Double Basis Set Research Articles

Design and synthesis of new thiobarbituric acid metal complexes as potent protease inhibitors: spectral characterization, thermal analysis and DFT calculations

Five novel metal complexes of thiobarbituric acid (TBAH) have been prepared with the general formulae: [Ti(TBA)2(H2O)2]Cl2·2H2O, [Pd(TBA)2]·4H2O, Na[Ag(TBA)2(H2O)2]·4H2O, [Hg(TBA)2(H2O)2] and [Ce(TBA)2(H2O)3]SO4·H2O. The complexes have been fully characterized employing physicochemical and diverse spectroscopic techniques (IR, UV–Vis, mass and 1H NMR) as well as thermal analysis. Elemental analyses and spectroscopic data have showed that the stoichiometries of all complexes were 1:2. Thermal analysis measurements indicated that the complexes have good thermal stability. Density functional theory calculations were carried out at the B3LYP levels of theory with a double basis set, LANL2DZ basis set for titanium, palladium, cerium atoms, or LANL2MB basis set for silver, mercury atoms and 6-31+G(d,p) basis set for the other atoms. The optimized geometry of the ligand and its complexes was obtained based on the optimized structures. The ligand and its metal complexes act as protease inhibitors and repressed their enzymatic activity significantly.

Sonochemical synthesis, in vitro evaluation and DFT study of novel phenothiazine base Schiff bases and their nano copper complexes as the precursors for new shaped CuO-NPs

The current work reports the ultrasound-assisted synthesis of two nano binuclear copper complexes derived from novel tetradentate (N2O2) phenothiazine based Schiff bases. The synthesized compounds were characterized using the physicochemical methods, including 1H NMR, 13C NMR, FE-SEM, Mass, FT-IR, UV–Vis, elemental analysis, magnetic moment and molar conductance measurements. It is found that the geometrical structure of CuII2LnCl4 is distorted tetrahedral around the copper atoms using the results of 1H NMR, UV–Vis and magnetic moment studies. In addition, CuO nano particles were produced in the nano range (14.3-12.1nm) by the thermal decomposition of the copper complexes CuO NPs were characterized using FT-IR, FE-SEM, XRD, UV–Vis and photoluminescence methods and indicated a close accordance with the standard pattern. Also, the antioxidant studies revealed that the copper complexes exhibit comparable scavenging effects (against O2 and OH) with the standard antioxidants, such as vitamin C, while, they show more antioxidant activity than ligands. Similarly, the complexes show more antibacterial activity against four gram positive and gram negative bacteria in comparison to their Schiff base ligands. furthermore, The optimized structure, Molecular orbital (M.O.), Mulliken population analysis (MPA), contour of Electrostatic Potential (ESP) and Molecular Electrostatic Potential (MEP) map of the titled compounds were calculated base on DFT calculations that were carried out at the B3LYP levels of theory with a double basis set LANL2DZ for copper, and 6-311+G(d,p) basis set for the other atoms.

Critical nuclear charge for two-electron atoms.

The critical nuclear charge Z(c) required to bind a nucleus plus two electrons in a heliumlike atom has recently been an area of active study, resulting in a disagreement with earlier calculations and with the value obtained from the radius of convergence 1/Z* of a 1/Z expansion of the energy. In order to resolve the disagreement, have performed high-precision variational calculations in Hylleraas coordinates. With the double basis set method, we have been able to obtain good convergence for Z very close to Z(c), which together with the Hellmann-Feynman theorem yields the value Z(c) = 0.911,028,224,077,255,73(4), corresponding to 1/Z(c) = 1.097,660,833,738,559,80(5). This value is in agreement with the value obtained by Baker et al. [Phys. Rev. A 41, 1247 (1990)]. A significant feature of the results is that the outer electron remains localized near the nucleus, even at Z = Z(c), and the bound state evidently changes smoothly into a shape resonance for Z<Z(c). A qualitative polarization potential is proposed to account for the resonance, and the radial distribution function for the electron density is calculated.

