Mixed Basis Set Research Articles

Conformational analysis of cellobiose by electronic structure theories

Adiabatic ϕ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each ϕ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-ϕH, syn-ψH), and the results from the solvated calculations were consistent with the (syn ϕH/ψH conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory.

Structures and potential energy functions of the ground states of YH,YD,YT molecules

Using the density functional theory(B3LYP) method, the 6-311++G(3df,2pd), AUG-cc-PVTZ, AUG-cc-PVQZ basis sets for H and effective core potentials for Y, the energies, equilibrium structure and harmonic frequency of the ground states of YH(D,T) molecules are calculated. Based on the theory of atomic and molecular reaction statics, the reasonable dissociation limits of the ground states of YH(D,T) molecules are derived. By comparing the calculation results with the existing experimental and theoretical values, we find that the mixed basis sets LANL2TZ/AUG-cc-PVQZ are most suited for the calculation of the molecules. Consequently, the potential energy surfaces of the ground states of YH(D,T) molecules are scanned at the B3LYP/LANL2TZ/AUG-cc-PVQZ level of theory. The potential energy curves of the ground states of YH(D,T) molecules are obtained by the least square fitting to the Murrell-Sorbie potential energy function. The spectroscopic constants (Be, e, e, ee, De) and force constants ((f2, f3, f4)are calculated and compared with experimental results, indicating that the calculation results are in good agreement with the experimental data.

Contribution of phonons to the line width of surface electronic states on Pd(111)

This paper reports on the results of calculations of the contributions from the electron-phonon interaction to the line width of the surface electronic states on Pd(111). The calculations have been performed both using an ab initio method based on the electron density functional theory and the linear response method in the pseudopotential representation with a mixed basis set and using a model that includes the description of the electronic structure of the surface by a one-dimensional model potential. The phonon contribution to the width of the lines has been analyzed for all the surface states under consideration. It has been demonstrated that the line width due to the electron-phonon interaction exhibits a weak anisotropy and that the character of changes in the line width with variations in the energy and the wave vector of the electron depends first of all on the particular surface energy band.

DFT study of crown ether-bridged Z-stilbenes and their complexes with alkali metal cations

A density functional theory (DFT) based on the interaction of alkali metal cations (Li+, Na+, K+, Rb+ and Cs+) with crown ether-bridged Z-stilbene has been investigated. The minimum energy structures, binding energies, and various thermodynamic parameters of free ligands and their metal cations complexes have been determined with B3LYP functional using mixed basis set (C, H, O, Li+, Na+ and K+ using 6-31+G(d), and the heavier cations: Rb+ and Cs+ using LANL2DZ). The optimized geometric structures are performed natural bond orbital (NBO) analysis. The main types of driving force host–guest interactions are investigated, the electron-donating O offers lone pair electrons to the contacting LP* (1-center valence lone pair) of alkali metal cations. In addition, the maximum absorption wavelength is studied on the time-dependent density functional theory (TD-DFT), the calculated results indicate that the wavelength is blue shifted when alkali cations incorporating into the ether rings. It is found that the crown ether-bridged Z-stilbene is good candidate for moderate alkali metal cations’ recognition regent.

Ab initio potential energy surface and bound states for the Kr–OCS complex

The first ab initio potential energy surface of the Kr-OCS complex is developed using the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)]. The mixed basis sets, aug-cc-pVTZ for the O, C, and S atom, and aug-cc-pVQZ-PP for the Kr atom, with an additional (3s3p2d1f) set of midbond functions are used. A potential model is represented by an analytical function whose parameters are fitted numerically to the single point energies computed at 228 configurations. The potential has a T-shaped global minimum and a local linear minimum. The global minimum occurs at R = 7.146 a(0), θ = 105.0° with energy of -270.73 cm(-1). Bound state energies up to J = 9 are calculated for three isotopomers (82)Kr-OCS, (84)Kr-OCS, and (86)Kr-OCS. Analysis of the vibrational wavefunctions and energies suggests the complex can exist in two isomeric forms: T-shaped and quasi-linear. The calculated transition frequencies and spectroscopic constants of the three isotopomers are in good agreement with the experimental values.

Density functional theory study of the bis‐3‐benzo‐crown ethers and their complexes with alkali metal cations Na+, K+, Rb+ and Cs+

The binding interactions of bis‐3‐benzo‐15‐crown‐5 ethers and bis‐3‐benzo‐18‐crown‐6 ethers (neutral hosts) with a series of alkali metal cations Na+, K+, Rb+ and Cs+ (charged guests) were investigated using quantum chemical density functional theory. Different optimized structures, binding energies and various thermodynamic parameters of free crown ethers and their metal cation complexes were obtained based on the Becke, three‐parameter, Lee–Yang–Parr functional using mixed basis set (C, H, O, Na+ and K+ using 6‐31 g, and the heavier cation Rb+ and Cs+ using effective core potentials). Natural bond orbital analysis is conducted on the optimized geometric structures. The main types of driving force host–guest interactions are investigated. The electron donating O offers a lone pair of electrons to the contacting LP* (1‐center valence antibond lone pair) orbitals of metal cations. The bis‐3‐benzocrown ethers are assumed to have sandwich‐like conformations, considering the binding energies to gauge the exact interactions with alkali cations. It is found that there are two different types of complexes: one is a tight ion pair and the other is a separated ion pair. Copyright © 2011 John Wiley & Sons, Ltd.

