Polarization Functions In Basis Set Research Articles

Partial and Complete Substitution of the 1,4-Benzenedicarboxylate Linker in UiO-66 with 1,4-Naphthalenedicarboxylate: Synthesis, Characterization, and H2-Adsorption Properties.

We describe the synthesis and corresponding full characterization of the set of UiO-66 metal-organic frameworks (MOFs) with 1,4-benzenedicarboxylate (C6H4(COOH)2, hereafter H2BDC) and 1,4-naphthalenedicarboxylate (C10H6(COOH)2, hereafter H2NDC) mixed linkers with NDC contents of 0, 25, 50, and 100%. Their structural (powder X-ray diffraction, PXRD), adsorptive (N2, H2, and CO2), vibrational (IR/Raman), and thermal stability (thermogravimetric analysis, TGA) properties quantitatively correlate with the NDC content in the material. The UiO-66 phase topology is conserved at all relative fractions of BDC/NDC. The comparison between the synchrotron radiation PXRD and 77 K N2-adsorption isotherms obtained on the 50:50 BDC/NDC sample and on a mechanical mixture of the pure BDC and NDC samples univocally proves that in the mixed linkers of the MOFs the BDC and NDC linkers are shared in each MOF crystal, discarding the hypothesis of two independent phases, where each crystal contains only BDC or NDC linkers. The careful tuning of the NDC content opens a way for controlled alteration of the sorption properties of the resulting material as testified by the H2-adsorption experiments, showing that the relative ranking of the materials in H2 adsorption is different in different equilibrium-pressure ranges: at low pressures, 100NDC is the most efficient sample, while with increasing pressure, its relative performance progressively declines; at high pressures, the ranking follows the BDC content, reflecting the larger internal pore volume available in the MOFs with a higher fraction of smaller linkers. The H2-adsorption isotherms normalized by the sample Brunauer-Emmett-Teller specific surface area show, in the whole pressure range, that the surface-area-specific H2-adsorption capabilities in UiO-66 MOFs increase progressively with increasing NDC content. Density functional theory calculations, using the hybrid B3LYP exchange correlation functional and quadruple-ζ with four polarization functions (QZ4P) basis set, show that the interaction of H2 with the H2NDC linker results in an adsorption energy larger by about 15% with respect to that calculated for adsorption on the H2BDC linker.

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.

Ab initio molecular dynamics thermal decomposition of methane on Ni-Cu/γ-Al2O3 catalysts for CNT production: Effect of Cu promoter

The decomposition of a single CH4 molecule on the surface of Ni-Cu/γ-Al2O3 catalyst with 1:0, 1:1, and 0:1 Ni-Cu molar ratios for carbon nanotubes (CNT) production was investigated via ab initio molecular dynamics (AIMD) simulations with supporting empirical data. The simulation model was based on the formation of Ni-Cu alloy on γ-Al2O3 from empirical data. Structural relaxation and AIMD simulations were performed using the Local Density Approximation – Vosko-Wilk-Nusair (LDA-VWM) exchange correlation functional, Gaussian double zeta plus polarization function basis set (DNP) at 2 × 2 × 1 k-point calculation and orbital cut-off of 3.5 Å, with simulation parameters: T = 850 °C, time step = 1.9 fs (78.5 a.u.), total simulation time = 0.38 ps, with the canonical NVT (constant amount (N), volume (V) and temperature (T)) thermodynamic ensemble and Generalized Gaussian Moment (GGM) thermostat. Simulations predicted an increase in catalytic activity in the presence of Cu with the lowest C deposition on 0:1 Ni-Cu and is supported by the marked decrease in CNT yield in the absence of Ni. Simulation data also suggest a weak metal – γ-Al2O3 interaction in favor of tip-growth CNTs. Calculations predicted a decrease in crystal size with the addition of Cu to Ni/γ-Al2O3 indicative of the formation of a Ni-Cu alloy, and is supported by a corresponding decrease in CNT diameter. Calculations also predicted a decrease in the reactant-product transition state energy difference in 1:1 Ni-Cu supported by an increase in catalytic activity from empirical data.