DFT study on C–C bond cleavage of nitriles by a silyl(silylene)iron complex

The unsaturated disilanyl iron (II) complex Cp∗Fe(CO)SiMe 2SiMes 2Me is regard as a key intermediate in the reactions of the C–C bond cleavage of nitriles. The C–C bond cleavage of nitriles occurs after 1,2- and 1,3-group migration reactions in the organosilicon moieties. This reaction mechanism of the cleavage of C–C bond of nitriles by the Silyl(silylene) iron complex was investigated in detail with Gaussian98 package at the Becke3LYP (B3LYP) level of the density functional theory. The effective core potentials of Hay and Wadt with a double-basis set (LanL2DZ) were used to describe Fe, Si atoms, and the standard 6-31 G basis set was used for H, C, N, and O atoms. Polarization functions were also added for Si ( ζd = 0.262), C ( ζd = 0.8) and those atoms directly involved in bond-forming and bond-breaking processes. The C–C bond rupture of nitriles by the Silyl(silylene) ruthenium complex was also studied and we found that the induction effect of Silyl(silylene) iron complex should be better.

Hyperfine structure of the 23P state of 3He with and without an external magnetic field

The hyperfine structure of the 23P state of 3He with and without an external magnetic field is precisely calculated. All the linear terms, diamagnetic terms and the α2 relativistic correction terms are included in the Zeeman Hamiltonian. The values of the fields for 32 crossings and 5 anticrossings of the magnetic sublevels are theoretically predicted for magnetic field strengths up to 10 000 gauss. The results are compared with experimental data and other theoretical works. All related matrix elements are calculated with high accuracy by the use of double basis set Hylleraas-type variational wavefunctions.

Furan−Formic Acid Dimers: An ab Initio and Matrix Isolation Study

The dimers formed by formic acid (FA) and furan are investigated by ab initio methods and matrix isolation spectroscopy. Nine complexes with binding energies between -3.91 and -0.82 kcal/mol (MP2/6-311++G(d,p) + ZPE + BSSE) are identified. Another five weaker bound complexes are localized at lower level of theory only. The binding in the furan-FA dimers can be described in terms of OH...O, C=O...H, HO...H, CH...O, OH...pi, and CH...pi interactions. Therefore, the furan-FA complexes are classified in two types: (1) the dimers where the OH hydrogen of formic acid interacts with the furan molecule and (2) the dimers where the main interactions of FA with the furan molecule are via the less acidic CH hydrogen. Duning's and Pople's triple and double basis sets were used to study the dependence of the geometries and energies of the complexes from the basis set. BSSE (basis set superposition error) counterpoise corrections (CP) were included during the geometry optimizations of all dimers at the MP2/6-31G(d,p) level of theory. Matrix isolation spectroscopy allowed us to record the IR spectrum of aggregates between FA and furan. By comparison of the experimental IR spectrum with calculated IR spectra of a variety of complexes, it was possible to identify the most stable furan-FA dimer as the major product of the aggregation.

Precision calculation of electronic gJ factors for n3S1 states of 4He and 7Li+ ion

Precisely calculated results of Zeeman gJ factors gJ/ge − 1 for n3S1 (n = 2–10) states of all helium isotopes and lithium ions are presented, relativistic and radiative corrections of orders α2, α2m/M and α3 are included. All necessary matrix elements are precisely evaluated by the use of variational wavefunctions constructed from double basis sets in Hylleraas coordinates.

High precision variational calculations for H+2

A double basis set in Hylleraas coordinates is used to obtain improved variational upper bounds for the nonrelativistic energy of the 1 1S (v = 0, R = 0), 2 1S (v = 1, R = 0) and 2 3P (v = 0, R = 1) states of H+2. This method shows a remarkable convergence rate for relatively compact basis set expansions. A comparison with the most recent work is made. The accuracy of the wavefunctions is tested using the electron–proton Kato cusp condition.

Note on the generation of a new basis set for band structure calculations of infinite stacks

The band structures of a formamide stack (in the DNA B stacking arrangement), as well of cytosine (C) and uracil (U) stacks were calculated at the ab initio Hartree–Fock (HF) level using first a double basis set. The resulting valence and conduction bands were corrected for correlation on the basis of the inverse Dyson equation in the diagonal approximation with a MP2 self-energy taking into account the relaxation effects.It has been found that if one supplements the double ζ basis with one belonging to a “phantom” molecule (a molecule without nuclear charges and electrons at the midway of the stacking distance, 3.36Å/2=1.68Å and at half the rotation angle, 18°) one obtains substantially larger correlation effects and the fundamental gap gets close to the values which can be estimated on the basis of the optical spectra. Most probably this finding will turn out to be important for other stacked systems.

Near-edge X-ray absorption and dichroism in amino acids.