Ab initio potential energy surface and bound states of the Ar–BH complex

A new potential energy surface for Ar–BH complex is calculated by CCSD(T) method. Mixed basis sets, aug-cc-pVQZ for the H, B and Ar atom with an additional (3s3p2d2f1g) set of midbond functions are used. There are two minima on the potential. The global minimum with energy −178.51cm−1 is found for a skew T-shaped geometry with R=6.40a0 and θ=75.5°. The shallower minimum is located at R=8.15a0 and θ=180° with well depth −75.98cm−1. Based on the potential, the bound state energies are calculated for the Ar–BH complex and the predicted spectroscopic constants are also present.

Rapidly calculated DFT relaxed iso-potential ϕ/ψ maps: β-cellobiose

New cellobiose ϕH/ψH maps are generated using a mixed basis set DFTr method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are created for different conformational states of cellobiose, showing how glycosidic bond dihedral angles vary as different sets of hydroxymethyl rotamers and hydroxyl directions are examined. These maps are generated, fixing the dihedral ϕH and ψH values at ten degree intervals and energy optimizing the remaining geometry using the B3LYP/6-31+G* functional for all atoms except carbon atoms, where the functional B3LYP was used with the mixed basis set, 4-31G. Mapping results are compared between in vacuo structures using the mixed basis set, in vacuo using the full basis set, and those in which the implicit solvent method, COSMO, is included with the mixed basis set. Results show significant changes in position of energy minima with variation in hydroxyl rotamers and with application of solvent. Unique to this study is the mapping of the hydration energy at each ϕH/ψH point on the map using the energy derived at each point by applying COSMO. Using hydration gradients as a guide one observes directional solvent driven changes in the minimum energy positions. Interesting internal coordinate variances are described.

A Proton Pathway in the Voltage Sensing Domain of K V Channels, with a Possible Relation of Gating to the Pore Cavity and to the T1 Moiety

Voltage gating of a channel is complex. Strong evidence links the activation gate to the intracellular T1 moiety (Minor et al, 2000, Cell,102,657), and to slow inactivation (Panyi and Deutsch, J. Gen’l. Physiol.,2007,129,403, and other references). Using quantum calculations (B3LYP with mixed basis set, plus frequency corrections to reach room temperature), we have found a large entropic barrier (81kJ) between pore cavity and selectivity filter. This barrier may relate to slow inactivation, but it could be overcome, allowing ion transport, by electrostatic interactions either with an incoming ion, or protons that move during gating. Some additional calculations are presented in the context of specific interactions of S6 and S3 with T1 and the S4-5 linker. Possible electrostatic relation to the pore, and slow inactivation, requires further calculations. The residues for relevant amino acid linkages include (numbering, 3LUT structure, Kv1.2 channel): 1) E420(S6):Q315(S4-S5):[possible water]:N253(S3):E142(T1) 2) Q319(S4-S5):E136(T1):R419(S6):Y415(S6) 3) E422(S6):K134(T1). Also involved: D259, and N256 (S3: the latter may require one water for network linkage). Moving protons would, in this hypothesis, neutralize charges on acid residues, breaking links in the network, leading to gating. The complete proton pathway forms a “box” with defined boundaries; limited water connects sections of the network, which reaches the S4 positively charged residues to continue the path. Unless there is a mutation RaH, protons do not exit the VSD. The residues comprising the proton pathway are conserved not only in Kv1.2 channels from multiple organisms, but in Kcna, Kv1.3 and Kv1.5 from chicken.

Local exact exchange potentials within the all-electron FLAPW method and a comparison with pseudopotential results

We present a general numerical approach to construct local Kohn-Sham potentials from orbital-dependent functionals within the all-electron full-potential linearized augmented-plane-wave (FLAPW) method, in which core and valence electrons are treated on an equal footing. As a practical example, we present a treatment of the orbital-dependent exact-exchange (EXX) energy and potential. A formulation in terms of a mixed product basis, which is constructed from products of LAPW basis functions, enables a solution of the optimized-effective-potential (OEP) equation with standard numerical algebraic tools and without shape approximations for the resulting potential. We find that the mixed product and LAPW basis sets must be properly balanced to obtain smooth and converged EXX potentials without spurious oscillations. The construction and convergence of the exchange potential are analyzed in detail for diamond. Our all-electron results for C, Si, SiC, Ge, and GaAs semiconductors as well as Ne and Ar noble-gas solids are in very favorable agreement with plane-wave pseudopotential calculations. This confirms the adequacy of the pseudopotential approximation in the context of the EXX-OEP formalism and clarifies a previous contradiction between FLAPW and pseudopotential results.