Direct production of 2-keto-l-gulonic acid from D-sorbitol by metabolic engineering of Gluconobacter oxydans WSH-003

The decomposition of a single CH4 molecule on the surface of Ni-Cu/γ-Al2O3 catalyst with 1:0, 1:1, and 0:1 Ni-Cu molar ratios for carbon nanotubes (CNT) production was investigated via ab initio molecular dynamics (AIMD) simulations with supporting empirical data. The simulation model was based on the formation of Ni-Cu alloy on γ-Al2O3 from empirical data. Structural relaxation and AIMD simulations were performed using the Local Density Approximation – Vosko-Wilk-Nusair (LDA-VWM) exchange correlation functional, Gaussian double zeta plus polarization function basis set (DNP) at 2 × 2 × 1 k-point calculation and orbital cut-off of 3.5 Å, with simulation parameters: T = 850 °C, time step = 1.9 fs (78.5 a.u.), total simulation time = 0.38 ps, with the canonical NVT (constant amount (N), volume (V) and temperature (T)) thermodynamic ensemble and Generalized Gaussian Moment (GGM) thermostat. Simulations predicted an increase in catalytic activity in the presence of Cu with the lowest C deposition on 0:1 Ni-Cu and is supported by the marked decrease in CNT yield in the absence of Ni. Simulation data also suggest a weak metal – γ-Al2O3 interaction in favor of tip-growth CNTs. Calculations predicted a decrease in crystal size with the addition of Cu to Ni/γ-Al2O3 indicative of the formation of a Ni-Cu alloy, and is supported by a corresponding decrease in CNT diameter. Calculations also predicted a decrease in the reactant-product transition state energy difference in 1:1 Ni-Cu supported by an increase in catalytic activity from empirical data.

All-electron double zeta basis sets for the most fifth-row atoms: Application in DFT spectroscopic constant calculations

Segmented all-electron contracted double zeta valence plus polarization function (DZP) basis sets for the elements Cs, Ba, La, from Hf to Ir, and from Au to Rn are constructed for using in conjunction with the non-relativistic and Douglas–Kroll–Hess (DKH) Hamiltonians. Using the B3LYP hybrid functional, the performance of the DZP–DKH basis set is assessed for predicting atomic ionization energy as well as spectroscopy constants of some compounds. Despite its compact size, this set demonstrates consistent, efficient, and reliable performance and will be especially useful in calculations of molecular properties that require explicit treatment of the core electrons.

Gaussian basis sets of quadruple zeta quality for potassium through xenon: application in CCSD(T) atomic and molecular property calculations

All-electron segmented contracted quadruple zeta valence plus polarization function (QZP) basis sets for the elements from K to Xe were constructed to be used in conjunction with the non-relativistic and Douglas–Kroll–Hess (DKH) Hamiltonians. The QZP-DKH set is obtained from the original QZP basis set, that is, the values of the contraction coefficients were re-optimized using the relativistic DKH Hamiltonian. This extends earlier works on segmented contracted QZ basis set for atoms H–Ar. At the coupled-cluster level of theory, the convergence of atomic ionization energy as well as of molecular spectroscopic constants as a function of basis set size is examined. Additional improvements on spectroscopic constants were achieved by applying corrections due to core–valence correlation and spin–orbit effects. This leads to estimates for the spectroscopic constants of various diatomics in gaseous phase. One verifies that the experimental and benchmark theoretical bond lengths, atomization energies, and harmonic vibrational frequencies can be reproduced well with the QZP-DKH set.

Triple zeta quality basis sets for atoms Rb through Xe: application in CCSD(T) atomic and molecular property calculations

Segmented all-electron contracted triple zeta valence plus polarization function (TZP) basis sets for the elements from Rb to Xe were constructed to be used in conjunction with the non-relativistic and Douglas–Kroll–Hess (DKH) Hamiltonians. This extends earlier work on segmented contracted TZ basis set for the atoms H-Kr. At the coupled cluster level of theory, ionization energy of some atoms as well as spectroscopic constants of a sample of diatomics were calculated and compared with benchmark theoretical values. One verifies that the benchmark bond length, dissociation energy, and harmonic vibrational frequency can be reproduced well with the TZP-DKZ set.

Exploring the surface reactivity of Ag nanoparticles with antimicrobial activity: A DFT study

AbstractThe preferential sites of electrophilic, nucleophilic, and radical attacks on the surface of highly spherical Ag nanoparticles with a diameter of ∼ 2 nm are studied via the Fukui functions and the molecular electrostatic potential; both are calculated using the density functional (DFT) generalized gradient approximation‐revised version of the Perdew, Burke, and Ernzerhof level of theory with the double‐numerical with polarization functions (DNP) basis set for the valence electrons, and DFT‐based semicore pseudopotentials for the core electrons. Because the interaction of Ag nanoparticles with virus and microorganisms takes place in an aqueous environment, the solvent (water) effect is also obtained using the Conductor‐like Screening Model. Three typical structures are chosen: cuboctahedral, icosahedral, and ino‐decahedral. All three present an “amphoteric” behavior against electrophiles, nucleophiles, and radicals. For the cuboctahedral and decahedral geometries, the highest susceptibility to attack is on the edges shared by a {111} face and a {100} face; for the icosahedral geometry, the highest susceptibility to attack is on the vertices. Ionization potentials, electron affinities, electronegativities, and chemical hardness are also reported. Comparison with experiments is presented. © 2012 Wiley Periodicals, Inc.