Nitrogen-containing organic compounds form a special group of compounds that have become of interest for spectroscopic research owing to their potential technical use and biological importance. Near edge X-ray absorption (NEXAFS) and circular dichroism (XCD) spectroscopies constitute two spectroscopies with capability of giving information on composition and structure of such sampies. In the present work we address a particular set of organic compounds with special relevance for biochemistry, namely the amino acids, and explore in what way NEXAFS and XCD spectra can fingerprint such compounds. We briefly review and discuss recent theoretical results on spectra at the K edges of C, N and O, that were presented in a series of papers (Plashkevych et al., 1998; Carravetta et al., 1998) These studies were also motivated by the observations (Kirtley et al., 1992) that the nitrogen edge NEXAFS spectrum of DNA can be understood as a weighted sum of the polynucleotide spectra, and by the suggestion that differences in the NEXAFS spectra might be used for mapping proteins which differ in their amino acid content (Boese et al., 1997). Except for glycine, all the amino acids investigated alanine, cysteine, serine, valine, glycine, phenylalanine, histidine, tyrosine and tryptophan exist in two optically active forms, namely as Dand Lisomers that are mirror images of one another. The rotatory X-ray absorption intensities have been computed and XCD spectra for this class of molecules are predicted (Plashkevych et al., to be published). The direct atomic orbital static exchange approach STEX is employed. It is based on a separate channel description of the absorption process, which allows an easy analysis of the spectra in terms of contributions from different molecular subunits. The STEX technique is implemented for fully relaxed core hole potentials of the different sites, and for using the double basis set algorithm, allowing for close to basis set limit results.

Variational eigenvalues for the S states of helium

The double basis set method in Hylleraas coordinates is used to obtain improved variational upper bounds for the l s ns 1S and 3S states of helium with n up to 10. The accuracy and stability of the results are discussed relative to an alternative basis set recently proposed by Kleindienst et al. [ Chem. Phy s. Letters 218(1994) 441].

Non-empirical calculations for the interaction of dihydrogen with hydride and alkyl complexes of boron, aluminium and titanium

The reaction X 2MR + H 2 → X 2MH + HR (MB, Al, Ti; RH, CH 3; XH, F) was studied by ab initio calculations with double-basis set. The electronic correlation according to the Möller-Plesset perturbation theory at the fourth-order was also taken into account. Influence of the active bond (MH, MCH 3), metal (B, Al, Ti) and nature of the ligands (H, F) on the possibility of reacting via the concerted mechanism and the value of activation energy were analyzed, the calculation results being the basis for the analysis. It is shown that due to the valence d-orbitals of the titanium atom, such an orbital structure of the transition state can be formed which always corresponds to the symmetry-allowed reaction.

Nonempirical calculations of potential-energy surfaces for nucleophilic addition of H? and F? to an acetylene molecule

The minimal energy paths for the nucleophilic addition of a hydride ion (H−) and a fluoride ion (F−) to a molecule of acetylene (A) have been calculated with the use of 3–21++G and 3–21+G double basis sets in the framework of the Hartree-Fock-Roothaan method. The values of the total energies of the reactants, transition states, and products have been refined by means of calculations with more complete basis sets [6–31++G// 3–21++G and 6–31++G*//3–21++G for reaction (1); 6–31+G*//3–21+G and 6–31++G**//3–21+G for reaction (2)] and by taking into account the correlation energy for reaction (1) in the framework of the SCEP/6–31++*//3–21++G method. It has been established that the activation energy of reaction (2) is 15.94 kJ/mole lower than that for reaction (1), that reaction (1) is exothermic, and that the enthalpy change accompanying reaction (2) is close to zero. The character of the distribution of the electron density along the minimal energy paths of both reactions has been analyzed, and the differences appearing as a result of the replacement of the soft nucleophile H− by the harder nucleophile F− have been ascertained. The results of the calculations have been compared with the results available in the literature for reaction (1).

High-precision eigenvalues for the 1s2p^1P and ^3P states of helium

The double basis set method in Hylleraas coordinates described previously [ Nucl. Instrum. MethodsB31, 7 ( 1988)] is applied to the calculation of high-precision eigenvalues for the 1s2p1P and 3P states of helium. Convergence to a few parts in 1014 is obtained for the nonrelativistic energies. The new wave functions are used to calculate mass-polarization, relativistic, relativistic reduced mass, and quantum-electrodynamic corrections. A comparison of the P-state energies, together with the previously calculated S- and D-state energies, with the experimental energy levels tabulated by Martin [ Phys. Rev A36, 3575 ( 1987)] yields well-defined discrepancies of the order of 0.001 cm−1, which can be attributed to higher-order relativistic and quantum-electrodynamic effects.

