and electrostatic scales of quantitative convergence. Using the molecular similarity field based in the local guantum similarity (LQS) with the Topo-Geometrical Superposition Algorithm (TGSA) alignment method and the chemical reactivity in the density function theory (DFT) context, all calculations were carried out with Amsterdam Density Functional (ADF) code, using the gradient generalized approximation (GGA) and local exchange correlations PW91, in order to characterize the electronic effect by atomic size in the halogens group using a standard Slater-type-orbital basis set. In addition, in this study we introduced news molecular bonding relationships in the inductive effect and the nature of the polar character in the C–H bond taking into account the global and local reactivity descriptors such as chemical potential, hardness, electrophilicity, and Fukui functions, respectively. These descriptors are used to find new alternative considerations on the inductive effect, unlike to the binding energy and dipole moment performed in the traditional organic chemical.

First Principles Study on Sino (N=14-18) and Si10-Mom(M=1-8) Clusters

Combining the full-potential linear–muffin–tin–orbital molecular-dynamics (FP-LMTO-MD) and the Amsterdam Density Functional (ADF) with TZ2P basis set in conjunction with self-consistent-field (SCF), we have studied the geometric features and stabilities of the SinO (n=14-18) clusters.. The total binding energy Etot, gap of HOMO (highest-occupied molecular orbital)-LUMO (lowest-unoccupied molecular orbital) Eg, dipole moment μ and total constant volume heat capacity Cv(tot) were also calculated. The results show that the one dopant oxygen atom tends to occupy the edge or the surface position in the middle size silicon clusters (Sin, n=14-18). To further understanding the evolutionary tendency of the physical characteristics for the Si-O clusters with different composition, the Si10-mOm (m=1-8) clusters were also studied using the same methods. It was found that the structures of the Si10-mOm (m=1-8) clusters evolve from compact three dimensions to chain-like with increasing of the O proportion. The binding energy curve of Si10-mOm clusters with different m shows a dip at m=6, which suggests that an optimal proportion of O and Si atoms may exist in the Si10-mOm(m=1-8) clusters.

The role of the exchange-correlation response kernel and scaling corrections in relativistic density functional nuclear magnetic shielding calculations with the zeroth-order regular approximation

The relativistic NMR module of the Amsterdam Density Functional (ADF) package, which is frequently utilised in studies of heavy atom NMR chemical shifts, is extended to calculate a hitherto neglected term from the response of the exchange-correlation (XC) potential. The term vanishes in the absence of spin-orbit coupling. Further, corrections to the shielding arising from scaling factors in the zeroth-order regular approximation (zora) relativistic framework are investigated. The XC response markedly improves calculated proton chemical shifts for hydrogen halides. Mercury chemical shifts for mercury dihalides are also noticeably altered. Contributions from density-gradient dependent terms in the response kernel contribute about 30–40%. New fully relativistic density functional theory (DFT) benchmark data are compared with zora and literature reference values. In line with previous work, it is found that absolute shielding constants for Hg are not accurately predicted with zora. However, chemical shifts agree well with fully relativistic calculations. The application of ‘scaled-zora’ scaling factors deteriorates the shielding constants and is therefore not recommended. The scaling hardly affects chemical shifts. zora calculations are not suitable for absolute shielding of heavy atoms but they can be used safely for chemical shifts in most application scenarios.

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.