XZP + 1d and XZP + 1d-DKH basis sets for second-row elements: application to CCSD(T) zero-point vibrational energy and atomization energy calculations

Recently, segmented all-electron contracted double, triple, quadruple, quintuple, and sextuple zeta valence plus polarization function (XZP, X = D, T, Q, 5, and 6) basis sets for the elements from H to Ar were constructed for use in conjunction with nonrelativistic and Douglas-Kroll-Hess Hamiltonians. In this work, in order to obtain a better description of some molecular properties, the XZP sets for the second-row elements were augmented with high-exponent d "inner polarization functions," which were optimized in the molecular environment at the second-order Møller-Plesset level. At the coupled cluster level of theory, the inclusion of tight d functions for these elements was found to be essential to improve the agreement between theoretical and experimental zero-point vibrational energies (ZPVEs) and atomization energies. For all of the molecules studied, the ZPVE errors were always smaller than 0.5%. The atomization energies were also improved by applying corrections due to core/valence correlation and atomic spin-orbit effects. This led to estimates for the atomization energies of various compounds in the gaseous phase. The largest error (1.2kcalmol(-1)) was found for SiH(4).

A DFT study on the standard electrode potentials of 2‐substituted imidazoles

AbstractExtensive density functional theory, calculations, with optimization of geometries and estimation of substituent effects, have been performed to investigate the electrode potentials of dimer and protonated cation structures of 2‐substituted imidazoles. The gas phase geometries of dimer, anion, protonated cation, and neutral structures of 2‐substituted imidazoles have been optimized using Boese‐Martin for kinetics (BMK) and the Minnesota 2005 (M05) hybrid functionals combined with the valence triple‐ζ quality with polarization function (TZVP) basis set. The geometries in the presence of acetonitrile solvent have been optimized using the conductor‐like polarizable continuum model model of solvation at the same levels of theory. Frequency calculations have been performed for all the structures and none of them is found to exhibit any imaginary frequency. NH‐‐‐H infrared harmonic frequencies have been calculated and compared with available experimental data. The substituent effects on the electrode potentials of imidazole have been investigated as electron donating CH3, OH, NH2, OCH3 and electron withdrawing NO2, Cl, F, Br groups, which are bonded to the second numbered carbon atom of the imidazole molecule. It has been found that electron donating substituents show more negative electrode potentials, whereas electron withdrawing substituents have the opposite effect. © 2012 Wiley Periodicals, Inc.

A Relativistic Density Functional Study of the U<sub>2</sub>F<sub>6</sub> Molecule

All-electronic relativistic density functional theory (DFT) method has been used to study the U2F6 molecule. Results from calculations predict the existence of U2F6 molecule, which has been found to be stable with a multiply bonded U2 unit. The calculations also predict that D3d symmetry of U2F6 is more stable than D3h. The optimized geometries, vibrational frequencies and infrared intensities are reported for D3d symmetry of U2F6 from Becke Three-parameter Lee-Yang-Parr (B3LYP) function with triple zeta valence plus polarization functions basis set (TZP). The bond dissociation energy (BDE) for U-U bond in the U2F6 was obtained using the same method. In addition, the entropies of U2F6 have been investigated at temperature rang from 0 to 3000K in 10 steps using the B3LYP method.

Gaussian basis set of sextuple zeta quality for hydrogen through argon

Segmented all-electron contracted sextuple zeta valence plus polarization function (6ZP) basis sets for the elements from H to Ar were constructed to be used in conjunction with the non-relativistic and Douglas–Kroll–Hess Hamiltonians. The scalar relativistic effect at the coupled cluster level of theory on atomization energy for a sample of molecules was discussed. Additional improvements in the atomization energies were achieved by applying corrections due to core/valence correlation, atomic spin–orbit effects, and addition of tight d and f functions on second-row elements. This leads to estimates for the heat of formation of gaseous boron and carbon tetrafluoride.