Structure and tunneling dynamics of malonaldehyde. A theoretical study

The geometry and harmonic vibrational frequencies of equilibrium malonaldehyde and of the transition state for the symmetric intramolecular hydrogen atom transfer have been determined at the SCF level of theory (using a slightly better than double-basis set). All geometrical parameters were fully and simultaneously optimized by using SCF gradient techniques. Comparison of the equilibrium structure with the structure determined from microwave spectra shows good agreement in most respects, although there are a few differences. At the C/sub s/ equilibrium geometry and the C/sub 2//sub v/ transition state large scale configuration interaction (all single and double excitations) calculations were carried out to determine the barrier height for the symmetric hydrogen atom transfer; including a correction for quadruple excitations, this gives a classical or ''bare'' barrier height of 8.0 kca./mol. A one-dimensional model for the tunneling dynamics of H-atom transfer leads to a tunneling splitting in the ground vibrational state of approx. 18 cm/sup -1/, in relatively good agreement with the experimental value. It is noted, though, that the value of the splitting is sensitive to the potential surface parameters (i.e., bare height, frequencies) and that there is also uncertainty about the accuracy of the one-dimensional description of the tunneling.

Generalized muffin-tin orbitals for electronic structure studies of surfaces, interfaces, and organic solids

We have developed an improvement formalism for carrying out electronic structure calculations for surfaces, interfaces, and organic solids using muffin-tin-orbital (MTO) basis sets. We will first show how the variational flexibility of MTO tail functions can be improved by introducing generalized MTO tail functions composed of modified spherical Bessel functions Kl(κ, r) and their derivatives with respect to κ. Next, we will show how energy dependent MTOs can be constructed by using double basis sets, the first partners being keyed to the radial solutions of the wave equation inside the MT spheres, and the second partners to the energy derivatives of these radial solutions. The energy dependence of these double MTO basis sets introduces additional variational flexibility. Since the first partners will normally be considerably larger than the second partners, the double-dimension secular equations can be solved economically by using the Löwdin partitioning scheme. Finally, we will indicate how the calculation of the interstitial matrix elements, which is usually the time-limiting step for open structures, can be approximated rather nicely by calculating these matrix elements inside a suitably chosen set of overlapping atomic spheres, and then extrapolating to a set of larger overlapping atomic spheres which enclose the most important portion of the interstitial region. With these improvements, it should be possible to carry out accurate calculations for open structures having large numbers of atoms per unit cell considerably more rapidly and economically than by existing MTO-type methods.

Model organometallic systems. The interaction of 2S beryllium(1+) ion, 1S beryllium, and 3P beryllium atoms with acetylene and ethylene

To model the interaction between metal atoms and unsaturated hydrocarbons, several electronic states of the Be-C/sub 2/H/sub 2/ and Be--C/sub 2/H/sub 4/ systems have been investigated using ab initio electronic structure theory. Double basis sets have been used (after some experimentation with polarization functions) at the self-consistent-field level of theory. For ten different electronic arrangements, potential energy curves have been predicted for the perpendicular approach of the Be nucleus to the midpoint of the carbon--carbon bond. The interaction of Be/sup +/ ion (ground /sup 2/S state) with both acetylene and ethylene is attractive, yielding equilibrium Be midpoint separations of 2.03 and 2.09 A and binding energies of 30 and 33 kcal/mole. In contrast the /sup 1/S ground state of the neutral Be atom has an essentially repulsive interaction. The threefold degenerate excited /sup 3/P state splits into /sup 3/A/sub 1/, /sup 3/B/sub 1/, and /sup 3/B/sub 2/ components as it approaches the ethylene molecule. The /sup 3/B/sub 2/ state is rather strongly bound, 19 kcal for Be--C/sub 2/H/sub 2/ and 25 kcal for Be-C/sub 2/H/sub 4/. the /sup 3/A/sub 1/ state is strongly repulsive, while the /sup 3/B/sub 1/ state assumes an intermediate role. These trends are readily explained bymore » qualitative molecular orbital concepts.« less

Small gaussian basis sets for second-row atoms

6s-type and 4p-type gaussian basis sets are obtained for the second row atoms by fitting, using a least squares criterion, to 12s-type and 9p-type gaussian basis sets which are close to the self-consistent field atomic orbital wave functions. The small gaussian expansions are considered to be more suited for molecular calculations using double basis sets. The differences between these sets and the 10s-type, 6p-type and 9s-type, 5p-type are analysed. For molecular calculations using single gaussian basis sets the 10s-type and 6p-type would seem to be the best compromise.