Theoretical Study on the Interaction Potential and Bound States of the Ne-Beh Complex

The first two-dimensional potential energy surface for the Ne-BeH van der Waals interaction is calculated by the single and double excitation coupled-cluster theory with noniterative treatment of triple excitations(CCSD(T)). Mixed basis sets, aug-cc-pVQZ for the Be , H and Ne atom, with an additional (3s3p2d1 f 1g) set of midbond functions are used. There is a single global minimum at Re =6.95a0 ande =72.5 ◦ with well depth -34.43607 cm −1 . Based on the potential, the rovibrational energy level structure of the

Calibration and applications of the ΔMP2 method for calculating core electron binding energies

We calibrated a method for the evaluation of core electron binding energies, based on the energy differences between the cation and neutral molecule evaluated at the level of Møller-Plesset perturbation theory. The central feature of the method is the use of a mixed basis set: a large all-electron basis set is used for the atom whose core electron is removed, while the model core potential basis set is employed for all remaining atoms. Calibration was carried out for 55 molecules and 114 binding energies of 1s core electrons for the atoms C, N, O, and F. The average absolute deviation for all the core electron binding energies is 0.163 eV. The method was applied to the calculation of the core electron binding energies of five nucleic acid bases (uracil, adenine, cytosine, guanine, and thymine) and several of their low-energy tautomers.

DFT Study of Nitrogen-Substituted FAU: Effects of Ion Exchange and Aluminum Content on Base Strength

We have studied base strengths of nitrogen-substituted (nitrided) zeolites with faujasite (FAU) structure by calculating sorption energies of probe molecules (BF3 and BH3) using density functional theory with mixed basis sets applied to embedded clusters. BH3 was found to be a better probe of base strength because it does not introduce competing metal−fluorine interactions that obfuscate trends. In all cases, the base strengths of nitrided zeolites (denoted M−N−Y) were found to exceed those of the corresponding standard M−Y zeolites, where M = Li, Na, K, Rb, or Cs charge-compensating cations. We have found that for a particular Si:Al ratio, BH3 sorption energies vary in the order Li < Na < K ∼ Rb ∼ Cs. Sorption energy and hence base strength was found to decrease with increasing Si:Al ratio from 1 to 3 beyond which the base strength was found to increase again. The initial regime (1 < Si:Al < 3) is consistent with the prevailing understanding that the base strength increases with Al content, while the lat...

The rovibrational structure of the Kr–HF complex from an ab initio interaction potential

The first high quality potential energy surface for the Kr–HF complex is calculated with the CCSD(T) method and avqz+33221 basis set. A mixed basis sets, aug-cc-pVQZ for the H and F atom, and aug-cc-pVQZ-PP for the Kr atom, with an additional (3s3p2d2f1g) set of midbond functions are used. It is found that there are two minima on the potential. The global minimum is located at Re=6.70a0 and θe=180° with well depth −252.3537cm−1. The shallower minimum is −106.1783cm−1 located at R=6.65a0 and θ=0°. We also calculate the bound states of Kr–HF complex. The theoretical spectroscopic constants agree with experimental counterparts.

Molecular structure and vibrational assignments of bis(4-aminopent-3-en-2-onato)copper(II): A detailed density functional theoretical study

Bis(4-aminopent-3-en-2-onato) copper(II), Cu(APO) 2, was synthesized and its total X-ray crystallographic data were determined. The molecular structure and vibrational spectra of this compound were investigated by means of density functional theory (DFT) calculations at the B3LYP level using 6-31G **, 6-311G *, and 6-31++G * basis sets, and the results were compared with the experimental data. For comparison, the geometrical parameters and vibrational wavenumbers of Cu(APO) 2 were also calculated at the HF and MPW1PW91 levels using mixed basis sets (GEN), 6-311+G * for the Cu atom and 6-31G ** for all the other atoms. All of the measured IR and Raman bands were interpreted in terms of the calculated vibrational modes. The scaled theoretical frequencies and the structural parameters were in good agreement with the experimental data.