An augmented Gaussian basis set for calculations of molecular polarizabilities on platinum compounds

Recently, segmented all-electron contracted double zeta valence plus polarization function (DZP) basis sets for the Pt element were constructed to be used in conjunction with the non-relativistic and Douglas–Kroll–Hess Hamiltonians. In this work, with the purpose of having a better description of electron affinity, polarizabities, and hydrogen bonding, the DZP set was augmented with diffuse (s, p, and d symmetries) and polarization (f symmetry) functions that were optimized for the anion at the Hartree–Fock and Mϕller–Plesset second-order levels, respectively. From optimized relativistic geometries and using non-hybrid and hybrid functionals, the performance of the augmented DZP (ADZP) set is assessed for predicting static electric dipole moment and polarizability of PtH, PtH 2, and antitumor drugs (cisplatin and carboplatin). Despite its compact size, the ADZP set demonstrates consistent, efficient, and reliable performance. ADZP electric property calculations showed to be as fast as those that use augmented effective core potential basis sets.

Determination of Structure and Dynamics of the Solvated Bisulfide (HS−) Ion by ab Initio QMCF Molecular Dynamics

The hydration structure of the bisulfide (HS(-)) ion in dilute aqueous solution was characterized by means of an ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation at the Hartree-Fock level employing Dunning double-ζ plus polarization function (DZP) basis sets. An average H-S bond distance of 1.35 Å resulted from the simulation and a hydration shell located at 2.42 Å S(HS(-))···H(w) and 3.97 Å HS(-) distances, respectively. At the sulfur site, the average coordination number is 5.9 ± 1.1, while the value for the hydrogen site is 9.2 ± 1.6. The calculated H(HS(-))-S(HS(-)) stretching frequency of 2752 cm(-1) obtained from the QMCF MD simulation is in good agreement with that reported from the Raman spectrum (2570 cm(-1)) only if a scaling factor of 0.89 is applied. The stability of the nondissociated HS(-) structure is reflected by the force constants of 436.1 and 4.5 N/m determined for the H(HS(-))-S(HS(-)) and H(HS(-))···O(w) bonds, respectively. A weak structure-making effect of the hydrated HS(-) ion results from the mean residence times of 1.5 and 2.1 ps of coordinated water molecules at the sulfur and hydrogen sites of the HS(-) ion, respectively.

All-electron double zeta basis sets for platinum: Estimating scalar relativistic effects on platinum(II) anticancer drugs

Segmented all-electron contracted double zeta valence plus polarization function (DZP) basis sets for the element Pt were constructed for use in conjunction with the non-relativistic and Douglas–Kroll–Hess (DKH) Hamiltonians. The DZP–DKH set is loosely contracted and thus offer computational advantages compared to the generally contracted relativistic basis sets, while their sufficiently small size allows it to be used in place of effective core potentials (ECP) for routine studies of molecules. Using the one-parameter hybrid functional mPW1PW, the performance of the basis sets is assessed for predicting the molecular structures and atomic charges of platinum(II) antitumor drugs, cisplatin and carboplatin. These results can be used as reference values to calibrate further ECP calculations. Despite their compact size, the DZP sets demonstrate consistent, efficient, and reliable performance and will be especially useful in calculations of molecular properties that require explicit treatment of the core electrons.

An ab initio quantum mechanical charge field molecular dynamics simulation of a dilute aqueous HCl solution

An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree-Fock level in conjunction with Dunning double-zeta plus polarization function basis sets. The simulation predicts an average H-Cl bond distance of 1.28 A, which is in good agreement with the experimental value. The H(HCl)...O(w) and Cl(HCl)...H(w) distances of 1.84 and 3.51 A were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure-making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively.

Factorial design analysis of the effects of wave function modifications on calculated HC and CC stretching frequencies in H 2C [dbnd]CHX and HC [tbnd]CX

Two-level factorial designs (FD) have been used to determine the effects of wave function modifications on calculated CH and CC harmonic stretching frequencies of the H 2C CHX and HC CX molecules with X = H, CH 3, F, Cl and CN. These modifications were treated at two levels, which consists in: (I) using either a double- or a triple-zeta valence basis set; (II) including or not diffuse functions in basis set, (III) including or not polarization functions in basis set, and (IV) performing a calculation with or without electron correlation beyond the Hartree–Fock level, i.e., MP2 or B3LYP. Our results have shown that valence (Val), diffuse (Dif), polarization (Pol) and electron correlation (Corr) main effects as well as the Pol/Corr second-order interaction effect are significant to build factorial models for these vibrational modes. When valence and diffuse functions are introduced in the basis set, the calculated HC and CC stretching frequencies are decreased in both the HC CX and H 2C CHX molecules. As expected, by far the correlation principal effect is the most important on the frequency values. This effect provokes a decrease of −281.4 cm −1 and −153.3 cm −1 in the C C and C C vibrational frequencies, respectively, using the MP2 calculations, whereas this decrease for the H C oscillator is −156.1 cm −1 and −116.1 cm −1 in HC CX and H 2C CHX, respectively. This same effect produces an important Pol/Corr interaction effect on HC and CC stretching frequencies, increasing their values by +45.3 cm −1 and +18.4 cm −1 in HC CX, respectively, whereas their corresponding values in H 2C CHX are +43.9 cm −1 and +11.0 cm −1, respectively. Finally, algebraic models were then established to explain how calculated HC and CC stretching frequencies in HC CX and H 2C CHX depend on the characteristics of the molecular orbital wave functions.