Ab initio potential energy surface and bound states of the Xe–HF complex

The two-dimensional potential energy surface for the Xe–HF van der Waals interaction is calculated by the single and double excitation coupled-cluster theory with noniterative treatment of triple excitations [CCSD(T)]. Mixed basis sets, aug-cc-pVQZ for the H and F atom and aug-cc-pVQZ-PP for the Xe atom, with an additional (3 s3 p2 d2 f1 g) set of midbond functions are used. There are two minima on the potential. The global minimum at R e = 7.05 a 0 and θ e = 180 ° with well depth −309.2906 cm −1. The shallower minimum is located at R = 7.00 a 0 and θ = 0 ° . Based on the potential, the predicted transition frequencies are in good agreement with the experimental results.

Coumarin derived chromophores in the donor–acceptor–donor format that gives fluorescence enhancement and large two-photon activity in presence of specific metal ions

Two coumarin derived dyes (compounds L a and L) have been synthesized in high yields by Schiff base condensation. On probing with a femtosecond laser, none of these compounds show any two-photon activity in the wavelength range, 760–860 nm. However, L a in presence of Zn(II) and L in presence of Mg(II), exhibit large two-photon absorption as well as emission in the same wavelength range. Theoretical calculations at the B3LYP functional with 6-31G∗ and LanL2DZ mixed basis set under DFT formalism support experimental results.

Interaction of N 2 with Kr: Potential energy surface and bound states

The first ab initio potential energy surface of the Kr–N 2 complex is developed using CCSD(T) method. A mixed basis sets, aug-cc-pVQZ for the C and O atom, and aug-cc-pVQZ-PP for the Kr atom, with an additional (3 s3 p2 d2 f1 g) set of midbond functions are used. The potential has a minimum of −111.79 cm −1 with R e = 7.30 a 0 at T-shaped geometry ( θ e = 90°). Based on the potential, the bound state energies are calculated up to J = 5 for seven isotopomers of 84Kr– 14N 2, 86Kr– 14N 2, 82Kr– 15N 2, 84Kr– 15N 2, 86Kr– 15N 2, 86Kr– 14N 15N, 84Kr– 14N 15N complex. Compared with available experimental data, all predicted transition frequencies agree within better than 2% with the experimental results.

Assessment of the "6-31+G** + LANL2DZ" mixed basis set coupled with density functional theory methods and the effective core potential: prediction of heats of formation and ionization potentials for first-row-transition-metal complexes.

Computational chemists have long demonstrated great interest in finding ways to reliably and accurately predict the molecular properties for transition-metal-containing complexes. This study is a continuation of our validation efforts of density functional theory (DFT) methods when applied to transition-metal-containing systems (Riley, K.E.; Merz, K. M., Jr. J. Phys. Chem. 2007, 111, 6044-6053). In our previous work we examined DFT using all-electron basis sets, but approaches incorporating effective core potentials (ECPs) are effective in reducing computational expense. With this in mind, our efforts were expanded to include evaluation of the performance of the basis set derived to approximate such an approach as well on the same set of density functionals. Indeed, employing an ECP basis such as LANL2DZ (Los Alamos National Laboratory 2 double zeta) for transition metals, while using all-electron basis sets for all other non-transition-metal atoms, has become more and more popular in computations on transition-metal-containing systems. In this study, we assess the performance of 12 different DFT functionals, from the GGA (generalized gradient approximation), hybrid-GGA, meta-GGA, and hybrid-meta-GGA classes, respectively, along with the 6-31+G** + LANL2DZ (on the transition metal) mixed basis set in predicting two important molecular properties, heats of formation and ionization potentials, for 94 and 58 systems containing first-row transition metals from Ti to Zn, which are all in the third row of the periodic table. An interesting note is that the inclusion of the exact exchange term in density functional methods generally increases the accuracy of ionization potential prediction for the hybrid-GGA methods but decreases the reliability of determining the heats of formation for transition-metal-containing complexes for all hybrid density functional methods. The hybrid-GGA functional B3LYP gives the best performance in predicting the ionization potentials, while the meta-GGA functional TPSSTPSS provides the most reliable and accurate results for heat of formation calculations. TPSSTPSS, a meta-GGA functional, which was constructed from first principles and subject to known exact constraints just like in an "ab initio" way, is successful in predicting both the ionization potentials and the heats of formation for transition-metal-containing systems.

Rapid convergence of crystalline energy bands by use of a plane-wave-gaussian mixed basis set

All of the crystalline electron wave functions are expanded in an analytic mixed LCAO-PW basis. The LCAO'S, expressed as contracted sets of non-overlapping even-tempered Gaussians, describe the short wave length part of the electron wave functions, while the plane waves describe the long wave length part. One LCAO is obtained from each isolated atom electron state (neglecting electron spin) for each atom in the unit cell. About 65 plane waves give valence and low conduction band convergence to 0.2 eV for both C and zinc-blende ZnO, whereas over a thousand terms would be required for comparable OPW convergence. The analytic mixed basis set should be applicable to the calculation of electron energy bands in a wide variety of crystalline compounds.