Dispersion-corrected DFT calculations on C60-porphyrin complexes

The quality of the newly added, empirical dispersion correction in density functional theory (DFT) calculations is examined for several supramolecular complexes of fullerene (C(60)) with free-base and metal porphyrins (Por). The benzene dimer (C(6)H(6))(2), naphthalene dimer (C(10)H(8))(2), and anthracene dimer (C(14)H(10))(2) were also included in the study for comparison. Three density functionals, two damping functions, and two types of basis sets were employed in the computations. The estimated dispersion energies in the fullerene-porphyrin systems are rather large, ranging from 0.5 eV in C(60).ZnP to 1 eV in C(60).H(2)TPP. Any dispersion-corrected DFT (DFT + E(disp)) method is shown to perform well for C(60).H(2)TPP, C(60).ZnTPP, and C(60).ZnP, where the intermolecular distances are relatively large. But large basis sets, e.g. TZP (triple-zeta + one polarization function), are required in order to obtain reliable results with DFT + E(disp). In the case of C(60).FeP, where the intermolecular distance R is short, the DFT + E(disp) calculated R depends on the damping function as well as on the DFT method, and all the DFT + E(disp) calculations lead to significant changes in the relative energies of the various spin states. The quality of the DFT + E(disp) calculated results on C(60).FeP is hard to judge here without detailed experimental data on a C(60).FePor complex. Owing to error cancellation, the pure DFT calculations with a smaller DZP (double-zeta + one polarization function) basis set without any correction are shown to give quite accurate results.

Efficiency of numerical basis sets for predicting the binding energies of hydrogen bonded complexes: Evidence of small basis set superposition error compared to Gaussian basis sets

Binding energies of selected hydrogen bonded complexes have been calculated within the framework of density functional theory (DFT) method to discuss the efficiency of numerical basis sets implemented in the DFT code DMol3 in comparison with Gaussian basis sets. The corrections of basis set superposition error (BSSE) are evaluated by means of counterpoise method. Two kinds of different numerical basis sets in size are examined; the size of the one is comparable to Gaussian double zeta plus polarization function basis set (DNP), and that of the other is comparable to triple zeta plus double polarization functions basis set (TNDP). We have confirmed that the magnitudes of BSSE in these numerical basis sets are comparative to or smaller than those in Gaussian basis sets whose sizes are much larger than the corresponding numerical basis sets; the BSSE corrections in DNP are less than those in the Gaussian 6-311+G(3df,2pd) basis set, and those in TNDP are comparable to those in the substantially large scale Gaussian basis set aug-cc-pVTZ. The differences in counterpoise corrected binding energies between calculated using DNP and calculated using aug-cc-pVTZ are less than 9 kJ/mol for all of the complexes studied in the present work. The present results have shown that the cost effectiveness in the numerical basis sets in DMol3 is superior to that in Gaussian basis sets in terms of accuracy per computational cost.

Density functional theory calculations of optical rotation: Employment of ADZP and its comparison with other basis sets

Density function theory calculations of frequency dependent optical rotations ([alpha]omega) for 30 rigid chiral molecules are reported. Calculations have been carried out at the sodium D line frequency, using the augmented double zeta valence quality plus polarization functions (ADZP) basis set and the BP86 nonhybrid and B3LYP hybrid functionals. Gauge-invariant atomic orbitals were used to guarantee origin-independent values of [alpha]D. Comparison between corresponding results obtained with nonhybrid and hybrid functionals as well as with theoretical optical rotations reported in the literature is done. Excited electronic states of three molecules are also discussed in light of circular dichroism spectra and B3LYP and BP86 calculated excitation energies and rotatory strengths. One verifies that the B3LYP/ADZP results are in better agreement with experiment.